Method of identifying molecules that bind to the large ribosomal subunit

[0001] This application is a continuation-in-part of co-pending U.S. application Ser. No. 10/072,634, filed Feb. 8, 2002, which is a continuation-in-part of co-pending U.S. application Ser. No. 09/922,251, filed Aug. 3, 2001, and claims the benefit of (i) U.S. Provisional Application No. 60/348,731, filed Jan. 14, 2002, and (ii) U.S. Provisional Application No. 60/352,024, filed Jan. 25, 2002, the disclosures of each of which are incorporated by reference herein.

[0002] Certain work described herein was supported, in part, by Federal Grant Nos. NIH-GM22778 and NIH-GM54216, awarded by the National Institutes of Health. The Government may have certain rights in the invention.

[0003] The present invention relates generally to the field of protein biosynthesis and to modulators, for example, inhibitors, of protein biosynthesis. More particularly, the invention relates to: methods and compositions for elucidating the three-dimensional structure of the large ribosomal subunit, either alone or in combination with a protein synthesis inhibitor; the three-dimensional structure of the large ribosomal subunit, either alone or in combination with a protein synthesis inhibitor; the use of such structures in the design and testing of novel protein synthesis inhibitors; and novel protein synthesis inhibitors.

I. Ribosomes: Structure, Function, and Composition

[0004] Ribosomes are ribonucleoproteins which are present in both prokaryotes and eukaryotes. They comprise about two-thirds RNA and one-third protein. Ribosomes are the cellular organelles responsible for protein synthesis. During gene expression, ribosomes translate the genetic information encoded in a messenger RNA into protein (Garrett et al (2000) “The Ribosome: Structure, Function, Antibiotics and Cellular Interactions, “American Society for Microbiology, Washington, D.C.).

[0005] Ribosomes comprise two nonequivalent ribonucleoprotein subunits. The larger subunit (also known as the “large ribosomal subunit”) is about twice the size of the smaller subunit (also known as the “small ribosomal subunit”). The small ribosomal subunit binds messenger RNA (mRNA) and mediates the interactions between mRNA and transfer RNA (tRNA) anticodons on which the fidelity of translation depends. The large ribosomal subunit catalyzes peptide bond formation—the peptidyl-transferase reaction of protein synthesis—and includes (at least) two different tRNA binding sites: the A-site which accommodates the incoming aminoacyl-tRNA, which is to contribute its amino acid to the growing peptide chain, and the P-site which accommodates the peptidyl-tRNA complex, i.e., the tRNA linked to all the amino acids that have so far been added to the peptide chain. The large ribosomal subunit also includes one or more binding sites for G-protein factors that assist in the initiation, elongation, and termination phases of protein synthesis. The large and small ribosomal subunits behave independently during the initiation phase of protein synthesis; however, they assemble into complete ribosomes when elongation is about to begin.

[0006] The molecular weight of the prokaryotic ribosome is about 2.6×10⁶ daltons. In prokaryotes, the small ribosomal subunit contains a 16S (Svedberg units) ribosomal RNA (rRNA) having a molecular weight of about 5.0×10⁵ daltons. The large ribosomal subunit contains a 23S rRNA having a molecular weight of about 1.0×10⁶ daltons and a 5S rRNA having a molecular weight of about 4.0×10⁵ daltons. The prokaryotic small subunit contains about 20 different proteins and its large subunit contains about 35 proteins. The large and small ribosomal subunits together constitute a 70S ribosome in prokaryotes.

[0007] Eukaryotic ribosomes generally are bigger than their prokaryotic counterparts. In eukaryotes, the large and small subunits together make an 80S ribosome. The small subunit of a eukaryotic ribosome includes a single 18S rRNA, while the large subunit includes a 5S rRNA, a 5.8S rRNA, and a 28S rRNA. The 5.8S rRNA is structurally related to the 5′ end of the prokaryotic 23S rRNA, and the 28S rRNA is structurally related to the remainder of the prokaryotic 23S rRNA (Moore (1998) Annu. Rev. Biophys. 27: 35-58). Eukaryotic ribosomal proteins are qualitatively similar to the prokaryotic ribosomal proteins; however, the eukaryotic proteins are bigger and more numerous (Moore (1998) supra).

II. Structural Conservation of the Large Ribosomal Subunit

[0008] While the chemical composition of large ribosomal subunits vary from species to species, the sequences of their components provide unambiguous evidence that they are similar in three-dimensional structure, function in a similar manner, and are related evolutionarily. The evolutionary implications of rRNA sequence data available are reviewed in the articles of Woese and others in part II of Ribosomal RNA, Structure, Evolution, Processing and Function in Protein Biosynthesis, (Zimmermann and Dahlberg, eds., CRC Press, Boca Raton, Fla., 1996). The article by Garret and Rodriguez-Fonseca in part IV of the same volume discusses the unusually high level of sequence conservation observed in the peptidyl transferase region of the large ribosomal subunit. The ribosomes of archeal species like Haloarcula marismortui resemble those obtained from eubacterial species like E. coli in size and complexity. However, the proteins in H. marismortui ribosomes are more closely related to the ribosomal proteins found in eukaryotes (Wool et al. (1995) Biochem. Cell Biol. 73: 933-947).

III. Determination of the Structure of Ribosomes

[0009] Much of what is known about ribosome structure is derived from physical and chemical methods that produce relatively low-resolution information. Electron microscopy (EM) has contributed to an understanding of ribosome structure ever since the ribosome was discovered. In the 1970s, low resolution EM revealed the shape and quaternary organization of the ribosome. By the end of 1980s, the positions of the surface epitopes of all the proteins in the E. coli small subunit, as well as many in the large subunit, had been mapped using immunoelectron microscopy techniques (Oakes et al. (1986), Structure, Function and Genetics of Ribosomes, (Hardesty, B. and Kramer, G., eds.) Springer-Verlag, New York, N.Y., pp. 47-67; Stoeffler et al. (1986), Structure. Function and Genetics of Ribosomes, (Hardesty, B. and Kramer, G., eds.) Springer-Verlag, New York, N.Y., pp. 28-46). In the last few years, advances in single-particle cryo-EM and image reconstruction have led to three-dimensional reconstructions of the E. coli 70S ribosome and its complexes with tRNAs and elongation factors to resolutions of between 15 Å and 25 Å (Stark et al. (1995) Structure 3: 815-821; Stark et al. (1997) Nature 3898: 403-406; Agrawal et al. (1996) Science 271: 1000-1002; Stark et al. (1997) Cell 28: 19-28). Additionally, threedimensional EM images of the ribosome have been produced at resolutions sufficiently high so that many of the proteins and nucleic acids that assist in protein synthesis can be visualized bound to the ribosome. An approximate model of the RNA structure in the large subunit has been constructed to fit a 7.5 Å resolution electron microscopic map of the 50S subunit from E. coli and available biochemical data (Mueller et al. (2000) J. Mol. Biol. 298: 35-59).

[0010] While the insights provided by EM have been useful, it has long been recognized that a full understanding of ribosome structure would derive only from X-ray crystallography. In 1979, Yonath and Wittman obtained the first potentially useful crystals of ribosomes and ribosomal subunits (Yonath et al. (1980) Biochem. Internat. 1: 428-435). By the mid 1980s, scientists were preparing ribosome crystals for X-ray crystallography (Maskowski et al. (1987) J. Mol. Biol. 193: 818-822). The first crystals of 50S ribosomal subunit from H. marismortui were obtained in 1987. In 1991, improvements were reported in the resolution of the diffraction data obtainable from the crystals of the 50S ribosomal subunit of H. marismortui (van Bohlen, K. (1991) J Mol. Biol. 222: 11).

[0011] In 1995, low resolution electron density maps for the large and small ribosomal subunits from halophilic and thermophilic sources were reported (Schlunzen et al. (1995) Biochem. Cell Biol. 73: 739-749). However, these low resolution electron density maps proved to be spurious (Ban et al. (1998) Cell 93: 1105-1115).

[0012] The first electron density map of the ribosome that showed features recognizable as duplex RNA was a 9 Å resolution X-ray crystallographic map of the large subunit from Haloarcula marismortui (Ban et al. (1998) supra). Extension of the phasing of that map to 5 Å resolution made it possible to locate several proteins and nucleic acid sequences, the structures of which had been determined independently (Ban et al. (1999) Nature 400: 841-847).

[0013] At about the same time, using similar crystallographic strategies, a 7.8 Å resolution map was generated of the entire Thermus thermophilus ribosome showing the positions of tRNA molecules bound to its A-, P-, and E- (protein exit site) sites (Cate et al. (1999) Science 285: 2095-2104), and a 5.5 Å resolution map of the 30S subunit from T. thermophilus was obtained that allowed the fitting of solved protein structures and the interpretation of some of its RNA features (Clemons, Jr. et al. (1999) Nature 400: 833-840). Subsequently, a 4.5 Å resolution map of the T. thermophilus 30S subunit was published, which was based in part on phases calculated from a model corresponding to 28% of the subunit mass that had been obtained using a 6 Å resolution experimental map (Tocilj et al. (1999) Proc. Natl. Acad. Sci. USA 96: 14252-14257).

IV. Location of the Peptidyl Transferase Site in the Large Ribosomal Subunit

[0014] It has been known for about 35 years that the peptidyl transferase activity responsible for the peptide bond formation that occurs during messenger RNA-directed protein synthesis is intrinsic to the large ribosomal subunit (Traut et al. (1964)J. Mol. Biol. 10: 63; Rychlik (1966) Biochim. Biophys. Acta 114: 425; Monro (1967) J. Mol. Biol. 26: 147-15; Maden et al. (1968) J. Mol. Biol. 35: 333-345) and it has been understood for even longer that the ribosome contains proteins as well as RNA. In certain species of bacteria, for example, the large ribosomal subunit contains about 35 different proteins and two RNAs (Noller (1984) Ann. Rev. Biochem. 53: 119-162; Wittmann-Liebold et al. (1990) The Ribosome: Structure, Function, and Evolution, (W. E. Hill et al., eds.) American Society for Microbiology, Washington, D.C. (1990), pp. 598-616). These findings posed three related questions. Which of the almost 40 macromolecular components of the large ribosomal subunit contribute to its peptidyl transferase site, where is that site located in the large subunit, and bow does it work?

[0015] By 1980, the list of components that might be part of the ribosome's peptidyl transferase had been reduced to about half a dozen proteins and 23S rRNA (see Cooperman (1980) Ribosomes: Structure, Function, and Genetics, (G. Chambliss et al., eds.) University Park Press, Baltimore, Md. (1980), 531-554), and following the discovery of catalytic RNAs (Guerrier-Takada et al. (1983) Cell 35: 849-857; Kruger et al. (1982) Cell 31: 147-157), the hypothesis that 23S rRNA might be its sole constituent, which had been proposed years earlier, began to gain favor. In 1984, Noller and colleagues published affinity labeling results which showed that U2619 and U2620 (in E. coli: U2584, U2585) are adjacent to the CCA-end of P-site-bound tRNA (Barta et al. (1984) Proc. Nat. Acad. Sci. USA 81: 3607-3611; Vester et al. (1988) EMBO J. 7: 3577-3587). These nucleotides appear to be part of a highly conserved internal loop in the center of domain V of 23S rRNA. The hypothesis that this loop is intimately involved in the peptidyl transferase activity was supported by the observation that mutations in that loop render cells resistant to many inhibitors of peptidyl transferase, and evidence implicating it in this activity has continued to mount (see, Noller (1991) Ann. Rev. Biochem. 60: 191-227; Garrett et al. (1996) Ribosomal RNA: Structure, Evolution, Processing and Function in Protein Biosynthesis, (R. A. Zimmerman and A. E. Dahlberg, eds.) CRC Press, Boca Raton, Fla. (1996), pp. 327-355).

[0016] Definitive proof that the central loop in domain V is the sole component of the ribosome involved in the peptidyl transferase activity has remained elusive, however. Studies have shown that it was possible to prepare particles that retained peptidyl transferase activity by increasingly vigorous deproteinizations of large ribosomal subunits, however, it was not possible to produce active particles that were completely protein-free. Nevertheless, combined with earlier reconstitution results (Franceschi et al. (1990) J. Biol. Chem. 265: 6676-6682), this work reduced the number of proteins that might be involved to just two: L2 and L3 (see, Green et al. (1997) Annu. Rev. Biochem. 66: 679-716). More recently, Watanabe and coworkers reported success in eliciting peptidyl transferase activity from in vitro synthesized, protein-free 23S rRNA (Nitta et al. (1998) RNA 4: 257-267), however, their observations appear not to have withstood further scrutiny. Thus the question still remained: is the ribosome a zibozyme or is it not?

[0017] Over the years, the location of the peptidyl transferase site in the ribosome has been approached almost exclusively by electron microscopy. In the mid-1980s evidence that there is a tunnel running through the large ribosomal subunit from the middle of its subunit interface side to its back (Milligan et al (1986) Nature 319: 693-695; Yonath et al. (1987) Science 236: 813-816) began to accumulate, and there has been strong reason to believe that polypeptides pass through it as they are synthesized (Bernabeu et al. (1982) Proc. Nat. Acad. Sci. USA 79: 3111-3115; Ryabova et al. (1988) FEBS Letters 226: 255-260; Beckmann et al. (1997) Science 278: 2123-2126). More recent cryo-EM investigations (Frank et al (1995) Nature 376: 441-444; Frank et al. (1995) Biochem. Cell Biol. 73: 757-765; Stark et al. (1995) supra) confirmed the existence of the tunnel and demonstrated that the CCA-ends of ribosome-bound tRNAs bound to the A- and P-sites are found in the subunit interface end of the tunnel. Consequently, the peptidyl transferase site must be located at that same position, which is at the bottom of a deep cleft in the center of the subunit interface surface of the large subunit, immediately below its central protuberance.

[0018] The substrates of the reaction catalyzed at the peptidyl transferase site of the large subunit are an aminoacyl-tRNA (aa-tRNA) and a peptidyl-tRNA. The former binds in the ribosome's A-site and the latter in its P-site. The α-amino group of the aa-tRNA attacks the carbon of the carbonyl acylating the 3′ hydroxyl group of the peptidyl-tRNA, and a tetrahedral intermediate is formed at the carbonyl carbon. The tetrahedral intermediate resolves to yield a peptide extended by one amino acid esterified to the A-site bound tRNA and a deacylated tRNA in the P-site.

[0019] This reaction scheme is supported by the observations of Yarus and colleagues who synthesized an analogue of the tetrahedral intermediate by joining an oligonucleotide having the sequence CCdA to puromycin via a phosphoramide group (Welch et al. (1995) Biochemistry 34: 385-390). The sequence CCA, which is the 3′ terminal sequence of all tRNAs, binds to the large subunit by itself, consistent with the biochemical data showing that the interactions between tRNAs and the large subunit largely depend on their CCA sequences (Moazed et al. (1991) Proc. Natl. Acad. Sci. USA 88: 3725-3728). Puromycin is an aa-tRNA analogue that interacts with the ribosomal A-site, and the phosphoramide group of the compound mimics the tetrahedral carbon intermediate. This transition state analogue, CCdA-phosphate-puromycin (CCdA-p-Puro), binds tightly to the ribosome, and inhibits its peptidyl transferase activity (Welch et al. (1995) supra).

V. Structure Determination of Macromolecules Using X-Ray Crystallography

[0020] In order to better describe the efforts undertaken to determine the structure of ribosomes, a general overview of X-ray crystallography is provided below.

[0021] Each atom in a crystal scatters X-rays in all directions, but crystalline diffraction is observed only when a crystal is oriented relative to the X-ray beam so that the atomic scattering interferes constructively. The orientations that lead to diffraction may be computed if the wavelength of the X-rays used and the symmetry and dimensions of the crystal's unit cell are known (Blundell et al. (1976) Protein Crystallography (Molecular Biology Series), Academic Press, London). The result is that if a detector is placed behind a crystal that is being irradiated with monochromatic X-rays of an appropriate wavelength, the diffraction pattern recorded will consist of spots, each spot representing one of the orientations that gives rise to constructive interference.

[0022] Each spot in such a pattern, however it is recorded, is characterized by (i) an intensity (its blackness); (ii) a location, which encodes the information about diffraction orientation; and (iii) a phase. If all of those things are known about each spot in a crystal diffraction pattern, the distribution of electrons in the unit cell of the crystal may be computed by Fourier transformation (Blundell et al. (1976) supra), and from that distribution or electron density map, atomic positions can be determined.

[0023] Unfortunately, the phase information essential for computing electron distributions cannot be measured directly from diffraction patterns. One of the methods routinely used to determine the phases of macromolecules, such as proteins and nucleic acids, is called multiple isomorphous replacement (MIR) which involves the introduction of new X-ray scatterers into the unit cell of the crystal. Typically, these additions are heavy atoms, which make a significant contribution to the diffraction pattern. It is important that the additions be sufficiently low in number so that their positions can be located and that they leave the structure of the molecule or of the crystal cell unaltered, i.e. the crystals should be isomorphous. Isomorphous replacement usually is performed by diffusing different heavy-metal complexes into the channels of the preformed protein crystals. Macromolecules expose side chains (such as SH groups) in these solvent channels that are able to bind heavy metals. It is also possible to replace endogenous light metals in metalloproteins with heavier ones, e.g., zinc by mercury, or calcium by samarium. Alternatively, the isomorphous derivative can be obtained by covalently attaching a heavy metal to the macromolecule in solution and then subjecting it to crystallization conditions.

[0024] Heavy metal atoms routinely used for isomorphous replacement include but are not limited to mercury, uranium, platinum, gold, lead, and selenium. Specific examples include mercury chloride, ethyl-mercury phosphate, and osmium pentamine, iridium pentamine. Since such heavy metals contain many more electrons than the light atoms (H, N, C, O, and S) of the protein, the heavy metals scatter x-rays more strongly. All diffracted beams would therefore increase in intensity after heavy-metal substitution if all interference were positive. In fact, however, some interference is negative; consequently, following heavy-metal substitution, some spots increase in intensity, others decrease, and many show no detectable difference.

[0025] Phase differences between diffracted spots can be determined from intensity changes following heavy-metal substitution. First, the intensity differences are used to deduce the positions of the heavy atoms in the crystal unit cell. Fourier summations of these intensity differences give maps, of the vectors between the heavy atoms, the so-called Patterson maps. From these vector maps, the atomic arrangement of the heavy atoms is deduced. From the positions of the heavy metals in the unit cell, the amplitudes and phases of their contribution to the diffracted beams of protein crystals containing heavy metals is calculated.

[0026] This knowledge then is used to find the phase of the contribution from the protein in the absence of the heavy-metal atoms. As both the phase and amplitude of the heavy metals and the amplitude of the protein alone is known, as well as the amplitude of the protein plus heavy metals (i.e., protein heavy-metal complex), one phase and three amplitudes are known. From this, the interference of the X-rays scattered by the heavy metals and protein can be calculated to determine if the interference is constructive or destructive. The extent of positive or negative interference, with knowledge of the phase of the heavy metal, give an estimate of the phase of the protein. Because two different phase angles are determined and are equally good solutions, a second heavy-metal complex can be used which also gives two possible phase angles. Only one of these will have the same value as one of the two previous phase angles; it therefore represents the correct phase angle. In practice, more than two different heavy-metal complexes are usually made in order to give a reasonably good estimate of the phase for all reflections. Each individual phase estimate contains experimental errors arising from errors in the measured amplitudes. Furthermore, for many reflections, the intensity differences are too small to measure after one particular isomorphous replacement, and others can be tried.

[0027] The amplitudes and the phases of the diffraction data from the protein crystals are used to calculate an electron-density map of the repeating unit of the crystal. This map then is interpreted to accommodate the residues of the molecule of interest. That interpretation is made more complex by several limitations in the data. First, the map itself contains errors, mainly due to errors in the phase angles. In addition, the quality of the map depends on the resolution of the diffraction data, which, in turn, depends on how well-ordered the crystals are. This directly influences the quality of the map that can be produced. The resolution is measured in angstrom units (Å); the smaller this number is, the higher the resolution and, therefore, the greater the amount of detail that can be seen.

[0028] Building the initial model is a trial-and-error process. First, one has to decide how a polypeptide chain or nucleic acid weaves its way through the electron-density map. The resulting chain trace constitutes a hypothesis by which one tries to match the density of side chains to the known sequence of the polypeptide or nucleic acid. When a reasonable chain trace has finally been obtained, an initial model is built that fits the atoms of the molecule into the electron density. Computer graphics are used both for chain tracing and for model building to present the data and manipulated the models.

[0029] The initial model will contain some errors. Provided the crystals diffract to high enough resolution (e.g., better than 3.5 Å), most or substantially all of the errors can be removed by crystallographic refinement of the model using computer algorithms. In this process, the model is changed to minimize the difference between the experimentally observed diffraction amplitudes and those calculated for a hypothetical crystal containing the model (instead of the real molecule). This difference is expressed as an R factor (residual disagreement) which is 0.0 for exact agreement and about 0.59 for total disagreement.

[0030] In general, the R factor for a well-determined macromolecular structure preferably lies between 0.15 and 0.35 (such as less than about 0.24-0.28). The residual difference is a consequence of errors and imperfections in the data. These derive from various sources, including slight variations in the conformation of the protein molecules, as well as inaccurate corrections both for the presence of solvent and for differences in the orientation of the microcrystals from which the crystal is built. This means that the final model represents an average of molecules that are slightly different both in conformation and orientation.

[0031] In refined structures at high resolution, there are usually no major errors in the orientation of individual residues, and the estimated errors in atomic positions are usually around 0.1-0.2 Å, provided the sequence of the protein or nucleic acid is known. Hydrogen bonds, both within the molecule of interest and to bound ligands, can be identified with a high degree of confidence.

[0032] Typically, X-ray structures can be determined provided the resolution is better than 3.5 Å. Electron-density maps are interpreted by fitting the known amino acid and/or nucleic acid sequences into regions of electron density.

VI. The Need for Higher Resolution for the 50S Ribosomal Subunit

[0033] Although the art provides crystals of the 50S ribosomal subunit, and 9 Å and 5 Å resolution X-ray crystallographic maps of the structure of the 50S ribosome, the prior art crystals and X-ray diffraction data are not sufficient to establish the three-dimensional structures of all 31 proteins and 3,043 nucleotides of the 50S ribosomal subunit. Thus, the prior art crystals and maps are inadequate for the structure-based design of active agents, such as herbicides, drugs, insecticides, and animal poisons.

[0034] More detailed, higher resolution X-ray crystallographic maps are necessary in order to determine the location and three-dimensional structure of the proteins and nucleotides in ribosomes and ribosomal subunits, particularly for the 50S ribosomal subunit. An accurate molecular structure of the 50S ribosomal subunit will not only enable further investigation and understanding of the mechanism of protein synthesis, but also the development of effective therapeutic agents and drugs that modulate (e.g., induce or inhibit) protein synthesis.

[0035] The present invention is based, in part, upon the determination of a high resolution atomic structure of a ribosomal subunit, more particularly, a large subunit of a ribosome. In addition, the invention is based, in part, upon the determination of high resolution atomic structures of certain protein synthesis inhibitors, namely antibiotics, when they are interacting with the large subunit of the ribosome.

[0036] The invention provides the structure of the large subunit of a ribosome isolated from the organism, Haloarcula marismortui. However, in view of the high level o f sequence and structural homology between ribosomes of organisms in different kingdoms, the structural information disclosed herein can be used to produce, using routine techniques, high resolution structural models of large ribosomal units for any organism of interest.

[0037] Although there is significant homology between ribosomes of different organisms, for example, between ribosomes of humans and certain human pathogens, there still are differences that can be exploited therapeutically. For example, many clinically and commercially significant protein synthesis inhibitors, for example, antibiotics such as streptomycin, tetracycline, chioramphenicol and erythromycin, selectively target bacterial ribosomes and disrupt bacteria) protein synthesis but at the same time do not target or otherwise significantly affect human ribosome function. As a result, over the years antibiotics have proven to be invaluable in the treatment of microbial infections in humans. However, there is still an ongoing need for new protein synthesis inhibitors, particularly because of the development of strains of pathogens that are resistant to known antibiotics. The information provided herein provides insights into the design of new protein synthesis inhibitors.

[0038] The invention provides computer systems containing atomic co-ordinates that define at least a portion of the three-dimensional structure of a ribosome, more specifically, a large ribosomal subunit. In addition, the invention provides methods of using the atomic co-ordinates to identify new molecules that can selectively bind ribosomes, and that preferably act as selective inhibitors of protein synthesis. In addition, the invention provides computer systems containing atomic co-ordinates that define at least a portion of certain antibiotics when interacting with their binding sites in the large ribosomal subunit. In addition, the invention provides methods of using the atomic co-ordinates of the antibiotics to identify new molecules that selectively bind ribosomes, and that preferably act as selective inhibitors of protein synthesis. In addition, the invention provides new families of protein synthesis inhibitors. Each of these aspects of the invention is discussed in more detail below.

[0039] In one aspect, the invention provides a computer system comprising: (a) a memory having stored therein data indicative of atomic co-ordinates derived from an electron density map having a resolution of at least about 4.5 Å, more preferably of at least about 3.0 Å, and most preferably of about 2.4 Å and defining a ribofunctional locus of a large subunit of a ribosome; and (b) a processor in electrical communication with the memory, the processor comprising a program for generating a three-dimensional model representative of the ribofunctional locus. In a preferred embodiment, the computer system further comprises a device, for example, a computer monitor, or terminal for providing a visual representation of the molecular model. In another preferred embodiment, the processor further comprises one or more programs to facilitate rational drug design.

[0040] In a preferred embodiment, the computer system further comprises at least a portion of the atomic co-ordinates deposited at the Protein Data Bank under accession number PDB ID: 1FFK (large ribosomal subunit), I FFZ (large ribosomal subunit complexed with CCdA-p-Puro), 1FG0 (large ribosomal subunit complexed with a mini-helix analogue of aminoacyl-tRNA), 1 JJ2 (large ribosomal structure), 1K73 (large ribosomal subunit complexed with anisomycin), 1KC8 (large ribosomal subunit complexed with blasticidin), 1K8A (large ribosomal subunit complexed with carbomycin), 1KD1(large ribosomal subunit complexed with spiramycin); or 1K9M (large ribosomal subunit complexed with tylosin) or recorded on compact disk, Disk No. 1 of 1.

[0041] In a preferred embodiment, the atomic co-ordinates further define at least a portion of a protein synthesis inhibitor, for example, an antibiotic, more specifically an antibiotic selected from the group consisting of anisomycin, blasticidin, carbomycin A, sparsomycin, spiramycin, tylosin, virginiamycin M, azithromycin, linezolid, chloramphenicol and erythromycin, complexed with a ribofunctional locus. More specifically, the invention provides atomic co-ordinates of the large ribosomal subunit together the atomic co-ordinates of antibiotics interacting with the large ribosomal subunit. These atomic co-ordinates are recorded on compact disk, Disk No. 1, and correspond to: large ribosomal subunit complexed with anisomycin (file name: anisomysin.pdb or ANISOMYC.PDB); large ribosomal subunit complexed with blasticidin (file name: blasticidin.pdb or BLASTICI.PDB); large ribosomal subunit complexed with carbomycin (file name: carbomycin.pdb or CARBOMYC.PDB); large ribosomal subunit complexed with tylosin (file name: tylosin.pdb or TYLOSIN.PDB); large ribosomal subunit complexed with sparsomycin (file name: sparsomycin.pdb or SPARSOMY.PDB); large ribosomal subunit complexed with virginiamycin M (file name: virginiamycin.pdb or VIRGINIA.PDB); large ribosomal subunit complexed with spiramycin (file name: spiramycin.pdb or SPIRAMYC.PDB); large ribosomal subunit complexed with azithromycin (file name: AZITHROM.PDB or azithromycin.pdb); or large ribosomal subunit complexed with linezolid (file name: LINEZOLI.PDB or linezolid.pdb); or large ribosomal subunit complexed with erythromycin (file name: erythromycin.pdb).

[0042] In a preferred embodiment, the ribofunctional locus comprises at least a portion of an active site in the ribosomal subunit, for example, at least a portion of one or more of: a peptidyl transferase site (a portion of which may be defined by a plurality of residues set forth in Table 5A or 5B); an A-site (a portion of which may be defined by a plurality of residues set forth in Table 6A or 6B); a P-site (a portion of which may be defined by a plurality of residues set forth in Table 7A or 7B); a polypeptide exit tunnel (a portion of which may be defined by a plurality of residues set forth in Table 8A or 8B, Table 9, or Table 10); or an antibiotic binding domain (a portion of which may be defined by a plurality of residues set forth in Table 11A or 11B, Table 12A or 12B, Table 13A or 13B, Table 14A or 14B, Table 15A or 15B, Table 16A or 16B, Table 17A or 17B, Table 18A or 18B, Table 19A or 19B, or Table 20A or 20B). A plurality of residues shall be considered to include at least 3 residues, preferably at least 5 residues, and more preferably at least 10 residues. The ribofunctional locus may be defined by atoms of ribosomal RNA, one or more ribosomal proteins, or a combination of ribosomal RNA and one or more ribosomal proteins.

