Method for identifying protein synthesis inhibitors by ribosome structure

Abstract

The invention provides methods for producing high resolution crystals of ribosomes and ribosomal subunits as well as crystals produced by such methods. The invention also provides high resolution structures of ribosomal subunits either alone or in combination with protein synthesis inhibitors. The invention provides methods for identifying ribosome-related ligands and methods for designing ligands with specific ribosome-binding properties as well as ligands that may act as protein synthesis inhibitors. Thus, the methods and compositions of the invention may be used to produce ligands that are designed to specifically kill or inhibit the growth of any target organism.

1 - 46 . (canceled) 
     
     
         47 . 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 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.   
     
     
         48 . The computer system of  claim 47 , further comprising a device for providing a visual representation of the model. 
     
     
         49 . The computer system of  claim 47 , wherein the atomic co-ordinates comprise at least a portion of the atomic co-ordinates deposited at the Protein Data Bank under accession number PDB ID: 1FFK, 1FFZ, 1FG0, or 1JJ2. 
     
     
         50 . The computer system of  claim 47 , wherein the atomic co-ordinates further define at least a portion of a protein synthesis inhibitor complexed with a ribofunctional locus. 
     
     
         51 . The computer system of  claim 50 , wherein the protein synthesis inhibitor is an antibiotic. 
     
     
         52 . The computer system of  claim 51 , wherein the atomic co-ordinates comprise at least a portion of the atomic co-ordinates recorded on Disk No. 3 of 3 under file number anisomycin.pdb, blasticidin.pdb, carbomycin.pdb, sparsomycin.pdb, spiramycin.pdb, tylosin.pdb, or virginiamycin.pdb. 
     
     
         53 . The computer system of  claim 47 , where in ribofunctional locus comprises at least a portion of an active site in the ribosomal subunit. 
     
     
         54 . The computer system claim of  53 , wherein the active site comprises at least a portion of a peptidyl transferase site. 
     
     
         55 . The computer system of  claim 54 , wherein the peptidyl transferase site is defined by a plurality of residues set forth in Table 5. 
     
     
         56 . The computer system of  claim 47 , wherein the ribofunctional locus comprises at least a portion of an A-site. 
     
     
         57 . The computer system of  claim 56 , wherein the A-site is defined by a plurality of residues set forth in Table 6. 
     
     
         58 . The computer system of  claim 47 , wherein the ribofunctional locus comprises at least a portion of a P-site. 
     
     
         59 . The computer system of  claim 58 , wherein the P-site is defined by a plurality of residues set forth in Table 7. 
     
     
         60 . The computer systems of  claim 47 , wherein the ribofunctional locus comprises at least a portion of a polypeptide exit tunnel. 
     
     
         61 . The computer system of  claim 60 , wherein the exit tunnel is defined by a plurality of residues set forth in Table 8, Table 9 or Table 10. 
     
     
         62 . The computer system of  claim 58 , wherein the ribofunctional locus comprises at least a portion of a polypeptide exit tunnel. 
     
     
         63 . The computer system of