[0043] In another preferred embodiment, the atomic co-ordinates are produced by molecular modeling. Using the atomic co-ordinates provided herein, the skilled artisan may generate models of any ribosome of interest using conventional techniques, for example, conventional homology modeling, and or molecular replacement techniques. In another embodiment, the atomic co-ordinates are produced by homology modeling using at least a portion of the atomic co-ordinates deposited at the Protein Data Bank under accession number PDB ID: 1 FFK, 1 FFZ, 1FG0, 1JJ2, 1K73, 1KC8, 1K8A, 1KD1, or 1K9M, or any of the atomic co-ordinates included in compact disk, Disk No. 1. In another embodiment, the atomic co-ordinates are produced by molecular replacement using at least a portion of the atomic co-ordinates deposited at the Protein Data Bank under accession number PDB ID: 1FFK, 1FFZ, 1FG0, 1JJ2, 1K73, 1KC8, 1K8A, 1KD1 or 1K9M, or any of the atomic co-ordinates recorded on compact disk, Disk No. 1.

[0044] In a preferred embodiment, the atomic co-ordinates define residues that are conserved between ribosomes or ribosomal subunits of pathogens, for example, prokaryotic organisms, and, optionally but more preferably, are also absent from ribosomes or ribosomal subunits of a host organism, for example, a human. In another preferred embodiment, the atomic co-ordinates may define residues that are conserved between ribosomes or ribosomal subunits of prokaryotic organisms, for example, bacteria, and, optionally but more preferably, are also absent from ribosomal subunits of eukaryotes, for example, a mammal, more preferably, a human. This information can be used, for example, via the use of one or more molecular models, to identify targets for rational drug design that may be exploited to develop new molecules, for example, protein synthesis inhibitors, that disrupt protein synthesis in a pathogen, for example, a bacteria, but do not disrupt or otherwise substantially affect protein synthesis in a host organism, for example, a human.

[0045] In another aspect, the invention provides a variety of methods for designing, testing and refining new molecules via rational drug design. For example, the invention provides a method that comprises the steps of: (a) providing a model, for example, a molecular model, having a ribofunctional locus of a large subunit of a ribosome, wherein the model is defined by the spatial arrangement of atoms derived from an electron density map having a resolution of at least about 4.5 Å, more preferably to at least about 3.0 Å, and most preferably to about 2.4 Å; and (b) using the model to identify a candidate molecule having a surface complementary to the ribofunctional locus. Preferably, the candidate molecule stereochemically interfits and more preferably binds with the ribofunctional locus of the large subunit of the ribosome.

[0046] In a preferred embodiment, the method comprises one or more additional steps of: producing the candidate molecule identified in such a method; determining whether the candidate molecule, when produced, modulates (for example, induces or reduces) ribosomal activity; identifying a modified molecule; producing the modified molecule; determining whether the modified molecule, when produced, modulates ribosomal activity; and producing the modified molecule for use either alone or in combination with a pharmaceutically acceptable carrier. The candidate molecule and/or the modified molecule may be an antibiotic or antibiotic analogue, for example, a macrolide antibiotic or a macrolide analogue.

[0047] In a preferred embodiment, the ribofunctional locus used in such a method comprises at least a portion of an active site in the ribosomal subunit. In another preferred embodiment, the ribofunctional locus is defined by at least a portion of one or more of: a peptidyl transferase site (a portion of which may be defined by a plurality of residues set forth in Table 5A or Table 5B); an A-site (a portion of which may be defined by a plurality of residues set forth in Table 6A or Table 6B); a P-site (a portion of which may be defined by a plurality of residues set forth in Table 7A or Table 7B); a polypeptide exit tunnel (a portion of which may be defined by a plurality of residues set forth in Table 8A, Table 8B, Table 9, Table 10); or an antibiotic binding domain (a portion of which may be defined by a plurality of residues set forth in Table 11A, Table 11B, Table 12A, Table 12B, Table 13A, Table 13B, Table 14A, Table 14B, Table 15A, Table 15B, Table 16A, Table 16B, Table 17A, Table 17B, Table 18A, Table 18B, Table 19A, Table 19B, Table 20A or Table 20B). The ribofunctional locus may be defined by atoms of ribosomal RNA, one or more ribosomal proteins, or a combination of ribosomal RNA and one or more ribosomal proteins.

[0048] In another preferred embodiment, the atomic co-ordinates are used to produce a molecular model in an electronic form. The atomic co-ordinates preferably are produced by molecular modeling. In another embodiment, the atomic co-ordinates are produced by homology modeling using at least a portion of the atomic co-ordinates deposited at the Protein Data Bank under accession number PDB ID: 1FFK, 1FFZ, 1FG0, 1JJ2, 1K73, 1KC8, 1K8A, 1KD, or 1K9M, or the atomic co-ordinates recorded on compact disk, Disk No. 1. In another embodiment, the atomic co-ordinates are produced by molecular replacement using at least a portion of the atomic co-ordinates deposited at the Protein Data Bank under accession number PDB ID: 1FFK, 1FFZ, 1FG0, 1JJ2, 1K73, 1KC8, 1K8A, 1KD1, or 1K9M or any of the atomic co-ordinates included on compact disk, Disk No. 1.

[0049] In a preferred embodiment, the atomic co-ordinates may define residues that are conserved among ribosomes or ribosomal subunits of pathogens, for example, prokaryotic organisms, and, optionally but more preferably, are also absent in ribosomes or ribosomal subunits of a host organism, for example, a human. In another preferred embodiment, the atomic co-ordinates may define residues that are conserved between ribosomes or ribosomal subunits of prokaryotic organisms, for example, bacteria, and, optionally but more preferably, are also absent from ribosomes or ribosomal subunits of eukaryotes, for example, a mammal, more preferably a human. This information can be used, for example, via the use of one or more molecular models, to identify targets for rational drug design that may be exploited to develop new molecules, for example, protein synthesis inhibitors, that disrupt protein synthesis in a pathogen, for example, a bacteria but do not disrupt or otherwise substantially affect protein synthesis in a host organism, for example, a human.

[0050] In a preferred embodiment, the computer system further comprises at least a portion of the atomic co-ordinates deposited at the Protein Data Bank under accession number PDB ID: 1FFK (large ribosomal subunit), 1FFZ (large ribosomal subunit complexed with CCdA-p-Puro), 1FG0 (large ribosomal subunit complexed with a mini-helix analogue of aminoacyl-tRNA), 1JJ2 (large ribosomal subunit), 1K73 (large ribosomal subunit complexed with anisomycin), 1KC8 (large ribosomal subunit complexed with blasticidin), 1K8A (large ribosomal subunit complexed with carbomycin), 1KD1(large ribosomal subunit complexed with spiramycin); or 1K9M (large ribosomal subunit complexed with tylosin), or recorded on compact disk, Disk No. 1.

[0051] In another aspect, the invention provides a computer system comprising: (a) a memory having stored therein data indicative of atomic co-ordinates derived from an electron density map defining at least a portion of a protein synthesis inhibitor when the protein synthesis inhibitor is interacting with a ribofunctional locus of a large subunit of a ribosome; and (b) a processor in electrical communication with the memory, the processor comprising a program for generating a three-dimensional model representative of at least a portion of the protein synthesis inhibitor. In a preferred embodiment, the computer system further comprises a device, for example, a computer monitor, or terminal for providing a visual representation of the molecular model. In another preferred embodiment, the processor further comprises one or more programs to facilitate rational drug design.

[0052] In a preferred embodiment, the atomic co-ordinates further define at least a portion of a protein synthesis inhibitor, for example, an antibiotic, more specifically an antibiotic selected from the group consisting of anisomycin, blasticidin, carbomycin A, sparsomycin, spiramycin, tylosin, virginiamycin M, azithromycin, linezolid and erythromycin, complexed with a ribofunctional locus. In a preferred embodiment, the ribofunctional locus comprises at least a portion of an active site of a ribosome, for example, at least a portion of one or more of (i) a peptidyl transferase site, (ii) an A-site, (iii) a P-site, (iv) a polypeptide exit tunnel.

[0053] More specifically, the invention provides atomic co-ordinates of antibiotics interacting with the large ribosomal subunit. These atomic co-ordinates are recorded on compact disk, Disk No. 1, and correspond to: large ribosomal subunit complexed with anisomycin (file name: anisomysin.pdb or ANISOMYC.PDB); large ribosomal subunit complexed with blasticidin (file name: blasticidin.pdb or BLASTICI.PDB); large ribosomal subunit complexed with carbomycin A (file name: carbomycin.pdb or CARBOMYC.PDB); large ribosomal subunit complexed with tylosin (file name: tylosin.pdb or TYLOSIN.PDB); large ribosomal subunit complexed with sparsomycin (file name: sparsomycin.pdb or SPARSOMY.PDB); large ribosomal subunit complexed with virginiamycin M (file name: virginiamycin.pdb or VIRGINIA.PDB); large ribosomal subunit complexed with spiramycin (file name: spiramycin.pdb or SPIRAMYC.PDB); large ribosomal subunit complexed with azithromycin (file name: AZITHROM.PDB or azithromycin.pdb); or large ribosomal subunit complexed with linezolid (file name: LINEZOLI.PDB or linezolid.pdb); or large ribosomal subunit complexed with erytiromycin (file name: erythromycin.pdb).

[0054] In another aspect, the invention provides a method of identifying a lead candidate for a new protein synthesis inhibitor. The method comprises the steps of (a) providing a molecular model of at least a portion of a protein synthesis inhibitor when the protein synthesis inhibitor is interacting with a ribofunctional locus of a large subunit of a ribosome; and (b) using the model to identify the lead candidate. In a preferred embodiment, the lead candidate is capable of interacting, and still more preferably binding a ribofunctional locus.

[0055] In another preferred embodiment, the method comprises the additional step of producing the lead compound. After synthesis, the lead compound can be tested for biological activity, for example, modulation of ribosome activity in an in vitro assay or growth inhibition of micro-organisms of interest. Based on the results of such studies, it is possible to determine structure-activity relationships, which may then be used to design further modifications of the lead compound in order to improve a particular feature of interest. The modified lead compounds then can be produced and assessed for biological activity, as before. Once a compound of interest has been designed, synthesized and tested for activity, it may then be produced in commercially feasible quantities for use as a pharmaceutical.

[0056] In a preferred embodiment, the starting molecule (i.e., the protein synthesis inhibitor), the lead compound and the penultimate compound is an antibiotic or antibiotic analogue. In another embodiment, the lead compound and also the penultimate compound is a hybrid antibiotic (i.e., comprises a portion of a first antibiotic and a portion of a second, different antibiotic).

[0057] In another preferred embodiment, the model used in the practice of the invention is a model of an antibiotic selected from the group consisting of anisomycin, blasticidin, carbomycin A, sparsomycin, spiramycin, tylosin, virginiamycin M, azithromycin, linezolid, or erythromycin. The model preferably comprises a portion of the atomic co-ordinates recorded on compact disk, Disk No. 1 of 1 under file name: anisomycin.pdb, blasticidin.pdb, carbomycin.pdb, sparsomycin.pdb, spiramycin.pdb, tylosin.pdb, virginiamycin.pdb, ANISOMYC.PDB, BLASTICI.PDB, CARBOMYC.PDB, SPARSOMY.PDB, SPIRAMYC.PDB, TYLOSIN.PDB, VIRGINIA.PDB, AZITHROM.PDB, LINEZOLI.PDB, azithromycin.pdb, linezolid.pdb, or erythromycin.pdb. In another preferred embodiment, the penultimate compound is an analogue of an antibiotic selected from the group consisting of anisomycin, blasticidin, carbomycin A, sparsomycin, spiramycin, tylosin, virginiamycin M, azithromycin, linezolid, or erythromycin.

[0058] In a preferred embodiment, the ribofunctional locus comprises at least a portion of an active site of a ribosome, for example, at least a portion of one or more of (i) a peptidyl transferase site, (ii) an A-site, (iii) a P-site, and (iv) a polypeptide exit tunnel. In another embodiment, the molecular model useful in the practice of the invention is in an electronic form, in which case the molecular model preferably is generated by molecular modeling.

[0059] In another aspect, the invention provides new protein synthesis inhibitors that disrupt the function of a target ribosome. These inhibitors can be readily designed and tested as disclosed herein.

[0060] One type of protein synthesis inhibitor of the invention comprises: a first binding domain having a surface, for example, a solvent accessible surface, that mimics or duplicates a surface of a known first molecule, for example, a first antibiotic, that binds with a first contact site, for example, a first ribofunctional locus, in or on a large ribosomal subunit; and a second binding domain having a surface, for example, a solvent accessible surface, that mimics or duplicates a surface of a known second molecule, for example, a second antibiotic, that binds with a second contact site, for example, a second ribofunctional locus, in or on the ribosomal subunit. The first domain is attached to the second domain so as to permit both the first domain and the second domain to bind simultaneously with their respective contact sites within or on the ribosomal subunit so as to disrupt protein synthesis in a ribosomal subunit. In a preferred embodiment, the protein synthesis inhibitor has a molecular weight of less than about 1,500 and an IC₅₀ of lower than about 50 μM, more preferably less than about 10 μM.

[0061] Another type of protein synthesis inhibitor is a synthetic, engineered molecule that comprises: (i) a binding domain having a surface, for example, a solvent accessible surface, that mimics or duplicates a solvent accessible surface of a known molecule, for example, a first known antibiotic, which binds with a contact site, for example, a ribofunctional locus in or on a ribosomal subunit; and (ii) a novel effector domain attached to the binding domain which, upon binding of the binding domain with the contact site, occupies a space within or adjacent to the ribosomal subunit thereby disrupting protein synthesis in the ribosomal subunit. In a preferred embodiment, the protein synthesis inhibitor has a molecular weight of less than about 1,500 and an IC₅₀ of lower than about 50 μM, more preferably less than about 10 μM.

[0062] In another aspect, the invention provides new protein synthesis inhibitors, for example, a molecule capable of contacting at least three residues but less than thirteen contact residues in Table 11A that together define an anisomycin binding pocket of a large ribosomal subunit, a molecule capable of contacting at least three residues but less than ten contact residues in Table 12A that together define a blasticidin binding pocket of a large ribosomal subunit, a molecule capable of contacting at least three residues but less than sixteen contact residues in Table 13A that together define a carbomycin A binding pocket of a large ribosomal subunit, a molecule capable of contacting at least three residues but less than twenty contact residues in Table 14A that together define a tylosin binding pocket of a large ribosomal subunit, a molecule capable of contacting at least three residues but less than nine contact residues in Table 15A that together define a sparsomycin binding pocket of a large ribosomal subunit, a molecule capable of contacting at least three residues but less than thirteen contact residues in Table 16A that together define a virginiamycin M binding pocket of a large ribosomal subunit, a molecule capable of contacting at least three residues but less than fifteen contact residues in Table 17A that together define a spiramycin binding pocket of a large ribosomal subunit, a molecule capable of contacting at least three residues but less than thirteen contact residues in Table 18A that together define an erythromycin binding pocket of a large ribosomal subunit, a molecule capable of contacting at least three but less than eleven contact residues in Table 19A that together define an azithromycin binding pocket of a large ribosomal subunit, or a molecule capable of contacting at least three residues but less than fifteen contact residues in Table 20A that together define a linezolid binding pocket of a large ribosomal subunit. The contact residues are those residues in the large ribosomal subunit that are in van der Waals contact with the antibiotic of interest.

[0063] In yet another aspect, the invention provides a protein synthesis inhibitor comprising, for example, a molecule capable of contacting a plurality of residues in Table 11A that together define an anisomycin binding pocket of a large ribosomal subunit, but lacking one or more atoms present in the anisomycin molecule, the atomic co-ordinates of which are recorded on Disk No. 1 under file name ANISOMYC.PDB; a molecule capable of contacting a plurality of residues in Table 12A that together define a blasticidin binding pocket of a large ribosomal subunit, but lacking one or more atoms present in the blasticidin molecule, the atomic co-ordinates of which are recorded on Disk No. 1 under file name BLASTICI.PDB; a molecule capable of contacting a plurality of residues in Table 13A that together define a carbomycin A binding pocket of a large ribosomal subunit, but lacking one or more atoms present in carbomycin A, the atomic co-ordinates of which are recorded on Disk No. 1 under file name CARBOMYC.PDB; a molecule capable of contacting a plurality of residues in Table 14A that together define a tylosin binding pocket of a large ribosomal subunit, but lacking one or more atoms present in tylosin, the atomic co-ordinates of which are recorded on Disk No. 1 under file name TYLOSIN.PDB; a molecule capable of contacting a plurality of residues in Table 15A that together define a sparsomycin binding pocket of a large ribosomal subunit, but lacking one or more atoms present in sparsomycin, the atomic co-ordinates of which are recorded on Disk No. 1 under file name SPARSOMY.PDB; a molecule capable of contacting a plurality of residues in Table 16A that together define a virginiamycin M binding pocket of a large ribosomal subunit, but lacking one or more atoms present in virginiamycin M, the atomic co-ordinates of which are recorded on Disk No. 1 under file name VIRGINIA.PDB; a molecule capable of contacting a plurality of residues in Table 17A that together define a spiramycin binding pocket of a large ribosomal subunit, but lacking one or more atoms present in spiramycin, the atomic co-ordinates of which are recorded on Disk No. 1 under file name SPIRAMYC.PDB; a molecule capable of contacting a plurality of residues in Table 18A that together define an erythromycin binding pocket of a large ribosomal subunit, but lacking one or more atoms present in erytliromycin, the atomic co-ordinates of which are recorded on Disk No. 1 under file name erythromycin.pdb; a molecule capable of contacting a plurality of residues in Table 19A that together define an azithromycin binding pocket of a large ribosomal subunit, but lacking one or more atoms present in azithromycin, the atomic co-ordinates of which are recorded on Disk No. 1 under file name azithromycin.pdb; or a molecule capable of contacting a plurality of residues in Table 20A that together define a linezolid binding pocket of a large ribosomal subunit, but lacking one or more atoms present in linezolid, the atomic co-ordinates of which are recorded on Disk No. 1 under file name linezolid.pdb.

[0064] The foregoing aspects and embodiments of the invention may be more fully understood by reference to the following figures, detailed description and claims. Further advantages are evident from the drawings.

I. Definitions

[0109] As used herein, the term “active site” refers to regions on a ribosome or ribosomal subunit that are directly involved in protein synthesis, e.g., the peptidyl transferase site, the A-site, the P-site, the polypeptide exit tunnel, the elongation factor binding site, and other similar sites.

[0110] As used herein, the terms “agent,” “ligand” and “lead candidate” are used synonymously and refer to any atom, molecule, or chemical group which binds or interacts with a ribosome, ribosomal subunit or ribosome fragment. Thus, ligands include, but are not limited to, a single heavy atom, an antibiotic or an analogue or derivative thereof, a tRNA, a peptidyl tRNA, an aminoacyl tRNA, or a signal recognition particle (“SRP”).

[0111] As used herein, “archaebacteria” refers to the kingdom of monerans that includes methane producers, sulfur-dependent species, and many species that tolerate very salty or hot environments.

[0112] As used herein, the term “A-site” refers to the locus occupied by an aminoacyl-tRNA molecule immediately prior to its participation in the peptide-bond forming reaction.

[0113] As used herein, the term “asymmetric unit” refers to a minimal set of atomic co-ordinates that when operated upon by the symmetry operations of a crystal will regenerate the entire crystal.

[0114] As used herein, “at least a portion of” or “at least a portion of the three-dimensional structure of” is understood to mean a portion of the three-dimensional structure of a ribosome or ribosomal subunit, including charge distribution and hydrophilicity/hydrophobicity characteristics, formed by at least three, more preferably at least three to ten, and most preferably at least ten amino acid and/or nucleotide residues of the ribosome or ribosomal subunit. The residues forming such a portion may be, for example, residues which form a contiguous portion of the primary sequence of a ribosomal RNA or ribosomal protein, residues which form a contiguous portion of the three-dimensional structure of the ribosome or ribosomal subunit, or a combination thereof. As used herein, the residues forming “a portion of the three-dimensional structure of” a ribosome or ribosomal subunit, form a three-dimensional shape in which each atom or functional group forming the portion of the shape is separated from the nearest atom or functional group forming the portion of the shape by no more than 40 Å, preferably by no more than 20 Å, more preferably by no more than 5-10 Å, and most preferably by no more than 1-5 Å.

[0115] As used herein, the term “atomic co-ordinates” or “structure co-ordinates” refers to mathematical co-ordinates (represented as “X,” “Y” and “Z” values) that describe the positions of atoms in a crystal of a ribosome or ribosomal subunit. The diffraction data obtained from the crystals are used to calculate an electron density map of the repeating unit of the crystal. The electron density maps are used to establish the positions of the individual atoms within a single ribosomal subunit. Those of skill in the art understand that a set of structure co-ordinates determined by X-ray crystallography is not without standard error. For the purpose of this invention, the structures of two ribosomes, ribosomal subunits or portions thereof are considered to be the same if they satisfy one of the following two tests. In a first test, the structures are considered to be the same if a set of structure co-ordinates for a ribosome or ribosomal subunit from any source has a root mean square deviation of non-hydrogen atoms of less than about 2.0 Å, or more preferably less than about 0.75 Å, when superimposed on the non-hydrogen atom positions of the atomic co-ordinates deposited at the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) (Berman et al. (2000) Nucleic Acids Research 28, 235-242; see also, the web page at the URL resb.org/pdb/) with the accession numbers PDB ID: 1FFK; PDB ID: 1FFZ; PDB ID: 1FG0; PDB ID: 1JJ2;PDB ID: 1K73; PDB ID: 1KC8; PDB ID: 1K8A; PDB ID: 1KD1; or PDB ID: 1K9M, or contained on Disk 1 of 1, the disclosure of each of the foregoing of which is incorporated herein by reference in its entirety. In a second test, the structures are considered to be the same if the r.m.s. deviation between a set of atoms in a test structure and a corresponding set of atoms in a reference structure is less than 2.0 Å. For the purposes of this test, the set of atoms in the reference structure comprises at least five of the series of 23S rRNA residues listed below as 631-633, 835-841, 844-846, 882-885, 1836-1839, 2095-2105, 2474-2478, 2485-2490, 2528-2530, 2532-2543,2607-2612, 2614-2623, 2642-2648 of the structure deposited in the PDB under accession number PDB ID: 1JJ2 or contained as file name 1JJ2.RTF on Disk 1 of 1. The residues in the test structure corresponding to the ones listed above are identified by sequence alignment using the program Lasergene v. 5.0 (DNA Star, Inc., Madison, Wis.) with the default settings. Specifically, the computer program is used to align those residues listed above in the Haloarcula marismortui 23S rRNA sequence with those in the test organism's rRNA. Once aligned, the corresponding residues in the test organism's rRNA are identified. The atomic co-ordinates of backbone atoms (P, C5′, 05′, C4′, C3′, 03′) of atoms in the test structure are superimposed upon the corresponding backbone atoms (P, C5′, 05′, C4′, C3′, 03′) of the reference structure using the program MIDAS Plus (Ferrin et al. (1988) J. Mol. Graphics 6: 13-27 and 36-37). The test and reference structures are considered the same if the r.m.s. deviation between the two sets of atoms after superpositioning is less than 2.0 Å, as determined by MIDAS Plus.

[0116] In the list of atomic co-ordinates deposited at the RCSB Protein Data Bank or included herein as files recorded on the compact disks, the term “atomic co-ordinate” or structure co-ordinates refer to the measured position of an atom in the structure in Protein Data Bank (PDB) format, including X, Y, Z and B, for each. The term “atom type” refers to the element whose co-ordinates are measured. The first letter in the column defines the element. The term “X”, “Y”, “Z” refers to the crystallographically defined atomic position of the element measured with respect to the chosen crystallographic origin. The term “B” refers to a thermal factor that measures the mean variation of an atom's position with respect to its average position.

[0117] Reference is made to the sets of atomic co-ordinates and related tables included with this specification and submitted on compact disk (two total compact disks including one original compact disk, and a duplicative copy of original compact disks). Disk No. 1 contains thirty-nine files. Disk No 1 contains the files identified as PDB1FFK.DOC and PDB1FFK.ENT which represent files of co-ordinates defining the large ribosomal subunit; PDB1FFZ.DOC and PDB1FFZ.ENT which represent files of the co-ordinates defining the large ribosomal subunit—CCdA-p-Puro complex; and PDB1FGO.DOC and PDB1FGO.ENT which represent files of the co-ordinates defining the large ribosomal subunit—aa-tRNA analogue complex; 1JJ2.RTF and 1JJ2.TXT which represent files of the co-ordinates defining the completely refined large ribosomal subunit; anisomycin.pdb, blasticidin.pdb, carbomycin.pdb, sparsomycin.pdb, spiramycin.pdb, tylosin.pdb and virginiamycin.pdb which represent files of the co-ordinates defining the large ribosomal subunit bound to anisomycin, blasticidin, carbomycin, sparsomycin, spiramycin, tylosin, and virginiamycin, respectively; three folders: FOLDERA contains the file identified as 1JJ2.PDB (which represents a file of a more highly refined co-ordinates defining the large ribosomal subunit), FOLDERB contains the files identified as ANISOMYC.PDB, BLASTICI.PDB, CARBOMYC.PDB, SPARSOMY.PDB, SPIRAMYC.PDB, TYLOSIN.PDB, and VIRGINIA.PDB (which represent files of the refined co-ordinates defining the large ribosomal subunit bound to anisomycin, blasticidin, carbomycin, sparsomycin, spiramycin, tylosin, and virginiamycin, respectively), FOLDERC contains the files identified as AZITHROM.PDB, and LINEZOLI.PDB (which represent files of the co-ordinates defining the large ribosomal subunit bound to azithromycin and linezolid, respectively); the file identified as erythromycin.pdb (which represents a file of the co-ordinates defining the large ribosomal subunit bound to erythromycin), and azithromycin.pdb and linezolid.pdb (which represent files of the refined co-ordinates defining the large ribosomal subunit bound to azithromycin and linezolid, respectively).

[0118] As will be apparent to those of ordinary skill in the art, the atomic structures presented herein are independent of their orientation, and that the atomic co-ordinates identified herein merely represent one possible orientation of a particular large ribosomal subunit. It is apparent, therefore, that the atomic co-ordinates identified herein may be mathematically rotated, translated, scaled, or a combination thereof, without changing the relative positions of atoms or features of the respective structure. Such mathematical manipulations are intended to be embraced herein.

[0119] As used herein, the terms “atomic co-ordinates derived from” and “atoms derived from” refers to atomic co-ordinates or atoms derived, either directly or indirectly, from an electron density map. It is understood that atomic co-ordinates or atoms derived “directly” from an electron density map refers to atomic co-ordinates or atoms that are identified from and/or fitted to an electron density map by using conventional crystallographic and/or molecular modeling techniques and thus can be considered to be primary atomic co-ordinates or atoms. It is understood that atomic co-ordinates or atoms derived “indirectly” from an electron density map refers to atomic co-ordinates or atoms that are derived from and thus are derivatives or transforms of the primary atomic co-ordinates or atoms and thus can be considered to be secondary atomic co-ordinates or atoms. The secondary atomic co-ordinates or atoms may be generated from the primary atomic co-ordinates or atoms by using conventional molecular modeling techniques. By way of a non limiting example, the atomic co-ordinates for the H. marismortui large ribosomal subunit as described hereinbelow are considered to be primary co-ordinates, whereas the atomic co-ordinates of a mammalian large ribosomal subunit which can be derived from H. marismortui atomic co-ordinates by molecular modeling, including, for example, homology modeling and/or molecular replacement, are considered to be secondary co-ordinates. Both types of atomic co-ordinates and atoms are considered to be embraced by the invention.

[0120] As used herein the terms “bind,” “binding,” “bound,” “bond,” or “bonded,” when used in reference to the association of atoms, molecules, or chemical groups, refer to any physical contact or association of two or more atoms, molecules, or chemical groups (e.g., the binding of a ligand with a ribosomal subunit refers to the physical contact between the ligand and the ribosomal subunit). Such contacts and associations include covalent and non-covalent types of interactions.

[0121] As used herein, the terms “complex” or “complexed” refer to the assembly of two or more molecules to yield a higher order structure, such as, a 50S ribosomal subunit bound to a ligand.

[0122] As used herein, the term “computational chemistry” refers to calculations of the physical and chemical properties of the molecules.

[0123] As used herein, the term “conjugated system” refers to more than two double bonds that are positioned spatially so that their electrons are completely delocalized with the entire system. Aromatic residues contain conjugated double bond systems.

[0124] As used herein, the terms “covalent bond” or “valence bond” refer to a chemical bond between two atoms in a molecule created by the sharing of electrons, usually in pairs, by the bonded atoms.

[0125] As used herein, the term “crystal” refers to any three-dimensional ordered array of molecules that diffracts X-rays.

[0126] As used herein, the term “crystallographic origin” refers to a reference point in the unit cell with respect to the crystallographic symmetry operation.

[0127] As used herein, the term “elongation factor binding domain” refers to the region of the ribosome that interacts directly with elongation factors, including, for example, the elongation factors, EF-Tu and EF-G.

[0128] As used herein, the term “E-site” refers to the locus occupied by a deacylated tRNA molecule as it leaves the ribosome following its participation in peptide-bond formation.

[0129] As used herein, the term “heavy atom derivatization” refers to the method of producing a chemically modified form, also known as a “heavy atom derivative”, of a crystal of the ribosome and the ribosomal subunit and its complexes. In practice, a crystal is soaked in a solution containing heavy metal atom salts, or organometallic compounds, e.g., mercury chlorides, ethyl-mercury phosphate, osmium pentamine, or iridium pentamine, which can diffuse through the crystal and bind to the ribosome or ribosomal subunit. The location(s) of the bound heavy metal atom(s) can be determined by X-ray diffraction analysis of the soaked crystal. This information, in turn, is used to generate the phase information used to construct three-dimensional structure of the complex (Blundell et al. (1976) supra).

[0130] As used herein, the term “homologue” is understood to mean any one or combination of (i) any protein isolated or isolatable from a ribosome or a ribosomal subunit (i.e., a ribosomal protein), (ii) any nucleic acid sequence isolated or isolatable from a ribosome or ribosomal subunit (i.e., a ribosomal RNA), (iii) any protein having at least 25% sequence identity to a ribosomal protein isolated from E. coli or Rattus norvegicus as determined using the computer program “BLAST” version number 2.1.1 implementing all default parameters, or (iv) any nucleic acid having at least 30% sequence identity to a ribosomal RNA isolated from E. coli or Rattus norvegicus as determined using the computer program “BLAST” version number 2.1.1 implementing all default parameters. “BLAST” version number 2.1.1 is available and accessible via the world wide web at the URL ncbi.nlm.nih.gov/BLAST/ or can be run locally as a fully executable program on a standalone computer.

[0131] As used herein, the term “homology modeling” refers to the practice of deriving models for three-dimensional structures of macromolecules from existing three-dimensional structures for their homologues. Homology models are obtained using computer programs that make it possible to alter the identity of residues at positions where the sequence of the molecule of interest is not the same as that of the molecule of known structure.

[0132] As used herein, the term “hydrogen bond” refers to two electronegative atoms (either O or N), which share a hydrogen that is covalently bonded to only one atom, while interacting with the other.

[0133] As used herein, the term “hydrophobic interaction” refers to interactions made by two hydrophobic residues.

[0134] As used herein, the terms “IC ₅₀ or “inhibitory concentration ₅₀” are understood to mean the concentration of a molecule that inhibits 50% of the activity of a biological process of interest, including, without limitation, cell viability and/or protein translation activity.

[0135] As referred to herein, ribosomal proteins are designated “LX” or “SX”, where L stands for “large subunit; S stands for “small subunit”; and X in either case is an integer.

[0136] As used herein, the term “MIR” refers to multiple isomorphous replacement, a technique used for deriving phase information from crystals treated with heavy atom compounds.

[0137] As used herein, the term “molecular graphics” refers to three dimensional representations of atoms, preferably on a computer screen.

[0138] As used herein, the terms “molecular model” or “molecular structure” refer to the three-dimensional arrangement of atoms within a particular object (e.g. the three-dimensional structure of the atoms that comprise a ribosome or ribosomal subunit, and the atoms that comprise a ligand that interacts with a ribosome or ribosomal subunit, particularly with a large ribosomal subunit, more particularly with a 50S ribosomal subunit).

[0139] As used herein, the term “molecular modeling” refers to a method or procedure that can be performed with or without a computer to make one or more models, and, optionally, to make predictions about structure activity relationships of ligands. The methods used in molecular modeling range from molecular graphics to computational chemistry.

[0140] As used herein, the term “molecular replacement” refers to a method that involves generating a model of a ribosome or ribosomal subunit whose atomic co-ordinates are unknown, by orienting and positioning the atomic co-ordinates described in the present invention in the unit cell of the crystals of the unknown ribosome so as best to account for the observed diffraction pattern of the unknown crystal. Phases can then be calculated from this model and combined with the observed amplitudes to give the atomic coordinates of the unknown ribosome or ribosomal subunit. This type of method is described, for example, in The Molecular Replacement Method, (Rossmann, M. G., ed.), Gordon & Breach, New York, (1972).

[0141] As used herein, “noncovalent bond” refers to an interaction between atoms and/or molecules that does not involve the formation of a covalent bond between them.

[0142] As used herein, the term “peptidyl transferase site” refers to the locus in the large ribosomal subunit where peptide bonds are synthesized.

[0143] As used herein, the term “polypeptide exit tunnel” refers to the channel that passes through the large ribosomal subunit from the peptidyl transferase site to the exterior of the ribosome through which newly synthesized polypeptides pass.

[0144] As used herein, the term “protein synthesis inhibitor” refers to any molecule that can reduce, inhibit or otherwise disrupt protein or polypeptide synthesis in a ribosome.

[0145] As used herein, the term “P-site” refers to the locus occupied by a peptidyl-tRNA at the time it participates in the peptide-bond forming reaction.

[0146] As used herein, the term “ribofunctional locus” refers to a region of the ribosome or ribosomal subunit that participates, either actively or passively, in protein or polypeptide synthesis within the ribosome or ribosomal subunit and/or export or translocation of a protein or polypeptide out of a ribosome. The ribofunctional locus can include, for example, a portion of a peptidyl transferase site, an A-site, a P-site, an E-site, an elongation factor binding domain, a polypeptide exit tunnel, and a signal recognition particle (SRP) binding domain. It is understood that the ribofunctional locus will not only have a certain topology but also a particular surface chemistry defined by atoms that, for example, participate in hydrogen bonding (for example, proton donors and/or acceptors), have specific electrostatic properties and/or hydrophilic or hydrophobic character.

[0147] As used herein, the term “ribosomal subunit” refers to one of the two subunits of the ribosome that can function independently during the initiation phase of protein synthesis but which both together constitute a ribosome. For example, a prokaryotic ribosome comprises a 50S subunit (large subunit) and a 30S subunit (small subunit).

[0148] As used herein, the term “ribosome” refers to a complex comprising a large ribosomal subunit and a small ribosomal subunit.

[0149] As used herein, the term “signal recognition particle binding domain” refers to the portion of the ribosome that interacts directly with the signal recognition particle.

[0150] As used herein, the term “space group” refers to the arrangement of symmetry elements of a crystal.

[0151] As used herein, the term “symmetry operation” refers to an operation in the given space group that places the atoms in one asymmetric unit on the corresponding atoms in another asymmetric unit.

[0152] As used herein, the term “twinned” refers to a single macroscopic crystal that contains microscopic domains of the same symmetry that differ significantly in orientation in such a way that the diffraction patterns of all are superimposed. In a twinned crystal the mosaic blocks, or domains, are orientated so that some point in one direction and others point in a second, distinctly different direction, and the directions are such that the diffraction pattern generated by one group of blocks falls exactly on top of the diffraction pattern of the other group.

[0153] As used herein, the term “untwinned” refers to a crystal cell the domains of which are aligned. The domains are also known as the “mosaic blocks.” Most crystals diffract as though they were assemblies of mosaic blocks. One can think of them as small, perfectly ordered regions within the larger crystal, which, overall, is not so well ordered. Each block has the same symmetry and unit cell packing as all the others.

[0154] As used herein, the term “unit cell” refers to a basic parallelepiped shaped block. The entire volume of crystal may be constructed by regular assembly of such blocks. Each unit cell comprises a complete representation of the unit of pattern, the repetition of which builds up the crystal.

II. Structure and Use of the Large Ribosomal Subunit

[0155] A. Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution, Initial Refinement

[0156] The present invention is based, in part, on the development of a novel method for preparing crystals of ribosomes. The novel method provides crystals of the 50S ribosomal subunit that are much thicker than those available earlier and that can diffract X-rays to a resolution of about 2.4 Å. The method eliminates the twinning of crystals that obstructed progress in determining the crystal structure of the 50S ribosomal subunit from H. marismortui for many years. The method of preparing the crystals of the 50S ribosomal subunit is discussed below.

[0157] The present invention is also based, in part, on the atomic structure of the crystal of the 50S ribosomal subunit from H. marismortui that has been derived from a 2.4 Å resolution electron density map that was experimentally phased using heavy atom derivatives. The atomic co-ordinates defining the large ribosomal unit were deposited on Jul. 10, 2000, at Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) (Berman et al. (2000) Nucleic Acid Research 28, 235-242; see also, the web page at the URL rcsb.org/pdb/) with accession number PDB ID: 1FFK.

[0158] Moreover, the present invention is based, in part, on the derivation from the atomic co-ordinates of the following model which is briefly summarized here and discussed in detail in the following sections of the specification. This model includes 2,811 of the 2,923 nucleotides of 23S rRNA, all 122 nucleotides of its 5S rRNA, and structures for the 27 proteins that are well-ordered in the subunit.

[0159] The secondary structures of both 5S and 23S rRNA are remarkably close to those deduced for them by phylogenetic comparison. The secondary structure of the 23S rRNA divides it into 6 large domains, each of which has a highly asymmetric tertiary structure. The irregularities of their shapes notwithstanding, the domains fit together in an interlocking manner to yield a compact mass of RNA that is almost isometric. The proteins are dispersed throughout the structure, concentrated largely on its surface, but they are much less abundant in the regions of the subunit that are of primary functional significance to protein syntheses—the 30S subunit interface, the binding regions for tRNA and the peptidyl transferase active site. The most surprising feature of many of these proteins are the extended, irregular structures of their loops and termini, which penetrate between RNA helices. The primary role of most of the protein s in the subunit appears to be stabilization of the three-dimensional structure of its rRNA.

[0160] 1. Preparation of the Crystal for the 50S Ribosomal Subunit and Structure Determination.

[0161] Several experimental approaches were used t o extend the resolution of the electron density maps of the H. marismortui 50S ribosomal subunit from 5 Å to 2.4 Å including improvements in the crystals. A back-extraction procedure was developed for reproducibly growing crystals that are much thicker than those available earlier and can diffract to 2.2 Å resolution (see, Example 1). Briefly, the crystals were grown at room temperature in hanging drops by vapor diffusion from seeded solutions back-extracted from precipitated subunits. The crystals that resulted had maximum dimensions of 0.5×0.5×0.2 mm and were harvested after three weeks. The twinning of crystals that obstructed progress for many years (Ban et al. (1999) supra) was eliminated by adjusting crystal stabilization conditions (see, Example 1). Crystals were stabilized by gradual transfer into a solution containing 12%, PEG 6000, 22% ethylene glycol, 1.7 M NaCl, 0.5 M NH₄Cl, 100 mM potassium acetate, 30 mM MgCl₂ and 1 mM CdCl₂, pH 6.2, and flash frozen in liquid propane. Reducing the salt concentration below 1.7 M NaCl (KCl) increased the tendency of crystals to become twinned. At salt concentrations as low as 1.2 M nearly all of the crystals were twinned.

[0162] All the X-r ay data used for high resolution phasing were collected at the Brookhaven National Synchrotron Light Source except for two native data sets used, which were collected at the Advanced Photon Source at Argon ne (see, Example 2) (Table 1). Osmium pentamine 132 sites) and Iridium hexamine (84 sites) derivatives proved to be the most effective in producing both isomorphous replacement and anomalous scattering phase information to 3.2 Å resolution (see, Example 2). Inter-crystal density averaging which had contributed significantly at lower resolution, was not helpful beyond about 5 Å resolution. Electron density maps were dramatically improved and their resolutions extended, eventually to 2.4 Å, using the solvent flipping procedure in CNS (Abrahams et al. (1996) Acta Crystollogr. D 52: 30; Brünger et al. (1998) Acta Crystallogr. D Biol. Crystallogr. 54: 905-921).

[0163]

TABLE 1
Statistics for Data Collection, Phase Determination, and Model Construction
Data Statistics
	MIRAS1	MIRAS2
	Native1	Os(NH3)52+	UO2F53−	Native2	Ir(NH3)63+	Os(NH3)63+	Ta6Br122+
Heavy atom	—	30.0	0.5	—	20.0	4.5	3.0
conc. (mM)
Soaking time (hrs)	—	1.5	4	—	24 hrs	24 hrs	24 hrs
Sites no.	—	132	20	—	84	38	9
Resolution (Å)	90-2.4	40-3.5	40-3.8	30-2.9	30-3.2	30-3.5	30-3.8
(*)	(2.5-2.4)	(3.6-3.5)	(3.9-3.8)	(3.0-2.9)	(3.27-3.20)	(3.6-3.5)	(3.97-3.80)
				(3.32-3.22)
λ (Å)	1.00	1.14	1.30	1.00	1.075	1.14	1.255
Observations	6,089,802	1,308,703	596,166	2,832,360	1,823,861	1,646,468	1,288,524
Unique	665,928	429,761	313,863	390,770	541,488	488,275	346,745
Redun. (*)	9.1 (6.5)	3.0 (2.5)	1.9 (1.6)	7.2	3.4	4.3 (4.2)	3.7
Completeness (*)	95.6 (71.0)	99.4 (96.8)	92.0 (54.1)	97.1	93.8	98.1 (99.0)	99.5
1/σl (Last bin)	25.5 (1.9)	13.5 (3.3)	8.9 (1.6)	18.0 (6.4)	12.0 (2.6)	10.6 (2.7)	10.8 (3.2)
Rmerge (*)	8.6 (69.1)	7.2 (32.0)	9.1 (37.9)	11.2 (36.9)	8.5 (29.5)	12.1 (46.0)	12.1 (40.5)
02 (ano)(*)	—	2.8 (1.0)	1.5 (1.0)	—	2.63 (1.48)	1.8 (1.0)	2.42 (1.18)
Rmerge (ano)	—	6.2	8.0	—	6.7	6.9
Riso	—	14.1 (22.7)	26.4 (47.0)	—	12.9 (28.1)	19.5 (39.4)
Phasing Statistics
	Resolution shells (Å): ˜73,200 reflections per bin
	30.0		5.1		4.0		3.5		3.2	Total
MIRAS1 (FOM)		0.52		0.31		0.14		—		0.32
Os(NH3)52+
Phasing power		0.87		0.72		0.66		—		0.75
Phasing power (SAD)		1.40		0.58		0.26		—		0.75
Rcullis (centric)		0.62		0.65		0.67		—		0.65
UO2F53−
Phasing Power		0.47		0.33		0.28		—		0.36
Phasing power (SAD)		0.46		0.25		—		—		0.36
Rcullis (centric)		0.72		0.77		0.75		—		0.75
MIRAS2 (FOM)		0.48		0.40		0.28		0.12		0.33
Ir(NH3)63+
Phasing power		1.02		0.92		0.78		0.66		0.89
Phasing power (SAD)		2.02		1.60		1.22		0.83		1.47
Rcullis (centric)		0.58		0.63		0.70		0.74		0.63
Os(NH3)63+
Phasing power		0.62		0.57		0.58		0.58		0.59
Phasing power (SAD)		0.47		0.39		—		—		0.42
Rcullis (centric)		0.78		0.78		0.78		0.76		0.78
Ta6Br122+ (Used for SAD phasing only)
Phasing power (SAD)		2.77		0.35		0.13		—		1.19
FOM(MIRAS1+MIRAS2+SAD)		0.76		0.51		0.31		0.14		0.37
Model Statistics
	rms deviations:	Average B factors (Å2)
Resolution range (Å)	90.0-2.4	Bonds (Å)	0.0064	All atoms	37.4
Reflections	577,304	Angles (°)	1.19	23S rRNA	32.3
Rcryst (%)	25.2	Dihedrals (°)	28.8	5S rRNA	43.2
Rfree (%)	26.1	Impropers (°)	1.68	Minimum/Max B factors (Å2)	70/107.9
λ, wavelength; Redun., redundancy; (*) last-resolution shell.
Riso: Σ|FPH − FP|/ΣFPH, where FPH and FP are the derivative and the native structure factor amplitudes, respectively. Rsym: ΣΣi|l(h) − I(h)i|/ΣΣ:I(h)i, where l(h) is the mean intensity after reflections. Phasing power: r.m.s. isomorphous difference divided by the r.m.s.
# residual lack of closure. Rcullis: Σ(∥FPH − FP|−|FH(calc)∥)/Σ|FPH −FP|, where FPH is the structure factor of the derivative and FP is that of the native data. The summation is valid only for centric reflection. FOM (figure of merit): mean value of the cosine of the error in phase angles. Abbreviations: MIRAS: multiple isomorphous replacement, anomalous scattering; SAD: single wavelength
# anomalous diffraction; FOM: figure of merit. Except for regions obscured by disorder, the experimentally-phased, 2.4 Å resolution electron density map was of sufficient quality so that both protein and nucleic acid sequencing errors could be identified and corrected. Each nucleotide could be fitted individually and the difference between A and G was usually clear without reference to the chemical sequence, as was the distinction between purines and pyrimidines (FIG. 1).

[0164] Subtraction of the atomic model from the experimental electron density map leaves no significant density except for water and ions, showing that the model accounts for all the macromolecular density. Preliminary refinement of the model was achieved using a mixed target in the program CNS (Brünger et al. (1998) supra). The model was further refined in real space against the 2.4 Å electron density map using the program TNT (Tronrud (1997), Macromolecular Crystallography, Part B, Methods In Enzymology), which yielded a model with a free R-factor of 0.33. One additional round of mixed target refinement of both atomic positions and B-factors using CNS led to the structure described below. Its free R-factor is 0.27 (Table 1).

[0165] 2. Sequence Fitting and Protein Identification.

[0166] The sequence of 23S rRNA was fit into the electron density map nucleotide by nucleotide starting from its sarcin/ricin loop sequence (A2691-A2702) (E. coli numbers A2654 to A2665), whose position had been determined at 5 Å resolution (Ban et al. (1999) supra). Guided by the information available about the secondary structures of 23S rRNAs (Gutell, R.R. (1996), “Comparative Sequence Analysis and the Structure of 16S and 23S rRNA,” Ribosomal RNA. Structure Evolution, Processing, and Function in Protein Biosynthesis, (Dahlberg A. and Zimmerman B., eds.), CRC Press, Boca Raton, Fla. pp. 11-128), the remaining RNA electron density neatly accommodated the sequence of 5S rRNA. The interpretation of protein electron density corresponding to the protein was more complicated because each protein region had to be identified chemically before the appropriate sequence could be fit into it, but about 4,000 amino acid residues were fit into electron density.

[0167] The H. marismortui 50S subunit appears to contain thirty-one proteins, and there are sequences in the Swiss-Prot data bank for twenty eight of those thirty one proteins, including one, HMS6 or L7ae, that was originally assigned to the small ribosomal subunit (Whittmann-Liebold et al. (1990) supra). The three remaining proteins were identified using the sequences of the ribosomal proteins from eukaryotes and other archeal species as guides. No electron density was found for one of the H. marismortui large ribosomal subunit proteins in the sequence database, LX. Either the assignment of LX to the large subunit is in error, or LX is associated with a disordered region of the subunit, or LX is absent from the subunits examined altogether.

[0168] The 2.4 Å resolution electron density map lacks clear electron density for proteins L1, L10, L11, and L12, the positions of which are known from earlier low resolution X-ray and/or electron microscopic studies. These proteins are components of the two lateral protuberances of the subunit, which are both poorly ordered in these crystals. L1 is the sole protein component of one of them (Oakes, M. et al. (1986)), Structure, Function and Genetics of Ribosomes, (Hardesty, B. and Kramer, G., eds.) Springer-Verlag, New York, N.Y., 47-67) and is evident in 9 Å resolution density maps of the subunit (Ban et al. (1998) supra), but not at higher resolutions. L10, L11 and L12 are components of the other protuberance, which is often referred to as the L7/L12 “stalk” (Oakes et al. (1986) supra). L11 and the RNA to which it binds were located in the 5 Å resolution electron density map of the H. marismortui large subunit (Ban et al. (1999) supra) using the independently determined crystal structures of that complex (Conn GL et al. (1999) Science 284: 1171-1174; Wimberly et al. (1999) Cell 97: 491-502). A protein fragment (about 100 residues) that is associated with the RNA stalk that supports the L11 complex can be seen in the 2.4 Å resolution map. Based on location, it must be part of L₁₀. There is no electron density corresponding to L 12 seen at any resolution, but the L 12 tetramer is known to be attached to the ribosome through L10, and the L10/L12 assembly is known to be flexible under some circumstances (Moller et al. (1986) Structure, Function, and Genetics of Ribosomes, Supra, pp. 309-325), which may explain its invisibility here.

[0169] The structures of eubacterial homologues of proteins L2, L4, L6, L14, and L22 have previously been determined in whole or in part (see, Table 2). L2, L6 and L14 were initially located in the 5 Å resolution map (Ban et al. (1999) supra). L4 and L22 have now been identified and positioned the same way. Electron density corresponding to most of the remaining proteins was assigned by comparing chain lengths and sequence motifs deduced from the electron density map with known sequence lengths, guided by the information available about relative protein positions (Walleczek et al. (1988) EMBO J. 7: 3571-3576) and protein interactions with 23S rRNA and 5S rRNA (Ostergaard et al. (1998) J. Mol. Biol. 284: 227-240). Each of the protein electron density regions so identified is well accounted for by its amino acid sequence.

[0170] The most interesting of the proteins identified by sequence similarity was L7ae, which first appeared to be L30e. The L30e identification seemed plausible because the structure of yeast L30 superimposes neatly on the electron density of L7ae, and the structure of the RNA to which L7ae binds closely resembles that of the RNA to which yeast L30 binds (Mao, H. et al. (1999) Nat. Struct. Biol. 6: 1139-1147). Nevertheless, the sequence of HMS6, which by sequence similarity is a member of the L7ae protein family, fits the electron density better. Four of the other proteins identified by sequence similarity, L24e, L37e, L37ae, and L44e, contain zinc finger motifs. The rat homologues of L37e and L37ae were predicted to be zinc finger proteins on the basis of their sequences (Wool et al. (1995) supra), and this prediction helped identify their homologues in H. marismortui.

[0171]

TABLE 2
Large Subunit Proteins from Haloarcula marismortui
	Interactions
Name1	Hmlg2	Lgth3	Conf4	1	2	3	4	5	6	5S	Proteins
L1*		211	glb.					+			none
L2†	RL8	239	glb + ext		+	+	+	+			(L37ae)
L3	RL3	337	glb + ext		+		+	+	+		L14, L24e, (L13)
L4†	RL4	246	glb + ext	+	+			Å			(L18e), (L24), (L37e)
L5	RL11	176	glb					+		+	L18
L6	RL9	177	glb		Å			Å	+		(L13)
L10*	RP0	348	glb?		+						L12
L11*	RL12	161	glb		+						none
L12*	RL1/2	115	glb								L10
L13	RL13a	145	glb		+			Å	Å		(L3), (L6)
L14	RL23	132	glb				+	+	+		L3, L24e
L15	RL27a	164	glb + ext	+	+			+			(L18e), (L32e)
L18	RL5	186	glb + ext		Å			+		+	L5, L21e
L19	RL19	148	glb + ext		+	+	+		Å		none
L22	RL17	154	glb + ext	+	Å	+	+	+	+		none
L23	RL23a	84	glb	Å		+					L29, (L39e)
L24	RL26	119	glb + ext	+							(L4)
L29	RL35	70	glb	+							L23
L30	RL7	154	glb		+					+	none
L18e	RL18	115	glb		+						(L4), (L15)
L21e	RL21	95	glb		+			+		Å	L18
L24e	RL24	66	glb				Å		+		L3, L14
L31e	RL31	91	glb			+	+		+		none
L32e	RL32	240	glb	Å	+						(L15)
L37e	RL37	56	glb + ext	+	+	+	Å				(L4)
L39e	RL39	49	ext	+		+					(L23)
L44e	RL36a	92	glb + ext	+			Å	+			(L15e)
L7ae	R17a	110	glb	Å							L15e
L10e	RL10	163	glb		+			+		Å	none
L15e	RL15	184	glb + ext	+	Å	Å	Å	+			(L44e), L7ae
L37ae	RL37a	72	glb + ext		+	+	+				L2
The top block of proteins include all those known to have eubacterial homologues of the same name. The second block lists proteins found in the H. marismortui large ribosomal subunit that have only eukaryotic homologues (Wittmann-Liebold et al. (1990) supra). Their names are all followed by the letter “e” to distinguish them from eubacterial proteins that would otherwise have the same name. The third block are large subunit proteins for which no H. marismortui sequence
# yet exists. They are identified by sequence homology using standard L names.
1The structures of all or part of homologues of the following proteins were previously determined: L1 (Nevskaya et al. (2000) Struct. Fold. Des. 8: 363), L2 (Nakagawa, A. et al. (1999) EMBO J. 18: 1459-1467), L4 (Wahl et al. (2000) EMBO J. 19: 807-818), L6 (Golden et al. (1993) EMBO J. 12: 4901-4908), L11 (Conn et al. (1999) supra; Wimberly et al. (1999) supra; Markus et al. (1997) Nature Struct. Biol. 4: 70-77), L12 (Leijonmarck, M. et al.
# (1980) Nature 286: 824-827), L14 (Davies et al. (1996) Structure 4: 55-66), L22 (Unge et al. (1998) Structure 6: 1577-1586), L30 (Wilson et al. (1986) Proc. Nat. Acad. Sci. USA 83: 7251-7255). All other structures, except 10, have been newly determined in this study.
2Rat homologue. Rat equivalents to H. marismortui proteins are from (Mao et al. (1999) supra).
3Sequence chain length.
4Conformation: glb = globular; ext = extension
5The protein interactions with the 6 domains of 23S rRNA, 5S rRNA and other proteins are specified. (+) implies that the interaction is substantial. (Å) implies a weak, tangential interaction. Protein names are shown in parentheses implies that the interactions are weak; otherwise, the interaction is substantial.
*All entries so designated describe proteins that are not fully represented in the electron density maps described here. The summary information provided is derived from literature sources and is included here for completeness only.
†The structure available for this protein in isolation does not include the extension(s) reported here.

[0172] 3. General Appearance of the Subunit

[0173] In its crown view (see FIG. 2), the large ribosomal subunit, which is about 250 Å across, presents its surface that interacts with the small subunit to the viewer with the three projections that radiate from that surface pointed up. Although the protuberance that includes L1 is not visible in the 2.4 Å resolution electron density map, the structure of L1, which has been determined independently (Nikonov et al. (1996) EMBO J. 15: 1350-1359), has been positioned approximately in lower resolution maps (Ban et al. (1998) supra) and is included here to orient the reader. It is evident that, except for its two lateral protuberances, the large ribosomal subunit is monolithic. There is no hint of a division of its structure into topologically separate domains. In addition, partly because it lacks obvious domain substructure but also because it is so large, it is impossible to comprehend looking at it as a whole. In order to convey to the reader a sense of how it is put together, the subunit must be dissected into its chemical components.

[0174] 4. RNA Secondary Structure.

[0175] All the base pairs in H. marismortui 23S rRNA stabilized by at least two hydrogen bonds were identified using a computer program that searched the structure for hydrogen bond donors and acceptors separated by less than 3.2 Å. Bases linked by at least two such bonds were considered paired if the angle between their normals was less than 45°, and the angle between bonds and base normals was also less than 45°. Based on the results of this analysis, a secondary structure diagram has been prepared in the format standard for 23S/28S rRNAs (see, FIG. 3). The secondary structure predicted for this molecule by phylogenetic comparison was remarkably accurate, but it did not find all of the tertiary pairings and failed to identify interactions involving conserved bases. In addition to base pairs of nearly every type, the RNA contains numerous examples of well-known secondary structure motifs such as base triplets, tetraloops, and cross-strand purine stacks, but no dramatically new secondary structure motifs have been identified so far.

[0176] The secondary structure of this 23S rRNA consists of a central loop that is closed by a terminal stem, from which 11 more or less complicated stem/loops radiate. It is customary to describe the molecule as consisting of 6 domains, and to number its helical stems sequentially starting from the 5′ end (see, FIG. 4) (Leffers et al. (1987) supra). The division of the molecule into domains shown in FIG. 4 deviates from standard practice with respect to helix 25, which is usually considered to be part of domain I. It is placed in domain II because it interacts more strongly with domain II than it does with the other elements of domain I.

[0177] There are five sequences longer than 10 nucleotides in 23S rRNA whose structures cannot be determined from the 2.4 Å resolution map due to disorder. Altogether they account for 207 out of the 232 nucleotides missing from the final model. The disordered regions are: (1) all of helix 1, (2) the distal end of helix 38, (3) helix 43/44 to which ribosomal protein L11 binds, (4) the loop end of stem/loop 69, and (5) helix 76/77/78, which is the RNA structure to which L1 binds. For completeness, these regions are included in FIG. 3 (in gray) with their secondary structures determined phylogenetically.

[0178] 5. Overall Architecture of rRNA.

[0179] The six domains of 23S rRNA and 5S rRNA all have complicated, convoluted shapes that nevertheless fit together to produce a compact, monolithic RNA mass (see FIGS. 4(A) and 4(B)). Thus despite the organization of its RNAs at the secondary structure level, in three-dimensions, the large subunit is a single, gigantic domain. In this respect, it is quite different from the small subunit, which is a flatter object that is not at all monolithic. Even in low resolution electron micrographs the small subunit consists of three structural domains, each of which, it turns out, contains one of the three secondary structure domain of its RNA (Noller et al. (1990) The Ribosome: Structure, Function, and Evolution, supra, pp. 73-92). This qualitative difference between the two subunits may reflect a requirement for conformational flexibility that is greater for the small subunit.

[0180] Domain I, which looks like a mushroom (see, FIG. 4E)), lies in the back of the particle, behind and below the L1 region. The thin part of the domain starts in the vicinity of domain VI, which is where its first and last residues are located. Helices 1 and 25 span the particle in the back and then the domain expands into a larger, more globular structure below and behind the L1 region.

[0181] The largest of the six 23S rRNA domains, domain II, which accounts for most of the back of the particle, has three protrusions that reach towards the subunit interface side of the particle (see, FIG. 4(F)). One of them (helix 42-44) is the RNA portion of the L7/L12 stalk, which is known to interact with elongation factors, is not well-ordered in these crystals. The second domain II protrusion is helix 38, which is the longest, unbranched stem in the particle. It starts in the back of the particle, bends by about 90 degrees and protrudes towards the small subunit between domains V and 5S rRNA. The third region, helix 32-35.1, points directly towards the small subunit and its terminus, the loop of stem/loop 34, interacts directly with the small ribosomal subunit (Culver et al. (1999) Science 285: 2133-2135). This loop emerges at the subunit interface between domains III and IV.

[0182] Domain III is a compact globular domain that occupies the bottom left region of the subunit in the crown view (see, FIG. 4(G)). It looks like a four pointed star with the origin of the domain (stem/loop 48) and stem/loops 52, 57, and 58 forming the points. The most extensive contacts of domain III are with domain II, but it also interacts with domains I, IV and VI. Unlike all the other domains, domain III hardly interacts with domain V at all; the sole contact is a single van der Waals contact involving a single base from each domain.

[0183] Domain IV accounts for most of the interface surface of the 50S subunit that contacts the 30S subunit (see, FIG. 4(H)). It forms a large diagonal patch of flat surface on that side of the subunit, and connects to domains III and V in the back of the particle. Helices 67-71 are the most prominent feature of domain IV, and form the front rim of the active site cleft, which is clearly visible at low resolution (see, FIG. 2). This is one of the few regions of the 23S rRNA that is not extensively stabilized by ribosomal proteins. Helix 69 in the middle of this ridge interacts with the long penultimate stem of 16S rRNA in the small ribosomal subunit and can be viewed as a divider separating A-site bound tRNAs from P-site bound tRNAs.

[0184] Domain V, which is sandwiched between domains IV and II in the middle of the subunit, is known to be intimately involved in the peptidyl transferase activity of the ribosome. Structurally the domain can be divided into three regions (see, FIGS. 4(I) and 4(J)). The first starts with helix 75 and ultimately forms the binding site for protein L 1. The second, which consists of helices 80-88, forms the bulk of the central protuberance region, and is supported in the back by the 5S rRNA and domain II. The third region, which includes helices 89-93, extends towards domain VI and helps stabilize the elongation factor binding region of the ribosome.

[0185] The smallest domain in 23S rRNA, domain VI, which forms a large part of the surface of the subunit immediately below the L7/L12 stalk, resembles a letter X with a horizontal bar at the bottom (see, FIG. 4(K)). An interesting region of this domain is the sarcin-ricin loop (SRL) (stem/loop 95), the structure of which has been extensively studied in isolation (Szewczak et al. (1995) J. Mol. Biol. 247: 81-98). The SRL is essential for factor binding, and ribosomes can be inactivated by the cleavage of single covalent bonds in this loop (Wool et al (1992) TIBS 17: 266-269). As suggested by nucleotide protection data, the major groove of this loop is exposed to solvent (Moazed et al. (1988) Nature 334: 362-364), and its conformation is stabilized by proteins and through interaction with domain V that involves two bases on the minor grove side. The nucleotides involved are A 2699 and G 2700 in domain VI, and A 2566 and G 2567 in domain V.

[0186] 5S ribosomal RNA, which is effectively the seventh RNA domain in the subunit, consists of three stems radiating out from a common junction called loop A (see, FIG. 4(D)). In contrast to what is seen in the crystal structure of fragment 1 from E. coli 5S rRNA (Correll et al. (1997) Cell 91: 705-712), the helix 2/3 arm of the molecule stacks on its helix 4/5 arm, not helix 1 (see, FIG. 4(L)). This arrangement results from a contorted conformation of loop A residues that involves two stacked base triples. Indeed, from the secondary structure point of view, the loopA-helix 2,3 arm of 5S rRNA is quite remarkable. Nowhere else in the subunit is there a higher concentration of unusual pairings and of convoluted RNA secondary structure.

[0187] 6. Sequence Conservation and Interactions in 23S rRNA.

[0188] While 23S/28S rRNAs contain many conserved sequences, they also vary substantially in chain length. Shorter 23S/28S rRNAs are distinguished from their longer homologues by the truncation of, or even the elimination of entire stem/loops, and by comparing sequences, one can identify a minimal structure that is shared by all (Gerbi (1995) Ribosomal RNA: Structure, Evolution, Processing and Function in Protein Biosynthesis, supra, pp. 77-88). The expansion sequences in the 23S rRNA of H. marismortui, i.e., the sequences it contains that are larger than the minimum, are shown in FIG. 5 in green. They are largely absent from the subunit interface surface of the particle, but they are abundant on its back surface, far from its active sites. This is consistent with low resolution electron microscopic observations suggesting that the region of the large subunit whose structure is most conserved is the surface that interacts with the small subunit (Dube et al. (1998) Structure 6: 389-399).

[0189] There are two classes of conserved sequences in 23S rRNA. One contains residues concentrated in the active site regions of the large subunit. The second class consists of much shorter sequences scattered throughout the particle (FIG. 5: red sequences). The SRL sequence in domain VI and the cluster of conserved residues belonging to domain V that are located at the bottom of the peptidyl transferase cleft are members of the first class. They are conserved because they are essential for substrate binding, factor binding and catalytic activity. Most of the residues in the second class of conserved residues are involved in the inter- and intra-domain interactions that stabilize the tertiary structure of 23S rRNA. Adenosines are disproportionately represented in this class. The predominance of A's among the conserved residues in rRNAs has been pointed out in the past (Ware et al. (1983) Nucl. Acids. Res. 22: 7795-7817).

[0190] In addition to its reliance on A-dependent motifs, the tertiary structure of the domains of 23S rRNA and their relative positions are stabilized by familiar tertiary structure elements like RNA zippers and tetraloop/tetraloop receptor motifs (Moore, P. B. (1999) Annu. Rev. Biochem. 68: 287-300), and in many places, base pairs and triples stabilize the interactions of sequences belonging to different components of the secondary structure of 23S rRNA.

[0191] Interestingly, 5S rRNA and 23S rRNA do not interact extensively with each other. The few RNA/RNA interactions there are involve the backbones of the helix 4/5 arm of 5S rRNA and the backbone of helix 38 of 23S rRNA. Most of the free energy and all of the specificity of 5S rRNA binding to the large ribosomal subunit appears to depend on its extensive interactions with proteins that act as modeling clay sticking it to the rest of ribosome.

[0192] 7. Proteins in the 50S Ribosomal Subunit.

[0193] The structures of twenty seven proteins found in the large ribosomal subunit of H marismortui (Table 2) have been determined. Twenty-one of these protein structures have not been previously established for any homologues, and the structures of the six that do have homologues of known structure have been rebuilt into the electron density map using their H. marismortui sequences. In addition, there are structures available for homologues of H. marismortui L1, L11 and L12, which cannot be visualized in the 2.4 Å resolution electron density map. Only the structure of L10 is still unknown among the thirty one proteins known to be present.

[0194] Not every one of these structures is complete. For example, an entire domain of L5 is missing from the electron density, presumably because of disorder. L32e is also noteworthy in this regard. About twenty residues from its N-terminus are not seen in the electron density map, and the electron density map suggests that its C-terminal residue is covalently bound to the most N-terminal of its visible residues.

[0195] Of the thirty large subunit ribosomal proteins whose structures are known, 17 are globular proteins, similar in character to thousands whose structures are in the Protein Data Bank (Table 2). The remaining thirteen proteins either have globular bodies with extensions protruding from them (“glb+ext”) or are entirely extended (“ext”). Their extensions often lack obvious tertiary structure and in many regions are devoid of secondary structure as well (see FIG. 6). These extensions may explain why many ribosomal proteins have resisted crystallization in isolation. The exceptions that prove the rule are L2 and L4, both of which are proteins belonging to the “glb+ext” class. Protein L2 was crystallized and its structure solved only after its extensions had been removed (Nakagawa et al. (1999) supra), and one of the two regions of L4 that are extended in the ribosome is disordered in the crystal structure of intact L4 (Wahl et al. (2000) supra).

[0196] Except for proteins L1, L7, L10 and L11, which form the tips of the two lateral protuberances, the proteins of the 50S subunit do not extend significantly beyond the envelope defined by the RNA (see, FIG. 7). Their globular domains are found largely on the particle's exterior, often nestled in the gaps and crevices formed by the folding of the RNA. Thus, unlike the proteins in spherical viruses, the proteins of the large ribosomal subunit do not form a shell around the nucleic acid with which they associate, and unlike the proteins in nucleosomes, they do not become surrounded by nucleic acid either. Instead, the proteins act like mortar filling the gaps and cracks between “RNA bricks.”

[0197] The distribution of proteins on the subunit surface is nearly uniform, except for the active site cleft and the flat surface that interacts with the 30S subunit. In the crown view the proteins lie around at the periphery of the subunit (see, FIG. 7(A)), but when viewed from the side opposite the 30S subunit binding site (the “back side”), they appear to form an almost uniform lattice over its entire surface (see, FIG. 7(B)). Similarly, the bottom surface of the subunit, which includes the exit of polypeptide tunnel, is studded with proteins (see, FIG. 7(C)). Indeed, the 5 proteins that surround the tunnel exit may play a role in protein secretion since they are part of the surface that faces the membrane and the translocon when membrane and secreted proteins are being synthesized.

[0198] Although FIG. 7 shows protein chains disappearing into the ribosome interior, the degree to which proteins penetrate the body of the particle can only be fully appreciated when the RNA is stripped away. The interior of the particle is not protein-free, but it is protein-poor compared to the surface of the particle. Extended tentacles of polypeptide, many of which emanate from globular domains on the surface, penetrate into the interior, filling the gaps between neighboring elements of RNA secondary structure (see, FIG. 8(E)). The bizarre structures of these extensions are explained by their interactions with RNA.

[0199] Although extended, non-globular structures are rare in the protein data base, they are not unknown. Extended protein termini often form inter-protein contacts, e.g., in viral capsids, presumably adopting fixed structures only upon capsid formation. The basic “tails” of histones may behave the same way when nucleosomes form. The N-terminal sequences of capsid proteins are often positively charged, and in virus crystal structures, the electron density for these sequences often disappears into the interior of the virus where these sequences presumably interact with asymmetrically arranged nucleic acid. The interactions observed in the ribosome could be useful models for these viral interactions.

[0200] The interactions of extended polypeptides and RNA in the large subunit, which stabilizes its massive nucleic acid structure, result in a tangle of RNA and protein in the center of the subunit (see, FIGS. 8(A) and 8(B)). It is hard to imagine such an object assembling from its components efficiently in anything other than a highly ordered manner. Chaperones may well be required to prevent the aggregation of the extended regions of these proteins, which are likely to be disordered outside the context provided by rRNA, and to manage the folding of rRNA.

[0201] 8. Protein and RNA Interactions.

[0202] Because protein permeates the large subunit to a surprising degree, there are only a few segments of the 23S rRNA that do not interact with protein at all. Of the 2923 nucleotides in 23S rRNA, 1157 nucleotides make at least van der Waals contact with protein (see, FIG. 8(D)), and there are only ten sequences longer than twenty nucleotides in which no nucleotide contacts protein. The longest such sequence contains forty-seven nucleotides, and is the part of domain IV that forms the ridge of the active site cleft.

[0203] The extent of the interactions between RNA and protein that occur when the large subunit assembles can estimated quantitatively. Using the Richards algorithm (Lee, B. et a. (1971) J. Mol. Biol. 55: 379-400) and a 1.7 Šradius probe to compute accessible surface areas, it can be shown that 180,000 Ų of surface becomes buried when the subunit forms from its isolated, but fully structured components. This is about half their total surface area. The average is about 6,000 Ų per protein. While this is an enormous amount compared to the surface buried when most protein oligomers form, it should be recognized that ribosome assembly must be accompanied by a large loss in conformational entropy that does not occur when most proteins oligomerize. The extended protein termini and loops of the ribosomal proteins are almost certainly flexible in isolation, and in the absence of protein, the RNA is probably quite flexible as well. Thus, the burial of a large amount of surface area may be required to provide the energy necessary to fix of the structures of these molecules.

[0204] All of the proteins in the particle except L12, interact directly with RNA and all but seven of the remaining thirty proteins interact with two rRNA domains or more (Table 2). The “champion” in this regard is L22, which is the only protein that interacts with RNA sequences belonging to all 6 domains of the 23S rRNA (see, FIG. 8(C)). The protein-mediated interactions between 5S rRNA and 23S rRNA are particularly extensive. Protein L18 attaches helix 1 and helix 2/3 of 5S rRNA to helix 87 of 23S rRNA. Protein L31e mediates an interaction between the same part of 5S rRNA and domains II and V. Loop C is linked to domain V by protein L5 and loop D is attached to domains II and V by protein L10e. Whatever else they may do, it is evident that an important function of these proteins is stabilization of the relative orientations of adjacent RNA domains. Several also help secure the tertiary structures of the domains with which they interact.

[0205] Since most ribosomal proteins interact with many RNA sequences and the number of proteins greatly exceeds the number of RNA domains, it can hardly come as a surprise that every rRNA domain interacts with multiple proteins (Table 2). Domain V, for example, interacts with thirteen proteins, some intimately and a few in passing.

[0206] It is clear that the oligonucleotide binding experiments long relied on for information about the RNA binding properties of ribosomal proteins have underestimated their potential for interacting with RNA. The high-affinity RNA binding site identified on a protein by such an experiment may indeed be important for ribosome assembly, but its many, weaker interactions with other sequences are likely to be missed, and they too may be vital for ribosome structure. Most ribosomal proteins crosslink RNA and crosslinking is impossible without multiple interactions. Similar considerations may apply to proteins that are components of other ribonucleoproteins such as the sliceosome.

[0207] Of the seven proteins that interact with only one domain, three (L1, L10, L11) participate directly in the protein synthesis process. Rather than being included in the ribosome to ensure that the RNA adopts the proper conformation, it seems more appropriate to view the RNA as being structured to ensure their correct placement. Another three (24, L29, L18e) interact with several secondary structure elements within the domains to which they bind, and presumably function to stabilize the tertiary structures of their domains. The last of the single RNA domain proteins, L7ae, is puzzling. On the one hand, it cannot function as an RNA stabilizing protein because it interacts with only a single, short sequence in domain I, and on the other hand, it is far from the important functional sites in the subunit, the peptidyl transferase site and factor binding site. It is quite close to L1, however, which appears to be important for E-site function (Agrawal et al., (1999) J. Biol. Chem. 274: 8723-8729), and maybe it is involved in that activity.

[0208] While many ribosomal proteins interact primarily with RNA, a few interact significantly with other proteins. The most striking structure generated by protein-protein interactions is the protein cluster composed of L3, L6, L14, L19 and L24e that is found close to the factor binding site. The protein surface they provide may be important for factor interactions.

[0209] The structure presented above illuminates both the strengths and weaknesses of approaches to complex assemblies that depend on determining the structures of components in isolation. The structures of the globular domains of homologues of the proteins in large ribosomal subunit from H. marismortui are largely the same as those of the corresponding domains in the intact subunit, though adjustments in domain positions are sometimes required. Consequently, these structures were very useful for locating proteins and interpreting lower resolution electron density maps. However, for obvious reasons, the structures of the extended tails and loops of ribosomal proteins cannot be determined in the absence of the RNAs that give them structure, and the feasibility of strategies that depend on producing low molecular weight RNA-protein complexes that have all the RNA contacts required to fix the structures of such proteins seems remote. RNA is also a problem. While the sarcin/ricin loop has much the same structure in isolation as it does in the ribosome, the structure of 5S rRNA in isolation differs in some respects from what is seen in the ribosome, and the structure of the isolated P-loop (Puglisi et al. (1997) Nat. Struct. Biol. 4: 775-778) does not resemble the structure of the P-loop in the ribosome at all. Clearly a “structural genomics” approach to the ribosome, which would have entailed determining the structures of all its proteins and all possible rRNA fragments, would not have worked. It may not be successful for other macromolecular assemblies either.

[0210] B. The Structural Basis of Ribosome Activity in Peptide Bond Synthesis

[0211] Analysis of the atomic co-ordinates discussed in section IIA above together with additional atomic co-ordinates of a ribosomal subunit complexed with various analogues, similarly refined, permit an analysis of ribosome function. Accordingly, the present invention is also based on the crystals of Haloarcula marismortui 50S ribosomal subunit complexed either with the Yarus transition state analogue, CCdA-p-Puro, or with a mini-helix analogue of an aminoacyl-tRNA. The present invention provides the structures of both complexes. The atomic co-ordinates of the structure of both complexes were deposited on Jul. 26, 2000, at Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) (Berman et al (2000) Nucleic Acid Research 28: 235-242; see also, the web page at the URL rcsb.org/pdb/) with accession numbers PDB ID: 1FFZ (50S ribosome/ CCdA-p-Puro complex) and PDB ID: 1FG0 (50S ribosome/aa-tRNA analogue).

[0212] As discussed below, the complete atomic structures of the large ribosomal subunit and its complexes with two substrate analogues show that the ribosome is a ribozyme. The complete atomic structures also provide information regarding the catalytic properties of its all-RNA active site. Both substrate analogues are contacted exclusively by conserved rRNA residues from domain V of 23S rRNA; there are no protein side-chains closer than about 18 Å to the peptide bond being synthesized. The mechanism of peptide bond synthesis appears to resemble the reverse of the deacylation step in serine proteases, with the base of A2486 (A2451) in E. coli playing the same general base role as His57 in chymotrypsin. The unusual pKa that A2486 must possess to perform this function probably derives from its hydrogen bonding to G2482 (G2447) which interacts with a buried phosphate that could stabilize the unusual tautomers of two bases which is required for catalysis. The polypeptide exit tunnel is largely formed by RNA but has significant contributions from proteins L22, L39 and L4 and its exit is encircled by proteins L19, L22, L23a, L24 and L29.

[0213] The CCdA from the Yarus analogue binds to the so-called P-loop and hence must be in the P-site. Only the terminal-CCA of the aa-tRNA analogue is visible, but since it interacts appropriately with the A-loop (Kim et al. (1999) Molec. Cell 4: 859-864), it must be in the A-site. The puromycin group occupies the same location in both structures, and there are no proteins near that site. Hence, the catalytic activity of the active site must depend entirely on RNA. The N3 of A2486 (E. coli A2451) is the titratable group nearest to the peptide bond being synthesized and is likely functioning as a general base to facilitate the nucleophilic attack by the α-amino group of the A-site substrate. In order to function in this capacity, the pKa of this base has to be roughly 5 units higher than normal.

[0214] 1. Structures of Substrate Analogue Complexes.

[0215] In order to establish how substrates interact at the A-site and P-site of the large subunit, two substrate analogues were used. One of the analogues, which was designed to mimic the acceptor stem of an aa-tRNA and bind to the A-site, was a twelve base-pair RNA hairpin with an aminoacylated, four-nucleotide extension on its 3′ end (see, FIG. 9). The sequence used was that of the tRNA tyr acceptor stem and it is terminated with puromycin, which itself is an analogue of tyrosyl-A76. The second analogue used was the Yarus transition state analogue, CCdA-p-puromycin. As in the case of the A-site substrate analogue, the puromycin of the Yarus inhibitor is expected to bind at the A-site, while its CCDA moiety should bind at the P-site.

[0216] The positions of the Yarus inhibitor and the tRNA acceptor stem analogue were determined by soaking these molecules into crystals of the H. marismortui 50S ribosomal subunit, measuring diffraction data to 3.2 Å resolution and calculating difference electron density maps (Welch et al. (1997) Biochemistry 36: 6614-6623). Maps of the complexes were also calculated using 2F_o(complexed)-F_o(uncomplexed) as coefficients, to examine the shifts in the positions of ribosome residues that occur when these analogues bind (see, FIG. 10(B) and Table 3).

[0217]

TABLE 3
Statistics for Data Collection and Scaling.
Crystal	Native A	Native B	CcdAp-Puro	Mini-helix
Soak time	—	—	24	24
(hours)
Soak	—	—	100	100
concentration
(μM)
Wavelength	1.0	1.0	1.0	1.0
(Å)
Observations	1,571,171	1,344,877	2,590,726	2,712,813
Unique	284,533	369,167	367,284	447,121
Redundancy	5.5	3.6	7.0	6.0
Resolution	70.0-3.2	70.0-3.0	70.0-3.0	70.0-2.8
limits (Å)
(High-	(3.26-3.20)	(3.05-3.00)	(3.23-3.17)	(3.08-3.02)
resolution bin)*
Completeness	94.1 (96.0)	98.9 (99.3)	98.6 (99.9)	99.6 (100)
1/σl	14.6 (4.0)	10.8 (3.1)	11.0 (2.8)	10.7 (2.9)
Rmerge†	10.2 (40)	11.5 (38)	18.8 (84)	14.3 (72)
Riso Native A‡	—	—	6.8 (20.8)	14.4 (25.2)
Riso Native B‡	—	—	12.6 (27.4)	17.5 (31.0)
*Statistics in parenthesis are calculated for the high-resolution bin used in map calculations, which, as indicated was sometimes lower in resolution than the high-resolution bin used in data reduction.
†Rmerge: ΣΣi|I(b) − I(h)i|ΣΣI(h)i where I(h) is the mean intensity after reflection.
‡Riso: Σ|FPH − FP|ΣFPH where FPH and FP are the soaked and the native crystal structure factor amplitudes respectively.

[0218] A model for the entire Yarus inhibitor could be fitted into the difference density (see, FIG. 10(A)), and the electron density map of the complex shows the N3 of A2486 (2451) within hydrogen bonding distance of a non-bridging oxygen of the phosphoramide (see, FIG. 10(B)). The inhibitor's two C's, which correspond to C74 and C75 of peptidyl-tRNA, are Watson-Crick base-paired with G2285 (2252) and G2284 (2251) in the P-loop, respectively (see, FIG. 11(A)). The C74-G2285 (2252) interaction was predicted by the results of Noller and coworkers (Noller et al. (1992) Science 256: 1416-1419). The dA, which corresponds to A76 of a tRNA in the P-site, is not base-paired, but rather stacks on the ribose of A2486 and hydrogen bonds to the 2′OH of nucleotide A2485 (see, FIG. 12(B)).

[0219] Only the CC-puromycin moiety of the mini-helix acceptor stem analogue showed ordered electron density in its difference electron density map (see, FIG. 10(C)). The C75 of the acceptor stem CCA is Watson-Crick base-paired with G2588 (2553) of the A-loop, whereas the C74 is more disordered and not base-paired but appears to stack on a ribosome base. The dimethyl A of the A-site inhibitor puromycin is positioned identically to the dimethyl A of the Yarus inhibitor. Further, the dimethyl A of puromycin, which is the A76 equivalent of an A-site tRNA, interacts with the A-loop in much the same way that the A76 from the P-site CCA interacts with the P-loop (see, FIG. 11(B)).

[0220] The most notable of the several conformational changes in the ribosome induced by the binding of the transition state analogue is the ordering of base A2637 (2602), which is disordered in the unliganded enzyme (see, FIG. 11(B)). It becomes positioned between the CCA bound at the A-site and the CCA bound at the P-site. The base of U2620 (2585) also moves so that it can make a hydrogen bond with the 2′ hydroxyl of the ribose of A76 in the A-site, and U2619 and G2618 shift to allow the A76 to be positioned. Smaller shifts in positions are observed in the positions of A2486, whose N3 is n ear to the non-bridging oxygen of the phosphate, and one of the G residues with which it interacts, G2102 (2482).

[0221] 2. Location and Chemical Composition of the Peptidyl Transferase Site.

[0222] The inhibitors are bound to a site made entirely of 23S rRNA with no proteins nearby, proving that the ribosome is a ribozyme. Both the Yarus inhibitor and the A-site analogue of aa-tRNA bind to the large subunit at the bottom of a large and deep cleft at the entrance to the 100 Å long polypeptide exit tunnel that runs through to the back of the subunit (see, FIG. 12). This site is surrounded by nucleotides belonging to the central loop of 23 S RNA domain V, the “peptidyl transferase loop.” Nucleotides from the single stranded portions of this loop make the closest approach to the phosphate that mimics the tetrahedral carbon intermediate. In general, the helices that extend from the peptidyl transferase loop in 2 secondary structure diagrams of 23S rRNA also extend away from the active site in the tertiary structure (see, FIG. 13). Although there are 13 proteins that interact with domain V (see, FIG. 14(A)), there are no globular proteins in the vicinity of the inhibitor. The closest polypeptides are the non-globular extensions of several proteins (L2, L3, L4, L10e) that penetrate deeply into domain V and approach the active site (see, FIG. 14(B)). These extensions fill many of the voids between the RNA helices of domain V, neutralize phosphate backbone charge, and presumably stabilize the structure of the domain and its association with other RNA regions. However, none of their side chain atoms is closer than about 18 Å to the phosphorus of the inhibitor's phosphate group, which marks the site where peptide bonds form. Furthermore, the substrate analogue is completely enclosed in an rRNA cavity that is so tightly packed that there is no possibility that an unidentified peptide could be lurking nearby (see, FIG. 15). Thus, the catalytic entity in the ribosome must be RNA.

[0223] Two of the proteins with long termini or loops penetrating the rRNA scaffold of domain V are proteins that could not previously be excluded from involvement in the peptidyl transferase reaction L2 and L3 (Noller (1991) Ann. Rev. Biochem. 60: 191-227). Noller and colleagues Noller et al. (1992) supra) found that under conditions which prevent RNA denaturation, extensive digestion of Thermus thermophilus 50S subunits with proteases followed by extraction with phenol and other agents that disrupt protein-RNA interactions did not remove several peptides from the subunit that were less than 10,000 in molecular weight. The structure makes it clear why these protein fragments were particularly resistant to protease treatments. While protease treatment could digest the globular protein domains on the surface of the large subunit, it could not remove the long termini or loops that penetrate deeply in the 23S rRNA because they are sequestered within the rRNA and thus protected from cleavage, independently of the globular domains.

[0224] 3. Peptidyl Transferase Active Site.

[0225] The RNA that surrounds the substrate analogues is closely packed, much like the active site region of a protein enzyme and the nucleotides in contact with the inhibitor are greater than 95% conserved in all three kingdoms of life (see, FIG. 15). Thus, it is clear that the ribosome is a ribozyme, but what gives the RNA its catalytic power?

[0226] Without wishing to be bound by theory, the residue most likely to be involved in catalysis, presumably as a general base, is A2486, whose N3 is about 3 Å from the phosphoramide oxygen of the Yarus inhibitor that is the analogue of the carbonyl oxygen of a nascent peptide bond and about 4 Å from the amide that corresponds to the amide nitrogen of the peptide bond being synthesized. Ordinarily, the pKa of the N1 of adenosine monophosphate is about 3.5 and that of its N3 is perhaps 2 pH units lower (Saenger (1984) Principles of nucleic Acid Structure, (C. R. Cantor, eds.), Springer Advanced Texts in Chemistry, Springer-Verlage, New York, N.Y.), and in order for A2486 to function as a general base, its pKa would have to be raised to 7 or higher. The crystal structure itself suggests that its pKa is, in fact, quite unusual. The N3 of A2486 can only hydrogen bond to the phosphate oxygen, as observed, if it (or the phosphate oxygen) is protonated. The distance between these two atoms is about 3 Å indicating that a hydrogen bond does, indeed, exist between them. Since the crystal is at pH 5.8, this implies that the pKa of the N3 is greater than 6. Muth and Strobel have measured the pKa of the corresponding A in E. coli 23S RNA by examining its dimethyl sulfate reactivity as a function of pH and have concluded that it is 7.6, though they cannot be sure from their experiments whether it is the N3 or N1 whose pKa they have measured (Muth et al. (2000) Science 289: 947-950). Because there is no other available, titratable RNA functional group closer than about 7 Å to the nascent peptide bond, there is not other group available to function as a general base.

[0227] There are several features of environment of A2486 (2451) that might affect its pKa. The pKa of the N3 of A2486 (2451) may be increased significantly in part by a charge relay mechanism, analogous to that which occurs in the active site of the serine proteases, with the buried phosphate of A2485 (2450) performing a similar function as the buried carboxylate of Asp 102 of chymotrypsin. The experimental 2.4 Å electron density map unambiguously establishes the hydrogen bonding interactions in this most critical region of the active site (see, FIG. 16(A)). The N6 of A2486 interacts with the O6 atoms of G2482 (2447) and G2102 (2061) (see, FIG. 16(B)). The N2 of G2482 is also interacting with a non-bridging oxygen of the phosphate group of A2485 (2450) that is among the total of 3 most solvent inaccessible phosphate groups (826, 1497 and 2485) in the large ribosomal subunit for which we do not see any neutralizing counterion in the 2.4 Å resolution map. Weak density that may correspond to a water molecule is hydrogen bonded to the other non-bridging oxygen. A neutralizing counterion is not apparent in this structure. The buried phosphate of A2485 could abstract the proton from the exocyclic N2 of G2482 in order to neutralize its energetically unfavorable buried negative charge. This, in turn, would stabilize the otherwise rare imino tautomer of that base. The interaction of an imino of G2482 with A2486 likewise can stabilize the imino tautomer of A2486 that would result in a negative charge on its N3 were it unprotonated (see, FIG. 16(C)). In this way, some of the negative electrostatic charge originating on the buried phosphate of A2485 could be relayed to the N3 of A2486, thereby increasing its pKa.

[0228] A second feature of the environment of the catalytic site that may affect its stability, tautomeric state and electrostatic charge distribution is a bound monovalent cation. A potassium or a sodium ion interacts with the O6 of G2482 and G2102 as well as with three other bases. Its identity as a potassium ion is established by its observed continuation and by an independent experiment showing that a rubidium ion can bind to this site. The monovalent ion might also stabilize non-standard tautomers, but its expected influence on the pKa of A2486 is less obvious. Early biochemical experiments have shown the importance of potassium for peptidyl transferase activity (Monro (1967) supra; Maden et al. (1968) supra) and this binding site could be responsible for that affect.

[0229] It may also be the case that stabilization of an imino tautomer by a buried phosphate explains the expected higher pKa of a catalytic cytosine in the active site of the hepatitis delta virus ribozyme (Ferre-D'Amare et al. (1998) Nature 395: 567-574; Naharo et al. (2000) Science 287: 1493-1497). In this case, a backbone phosphate, whose solvent accessibility is similar to that of A2485 in the ribosome, is observed to hydrogen bond to the N4 of C, and the protonated form of the imino tautomer of that C would neutralize the phosphate, promoting the function of its N3 as a general acid (Naharo et al. (2000) supra).

[0230] 4. Catalytic Mechanism of Peptide Bond Formation.

[0231] The proximity of the N3 of A2486 (2451) to the peptide bond being synthesized and the nature of the reaction catalyzed suggest a chemical mechanism of peptide synthesis that is analogous to the reverse of the deacylation step seen in serine proteases during peptide hydrolysis (Blow et al. (1969) Nature 221: 337-340; Steitz et al. (1982) Ann. Rev. Biophys. Bioeng. 11: 419-444). In that mechanism, the basic form of His57 abstracts a proton from the a-amino group of the peptide product as it attacks the acyl-Ser195. Formation of the tetrahedral carbonyl carbon intermediate is stabilized by interaction of the oxyanion formed with backbone amides (the “oxyanion hole”); His57 shuttles the proton acquired from the α-NH₂ to Ser195 as the tetrahedral intermediate breaks down.

[0232] The residue A2486 (2451) appears to be the analogous to His57 in chymotrypsin and that the peptidyl-tRNA is analogous to acyl-Ser195. Thus, the N3 of A2486, with its greatly elevated pKa, abstracts a proton from the α-amino group of the A-site bound aminoacyl-tRNA facilitating the nucleophilic attack of that amino group on the carbonyl carbon that acylates the 3′ OH of the tRNA in the P-site (see, FIG. 17(A)). In contrast to the serine proteases, however, the oxyanion of the tetrahedral intermediate is near to the protonated N3 of A2486 (A2451) rather than being proximal to a separate oxyanion binding site. Thus, it could be that the protonated N3 of A2486 stabilizes the formation of the oxyanion by hydrogen bonding to it, as we observe in the Yarus inhibitor complex (see, FIG. 17(B)). The N3 of A2486 could then subsequently transfer its proton to the 3′ hydroxyl of the P-site bound tRNA, which is liberated as the peptide shifts to the A-site bound tRNA (see, FIG. 17(C)).

[0233] An additional question is how is the catalyzed hydrolysis of the peptidyl tRNA in the P-site prevented prior to the delivery of the next appropriate aa-tRNA to the A-site? It appears from this complex that water would not be excluded from access to the peptidyl link to the P-site tRNA if the A-site were vacant. An analogous problem was discussed by Koshland in the 1960s (Koshland, Jr. (1963) Cold Spring Harbor Symp. Quant. Biol. 28: 473-489), who theorized why hexokinase does not hydrolyze ATP in the absence of glucose, since water should bind perfectly well to the binding site used by the 6-hydroxyl of glucose. The answer proposed was induced fit, i.e., hexokinase is not catalytically competent until the glucose binds and produces a conformational change that orients substrates and catalytic groups optimally. This indeed appears to be the case (Bennett, Jr. et al. (1978) Proc. Natl. Acad. Sci. USA 75: 4848-4852). Similarly, it could be that the catalytic A2486 and/or the peptidyl substrate are not properly oriented or that the binding site for the α-NH₂ group is blocked by a reoriented ribosome base in the absence of aa-tRNA in the A-site. The base of U2620 appears close to A2486 in the ligand free structure, and it may serve as the appropriate plug that prevents spontaneous hydrolysis of peptidyl-tRNA.

[0234] Thus, it appears that this RNA enzyme uses the same principles of catalysis as a protein enzyme. First, a large catalytic enhancement is achieved by precisely orienting the two reactants, the αNH₂ from the A-site aminoacyl-tRNA and the carbonyl carbon from the P-site peptidyl-tRNA. This may be accomplished, in part, by the interactions of the CCA ends of the A-site and P-site tRNAs with the A-loop and P-loop, respectively. Secondly, acid-base catalysis and transition state stabilization are achieved by an enzyme functional group (A2486 (2451) in this case) whose chemical properties are altered appropriately by the active site environment. Third, similar chemical principles may be used by RNA and protein enzymes to alter the pKa's of functional groups. A buried carboxylate of Asp102 acting through His57 alters the nucleophilicity of Ser195 in chymotrypsin (Blow et al. (1969) supra). In the ribosome a solvent inaccessible phosphate may act through G2482 (2447) alters the nucleophilicity of the N3 of A2486 (2451). It could be that RNA molecules “learned” how to use the chemical principles of catalysis significantly before protein molecules did.

[0235] 5. tRNA Binding.

[0236] While it is not possible to bind tRNA molecules to either the A-or P-sites in these crystals for steric reasons, it is possible to place the A-, P- and E-site tRNA molecules on the large ribosomal subunit in the same relative orientation that Cate et al. observed in their crystallographic study of the Thermus aquaticus 70S ribosome. The co-ordinates of the three tRNA molecules in the relative positions seen in the 70S ribosome can be docked on the Haloarcula marismortui large ribosomal subunit in a way that avoids steric clashes and places the acceptor stems of the A-site and P-site tRNAs near to the positions of the CCAs we have observed bound to the A-loop and P-loop (see FIG. 18). Although nucleotides C74 and C75 were modeled in a different conformation in the 7.8 Å ribosome map, the C74 residues from the CCAs in both the A- and P-sites can be connected to residue 72 of the docked A-site and P-site tRNAs through a modeled residue 73, and it appears that the tRNA molecules fit well onto the surface of the subunit. Unexpectedly, this modeling places the E-site, P-site and A-site bound tRNA molecules in close proximity to three ribosomal proteins. Proteins L5 and L10e are near tRNAs in the P-site and A-site. Since both of these proteins also interact with 5S rRNA, this observation raises the possibility that 5S rRNA and some of its associated proteins might help stabilize the positioning of ribosome bound tRNAs and is consistent with the fact that 5S rRNA enhances ribosomal activity, but is not absolutely essential for it (Moore, Ribosomal RNA & Structure, Evolution, Processing and Function in Protein Biosynthesis (1996), supra, pp. 199-236). Protein L44e appears to interact with the E-site tRNA and may contribute to E-site activity. According to this docking experiment the A-site tRNA interacts with the highly conserved stem-loop 2502-2518 (2467-2483) which together with L10e forms a large concave surface that contacts the tRNA on the T-stem, utilizing the exact same binding site exploited by EF-Tu (Gutell et al. (2000) supra).

[0237] Examination of the relationships between the CCAs bound in the A- and P-sites and the tRNAs to which they are connected as well as their interactions with the ribosome also leads to some insights into translocation. Immediately after formation of the new peptide bond and deacylation of the P-site tRNA, the acceptor end of the P-site tRNA is known to move to the E-side and that of the A-site tRNA moves to the P-site (Blobel etal. (1970) J. Cell. Biol. 45: 130-145). The approximate modeling of the 3 tRNA molecules on the large subunit suggests some possible contributions to this process. First, there are two base-pairs between the P-site tRNA and the P-loop and only one between the A-site and the A-loop. Moving from the A- to the P-site increases base-pairing, though there must be a concomitant attraction of the deacylated P-site tRNA to an E-site. Further, the CCAs bound to the A and P loops are related by 180° rotation, whereas the tRNAs to which they are attached are not. Thus, the relationships of the CCAs to the acceptor stems cannot be the same in both sites and may not be equally stable. If the conformation of the A-site tRNA is less stable, then moving a tRNA from the A- to the P-site might be energetically favored.

[0238] 6. Polypeptide Exit Tunnel.

[0239] It appears very likely from the structure that all nascent polypeptides pass through the polypeptide exit tunnel before emerging from the ribosome, because there appears to be no other way out. We are now able to address two important questions about the functioning of the polypeptide exit tunnel: (1) Why do nascent proteins not stick to its walls? Teflon has the marvelous property of not sticking to denatured egg proteins, so how has the ribosome achieved a similar non-stick surface for the denatured proteins that must pass through the tunnel? (2) Do proteins fold to any degree in the tunnel giving the ribosome a chaperon-like function?

[0240] The length of the tunnel from the site of peptide synthesis to its exit is about 100 Å, broadly consistent with the length of nascent polypeptide that is protected from proteolytic cleavage by the ribosome (Moazed et al. (1989) Nature 342: 142) and the minimum length required for antibody recognition at the exit (Picking et al. (1992) Biochemistry 31: 2368-2375). The tunnel is largely straight, except for a bend 20 to 35 Å from the peptidyl transferase center (see, FIG. 19). Its diameter varies from about 20 Å at its widest to a narrow point of about 10 Å at the very beginning and at a position 28 Å from the tunnel exit with an average diameter of about 15 Å. Since the smallest orifice through which the polypeptide product must pass only barely accommodates the diameter of an α-helix diameter, it seems unlikely that significant protein folding beyond the formation of α-helix could occur within the ribosome.

[0241] The majority of the tunnel surface is formed by domains I-V of 23S rRNA, but significant contributions are also made by the non-globular regions of proteins L22, L4 and L39 which not only fill some of the voids in the RNA scaffold, but also form significant portions of the tunnel wall (see, FIG. 19). The largest protein contributor to the surface of the tunnel is L22 whose long α-hairpin loop lies between RNA segments of domains I through IV and is approximately parallel with the axis of the tunnel. Unlike the other tunnel proteins, protein L39 does not have a globular domain at the surface of the particle and is almost entirely buried in domains I and III underneath protein L23. Interestingly, the nucleotides of 23S rRNA that form the tunnel wall are predominantly from loops in the 23S rRNA secondary structure (see, FIG. 19). As it progresses through the tunnel from the active site, a nascent polypeptide first encounters domain V followed 20 Å further along by domains II and IV and proteins L4 and L22. The last half of the tunnel is formed by domains I and III and the protein L39e.

[0242] The narrowest part of the tunnel is formed by proteins L22 and L4 which approach the tunnel from opposite sides forming what appears to be a gated opening (see, FIG. 19C). The function of this constriction, if any, is not obvious. It might be the place where the nature of the nascent chain is sensed and the information transmitted to the surface of the particle, perhaps through L22 or L4. The a-hairpin of L22 at the site of this orifice and the 23S rRNA interacting with it are highly conserved; its globular portion is located adjacent to the tunnel exit on the surface that must face the translocon during protein secretion (see, FIG. 19).

[0243] The “non-stick” character of the tunnel wall must reflect a lack of structural and polarity complementarity to any protein sequence or conformation that it encounters. The tunnel surface is largely hydrophilic and includes exposed hydrogen bonding groups from bases, backbone phosphates and polar protein side-chains (see, FIG. 19). While there are many hydrophobic groups (sugars, bases, protein side-chains) facing the tunnel as well, there are no patches of hydrophobic surface large enough to form a significant binding site for hydrophobic sequences in the nascent polypeptide. As the tunnel is some 20 Å in diameter and filled with water and the newly synthesized polypeptide is presumably freely mobile, the binding of a peptide to the tunnel wall would result in a large loss of entropy that would have to be compensated for by a large complementary interaction surface that is larger than 700 Å (Chothia et al. (1975) Nature 256: 705-708). Similarly, while Arg and Lys side-chains from a nascent peptide may indeed interact with the phosphates exposed in the tunnel, the degree of structural complementarity and the net binding energy obtained after displacing bound counterions must be too small to overcome the large unfavorable entropy of immobilization that would result from peptide binding. Thus, although the ribosome tunnel is made primarily of RNA, the nature of its surface is reminiscent of the interior surface of the chaperonin, GroEL (Xu et al. (1998) J. Struct. Biol. 124: 129-141) in its non-binding conformation. Only in the conformation that exposes a large hydrophobic surface does GroEL bind a denatured protein.

[0244] There are six proteins (L19, L22, L23, L24, L29 and L31e) located at the exit from the tunnel, facing the translocon onto which the ribosome docks during protein secretion. There is evidence that the ribosome binds the translocon even after extensive digestion of its protein by protease implying that interaction between the translocon and the ribosome is mediated by RNA. The proximity of these proteins to the translocon, however, leads us to wonder what role, if any, they might play in the protein secretion process. Recent data from the Dobberstein laboratory shows that the N-terminal domain of SRP54, the G-protein from the signal recognition particle involved in signal peptide binding, can be crosslinked to ribosomal proteins L23 and L29. These two proteins are adjacent to each other and at the tunnel exit (see, FIG. 19).

[0245] 7. Evolution.

[0246] In vitro evolution of RNA oligonucleotides has produced small RNA molecules that can bind molecules like the Yarus inhibitor effectively or catalyze the peptidyl transfer reaction (Zhaug et al. (1998) Chem. Biol. 5: 539-553; Welch et al. (1997) supra). The sequence and secondary structure of one of these selected RNAs is reminiscent of the peptidyl transferase loop in domain V of 23S rRNA (Zhaug et al. (1998) supra). The most striking similarity is a five nucleotide sequence that is identical to a sequence in domain V that includes the catalytic A2486, G2482 and the buried phosphate of A2485. Remarkably, all of the groups involved in the proposed charge relay system for activating A2486 in the ribosome, are present in the in vitro selected ribozyme. Thus, though the surrounding structural context is likely to be different, it seems plausible that this artificially evolved ribozyme uses the same mechanisms as the ribosome for shifting the pKa of an adenine and likewise uses it as a base for peptide synthesis. A second RNA (Welch et al. (1997) supra) contains a 12 nucleotide loop that includes a 9-base sequence identical to that found in the same region of the peptidyl transferase loop.

[0247] The striking similarities between the sequences containing the key catalytic elements found in the peptidyl-transferase active site of the ribosome and sequences of in vitro selected RNAs having related activities make it clear that the appearance of a small RNA domain capable of catalyzing peptidyl transferase was a plausible first step in the evolution of protein synthesis on the ribosome. The first peptides synthesized by this primordial peptide synthesizing enzyme might have been random polymers or copolymers, and it may have functioned with substrates as simple as an aminoacylated CCA. Basic peptides of the types observed to form the non-globular extensions that co-fold with the 23S rRNA might have been among the first peptides synthesized that were functionally useful. Such peptides may have enhanced the stability of the protoribosome and other early ribozymes as the more sophisticated peptides of the present day ribosome appear to do.

[0248] C. Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution, Complete Refinement

[0249] The three-dimensional structure of the large ribosomal subunit from Haloarcula marismortui has now been completely refined at 2.4 Å resolution. The model includes 2876 RNA nucleotides, 3701 amino acids from 28 ribosomal proteins, 117 magnesium ions, 88 monovalent cations, and 7898 water molecules. Many of its proteins consist of a surface-exposed globular domain and one or more basic, non-globular extensions that are buried in rRNA. Half of them include motifs common in non-ribosomal proteins including, for example: RRM domains, SH3-like barrels and zinc fingers. Proteins that have significant sequence and structural similarity, such as L15 and L18e, make essentially identical interactions with rRNA.

[0250] More particularly, the H. marismortui 50S subunit has been completely rebuilt and refined by successive rounds of gradient energy minimization and B-factor refinement using CNS (Brünger et al. (1998) supra). Ribosomal proteins and rRNA were completely rebuilt using the software program “O ” (Jones, T. A. et al. (1991) Acta Crystallogr. A46: 110-119) with 2F_o-Fc electron density maps prior to the modeling of solvent and metal ions. Modeling errors in the proteins were identified using PROCHECK (Laskowski et al.(1993) J. Appl. Cryst. 26: 283-291) and by inspection of F_o-Fc maps. Difference maps also aided in the identification of errors in the rRNA, most often associated with sugar puckers. In the process, some adjustments were made in amino acid conformations, sequence register and in sequences themselves. Sequence changes made were largely limited to L10e, L15e, and L37Ae, the only three proteins from the H. marismortui 50S that have not been sequenced directly. In addition, fifty-one amino acids were added to the model described in section IIA with forty-four of these coming from L10 at the base of the L7/L12 stalk and L39e which lines a portion of the wall of the polypeptide exit tunnel. Fewer adjustments were made to the rRNA structure. Forty-nine new nucleotides were modeled and refined, mainly in helices 43 and 44 in domain II of 23S rRNA. In addition, the sugar pucker or conformation about the glycosidic bond was adjusted for some nucleotides. The refinement process was monitored by the quality of electron density maps calculated using phases derived from the model as well as R/R_free values. The completely refined model now includes 2876 RNA nucleotides, 3701 amino acids, 210 metal ions, and 7898 water molecules. The model refines to an R/R_free of 18.9%/22.3% and has excellent geometry (Table 4).

[0251] Solvent modeling began with the generation of a list of possible magnesium ions obtained by an automatic peak selection using CNS. Peaks greater than 3.5σ in F_o-Fc maps positioned within the magnesium inner-sphere coordination distance of 1.9-2.1 Å from N or O atoms were selected. The resulting list was manually inspected and only peaks that displayed clear octahedral coordination geometry were selected as magnesium.

[0252] Monovalent cations were identified on the basis of isomorphous differences between rubidium-soaked and native crystals of the H. marismortui 50S subunit. Since native crystals were stabilized in the presence of 1.6M NaCl, these sites were initially modeled and refined as Na⁺¹. Refinement of these sites as K⁺¹ almost always resulted in unusually high temperature factors, with two exceptions where we have modeled K⁺¹. Most of the monovalent sites in the 50S subunit appear to occupied by Na₊₁ in our crystals, however, these sites are likely to be occupied by K⁺¹ in vivo.

[0253] Waters were selected as peaks greater than 3.5σ in F_o-Fc electron density maps and between 2.5 and 3.3 Å of O or N atoms. Individual B-factor values were used to assess the assignment of water molecules. A number of waters refined to B-factors significantly lower than surrounding RNA and protein atoms. In many cases these peaks were found to be metal or chloride ions. A small number of low B-factor water molecules were retained in the final model because they could not be unambiguously assigned as other species. As a result of adding metal ions and water molecules the final model now contains 98, 547 non-hydrogen atoms. The refinement and model statistics for the large ribosomal subunit are summarized in Table 4.

[0254]

TABLE 4
Refinement and Model Statistics for the H. marismortui 50S Subunit
Space Group	C2221
a = 211.66 Å, b = 299.67 Å, c = 573.77 Å
Total non-hydrogen atoms	98,542
RNA atoms	61,617
Protein atoms	28,800
Water molecules	7,893
Magnesium ions	117
Potassium ions	2
Sodium ions	86
Chloride ions	22
Cadmium ions	5
Refinement Statistics:
Resolution Range	15.0-2.4 Å
Number of reflections used in refinement	623,525
Number of reflections for cross-validation	6,187
Rworking	18.9%
Rfree	22.3%
σa coordinate error (cross-validated)	0.35Å (0.43 Å)
luzzati coordinate error (cross-validated)	0.29Å (0.35 Å)
Deviations from ideality:
r.m.s.d. bond lengths	0.0052 Å
r.m.s.d. bond angles	1.13°
r.m.s.d. dihedrals	15.7°
r.m.s.d. impropers	2.12°
Protein Statistics from Ramachandran Plot:
Residues in most favored regions	2704 (86.6%)
Residues in additional allowed regions	379 (12.1%)
Residues in generously allowed regions	27 (0.9%)
Residues in disallowed regions	13 (0.4%)
Average B-factor Statistics (Å2):
All atoms (high/low)	44.3 (10.1/133.7)
rRNA	41.2 (11.78/125.0)
proteins	49.7 (13.9/92.5)
waters	41.89 (9.58/115.4)

[0255] Refinement has also permitted additional modeling of L10, L39e, and the L11 binding site in 23S rRNA. Furthermore, it has been discovered that certain motifs, for example, RRM topologies, SH3-like barrels and zinc fingers are common in the 50S proteins and each recognizes rRNA in many different ways. Proteins that have significant three-dimensional homology, however, such as L15 and L18e as well as L18 and S11, make essentially identical interactions with rRNA. Additional structural homologies between 50S proteins and non-ribosomal proteins also are apparent. The solvent exposed surfaces of these globular protein domains are rich in aspartate and glutamate residues, while irregular protein extensions penetrate the RNA core of the ribosome. These extensions are often highly conserved, and their abundance of arginine, lysine, and glycine residues is important for their function. Collectively, the results show evolutionary connections between many ribosomal proteins and illustrate that protein-RNA interactions in the ribosome, although largely idiosyncratic, share some common principles.

[0256] D. Antibiotic Binding Sites

[0257] In addition to the foregoing structural studies, the structure of the large ribosomal subunit of H. marismortui has been determined complexed with each of nine different antibiotics. More specifically, crystals of the H. marismortui large ribosomal subunit have been soaked with one of the following antibiotics: anisomycin, blasticidin, carbomycin A, tylosin, sparsomycin, virginiamycin M, spiramycin, azithromycin, linezolid or erythromycin. The structure of the large ribosome subunit complexed with each antibiotic was then resolved based on X-ray diffraction data generated for each crystal.

[0258] Briefly, a small amount of a concentrated antibiotic solution was added to a large subunit crystal suspended in stabilization solution and incubated for several hours. Following freezing and the other procedures normally used to prepare such crystals for experimental use, X-ray diffraction data were collected from the antibiotic containing crystals. Because the crystals were isomorphous to those from which the structure described above was derived, the phases obtained for native crystal were combined with the diffraction intensities obtained from the antibiotic-soaked crystal to obtain a structure for the latter. The position of the antibiotic in the crystal to which was bound is revealed most clearly in difference electron density maps, which are electron density maps computed using the phases just referred to and amplitudes obtained by subtracting the amplitudes of crystals that contain no antibiotic from the (suitably scaled) amplitudes of those that contain antibiotic. By using the foregoing methods, it was possible to determine the atomic co-ordinates that show the spatial relationship between particular antibiotics and their binding sites within the large ribosomal subunit. It is contemplated that similar methods can be used to resolve the structure of other antibiotics complexed to the large ribosomal subunit.

[0259] The atomic co-ordinates of the large ribosomal subunit complexed with anisomycin are listed in a table on compact disk, Disk No. 1 under the file name anisomycin.pdb, a more refined set of which is represented in a table on compact disk, Disk No. 1 under the file name ANISOMYC.PDB, and deposited at the RCSB Protein Data Bank with the accession number PDB ID: 1K73. In addition, FIG. 20 shows the spatial relationship between the antibiotic anisomycin and the large ribosomal subunit.

[0260] The atomic co-ordinates of the large ribosomal subunit complexed with blasticidin are listed in a table on compact Disk No. 1 under the file name blasticidin.pdb, a more refined set of which is represented in a table on compact disk, Disk No. 1 under the file name BLASTICI.PDB, and deposited at the RCSB Protein Data Bank with the accession number PDB ID: 1KC8. FIG. 21 shows the spatial relationship between the antibiotic blasticidin and the large ribosomal subunit. For orientation, FIG. 21 also includes a substrate for the P-site.

[0261] The atomic co-ordinates of the large ribosomal subunit complexed with carbomycin A are listed in a table on compact disk, Disk No. 1 under the file name carbomycin.pdb, a more refined set of which is represented in a table on compact disk, Disk No. 1 under the file name CARBOMYC.PDB, and deposited at the RCSB Protein Data Bank with the accession number PDB ID: 1K8A. FIG. 22 shows the spatial relationship between the antibiotic carbomycin A and the large ribosomal subunit. FIG. 22 also shows a portion of the polypeptide exit tunnel.

[0262] The atomic co-ordinates of the large ribosomal subunit complexed with tylosin are listed in a table on compact disk, Disk No. 1 under the file name tylosin.pdb, a more refined set of which is represented in a table on compact disk, Disk No. 1 under the file name TYLOSIN.PDB, and deposited at the RCSB Protein Data Bank with the accession number PDB ID: 1K9M. FIG. 22 shows the spatial relationship between the antibiotic tylosin and the large ribosomal subunit. FIG. 22 also shows a portion of the polypeptide exit tunnel.

[0263] The atomic co-ordinates of the large ribosomal subunit complexed with sparsomycin are listed in a table on compact disk, Disk No. 1 under the file name sparsomycin.pdb, a more refined set of which is represented in a table on compact disk, Disk No. 1 under the file name SPARSOMY.PDB. FIG. 23 shows the spatial relationship between the antibiotic sparsomycin and the large ribosomal subunit. For orientation, FIG. 23 also shows a substrate for the P-site.

[0264] The atomic co-ordinates of the large ribosomal subunit complexed with virginiamycin M are listed in a table on compact disk, Disk No. 1 under the file name virginiamycin.pdb, a more refined set of which is represented in a table on compact disk, Disk No. 1 under the file name VIRGINIA.PDB. FIG. 24 shows the spatial relationship between the antibiotics virginiamycin M as well as carbomycin A, and the large ribosomal subunit.

[0265] The atomic co-ordinates of the large ribosomal subunit complexed with spiramycin are listed in a table on compact disk, Disk No. 1 under the file name spiramycin.pdb, a more refined set of which is represented in a table on compact disk, Disk No. 1 under the file name SPIRAMYC.PDB, and deposited at the RCSB Protein Data Bank with the accession number PDB ID: 1KD1. FIG. 25 shows the spatial relationship between the antibiotic spiramycin and the large ribosomal subunit.

[0266] The atomic co-ordinates of the large ribosomal subunit complexed with azithromycin are listed in a table on compact disk, Disk No. 1 under the file name AZITHROM.PDB, a more refined set of which is represented in a table on compact disk, Disk 1 under the file name azithromycin.pdb. FIG. 26 shows the spatial relationship between the antibiotic azithromycin and the large ribosomal subunit.

[0267] The atomic co-ordinates of the large ribosomal subunit complexed with linezolid are listed in a table on compact disk, Disk No. 1 under the file name LINEZOLI.PDB, a more refined set of which is represented in a table on compact disk, Disk No. 1 under the file name linezolid.pdb. FIG. 27 shows the spatial relationship between the antibiotic linezolid and the large ribosomal subunit.

[0268] The atomic coordinates of the large ribosomal subunit complexed with erythromycin are listed in a table on compact disk, Disk No. 1 under the file name erythromycin.pdb. FIG. 28 shows the spatial relationship between the antibiotic erythromycin and the large ribosomal subunit.

[0269] FIG. 29 shows the spatial orientations of several antibiotics, namely, blasticidin, anisomycin, virginiamycin M and carbomycin A, as they bind to their respective antibiotic binding sites within the large ribosomal subunit. For purposes of orienting the reader, the positions of the P-site, A-site and the polypeptide exit tunnel are shown in FIG. 29. As is apparent, these antibiotics bind to or contact specific locations within the large ribosomal subunit to disrupt protein biosynthesis. For example, it appears that blasticidin binds the large ribosomal subunit in the vicinity of the P-site; anisomycin and virginiamycin bind the large ribosomal subunit in the vicinity of the A-site; and carbomycin spiramycin, tylosin, azithromycin and erythromycin (macrolide 5) all binds the large ribosomal subunit in the vicinity of the polypeptide exit tunnel adjacent the peptidyl transferase site.

[0270] From FIG. 29, it is apparent that the skilled artisan may identify certain portions of each antibiotic that contact regions in the large ribosomal subunit. By knowing their spatial relationship with respect one another, the skilled artisan may generate a hybrid antibiotic molecule comprising a portion of a first template antibiotic and a portion of a second, different template antibiotic. The two portions may be linked by a chemical linker so as to maintain the spatial orientation of one portion with respect to the other portion. As a result, the hybrid antibiotic may simultaneously bind each of the regions of the ribosomal subunit typically bound by each template antibiotic. The design and testing of such molecules is discussed in more detail below.

[0271] FIG. 30(A) shows the tylosin molecule bound within the polypeptide exit tunnel. FIG. 30(A) shows an enlarged portion of the large ribosomal subunit with the antibiotic tylosin bound at the top of the polypeptide exit tunnel adjacent the peptidyl transferase site. FIGS. 30(B) and 30(C) are views showing each half of a large ribosomal subunit cut along the polypeptide exit tunnel and are provided to orient the reader to show the tylosin binding site relative to the large ribosomal unit as a whole. FIG. 30(A) also shows two cavities defined by the wall of the polypeptide exit tunnel and are denoted as “cavity 1” and “cavity 2.” In addition, FIG. 30(A) also shows a disaccharide binding pocket. The direction in which the newly synthesized polypeptide chains exits the ribosome through the polypeptide exit tunnel is denoted by an arrow.

[0272] E. Experimental Techniques Which Exploit X-Ray Diffraction Data

[0273] Based on the X-ray diffraction pattern obtained from the assemblage of the molecules or atoms in a crystalline solid, the electron density of that solid may be reconstructed using tools well known to those skilled in the art of crystallography and X-ray diffraction techniques. Additional phase information extracted either from the diffraction data and available in the published literature and/or from supplementing experiments may then be used to complete the reconstruction.

[0274] For basic concepts and procedures of collecting, analyzing, and utilizing X-ray diffraction data for the construction of electron densities see, for example, Campbell et al. (1984) Biological Spectroscopy, The Benjamin/Cummings Publishing Co., Inc., (Menlo Park, Calif.); Cantor et al. (1980) Biophysical Chemistry, Part II: Techniques for the study of biological structure and function, W. H. Freeman and Co., San Francisco, Calif.; A. T. Brünger (1993) X-PLOR Version 3.1: A system for X-ray crystallography and NMR, Yale Univ. Pr., (New Haven, Conn.); M. M. Woolfson (1997) An Introduction to X-ray Crystallography, Cambridge Univ. Pr., (Cambridge, UK); J. Drenth (1999) Principles of Protein X-ray Crystallography (Springer Advanced Texts in Chemistry), Springer Verlag; Berlin; Tsirelson et al. (1996) Electron Density and Bonding in Crystals: Principles, Theory and X-ray Diffraction Experiments in Solid State Physics and Chemistry, Inst. of Physics Pub.; U.S. Pat. No. 5,942,428; U.S. Pat. No. 6,037,117; U.S. Pat. No. 5,200,910 and U.S. Pat. No. 5,365,456 (“Method for Modeling the Electron Density of a Crystal”).

[0275] A molecular model may then be progressively built using the experimental electron density information and further refined against the X-ray diffraction data resulting in an accurate molecular structure of the solid.

[0276] F. Structural Determination Of Other Large Ribosomal Subunits

[0277] It is understood that the skilled artisan, when provided with the atomic co-ordinates of a first macromolecule may use this information to quickly and easily determine the three-dimensional structure of a different but structurally related macromolecule. For example, the atomic co-ordinates defining the large ribosomal subunit from H. marismortui can be used to determine the structure of the large ribosomal subunit from other species either as an isolated subunit, in complex with the small subunit, or either of these complexed with functionally important ligands, for example: aminoacyl tRNA; various protein synthesis factors, such as elongation factor G, elongation factor Tu, termination factor or recycling factor, in both their GTP and GDP conformational states; and protein synthesis inhibitors, for example, antibiotics. In addition, the H. marismortui subunit co-ordinates can also be used to solve the structures of ribosomal complexes with components of the protein secretion machinery, for example, the signal recognition particle, and the translocon.

[0278] If the crystal being examined contains a macromolecule of unknown structure and no additional information is available, additional experiments sometimes may be required to determine the relevant phases of the macromolecule. These studies can often be time consuming and uncertain of success (Blundell et al. (1976) supra). However, when additional information, for example, structural and/or crystallographic information, is available for molecules related in some way to the macromolecule of interest then the process of resolving the structure of the molecule of interest is a much less challenging and time-consuming task.

[0279] Accordingly, the skilled artisan may use information gleaned from the prior resolved structure to develop a three-dimensional model of a new molecule of interest. Furthermore, the skilled artisan may use a variety of approaches to elucidate the three-dimensional structure of the new molecule. The approaches may depend on whether crystals of the molecule of interest are available and/or whether the molecule of interest has a homologue whose structure has already been determined.

[0280] In one approach, if the molecule of interest forms crystals that are isomorphous, i.e., that have the same unit cell dimensions and space group as a related molecule whose structure has been determined, then the phases and/or co-ordinates for the related molecule can be combined directly with newly observed amplitudes to obtain electron density maps and, consequently, atomic co-ordinates of the molecule of interest. The resulting maps and/or atomic co-ordinates may then be refined using standard refinement techniques known in the art. In another approach, if the molecule of interest is related to another molecule of known three-dimensional structure, but crystallizes in a different unit cell with different symmetry, the skilled artisan may use a technique known as molecular replacement to obtain useful phases from the co-ordinates of the molecule whose structure is known (Blundell et al. (1976) supra). This approach reportedly was used in the determination of the structure of the 50S subunit of Deinococcus radiodurans (Harms J. et al., Cell 107(5): 679-88; Schlunzen F. et al., (2001) Nature 413(6858): 814-21). These phases can then be used to generate an electron density map and/or atomic co-ordinates for the molecule of interest. In another approach, if no crystals are available for the molecule of interest but it is homologous to another molecule whose three-dimensional structure is known, the skilled artisan may use a process known as homology modeling to produce a three-dimensional model of the molecule of interest. It is contemplated that other approaches may be useful in deriving a three-dimensional model of a molecule of interest. Accordingly, information concerning the crystals and/or atomic co-ordinates of one molecule can greatly facilitate the determination of the structures of related molecules.

[0281] The method of molecular replacement, developed initially by Rossmann and Blow in the 1960s, is now used routinely to establish the crystal structures of macromolecules of unknown structures using the structure of a homologous molecule, or one in a different state of ligation (M. G. Rossmann, ed. “The Molecular Replacement Methods,” Int. Sci. Rev. J No. 13, Gordon & Breach, New York, N.Y. (1972); Eaton Lattman, “Use of Rotation and Translation Functions,” H. W Wyckoff C. H. W. Hist. (S. N. Timasheff, ed.) Methods in Enzmmology, 115: 55-77 (1985)). For an example of the application of molecular replacement, see, for example, Rice, P. A. & Steitz, T. A. (1994) EMBO J. 13: 1514-24.

[0282] In molecular replacement, the three-dimensional structure of the known molecule is positioned within the unit cell of the new crystal by finding the orientation and position that provides the best agreement between observed diffraction amplitudes and those calculated from the co-ordinates of the positioned subunit. From this modeling, approximate phases for the unknown crystal can be derived. In order to position a known structure in the unit cells of an unknown, but related structure, three rotation angles and three translations relative to the unit cell origin have to be determined. The rotation search is carried out by looking for agreement between the Patterson function of the search and target structures as a function of their relative orientation (the rotation function). X-PLOR (Brünger et al. (1987) Science 235:458-460; CNS (Crystallography & NMR System, Brünger et al., (1998) Acta Cryst. Sect. D 54: 905-921), and AMORE: an Automatic Package for Molecular Replacement (Navaza, J. (1994) Acta Cryst. Sect. A, 50: 157-163) are computer programs that can execute rotation and translation function searches. Once the orientation of a test molecule is known, the position of the molecule must be found using a translational search. Once the known structure has been positioned in the unit cell of the unknown molecules, phases for the observed diffraction data can be calculated from the atomic co-ordinates of the structurally related atoms of the known molecules. By using the calculated phases and X-ray diffraction data for the unknown molecule, the skilled artisan can generate an electron density map and/or atomic co-ordinates of the molecule of interest.

[0283] By way of example, it is contemplated that a three-dimensional model of a ribosomal subunit other than that derived from H. marismortui can be generated via molecular replacement. In this method, the H. marismortui subunit structures are positioned within the unit cell of the new crystal by finding the orientation and position that provides the best agreement between observed diffraction amplitudes and those calculated from the co-ordinates of the positioned subunit. A starting electron density map calculated using 2F_hkl(observed)−F_hkl(calculated), where F(observed) are the diffraction amplitudes that have been measured from crystals of the unknown structure, and F(calculated) are the diffraction amplitudes calculated from the positioned H. marismortui subunit structure. Refinement of the initial model can be done as is standard in the field of macromolecular crystallography.

[0284] The H. marismortui 50S structure can also be used to establish the structure of a 70S ribosome or 50S ribosome for which an election density map has been calculated, at a resolution that would otherwise be too low to be interpreted, while a 5 Å resolution map could not be interpreted in atomic terms de novo, a plausible atomic model can be constructed by refitting the H. marismortui 50S structure to a lower resolution map (e.g., 4.5 Å to 8 Å). This refitting can be combined with homology modeling to obtain a three-dimensional model of a ribosome or ribosomal subunit from a different species. It is contemplated that similar procedures may be used to determine the structure of the eukaryotic 60S subunit and/or a eukaryotic ribosome.

[0285] In general, the success of molecular replacement for solving structures depends on the fraction of the structures that are related and their degree of identity. For example, if about 50% or more of the structure shows an r.m.s. difference between corresponding atoms in the range of about 2 Å or less, the known structure can be successfully used to solve the unknown structure.

[0286] Homology modeling, also known as comparative modeling or knowledge-based modeling, can be used to generate a three-dimensional model for a molecule based on the known structure of homologues. In general, the procedure may comprise one or more of the following steps: aligning the amino acid or nucleic acid sequence of an unknown molecule against the amino acid or nucleic acid sequence of a molecule whose structure has previously been determined; identifying structurally conserved and structurally variable regions; generating atomic co-ordinates for core (structurally conserved) residues of the unknown structure from those of the known structure(s); generating conformations for the other (structurally variable) residues in the unknown structure; building side chain conformations; and refining and/or evaluating the unknown structure.

[0287] By way of example, since the nucleotide sequences of all known 50S subunit rRNAs can be aligned relative to each other and to H. marismortui 23S and 5S rRNAs, it is possible to construct models of the structures of other 50S ribosomal rRNAs, particularly in the regions of the tunnel and active sites, using the H. marismortui structure. Likewise, homologous proteins can also be modeled using similar methodologies. Methods useful for comparative RNA sequence analysis are known in the art and include visual methods and number pattern methods, as well as methods employing chi-square statistics, phylogenetic algorithms, or empirical algorithms. Descriptions of some of the foregoing methods are available, for example, on the world wide web at the URL rna.icmb.utexas.edu/; Gutell (1996), “Comparative Sequence Analysis and the Structure of 16S and 23S rRNA,” Ribosomal RNA. Structure, Evolution, Processing, and Function in Protein Biosynthesis, (Dahlberg A. and Zimmerman B., eds.) CRC Press. Boca Raton, pp. 111-128; Guttell et al. (1993) Nucl. Acid Res. 21: 3055-3074; Schnare et al. (1996) J. Mol. Biol. 256: 701-719. Particularly useful visual inspection methods include comparison of a particular position in a H marismortui secondary structure diagram with the residues located at the analogous position on an E. coli secondary structure diagram. A software program that is particularly useful in homology modeling includes XALIGN (Wishart, D. et al., (1994) Cabios 10: 687-88). See also, U.S. Pat. No. 5,884,230.

[0288] To model the rRNA of a new species, bases of the H. marismortui rRNA can be replaced, using a computer graphics program such as “O ” (Jones et al., (1991) Acta Cryst. Sect. A, 47: 110-119), by those of the homologous rRNA, where they differ. In many if not most cases the same orientation of the base will be appropriate. Insertions and deletions may be more difficult and speculative, but the rRNA forming the peptidyl transferase site and the portion of the tunnel closest to it is very highly conserved with essentially no insertions and deletions. Automated web-based homology modeling can be performed using, for example, the computer programs SWISS-MODEL available through Glaxo Welcome Experimental Research in Geneva, Switzerland, and WHATIF available on EMBL servers.

[0289] For other descriptions of homology modeling, see, for example, Gutell R. R. (1996), supra; Gutell R. R., et al. (1993) Nucleic Acids Res. 21: 3055-3074; Schnare et al. (1996) J. Mol. Biol., 256: 701-719; Blundell et al. (1987) Nature 326: 347-352; Fetrow and Bryant (1993) Bio/Technology 11: 479-484; Greer (1991) Methods in Enzymology 202: 239-252; and Johnson et al. (1994) Crit. Rev. Biochem. Mol. Biol. 29: 1-68. An example of homology modeling can be found, for example, in Szklarz G. D. (1997) Life Sci. 61: 2507-2520.

[0290] As discussed earlier, the large ribosomal subunit from prokaryotes and eukaryotes and eukaryotic mitochondria are structurally conserved. The amino acid sequences of the large ribosomal subunit from prokaryotes and eukaryotes can be aligned due to the evolutionary conservation of amino acid residues that are important for three-dimensional structure, the nature and shape of the binding sites for substrates and the catalytic site. This similarity in amino acid sequence of the homologous large ribosomal subunit allows the construction of models, via homology modeling, for the molecules whose crystal structures have not been solved.

[0291] The new ribosome or large ribosomal subunit structures determined using the H. marismortui crystals and/or atomic co-ordinates can then be used for structure-based drug design using one or more of the approaches described hereinbelow. This information can then be used to design molecules that selectively bind and disrupt protein synthesis in the ribosomes of the pathogens while leaving the ribosomes of a host relatively unaffected.

[0292] G. Rational Drug Design

[0293] 1. Introduction

[0294] It is contemplated that the atomic co-ordinates defining a large ribosomal subunit of interest, whether derived from one or more of X-ray crystallography, molecular modeling, homology modeling or molecular replacement, may be used in rational drug design (RDD) to design a novel molecule of interest, for example, novel modulators (for example, inducers, mimetics or inhibitors) of ribosome function. Furthermore, it is contemplated that, by using the principles disclosed herein, the skilled artisan can design, make, test, refine and use novel protein synthesis inhibitors specifically engineered to reduce, disrupt, or otherwise or inhibit ribosomal function in an organism or species of interest. For example, by using the principles discussed herein, the skilled artisan can engineer new molecules that specifically target and inhibit ribosomal function in a pathogen, for example, a particular prokaryotic, organism, while preserving ribosomal function in a host, for example, a eukaryotic organism, specifically a mammal, and more specifically, a human. As a result, the atomic co-ordinates provided and discussed herein permit the skilled artisan to design new antibiotics that can kill certain pathogenic organisms while having little or no toxicity in the intended recipient, for example, a human.

[0295] It is contemplated that RDD using atomic co-ordinates of the large ribosomal subunit can be facilitated most readily via computer-assisted drug design (CADD) using conventional computer hardware and software known and used in the art. The candidate molecules may be designed de novo or may be designed as a modified version of an already existing molecule, for example, a pre-existing antibiotic, using conventional methodologies. Once designed, candidate molecules can be synthesized using standard methodologies known and used in the art. Following synthesis, the candidate molecules can be screened for bioactivity, for example, by their ability to reduce or inhibit ribosome function, their ability to interact with or bind a ribosome or a ribosomal subunit. Based in part upon these results, the candidate molecules may be refined iteratively using one or more of the foregoing steps to produce a more desirable molecule with a desired biological activity. The resulting molecules can be useful in treating, inhibiting or preventing the biological activities of target organisms, thereby killing the organism or impeding its growth. Alternatively, the resulting molecules can be useful for treating, inhibiting or preventing microbial infections in any organism, particularly animals, more particularly humans.

[0296] In summary, the tools and methodologies provided by the present invention may be used to identify and/or design molecules which bind and/or interact in desirable ways with ribosomes and ribosomal subunits. Basically, the procedures utilize an iterative process whereby the molecules are synthesized, tested and characterized. New molecules can be designed based on the information gained in the testing and characterization of the initial molecules and then such newly identified molecules can themselves be tested and characterized. This series of processes may be repeated as many times as necessary to obtain molecules with desirable binding properties and/or biological activities. Methods for identifying candidate molecules are discussed in more detail below.

[0297] 2. Identification of Candidate Molecules

[0298] It is contemplated that the design of candidate molecules of interest can be facilitated by conventional ball and stick-type modeling procedures. However, in view of the size and complexity of the large ribosomal subunit, it is contemplated that the ability to design candidate molecules may be enhanced significantly using computer-based modeling and design protocols.

[0299] 6a. Molecular Modeling.

[0300] It is contemplated that the design of candidate molecules, as discussed in detail hereinbelow, can be facilitated using conventional computers or workstations, available commercially from, for example, Silicon Graphics Inc. and Sun Microsystems, running, for example, UNIX based, Windows NT on IBM OS/2 operating systems, and capable of running conventional computer programs for molecular modeling and rational drug design.

[0301] It is understood that any computer system having the overall characteristics set forth in FIG. 31 may be useful in the practice of the invention. More specifically, FIG. 31, is a schematic representation of a typical computer work station having in electrical communication (100) with one another via, for example, an internal bus or external network, a central processing unit (101), a random access memory (RAM) (102), a read only memory (ROM) (103), a monitor or terminal (104), and optimally an external storage device, for example, a diskette, CD ROM, or magnetic tape (105).

[0302] The computer-based systems of the invention preferably comprise a data storage means having stored therein a ribosome or ribosomal subunit or fragment sequence and/or atomic co-ordinate/X-ray diffraction data of the present invention and the necessary hardware means and software means for supporting and implementing an analysis means. As used herein, “a computer system” or “a computer-based system” refers to the hardware means, software means, and data storage means used to analyze the sequence, X-ray diffraction data, and/or atomic co-ordinates of the invention. As used herein, the term “data storage means” is understood to refer to any memory which can store sequence data, atomic co-ordinates, and/or X-ray diffraction data, or a memory access means which can access manufactures having recorded thereon the atomic co-ordinates of the present invention.

[0303] In one embodiment, a ribosome or ribosomal subunit, or at least a subdomain thereof, amino acid and nucleic acid sequence, X-ray diffraction data and/or atomic co-ordinates of the present invention are recorded on computer readable medium. As used herein, the term “computer readable medium” is understood to mean any medium which can be read and accessed directly by a computer. Such media include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage medium, and magnetic tape; optical storage media such as optical discs or CD-ROM; electrical storage media such as RAM and ROM; and hybrids of these categories such as magnetic/optical storage media. A skilled artisan can readily appreciate how any of the presently known computer readable mediums can be used to create a manufacture comprising computer readable medium having recorded thereon an amino acid and/or nucleotide sequence, X-ray diffraction data, and/or atomic co-ordinates of the present invention.

[0304] As used herein, the term “recorded” is understood to mean any process for storing information on computer readable medium. A skilled artisan can readily adopt any of the presently known methods for recording information on computer readable medium to generate manufactures comprising an amino acid or nucleotide sequence, atomic co-ordinates and/or X-ray diffraction data of the present invention.

[0305] A variety of data storage structures are available to a skilled artisan for creating a computer readable medium having recorded thereon amino acid and/or nucleotide sequence, atomic co-ordinates and/or X-ray diffraction data of the present invention. The choice of the data storage structure will generally be based on the means chosen to access the stored information. In addition, a variety of data processor programs and formats can be used to store the sequence information, X-ray data and/or atomic co-ordinates of the present invention on computer readable medium. The foregoing information, data and co-ordinates can be represented in a word processing text file, formatted in commercially-available software such as WordPerfect and MICROSOFT Word, or represented in the form of an ASCII file, stored in a database application, such as DB2, Sybase, Oracle, or the like. A skilled artisan can readily adapt any number of data processor structuring formats (e.g. text file or database) in order to obtain computer readable medium having recorded thereon the information of the present invention.

[0306] By providing a computer readable medium having stored thereon a ribosome or ribosomal subunit sequence, and/or atomic co-ordinates, a skilled artisan can routinely access the sequence, and/or atomic co-ordinates to model a ribosome or ribosomal subunit, a subdomain thereof, mimetic, or a ligand thereof. Computer algorithms are publicly and commercially available which allow a skilled artisan to access this data provided in a computer readable medium and analyze it for molecular modeling and/or RDD. See, e.g., Biotechnology Software Directory, MaryAnn Liebert Publ., New York, N.Y. (1995).

[0307] Although computers are not required, molecular modeling can be most readily facilitated by using computers to build realistic models of a ribosome, ribosomal subunit, or a portion thereof. Molecular modeling also permits the modeling of new smaller molecules, for example ligands, agents and other molecules, that can bind to a ribosome, ribosomal subunit, or a portion therein. The methods utilized in molecular modeling range from molecular graphics i.e., three-dimensional representations) to computational chemistry (i.e., calculations of the physical and chemical properties) to make predictions about the binding of the smaller molecules or their activities; to design new molecules; and to predict novel molecules, including ligands such as drugs, for chemical synthesis.

[0308] For basic information on molecular modeling, see, for example, M. Schlecht, Molecular Modeling on the PC (1998) John Wiley & Sons; Gans et al., Fundamental Principals of Molecular Modeling (1996) Plenum Pub. Corp.; N. C. Cohen, ed., Guidebook on Molecular Modeling in Drug Design (1996) Academic Press; and W. B. Smith, Introduction to Theoretical Organic Chemistry and Molecular Modeling (1996). U.S. Patents which provide detailed information on molecular modeling include, for example: U.S. Pat. Nos. 6,093,573; 6,080,576; 6,075,014; 6,075,123; 6,071,700; 5,994,503; 5,884,230; 5,612,894; 5,583,973; 5,030,103; 4,906,122; and 4,812,12.

[0309] Three-dimensional modeling can include, but is not limited to, making three-dimensional representations of structures, drawing pictures of structures, building physical models of structures, and determining the structures of related ribosomes, ribosomal subunits and ribosome/ligand and ribosomal subunit/ligand complexes using the known co-ordinates. The appropriate co-ordinates are entered into one or more computer programs for molecular modeling, as known in the art. By way of illustration, a list of computer programs useful for viewing or manipulating three-dimensional structures include: Midas (University of California, San Francisco); MidasPlus (University of California, San Francisco); MOIL (University of Illinois); Yummie (Yale University); Sybyl (Tripos, Inc.); Insight/Discover (Biosym Technologies); MacroModel (Columbia University); Quanta (Molecular Simulations, Inc.); Cerius (Molecular Simulations, Inc.); Alchemy (Tripos, Inc.); LabVision (Tripos, Inc.); Rasmol (Glaxo Research and Development); Ribbon (University of Alabama); NAOMI (Oxford University); Explorer Eyechem (Silicon Graphics, Inc.); Univision (Cray Research); Molscript (Uppsala University); Chem-3D (Cambridge Scientific); Chain (Baylor College of Medicine); 0 (Uppsala University); GRASP (Columbia University); X-Plor (Molecular Simulations, Inc.; Yale University); Spartan (Wavefunction, Inc.); Catalyst (Molecular Simulations, Inc.); Molcadd (Tripos, Inc.); VMD (University of Illinois/Beckman Institute); Sculpt (Interactive Simulations, Inc.); Procheck (Brookhaven National Library); DGEOM (QCPE); RE_VIEW (Brunell University); Modeller (Birbeck College, University of London); Xmol (Minnesota Supercomputing Center); Protein Expert (Cambridge Scientific); HyperChem (Hypercube); MD Display (University of Washington); PKB (National Center for Biotechnology Information, NIH); ChemX (Chemical Design, Ltd.); Cameleon (Oxford Molecular, Inc.); and Iditis (Oxford Molecular, Inc.).

[0310] One approach to RDD is to search for known molecular structures that might bind to a site of interest. Using molecular modeling, RDD programs can look at a range of different molecular structures of molecules that may fit into a site of interest, and by moving them on the computer screen or via computation it can be decided which structures actually fit the site well (William Bains (1998) Biotechnology from A to Z, second edition, Oxford University Press, p. 259).

[0311] An alternative but related approach starts with the known structure of a complex with a small molecule ligand and models modifications of that small molecule in an effort to make additional favorable interactions with a ribosome or ribosomal subunit.

[0312] The present invention permits the use of molecular and computer modeling techniques to design and select novel molecules, such as antibiotics or other therapeutic agents, that interact with ribosomes and ribosomal subunits. Such antibiotics and other types of therapeutic agents include, but are not limited to, antifungals, antivirals, antibacterials, insecticides, herbicides, miticides, rodentcides, etc.

[0313] In order to facilitate molecular modeling and/or RDD the skilled artisan may use some or all of the atomic co-ordinates deposited at the RCSB Protein Data Bank with the accession number PDB ID: 1FFK, 1JJ2, 1FFZ, 1FG0, 1K73, 1KC8, 1K8A, 1KD1, or 1K9M, and/or those atomic co-ordinates contained on Disk No. 1. Furthermore, the skilled artisan, using the foregoing atomic co-ordinates, the skilled artisan can generate additional atomic co-ordinates via, for example, molecular modeling using, for example, homology modeling and/or molecular replacement techniques, that together define at least a portion of a model of a ribosome from another species of interest. By using the foregoing atomic co-ordinates, the skilled artisan can design inhibitors of protein synthesis that may be tailored to be effective against ribosomes from one or more species but which have little or no effect on ribosomes of other species. Such inhibitors may be competitive inhibitors. As used herein, the term “competitive inhibitor” refers to an inhibitor that binds to the active form of a ribosome or ribosomal subunit at the same sites as its substrate(s) or tRNA(s), thus directly competing with them. The term “active form” of a ribosome or ribosomal subunit refers to a ribosome or ribosomal subunit in a state that renders it capable of protein synthesis. Competitive inhibition can be reversed completely by increasing the substrate or tRNA concentration.

[0314] This invention also permits the design of molecules that act as uncompetitive inhibitors of protein synthesis. As used herein, the term “uncompetitive inhibitor” refers to a molecule that inhibits the functional activity of a ribosome or ribosomal subunit by binding to a different site on the ribosome or ribosomal subunit than does its substrates, or tRNA. Such inhibitors can often bind to the ribosome or ribosomal subunit with the substrate or tRNA and not to the ribosome or ribosomal subunit by itself. Uncompetitive inhibition cannot be reversed completely by increasing the substrate concentration. These inhibitors may bind to, all or a portion of, the active sites or other regions of the large ribosomal subunit already bound to its substrate and may be more potent and less non-specific than known competitive inhibitors that compete for large ribosomal subunit active sites or for binding to large ribosomal subunit.

[0315] Similarly, non-competitive inhibitors that bind to and inhibit protein synthesis whether or not it is bound to another chemical entity may be designed using the atomic co-ordinates of the large ribosomal subunits or complexes comprising large ribosomal subunit of this invention. As used herein, the term “non-competitive inhibitor” refers to an inhibitor that can bind to either the free or substrate or tRNA bound form of the ribosome or ribosomal subunit.

[0316] Those of skill in the art may identify inhibitors as competitive, uncompetitive, or non-competitive by computer fitting enzyme kinetic data using standard equation according to Segel, I. H., (1975) Enzyme Kinetics: Behaviour and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems, (Wiley Classics Library). It should also be understood that uncompetitive or non-competitive inhibitors according to the present invention may bind the same or different binding sites.

[0317] Alternatively, the atomic co-ordinates provided by the present invention are useful in designing improved analogues of known protein synthesis inhibitors or to design novel classes of inhibitors based on the atomic structures and co-ordinates of the crystals of the 50S ribosomal subunit/CCdA-p-Puro complex and the 50S ribosomal subunit/aa-tRNA analogue complex. This provides a novel route for designing inhibitors of protein synthesis with both high specificity, stability and other drug-like qualities (Lipinski et al. (1997) Adv. Drug Deliv. Rev. 23: 3).

[0318] The atomic co-ordinates of the present invention also permit probing the three-dimensional structure of a ribosome or ribosome subunit or a portion thereof with molecules composed of a variety of different chemical features to determine optimal sites for interaction between candidate inhibitors and/or activators and the ribosome or ribosomal subunit. For example, high resolution atomic co-ordinates based on X-ray diffraction data collected from crystals saturated with solvent allows the determination of where each type of solvent molecule sticks. Small molecules that bind to those sites can then be designed and synthesized and tested for their inhibitory activity (Travis, J. (1993) Science 262: 1374). Further, any known antibiotic, inhibitor or other small molecule that binds to the H marismortui large subunit can be soaked into H. marismortui large subunit crystals and their exact mode of binding determined from difference electron density maps. These molecules may represent lead compounds from which better drug-like compounds can be synthesized.

[0319] b. Identification of Target Sites.

[0320] The atomic co-ordinates of the invention permit the skilled artisan to identify target locations in a ribosome or large ribosomal subunit that can serve as a starting point in rational drug design. As a threshold matter, the atomic co-ordinates of the invention permit the skilled artisan to identify specific regions within a ribosome or ribosomal subunit that are involved with protein synthesis and/or protein secretion out of the ribosome. Furthermore, the atomic co-ordinates of the invention permit a skilled artisan to further identify portions of these regions that are conserved or are not conserved between different organisms. For example, by identifying portions of these regions that are conserved among certain pathogens, for example, certain prokaryotes, but are not conserved in a host organism, for example, a eukaryote, more preferably a mammal, the skilled artisan can design molecules that selectively inhibit or disrupt protein synthesis activity of the pathogen's but not the host's ribosomes. Furthermore, by analyzing regions that are either conserved or non-conserved between certain pathogens, it may be possible to design broad or narrow spectrum protein synthesis inhibitors, e.g., antibiotics, as a particular necessity arises.

[0321] FIG. 32, is a schematic representation of a large ribosomal subunit that identifies a variety of exemplary target sites that appear to participate in protein synthesis within the ribosome and/or the export or translocation of the newly synthesized protein out of the ribosome. The target sites include, for example, the P-site (200), the A-site (201), the peptidyl transferase center (202), the peptidyl transferase site (203) which includes at least a portion of the P-site and the A-site, a factor binding domain (204) including, for example, the EF-Tu binding domain and the EF-G binding domain, the polypeptide exit tunnel (205) including cavities defined by the wall of the exit tunnel, and the signal recognition particle binding domain (206).

[0322] By way of example, inspection of the atomic co-ordinates of the H. marismortui 50S ribosomal subunit has identified a variety of target regions that may serve as a basis for the rational drug design of new or modified protein synthesis inhibitors. The target regions include the peptidyl transferase site, A-site, the P-site, the polypeptide exit tunnel, certain cavities disposed in the wall of the polypeptide exit tunnel (for example, cavity I and cavity 2), and certain antibiotic binding pockets. The residues that together define at least a portion of each of the foregoing regions are identified in the following tables. However, it is contemplated that the same or similar target sites can be identified in a ribosome or a ribosomal unit of interest using the principles described herein. Furthermore, these principles can be employed using any of the primary sets of atomic co-ordinates provided herein or any additional atomic co-ordinate sets, for example, secondary atomic co-ordinate sets that may be generated by molecular modeling of any ribosome or ribosomal subunit of interest.

[0323] Table 5A identifies the residues in the H. marismortui 50S ribosomal subunit that together define at least a portion of the ribosomal peptidyl transferase site (5.8 Å shell). In addition, Table 5A identifies the corresponding residues that define at least a portion of the ribosomal peptidyl transferase site in E. coli, Ratius, human, and human mitochondria large subunit. Table 5B identifies the residues in the H. marismortui 50S ribosomal subunit that together define a broader portion of the ribosomal peptidyl transferase site (5.8 Å-1 2.6 Å shell). The non-conserved residues were identified by comparison of sequences from the structure of H. marismortui 23S rRNA or ribosomal protein that form the above-mentioned sites with the corresponding sequences of aligned genomic DNA encoding either the homologous 23S rRNA or ribosomal protein from the other organisms.

[0324]

TABLE 5A
Residues that Define the Ribosomal Peptidyl-Transferase Site (5.8 Å shell)
	Corre-	Corre-	Corre-	Corresponding
	sponding	sponding	sponding	Residue in
H. marismortui	Residue in	Residue in	Residue in	Human
Residue	E. coli	Rattus	Human	Mitochondria
23S rRNA
G2102	G2061	G3632	G3876	G1054
A2103	A2062	A3633	A3877	A1055
C2104	C2063	C3634	C3878	C1056
C2105	C2064	C3635	C3879	C1057
C2106	C2065	C3636	C3880	C1058
G2284	G2251	G3917	G4156	G1145
G2285	G2252	G3918	G4157	G1146
G2286	G2253	G3919	G4158	G1147
A2474	A2439	A4106	A4345	A1256
G2482	G2447	G4114	G4353	G1264
A2485	A2450	A4117	A4356	A1267
A2486	A2451	A4118	A4357	A1268
C2487	C2452	C4119	C4358	C1269
A2488	A2453	U4120	U4359	A1270
U2528	U2493	U4160	U4399	U1310
G2529	G2494	G4161	G4400	A1311
C2536	C2501	C4168	C4407	C1318
A2538	A2503	A4170	A4409	A1320
G2540	G2505	G4172	G4411	G1322
U2541	U2506	U4173	U4412	U1323
C2542	C2507	C4174	C4413	U1324
G2543	G2508	G4175	G4414	G1325
G2588	G2553	G4220	G4459	G1370
U2589	U2554	U4221	U4460	U1371
U2590	U2555	U4222	U4461	U1372
C2608	C2573	C4240	C4479	C1390
G2617	G2582	G4249	G4488	A1399
G2618	G2583	G4250	G4489	G1400
U2619	U2584	U4251	U4490	U1401
U2620	U2585	U4252	U4491	U1402
C2636	C2601	C4268	C4507	C1418
A2637	A2602	A4269	A4508	A1419
G2638	G2603	G4270	G4509	G1420
Residues that together define the peptidyl transferase site (5.8 Å shell) were determined to be those residues in the 50S ribosomal subunit that are within 5.8 angstroms of the atoms of the CC-Puromycin A-site ligand and the atoms of the CCdA-PO2 moiety of the CCdA-p-Puromycin transition state inhibitor (PDB accession codes: 1fg0 and 1ffz, respectively) using the program MIDASa.
# Conserved residues in 23S rRNA were determined by comparison of sequences from the H. marismortui 235 rRNAb with genomic DNA sequences encoding the homologous 23S rRNA (E. colic, Rattus norvegicusd, Humane or Human mitochondriaf). Sequence alignments were determined with the program MegAlign (DNASTAR, Madison, Wisconsin, USA) using default parameters.
aT. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge (1988) “The MIDAS Display System” J. Mol. Graphics, 6(1):13-27, 36-37.
bGenBank accession AF034619
cGenBank accession J01695
dGenBank accession 2624399
eGenBank accession M11167
fGenBank accession 13683

[0325]

TABLE 5B
Residues that Define the Ribosomal Peptidyl-Transferase Site
(5.8 Å-12.6 Å shell)
	Corre-	Corre-	Corre-	Corresponding
	sponding	sponding	sponding	Residue in
H. marismortui	Residue in	Residue in	Residue in	Human
Residue	E. coli	Rattus	Human	Mitochondria
23S rRNA
C1750	A1672	C2692	C2830	A732
C1982	C1941	C3513	C3757	A934
C1983	C1942	C3514	C3758	C935
U1984	U1943	U3515	U3759	U936
U1985	U1944	C3516	C3760	U937
U1996	U1955	U3527	U3771	U948
C2006	C1965	C3537	C3781	U958
A2007	A1966	A3538	A3782	A959
G2073	G2032	C3603	C3847	G1025
A2100	A2059	A3630	A3874	A1052
A2103	A2062	A3633	A3877	A1055
U2107	C2066	U3637	U3881	U1059
U2282	U2249	U3915	U4154	U1143
G2283	G2250	G3916	G4155	G1144
C2287	C2254	C3920	C4159	C1148
G2288	G2255	G3921	G4160	G1149
C2309	C2275	C3942	C4181	C1154
C2472	G2437	U4104	U4343	U1254
U2473	U2438	U4105	U4344	U1255
C2476	U2441	C4108	C4347	C1258
A2479	G2444	A4111	A4350	A1261
G2480	G2445	G4112	G4351	G1262
G2481	G2446	G4113	G4352	G1263
G2482	G2447	G4114	G4353	G1264
U2484	U2449	U4116	U4355	U1266
G2489	G2454	G4121	G4360	G1271
A2490	G2455	G4122	G4361	C1272
C2526	U2491	U4158	U4397	U1308
U2527	U2492	U4159	U4398	U1309
G2529	G2494	G4161	G4400	A1311
C2530	G2495	A4162	A4401	C1312
U2531	C2496	U4163	U4402	G1313
A2532	A2497	C4164	C4403	A1314
C2534	C2499	U4166	U4405	C1316
U2535	U2500	U4167	U4406	U1317
G2537	G2502	G4169	G4408	G1319
A2538	A2503	A4170	A4409	A1320
U2539	U2504	U4171	U4410	U1321
G2540	G2505	G4172	G4411	G1322
G2544	G2509	G4176	G4415	G1326
U2587	U2552	U4219	U4458	U1369
C2591	C2556	C4223	C4462	C1373
G2592	G2557	A4224	A4463	A1374
A2604	G2569	G4236	G4475	C1386
G2605	G2570	G4237	G4476	C1387
U2607	A2572	A4239	A4478	A1389
G2609	G2574	G4241	G4480	G1391
U2610	C2575	U4242	U4481	U1392
G2611	G2576	G4243	G4482	G1393
G2616	G2581	G4248	G4487	G1398
G2617	G2582	G4249	G4488	A1399
U2621	U2586	U4253	U4492	C1403
A2622	A2587	A4254	A4493	A1404
G2627	G2592	G4259	G4498	G1409
U2628	U2593	U4260	U4499	G1410
G2634	G2599	G4266	G4505	U1416
A2635	A2600	A4267	A4506	C1417
G2638	G2603	G4270	G4509	G1420
G2639	U2604	G4271	G4510	G1421
U2640	U2605	U4272	U4511	U1422
G2643	G2608	G4275	G4514	G1425
U2645	C2610	U4277	U4516	U1427
Protein L3
P1	NP*	S2	S2	P2
Protein L10E
D109	XX**	T113	T113	XX
G110	XX	G114	G114	XX
R112	XX	R116	R116	XX
Residues that together define the peptidyl transferase site (5.8 Å-12.6 Å shell) were determined to be those residues in the 50S ribosomal subunit that are within 5.8-12.6 angstroms of the atoms of the CC-Puromycin A-site ligand and the atoms of the CCdA-PO2 moiety of the CCdA-p-Puromycin transition state inhibitor (PDB accession codes: 1fg0 and 1ffz, respectively), using the program MIDASa.
# Conserved residues in 23S rRNA were determined by comparison of sequences from the structure of H. marismortui 23S rRNAb with the corresponding sequences of aligned genomic DNA encoding the homologous 23S rRNA (E. colic, Rattus norvegicusd, Humane or Human mitochondriaf). In cases of ribosomal proteins,
# comparisons were also made between the H. marismortui structural protein sequenceg and the corresponding sequences of aligned protein sequences encoding homologous proteins in E. colii, Rattus norvegicusj, Humank or Human mitochondrial. Sequence alignments were determined with the program MegAlign (DNASTAR, Madison, Wisconsin, USA) using default parameters.
*NP means that no homologous residue has been identified.
**XX means that no homologous protein has been identified in that species.
aa. T. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge (1988) “The MIDAS Display System” J. Mol. Graphics, 6(1):13-27, 36-37.
bGenBank accession AF034619
cGenBank accession J01695
dGenBank accession 2624399
eGenBank accession M11167
fGenBank accession 13683
gGenBank accession AAA86859 for protein L3; GenBank accession 15825950 for protein L10E.
iGenBank accession CAA26460 for protein L3.
jGenBank accession P21531 for protein L3; GenBank accession NP_112362 for protein L10E.
kGenBank accession NP_000958 for protein L3; GenBank accession NP_006004 for protein L10E.
lGenBank accession P09001 for protein L3.

[0326] Table 6A identifies the residues in the H. marismortui 50S ribosomal subunit that together define at least a portion of the ribosomal A-site (5.8 Å shell). In addition, Table 6A identifies the corresponding residues that define at least a portion of the ribosomal A-site in E. coli, Rattus, human, and human mitochondria large subunit. Table 6B identifies the residues in the H. marismortui 50S ribosomal subunit that together define a broader portion of the ribosomal A-site (5.8 Å-12.6 Å shell). The non conserved residues were identified as described previously with respect to Tables 5A and 5B.

[0327]

TABLE 6A
Residues that Define the Ribosomal A-site (5.8 Å shell)
	Corre-	Corre-	Corre-	Corresponding
	sponding	sponding	sponding	Residue in
H. marismortui	Residue in	Residue in	Residue in	Human
Residue	E. coli	Rattus	Human	Mitochondria
23S rRNA
G2102	G2061	G3632	G3876	G1054
C2104	C2063	C3634	C3878	C1056
A2485	A2450	A4117	A4356	A1267
A2486	A2451	A4118	A4357	A1268
C2487	C2452	C4119	C4358	C1269
A2488	A2453	U4120	U4359	A1270
U2528	U2493	U4160	U4399	U1310
G2529	G2494	G4161	G4400	A1311
C2536	C2501	C4168	C4407	C1318
U2541	U2506	U4173	U4412	U1323
C2542	C2507	C4174	C4413	U1324
G2543	G2508	G4175	G4414	G1325
G2588	G2553	G4220	G4459	G1370
U2589	U2554	U4221	U4460	U1371
U2590	U2555	U4222	U4461	U1372
C2608	C2573	C4240	C4479	C1390
G2618	G2583	G4250	G4489	G1400
U2619	U2584	U4251	U4490	U1401
U2620	U2585	U4252	U4491	U1402
Residues that together define the A-site (5.8 Å shell) were determined to be those residues in the 50S ribosomal subunit that are within 5.8 angstroms of the atoms of the CC-Puromycin A-site ligand (PDB accession code 1fg0) using the program MIDASa. Conserved residues in 23S rRNA were determined by comparison of sequences from the structure of H. marismortui 23S rRNAb with
# the corresponding sequences of aligned genomic DNA encoding the homologous 23S rRNA (E. colic, Rattus norvegicusd, Humane or Human mitochondriaf). Sequence alignments were determined with the program MegAlign (DNASTAR, Madison, Wisconsin, USA) using default parameters.
aT. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge (1988) “The MIDAS Display System” J. Mol. Graphics, 6(1):13-27, 36-37.
bGenBank accession AF034619
cGenBank accession J01695
dGenBank accession 2624399
eGenBank accession M11167
fGenBank accession 13683

[0328]

TABLE 6B
Residues that Define the Ribosomal A-site (5.8 Å-12.6 Å shell)
	Corre-	Corre-	Corre-	Corresponding
	sponding	sponding	sponding	Residue in
H. marismortui	Residue in	Residue in	Residue in	Human
Residue	E. coli	Rattus	Human	Mitochondria
23S rRNA
C1750	A1672	C2692	C2830	A732
C1982	C1941	C3513	C3757	A934
C1983	C1942	C3514	C3758	C935
U1984	U1943	U3515	U3759	U936
U1985	U1944	C3516	C3760	U937
U1996	U1955	U3527	U3771	U948
G2073	G2032	C3603	C3847	G1025
A2100	A2059	A3630	A3874	A1052
A2103	A2062	A3633	A3877	A1055
C2105	C2064	C3635	C3879	C1057
C2106	C2065	C3636	C3880	C1058
U2107	C2066	U3637	U3881	U1059
G2284	G2251	G3917	G4156	G1145
G2285	G2252	G3918	G4157	G1146
A2474	A2439	A4106	A4345	A1256
A2479	G2444	A4111	A4350	A1261
G2480	G2445	G4112	G4351	G1262
G2481	G2446	G4113	G4352	G1263
G2482	G2447	G4114	G4353	G1264
U2484	U2449	U4116	U4355	U1266
G2489	G2454	G4121	G4360	G1271
A2490	G2455	G4122	G4361	C1272
C2526	U2491	U4158	U4397	U1308
U2527	U2492	U4159	U4398	U1309
C2530	G2495	A4162	A4401	C1312
U2531	C2496	U4163	U4402	G1313
A2532	A2497	C4164	C4403	A1314
C2534	C2499	U4166	U4405	C1316
U2535	U2500	U4167	U4406	U1317
G2537	G2502	G4169	G4408	G1319
A2538	A2503	A4170	A4409	A1320
U2539	U2504	U4171	U4410	U1321
G2540	G2505	G4172	G4411	G1322
G2544	G2509	G4176	G4415	G1326
U2587	U2552	U4219	U4458	U1369
C2591	C2556	C4223	C4462	C1373
G2592	G2557	A4224	A4463	A1374
A2604	G2569	G4236	G4475	C1386
G2605	G2570	G4237	G4476	C1387
U2607	A2572	A4239	A4478	A1389
G2609	G2574	G4241	G4480	G1391
U2610	C2575	U4242	U4481	U1392
G2611	G2576	G4243	G4482	G1393
G2616	G2581	G4248	G4487	G1398
G2617	G2582	G4249	G4488	A1399
U2621	U2586	U4253	U4492	C1403
C2636	C2601	C4268	C4507	C1418
A2637	A2602	A4269	A4508	A1419
G2638	G2603	G4270	G4509	G1420
G2639	U2604	G4271	G4510	G1421
U2640	U2605	U4272	U4511	U1422
G2643	G2608	G4275	G4514	G1425
U2645	C2610	U4277	U4516	U1427
Protein L3
P1	NP*	S2	S2	P2
Residues that define the A-site (5.8 Å-12.6 Å shell) were determined to be those residues in the 50S ribosomal subunit that are within 5.8-12.6 angstroms of the atoms of the CC-Puromycin A-site ligand (PDB accession code 1fg0) using the program MIDASa. Conserved residues in 23S rRNA were determined by comparison of sequences from the structure of H. marismortui 23S rRNAb
# with the corresponding sequences of aligned genomic DNA encoding the homologous 23S rRNA (E. colic, Rattus norvegicusd, Humane or Human mitochondriaf). In cases of ribosomal proteins, comparisons were also made between the H. marismortui structural protein sequenceg and the corresponding sequences of aligned protein sequences encoding homologous proteins in
# E. coli, Rattus norvegicusj, Humank or Human mitochondrial. Sequence alignments were determined with the program MegAlign (DNASTAR, Madison, Wisconsin, USA) with default parameters. *NP means that no homologous residue has been identified.
aT. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge (1988) “The MIDAS Display System” J. Mol. Graphics, 6(1):13-27, 36-37.
bGenBank accession AF034619
cGenBank accession J01695
dGenBank accession 2624399
eGenBank accession M11167
fGenBank accession 13683
gGenBank accession AAA86859 for protein L3.
iGenBank accession CAA26460 for protein L3.
jGenBank accession P21531 for protein L3.
kGenBank accession NP_000958 for protein L3.
lGenBank accession P09001 for protein L3.

[0329] Table 7A identifies the residues in the H. marismortui 50S ribosomal subunit that together define at least a portion of the ribosomal P-site (5.8 Å shell). In addition, Table 7A identifies the corresponding residues that define at least a portion of the ribosomal P-site in E. coli, Rattus, human, and human mitochondria large subunit. Table 7B identifies the residues in the H. marismortui 50S ribosomal subunit that together define a broader portion of the ribosomal P-site (5.8 Å-12.6 Å shell). The non conserved residues were identified as described previously with respect to Tables 5A and 5B.

[0330]

TABLE 7A
Residues that Define the Ribosomal P-site (5.8 Å shell)
	Corre-	Corre-	Corre-	Corresponding
	sponding	sponding	sponding	Residue in
H. marismortui	Residue in	Residue in	Residue in	Human
Residue	E. coli	Rattus	Human	Mitochondria
23S rRNA
C2104	C2063	C3634	C3878	C1056
C2105	C1064	C3635	C3879	C1057
C2106	C2065	C3636	C3880	C1058
G2284	G2251	G3917	G4156	G1145
G2285	G2252	G3918	G4157	G1146
G2286	G2253	G3919	G4158	G1147
A2474	A2439	A4106	A4345	A1256
A2485	A2450	A4117	A4356	A1267
A2486	A2451	A4118	A4357	A1268
U2619	U2584	U4251	U4490	U1401
U2620	U2585	U4252	U4491	U1402
C2636	C2601	C4268	C4507	C1418
A2637	A2602	A4269	A4508	A1419
G2638	G2603	G4270	G4509	G1420
Residues that together define the P-site (5.8 Å shell) were determined to be those residues in the 50S ribosomal subunit that are within 5.8 angstroms of the atoms of the CCdA-PO2 moiety of the CCdA-p-puromycin transition state inhibitor (FIG. 10a) (PDB accession code 1ffz) using the program MIDASa.
# Conserved residues in 23S rRNA were determined by comparison of sequences from the structure of H. marismortui 23S rRNAb with the corresponding sequences of aligned genomic DNA encoding the homologous 23S rRNA (E. colic, Rattus norvegicusd, Humane or Human mitochondriaf).
# Sequence alignments were determined with the program MegAlign (DNASTAR, Madison, Wisconsin, USA) using default parameters.
aT. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge (1988) “The MIDAS Display System” J. Mol. Graphics, 6(1):13-27, 36-37.
bGenBank accession AF034619
cGenBank accession J01695
dGenBank accession 2624399
eGenBank accession M11167
fGenBank accession 13683

[0331]

TABLE 7B
Residues that Define the Ribosomal P-site (5.8 Å-12.6 Å shell)
	Corre-	Corre-	Corre-	Corresponding
	sponding	sponding	sponding	Residue in
H. marismortui	Residue in	Residue in	Residue in	Human
Residue	E. coli	Rattus	Human	Mitochondria
23S rRNA
C1982	C1941	C3513	C3757	A934
C2006	C1965	C3537	C3781	U958
A2007	A1966	A3538	A3782	A959
G2102	G2061	G3632	G3876	G1054
A2103	A2062	A3633	A3877	A1055
U2107	C2066	U3637	U3881	U1059
U2282	U2249	U3915	U4154	U1143
G2283	G2250	G3916	G4155	G1144
C2287	C2254	C3920	C4159	C1148
G2288	G2255	G3921	G4160	G1149
C2309	C2275	C3942	C4181	C1154
C2472	G2437	U4104	U4343	U1254
U2473	U2438	U4105	U4344	U1255
C2476	U2441	C4108	C4347	C1258
G2481	G2446	G4113	G4352	G1263
G2482	G2447	G4114	G4353	G1264
U2484	U2449	U4116	U4355	U1266
C2487	C2452	C4119	C4358	C1269
A2488	A2453	U4120	U4359	A1270
U2528	U2493	U4160	U4399	U1310
G2529	G2494	G4161	G4400	A1311
C2530	G2495	A4162	A4401	C1312
U2531	C2496	U4163	U4402	G1313
A2532	A2497	C4164	C4403	A1314
C2534	C2499	U4166	U4405	C1316
U2535	U2500	U4167	U4406	U1317
C2536	C2501	C4168	C4407	C1318
A2538	A2503	A4170	A4409	A1320
G2540	G2505	G4172	G4411	G1322
U2541	U2506	U4173	U4412	U1323
C2542	C2507	C4174	C4413	U1324
C2608	C2573	C4240	C4479	C1390
G2611	G2576	G4243	G4482	G1393
G2618	G2583	G4250	G4489	G1400
U2621	U2586	U4253	U4492	C1403
A2622	A2587	A4254	A4493	A1404
G2627	G2592	G4259	G4498	G1409
U2628	U2593	U4260	U4499	G1410
G2634	G2599	G4266	G4505	U1416
A2635	A2600	A4267	A4506	C1417
G2639	U2604	G4271	G4510	G1421
U2640	U2605	U4272	U4511	U1422
G2643	G2608	G4275	G4514	G1425
Protein L10E
D109	XX**	T113	T113	XX
G110	XX	G114	G114	XX
R112	XX	R116	R116	XX
Residues that together define the P-site (5.8 Å-12.6 Å shell) were determined to be those residues in the 50S ribosomal subunit that are within the atoms of the CCdA-PO2 moiety of the CCdA-p-puromycin transition state inhibitor (FIG. 10a) (PDB accession code 1ffz) using the program MIDASa.
# Conserved residues in 23S rRNA were determined by comparison of sequences from the structure of H. marismortui 23S rRNAb with the corresponding sequences of aligned genomic DNA encoding the homologous 23S rRNA (E. colic, Rattus norvegicusd, Humane or Human mitochondriaf).
# In cases of ribosomal proteins, comparisons were also made between the H. marismortui structural protein sequenceg and the corresponding sequences of aligned protein sequences encoding homologous proteins in E. colii, Rattus norvegicusj, Humank or Human mitochondrial.
# Sequence alignments were determined with the program MegAlign (DNASTAR, Madison, Wisconsin, USA) using default parameters. **XX means that no homologous protein has been identified in that species.
aT. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge (1988) “The MIDAS Display System” J. Mol. Graphics, 6(1):13-27, 36-37.
bGenBank accession AF034619
cGenBank accession J01695
dGenBank accession 2624399
eGenBank accession M11167
fGenBank accession 13683
gGenBank accession 15825950 for protein L10E.
iNo GenBank accession number for protein L10E.
jGenBank accession NP_112362 for protein L10E.
kGenBank accession NP_006004 for protein L10E.
lNo GenBank accession number that compares to protein L10E.

[0332] Table 8A identifies the residues in the H. marismortui 50S ribosomal subunit that are within 10 Å of a hypothetical, nascent polypeptide within the ribosomal exit tunnel (10 Å shell). In addition, Table 8A identifies the corresponding residues that define at least a portion of the ribosomal polypeptide exit tunnel in E. coli, Rattus, human, and human mitochondria large subunit. Further, Table 8B identifies the residues in the H. marismortui 50S ribosomal subunit that that are between 10-15 Å of a hypothetical, nascent polypeptide within the ribosomal exit tunnel (10 Å-15 Å shell). The non conserved residues were identified as described previously with respect to Tables 5A and 5B.

[0333]

TABLE 8A
Residues that Define the Ribosomal Peptide Exit Tunnel (10 Å shell)
	Corre-	Corre-	Corre-	Corresponding
	sponding	sponding	sponding	Residue in
H. marismortui	Residue in	Residue in	Residue in	Human
Residue	E. coli	Rattus	Human	Mitochondria
23S rRNA
A60	A64	C729	C682	NP*
G88	G93	G764	G713	NP
G89	A94	G765	G714	NP
A90	A95	C766	C715	NP
A462	C456	C1112	C1195	NP
U465	U459	G1116	G1199	NP
A466	A460	G1117	G1200	NP
G467	C461	G1118	G1201	NP
U468	C462	G1119	A1202	NP
G475	G469	U1127	U1208	NP
A476	A470	C1128	C1209	NP
A477	A471	A1129	U1210	NP
C478	A472	C1130	C1211	NP
U488	A482	C1140	C1221	NP
A497	G491	G1151	G1233	NP
A498	A492	G1152	A1234	NP
A513	A507	A1167	G1249	NP
G514	A508	A1168	A1250	NP
A767	A676	A1425	A1503	NP
U835	U744	U1491	U1570	NP
C839	U746	G1495	G1574	NP
U840	U747	U1496	U1575	NP
A841	G748	G1497	G1576	NP
A844	A751	A1500	A1579	NP
U845	A752	A1501	A1580	NP
U1359	U1255	U2191	U2327	U351
C1360	G1256	C2192	C2328	G352
C1361	C1257	U2193	U2329	U353
U1362	U1258	U2194	U2330	C354
G1363	G1259	G2195	G2331	C355
G1364	A1260	G2196	G2332	A356
A1424	U1318	G2255	G2391	G412
G1425	C1319	U2256	U2392	U413
C1426	C1320	G2257	G2393	A414
A1427	A1321	A2258	A2394	A415
C1428	A1322	A2259	A2395	A416
U1429	C1323	C2260	C2396	U417
G1430	G1324	A2261	A2397	NP
C1439	G1333	A2270	A2406	U426
U1440	G1334	C2271	C2407	A427
G1441	C1335	A2272	A2408	G428
A1442	A1336	U2273	U2409	U429
A1689	A1614	C2635	C2771	A680
C1690	C1615	A2636	A2772	U681
G1837	U1781	A3368	A3612	C831
U1838	U1782	U3369	U3613	C832
A2054	A2013	A3585	A3829	A1006
A2055	A2014	A3586	A3830	A1007
C2056	A2015	A3587	A3831	A1008
U2057	U2016	C3588	C3832	U1009
C2098	G2057	A3628	A3872	A1050
G2099	A2058	G3629	G3873	G1051
A2100	A2059	A3630	A3874	A1052
A2101	A2060	A3631	A3875	A1053
G2102	G2061	G3632	G3876	G1054
A2103	A2062	A3633	A3877	A1055
C2104	C2063	C3634	C3878	C1056
C2105	C2064	C3635	C3879	C1057
A2474	A2439	A4106	A4345	A1256
C2477	C2442	A4109	A4348	C1259
U2478	C2443	C4110	C4349	U1260
G2481	G2446	G4113	G4352	G1263
G2482	G2447	G4114	G4353	G1264
A2485	A2450	A4117	A4356	A1267
A2486	A2451	A4118	A4357	A1268
C2487	C2452	C4119	C4358	C1269
A2488	A2453	U4120	U4359	A1270
C2536	C2501	C4168	C4407	C1318
G2537	G2502	G4169	G4408	G1319
A2538	A2503	A4170	A4409	A1320
U2539	U2504	U4171	U4410	U1321
G2540	G2505	G4172	G4411	G1322
U2541	U2506	U4173	U4412	U1323
C2542	C2507	C4174	C4413	U1324
C2608	C2573	C4240	C4479	C1390
G2611	G2576	G4243	G4482	G1393
G2616	G2581	G4248	G4487	G1398
G2618	G2583	G4250	G4489	G1400
U2619	U2584	U4251	U4490	U1401
U2620	U2585	U4252	U4491	U1402
U2621	U2586	U4253	U4492	C1403
A2637	A2602	A4269	A4508	A1419
C2644	U2609	U4276	U4515	U1426
U2645	C2610	U4277	U4516	U1427
G2646	C2611	U4278	U4517	U1428
C2647	C2612	U4279	U4518	C1429
Protein L4
E59	E51	E65	E65	R70
S60	V52	S66	S66	G71
F61	T53	W67	W67	F72
G62	G54	G68	G68	E73
S63	S55	T69	T69	Q74
G64	G56	G70	G70	E75
R65	K57	R71	R71	R76
G66	NP*	A72	A72	G78
Q67	NP	V73	V73	L79
A68	NP	A74	A74	A80
H69	K58	R75	R75	D81
V70	P59	I76	I76	L82
P71	W60	P77	P77	H83
K72	R61	R78	R78	P84
L73	Q62	V79	V79	D85
D74	G64	G81	G81	F87
G75	T65	G82	G82	A88
R76	G66	G83	G83	T89
A77	R67	T84	T84	A90
Protein L22
E20	H9	N21	N21	Q73
E121	S81	K124	K124	P177
Q122	M82	M125	M125	P178
Q123	K83	R126	R126	P179
G124	R84	R127	R127	P180
R125	I85	R128	R128	E181
K126	M86	T129	T129	P182
P127	P87	Y130	Y130	P183
R128	R88	R131	R131	K184
A129	A89	A132	A132	A186
M130	K90	H133	H133	V187
G131	G91	G134	G134	A188
R132	R92	R135	R135	H189
A133	A93	I136	I136	A190
S134	D94	N137	N137	K191
A135	R95	P138	P138	E192
W136	I96	Y139	Y139	Y193
N137	L97	M140	M140	I194
Q140	T100	P143	P143	F197
Protein L39E
N18	XX**	N20	N20	N98
S19	XX	R21	R21	H106
R20	XX	P22	P22	R107
V21	XX	I23	I23	I108
P22	XX	P24	P24	G109
A23	XX	Q25	Q25	D110
Y24	XX	W26	W26	F111
V25	XX	I27	I27	I112
M26	XX	R28	R28	D113
L27	XX	M29	M29	V114
K28	XX	K30	K30	S115
T29	XX	T31	T31	E116
D30	XX	G32	G32	G117
E31	XX	N33	N33	P118
R35	XX	Y37	Y37	H135
N36	XX	N38	N38	N136
H37	XX	S39	S39	L137
K38	XX	K40	K40	Q138
R39	XX	R41	R41	R146
R40	XX	R42	R42	R147
H41	XX	H43	H43	H156
R44	XX	R46	R46	R170
N45	XX	T47	T47	S171
The residues in the 10 Å shell were determined to be those residues in the 50S ribosomal subunit that are within 10 angstroms of the atoms of a model of a newly synthesized peptide positioned in the center of the exit tunnel using the program MIDASa.
# Conserved residues in 23S rRNA were determined by comparison of sequences from the structure of H. marismortui 23S rRNAb with the corresponding sequences of aligned genomic DNA encoding the homologous 23S rRNA (E. colic, Rattus norvegicusd, Humane or Human mitochondriaf).
# In cases of ribosomal proteins, comparisons were also made between the H. marismortui structural protein sequenceg and the corresponding sequences of aligned protein sequences encoding homologous proteins in E. colii, Rattus norvegicusj, Humank or Human mitochondrial.
# Sequence alignments were determined with the program MegAlign (DNASTAR, Madison, Wisconsin, USA) using default parameters. *NP means that no homologous residue has been identified. **XX means that no homologous protein has been identified in that species.
aT. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge (1988) “The MIDAS Display System” J. Mol. Graphics, 6(1):13-27, 36-37.
bGenBank accession AF034619
cGenBank accession J01695
dGenBank accession 2624399
eGenBank accession M11167
fGenBank accession 13683
gGenBank accession P12735 for protein L4; GenBank accession R5HS22 for protein L22; GenBank accession P22452 for protein L39E.
iGenBank accession CAA26461 for protein L4; GenBank accession CAA26465 for protein L22; no GenBank accession for protein L39E.
jGenBank accession JC4277 for protein L4; GenBank accession P24049 for protein L22; GenBank accession CAA57900 for protein L39E.
kGenBank accessions P36578, NP_00959, S39803, and T09551 for protein L4; GenBank accession XP_057521 for protein L22; GenBank accession NP_000991 for protein L39E.
lGenBank accession XP_049502 for protein L4; GenBank accession XP_051279 for protein L22; GenBank accession NP_059142 and NP_542984 for protein L39E.

[0334]

TABLE 8B
Residues that Define the Ribosomal Peptide Exit Tunnel
(10 Å-15 Å shell)
	Corre-	Corre-	Corre-	Corresponding
	sponding	sponding	sponding	Residue in
H. marismortui	Residue in	Residue in	Residue in	Human
Residue	E. coli	Rattus	Human	Mitochondria
23S rRNA
U22	U25	G686	G637	NP*
G23	G26	G687	G638	NP
G24	G27	G688	G639	NP
C57	C61	C726	U679	NP
C58	U62	U727	U680	NP
A59	A63	U728	U681	NP
G61	U65	C730	C683	NP
A86	A91	A762	A711	NP
C87	U92	C763	C712	NP
G91	C96	U767	U716	NP
U454	U448	C1104	C1187	NP
C461	C455	C1111	C1194	NP
A463	A457	G1114	G1197	NP
G469	G463	G1120	G1203	NP
U470	U464	C1122	NP	NP
A473	G467	C1125	U1206	NP
C474	G468	G1126	C1207	NP
G479	G473	G1131	G1212	NP
C480	G474	C1132	G1213	NP
A485	A479	U1137	A1218	NP
A486	A480	C1138	C1219	NP
G487	G481	C1139	G1220	NP
A489	A483	U1141	G1222	NP
C490	C484	C1142	C1223	NP
C491	C485	C1143	G1224	NP
A495	G489	U1147	C1228	NP
G496	C490	C1148	C1229	NP
G499	G493	G1153	A1235	NP
G512	G506	G1166	G1248	NP
C515	C509	G1169	G1251	NP
C633	U576	G1284	G1365	NP
G634	G577	C1285	C1366	NP
A635	G578	A1286	A1367	NP
G636	G579	A1287	A1368	NP
C637	U580	U1288	U1369	NP
C638	C581	G1289	G1370	NP
C764	C673	C1422	C1500	NP
G765	G674	G1423	G1501	NP
A766	A675	A1424	A1502	NP
G836	G745	G1492	G1571	NP
U837	NP*	A1493	A1572	NP
C838	NP	C1494	C1573	NP
C842	A749	C1498	C1577	NP
A843	A750	A1499	A1578	NP
A846	A753	U1502	U1581	NP
A882	A789	A1538	A1617	NP
U883	U790	U1539	U1618	NP
C884	C791	C1540	C1619	NP
G885	A792	G1541	G1620	NP
C889	C796	C1545	C1624	NP
C890	G797	A1546	A1625	NP
A1358	A1254	A2190	A2326	U350
C1365	C1261	U2197	U2333	A357
C1366	A1262	G2198	G2334	G358
A1367	U1263	G2199	G2335	A359
U1368	A1264	U2200	U2336	U360
A1369	A1265	A2201	A2337	A361
U1419	U1313	U2250	U2386	C407
C1423	G1317	U2254	U2390	U411
U1432	U1326	C2263	C2399	U419
C1436	C1330	U2267	U2403	U423
A1437	G1331	G2268	G2404	G424
G1438	G1332	A2269	A2405	U425
G1443	G1337	G2274	G2410	C430
G1688	G1613	G2634	G2770	G679
A1691	A1616	G2637	G2773	U682
C1692	C1617	C2638	C2774	A683
A1836	A1780	A3367	A3611	A830
A1839	A1783	U3370	U3614	A833
U2052	U2011	C3583	C3827	U1004
G2053	G2012	G3584	G3828	G1005
G2058	U2017	C3589	C3833	U1010
U2059	G2018	NP	NP	G1011
G2073	G2032	C3603	C3847	G1025
G2097	G2056	A3627	A3871	G1049
C2106	C2065	C3636	C3880	C1058
U2107	C2066	U3637	U3881	U1059
G2284	G2251	G3917	G4156	G1145
G2285	G2252	G3918	G4157	G1146
U2473	U2438	U4105	U4344	U1255
C2475	C2440	C4107	C4346	C1257
C2476	U2441	C4108	C4347	C1258
A2479	G2444	A4111	A4350	A1261
G2480	G2445	G4112	G4351	G1262
U2484	U2449	U4116	U4355	U1266
G2489	G2454	G4121	G4360	G1271
U2528	U2493	U4160	U4399	U1310
G2529	G2494	G4161	G4400	A1311
U2531	C2496	U4163	U4402	G1313
A2532	A2497	C4164	C4403	A1314
C2534	C2499	U4166	U4405	C1316
U2535	U2500	U4167	U4406	U1317
G2543	G2508	G4175	G4414	G1325
G2588	G2553	G4220	G4459	G1370
U2607	A2572	A4239	A4478	A1389
U2610	C2575	U4242	U4481	U1392
A2612	A2577	A4244	A4483	A1394
G2613	G2578	G4245	G4484	U1395
C2614	C2579	C4246	C4485	C1396
U2615	U2580	U4247	U4486	U1397
G2617	G2582	G4249	G4488	A1399
A2622	A2587	A4254	A4493	A1404
C2636	C2601	C4268	C4507	C1418
G2639	U2604	G4271	G4510	G1421
G2642	G2607	A4274	A4513	G1424
G2643	G2608	G4275	G4514	G1425
U2648	U2613	A4280	A4519	U1430
Protein L4
T56	T48	T62	T62	E67
P57	R49	S63	R63/S63n	S68
A58	A50	A64	A64	L69
R78	A68	H85	H85	P91
R79	R69	R86	R86	R92
V80	S70	S87	S87	L96
Q82	NP	Q89	Q89	Q98
A83	S72	G90	G90	V99
V84	I73	A91	A91	A100
K85	K74	F92	F92	M101
Protein L22
R19	NP	S20	S20	R72
R21	A10	L22	L22	I74
Q22	R11	R23	R23	K75
V119	G79	A122	A122	G175
G120	P80	P123	P123	P176
S138	K98	S141	S141	Q195
P139	R99	S142	S142	Q196
Protein L24
K81	N74	K89	K89	Y95
R83	A76	N91	N91	Y97
G84	T77	G92	G92	I98
E85	G78	T93	T93	G99
Protein L29
G37	G35	G38	G38	XX**
G38	NP	G39	G39	XX
A39	Q36	A40	A40	XX
P40	L37	A41	A41	XX
E41	Q38	S42	S42	XX
P43	S40	L44	L44	XX
Protein L37E
G4	XX	G4	G4	XX
T5	XX	T5	T5	XX
Protein L39E
L14	XX	K16	K16	K94
D15	XX	Q17	Q17	A95
N16	XX	K18	K18	S96
Q17	XX	Q19	Q19	Q97
W24	XX	W26	W26	F111
W42	XX	W44	W44	L157
R43	XX	R45	R45	R158
D46	XX	K48	K48	R172
The residues in the 10-15 Å shell were determined to be those residues in the 50S ribosomal subunit that are within 10-15 angstroms of the atoms of a model of a newly synthesized peptide positioned in the center of the exit tunnel using the program MIDASa.
# Conserved residues in 23S rRNA were determined by comparison of sequences from the structure of H. marismortui 23S rRNAb with the corresponding sequences of aligned genomic DNA encoding the homologous 23S rRNA (E. colic, Rattus norvegicusd, Humane or Human mitochondriaf).
# In cases of ribosomal proteins, comparisons were also made between the H. marismortui structural protein sequenceg and the corresponding sequences of aligned protein sequences encoding homologous proteins in E. colii, Rattus norvegicusj, Humank or Human mitochondrial.
# Sequence alignments were determined with the program MegAlign (DNASTAR, Madison, Wisconsin, USA) with default parameters. *NP means that no homologous residue has been identified. **XX means that no homologous protein has been identified in that species.
aT. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge (1988) “The MIDAS Display System” J. Mol. Graphics, 6(1):13-27, 36-37.
bGenBank accession AF034619
cGenBank accession J01695
dGenBank accession 2624399
eGenBank accession M11167
fGenBank accession 13683
gGenBank accession P12735 for protein L4; GenBank accession R5HS22 for protein L22; GenBank accession R5HS22 for protein L24; GenBank accession R5HS29 for protein L29; GenBank accession P32410 for protein L37E; GenBank accession P22452 for protein L39E.
iGenBank accession CAA26461 for protein L4; GenBank accession CAA26465 for protein L22; GenBank accession R5EC24 for protein L24; GenBank accession R5EC29 for protein L29; no GenBank accession for protein L37E; no GenBank accession for protein L39E.
jGenBank accession JC4277 for protein L4; GenBank accession P24049 for protein L22; GenBank accession P12749 for protein L24; GenBank accession R5RT35 for protein L29; GenBank accession CAA47012 for protein L37E; GenBank accession CAA57900 for protein L39E.
kGenBank accessions P36578, NP_00959, S39803, and T09551 for protein L4; GenBank accession XP_057521 for protein L22; GenBank accession AAA60279 and NP_000978 for protein L24; GenBank accession AAA51648 for protein L29; GenBank accession NP_000988 for protein L37E; GenBank accession NP_000991 for protein L39E.
lGenBank accession XP_049502 for protein L4; GenBank accession XP_051279 for protein L22; GenBank accession XP_056350 for protein L24; no GenBank accession for protein L29; no GenBank accession for protein L37E; GenBank accessions NP_059142 and NP_542984 for protein L39E.
nR63 is present in GenBank sequences T09551 and S39803 whereas S63 is present in GenBank sequences P36578 and NP_000959.

[0335] FIG. 30 shows a region of the large ribosomal subunit in which an antibiotic binds. FIG. 30(A) shows an enlarged portion of the large ribosomal subunit with the antibiotic tylosin bound at the top of the polypeptide exit tunnel adjacent the peptidyl transferase site. FIGS. 30(B) and 30(C) are views showing each half of a large ribosomal subunit cut along the polypeptide exit tunnel and are provided to orient the reader to show the tylosin binding site relative to the large ribosomal unit as a whole. FIG. 30(A) also shows two cavities defined by the wall of the polypeptide exit tunnel and are denoted as “cavity 1” and “cavity 2.” In addition, FIG. 30(A) also shows a disaccharide binding pocket. The direction in which the newly synthesized polypeptide chains exits the ribosome through the polypeptide exit tunnel is denoted by an arrow.

[0336] Table 9 identifies the residues in the H. marismortui 50S ribosomal subunit that together define a first cavity within the wall of polypeptide exit tunnel (cavity 1). In addition, Table 9 identifies which of those residues that define corresponding residues from cavity 1 in E. coli, Rattus, human, and human mitochondria. The non-conserved residues were identified as described previously with respect to Tables 5A and 5B.

[0337]

TABLE 9
Residues that Define Cavity 1 in the Ribosomal Peptide Exit Tunnel
	Corre-	Corre-	Corre-	Corresponding
	sponding	sponding	sponding	Residue in
H. marismortui	Residue in	Residue in	Residue in	Human
Residue	E. coli	Rattus	Human	Mitochondria
23S rRNA
C474	G468	G1126	C1207	NP*
A766	A675	A1424	A1502	NP
A767	A676	A1425	A1503	NP
U768	A677	A1426	A1504	NP
U883	U790	U1539	U1618	NP
C884	C791	C1540	C1619	NP
G885	A792	G1541	G1620	NP
A886	A793	A1542	A1621	NP
U888	C795	C1544	C1623	NP
C889	C796	C1545	C1624	NP
C890	G797	A1546	A1625	NP
U1359	U1255	U2191	U2327	U351
G1837	U1781	A3368	A3612	C831
A2100	A2059	A3630	A3874	A1052
A2101	A2060	A3631	A3875	A1053
G2102	G2061	G3632	G3876	G1054
A2103	A2062	A3633	A3877	A1055
C2475	C2440	C4107	C4346	C1257
C2476	U2441	C4108	C4347	C1258
C2477	C2442	A4109	A4348	C1259
U2478	C2443	C4110	C4349	U1260
A2479	G2444	A4111	A4350	A1261
A2538	A2503	A4170	A4409	A1320
Protein L4
P57	R49	S63	R63/S63n	S68
A58	A50	A64	A64	L69
E59	E51	E65	E65	R70
S60	V52	S66	S66	G71
F61	T53	W67	W67	F72
G62	G54	G68	G68	E73
S63	S55	T69	T69	Q74
G64	G56	G70	G70	E75
R65	K57	R71	R71	R76
Q67	NP*	V73	V73	L79
V70	P59	I76	I76	L82
P71	W60	P77	P77	H83
K72	R61	R78	R78	P84
L73	Q62	V79	V79	D85
D74	G64	G81	G81	F87
G75	T65	G82	G82	A88
R76	G66	G83	G83	T89
Cavity residues were identified using the program MIDASa. Conserved residues in 23S rRNA were determined by comparison of sequences from the structure of H. marismortui 23S rRNAb with the corresponding sequences of aligned genomic DNA encoding the homologous 23S rRNA (E. colic, Rattus norvegicusd, Humane or Human mitochondriaf).
# In cases of ribosomal proteins, comparisons were also made between the H. marismortui structural protein sequenceg and the corresponding sequences of aligned protein sequences encoding homologous proteins in E. colii, Rattus norvegicusk, Humank or Human mitochondrial.
# Sequence alignments were determined with the program MegAlign (DNASTAR, Madison, Wisconsin, USA). *NP means that no homologous residue has been identified.
aT. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge (1988) “The MIDAS Display System” J. Mol. Graphics, 6(1):13-27, 36-37.
bGenBank accession AF034619
cGenBank accession J01695
dGenBank accession 2624399
eGenBank accession M11167
fGenBank accession 13683
gGenBank accession P12735 for protein L4.
iGenBank accession CAA26461 for protein L4.
jGenBank accession JC4277 for protein L4.
kGenBank accessions P36578 NP_00959, S39803, and T09551 for protein L4.
lGenBank accession XP_049502 for protein L4.
nR63 is present in GenBank sequences T09551 and S39803 whereas S63 is present in GenBank sequences P36578 and NP_000959.

[0338] Table 10 identifies the residues in the H. marismortui 50S ribosomal subunit that together define a second cavity in the wall of polypeptide exit tunnel (cavity 2). In addition, Table 10 identifies which of those residues that define corresponding residues from cavity 2 in E coli, Rattus, human, and human mitochondria. The non-conserved residues were identified as described previously with respect to Tables 5A and 5B.

[0339]

TABLE 10
Residues that Define Cavity 2 in the Ribosomal Peptide Exit Tunnel
	Corre-	Corre-	Corre-	Corresponding
	sponding	sponding	sponding	Residue in
H. marismortui	Residue in	Residue in	Residue in	Human
Residue	E. coli	Rattus	Human	Mitochondria
23S rRNA
U831	C740	U1488	U1567	NP*
U832	U741	C1489	C1568	NP
G833	A742	C1490	C1569	NP
G834	A743	NP	NP	NP
U835	U744	U1491	U1570	NP
G836	G745	G1492	G1571	NP
U837	NP	A1493	A1572	NP
C838	NP	C1494	C1573	NP
C839	U746	G1495	G1574	NP
U840	U747	U1496	U1575	NP
A841	G748	G1497	G1576	NP
A843	A750	A1499	A1578	NP
A844	A751	A1500	A1579	NP
U845	A752	A1501	A1580	NP
A846	A753	U1502	U1581	NP
C847	U754	C1503	C1582	NP
C848	U755	G1504	G1583	NP
C849	A756	G1505	G1584	NP
C1753	C1675	C2695	C2833	NP
A1754	A1676	A2696	A2834	U734
G1837	U1781	A3368	A3612	C831
U1838	U1782	U3369	U3613	C832
A1839	A1783	U3370	U3614	A833
G2099	A2058	G3629	G3873	G1051
A2100	A2059	A3630	A3874	A1052
A2103	A2062	A3633	A3877	A1055
U2615	U2580	U4247	U4486	U1397
G2616	G2581	G4248	G4487	G1398
U2621	U2586	U4253	U4492	C1403
A2622	A2587	A4254	A4493	A1404
G2643	G2608	G4275	G4514	G1425
C2644	U2609	U4276	U4515	U1426
U2645	C2610	U4277	U4516	U1427
G2646	C2611	U4278	U4517	U1428
C2647	C2612	U4279	U4518	C1429
Cavity residues were determined using the program MIDASa. Conserved residues in 23S rRNA were determined by comparison of sequences from the structure of H. marismortui 23S rRNAb with the corresponding sequences of aligned genomic DNA encoding the homologous 23S rRNA (E. colic, Rattus norvegicusd, Humane or Human mitochondriaf).
# Sequence alignments were determined with the program MegAlign (DNASTAR, Madison, Wisconsin, USA) using default parameters. *NP means that no homologous residue has been identified.
aT. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge (1988) “The MIDAS Display System” J. Mol. Graphics, 6(1):13-27, 36-37.
bGenBank accession AF034619
cGenBank accession J01695
dGenBank accession 2624399
eGenBank accession M11167
fGenBank accession 13683

[0340] Tables 9 and 10, however, define only two of many cavities disposed within the wall of the polypeptide exit tunnel. However, by using the atomic co-ordinates and molecular modeling methodologies described herein, the skilled artisan may identify the residues (contributed by amino acids, nucleotides or a combination of both) that together define other cavities within the wall of the polypeptide exit tunnel.

[0341] In addition, by using the atomic co-ordinates described herein, the skilled artisan can identify the antibiotic binding site of any antibiotic of interest. This information also provides contact sites between an antibiotic and the residues in a ribosome or ribosomal subunit, which can be used to advantage in the design of novel or modified protein synthesis inhibitors. The binding or contact sites for a variety of antibiotics are discussed in more detail below.

[0342] Table 11A identifies the residues in the H. marismortui 50S ribosomal subunit that together define at least a portion of an anisomycin binding pocket (5.8 Å shell). In addition, Table 11A identifies the corresponding residues that define at least a portion of the anisomycin binding pocket in E. coli, Rattus, human, and human mitochondria large subunit. Table 11B identifies the residues in the H. marismortui 50S ribosomal subunit that together define a broader portion of an anisomycin binding pocket (5.8 Å-12.6 Å shell). The non-conserved residues were identified as described previously with respect to Tables 5A and 5B.

[0343]

TABLE 11A
Residues that Define the Anisomycin Binding Pocket (5.8 Å shell)
	Corre-	Corre-	Corre-	Corresponding
	sponding	sponding	sponding	Residue in
H. marismortui	Residue in	Residue in	Residue in	Human
Residue	E. coli	Rattus	Human	Mitochondria
23S rRNA
A2100v	A2059	A3630	A3874	A1052
G2102v	G2061	G3632	G3876	G1054
A2103v	A2062	A3633	A3877	A1055
G2482v	G2447	G4114	G4353	G1264
A2486v	A2451	A4118	A4357	A1268
C2487h,v	C2452	C4119	C4358	C1269
A2488v	A2453	U4120	U4359	U1270
U2535h,v	U2500	U4167	U4406	U1317
C2536	C2501	C4168	C4407	C1318
A2538v	A2503	A4170	A4409	A1320
U2539h,v	U2504	U4171	U4410	U1321
G2540v	G2505	G4172	G4411	G1322
U2541v	U2506	U4173	U4412	U1323
U2620v	U2585	U4252	U4991	U1402
The residues that define the binding pocket (5.8 Å shell) were determined as those residues in the 50S ribosomal subunit that are located within 5.8 angstroms of the atoms of anisomysin using the program MIDASa.
# Conserved residues in 23S rRNA were determined by comparison of sequences from the structure of H. marismortui 23S rRNAb with the corresponding sequences of aligned genomic DNA encoding the homologous 235 rRNA (E. colic, Rattus norvegicusd, Humane or Human mitochondriaf).
# Sequence alignments were determined with the program MegAlign (DNASTAR, Madison, Wisconsin, USA) with default parameters.
aT. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge (1988) “The MIDAS Display System” J. Mol. Graphics, 6(1):13-27, 36-37.
bGenBank accession AF034619
cGenBank accession J01695
dGenBank accession 2624399
eGenBank accession M11167
fGenBank accession 13683
hIndicates residue that is within hydrogen-bonding distance (3.5 Å) of the ligand; for example, see Jorgensen, WL, Nguyen, TB. J. Comput. Chem. (1993) 14:195-205.
vResidues in van der Waals contact with the antibiotic are defined as those residues within rmin of any atom in the antibiotic, where rmin = 21/6s and is the minimum in the Lennard-Jones pair potential (see Computer Simulation of Liquids; Allen, M. P. and Tildesley, D. J.; Oxford University Press: New York, 1992, 11.).
# The Lennard-Jones ss are taken from the OPLS-AA force field (see, Jorgensen, W. L.; Maxwell, D. S. and Tirado-Rives, J. J. Am. Chem. Soc., 1996, 118, 11225-11236 and Jorgensen, W. L. BOSS, Version 4.3; Yale University: New Haven, CT, 2002).

[0344]

TABLE 11B
Residues that Define the Anisomycin Binding Pocket (5.8 Å-12.6 Å shell)
	Corre-	Corre-	Corre-	Corresponding
	sponding	sponding	sponding	Residue in
H. marismortui	Residue in	Residue in	Residue in	Human
Residue	E. coli	Rattus	Human	Mitochondria
23S rRNA
A631	A574	G1282	G1363	NP*
A632	A575	C1283	C1364	NP
C633	U576	G1284	G1365	NP
G2073	G2032	C3603	C3847	G1025
A2095	A2054	G3625	G3869	A1047
A2096	C2055	A3626	A3870	C1048
G2097	G2056	A3627	A3871	G1049
C2098	G2057	A3628	A3872	A1050
G2099	A2058	G3629	G3873	G1051
G2102	G2061	G3632	G3876	G1054
C2104	C2063	C3634	C3878	C1056
C2105	C2064	C3635	C3879	C1057
A2474	A2439	A4106	A4345	A1256
G2481	G2446	G4113	G4352	G1263
U2484	U2449	U4116	U4355	U1266
A2485	A2450	A4117	A4356	A1267
G2489	G2454	G4121	G4360	G1271
A2490	G2455	G4122	G4361	C1272
A2532	A2497	C4164	C4403	A1314
C2533	C2498	C4165	C4404	C1315
C2534	C2499	U4166	U4405	C1316
G2537	G2502	G4169	G4408	G1319
C2542	C2507	C4174	C4413	U1324
G2543	G2508	G4175	G4414	G1325
G2538	G2553	G4220	G4459	G1370
U2607	A2572	A4239	A4478	A1389
C2608	C2573	C4240	C4479	C1390
G2609	G2574	G4241	G4480	G1391
U2610	C2575	U4242	U4481	U1392
C2611	G2576	G4243	G4482	G1393
A2612	A2577	A4244	A4483	A1394
G2618	G2583	G4250	G4489	G1400
U2619	U2584	U4251	U4490	U1401
A2637	A2602	A4269	A4508	A1419
G2646	C2611	U4278	U4517	U1428
L3
W242	Q150	W257	W257	G246
The residues that define the binding pocket (5.8 Å-12.6 Å shell) were determined as those residues in the 50S ribosomal subunit that are located within 5.8-12.6 angstroms of the atoms of anisomysin using the program MIDASa.
# Conserved residues were determined by comparison between the proposed secondary structures of H. marismortuib, E. colib, and Rattus norvegicusc, Humand, and Human Mitochondriae.
# Sequence alignments were determined with the program MegAlign (DNASTAR, Madison, Wisconsin, USA) using default parameters. *NP means that no homologous residue has been identified.
aT. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge (1988) “The MIDAS Display System” J. Mol. Graphics, 6(1):13-27, 36-37.
bGenBank accession AF034619
cGenBank accession J01695
dGenBank accession 2624399
eGenBank accession M11167
fGenBank accession 13683
gGenBank accession AAA86859 for protein L3.
iGenBank accession CAA26460 for protein L3.
jGenBank accession P21531 for protein L3.
kGenBank accession NP_000964 for protein L3.
lGenBank accession P09001 for protein L3.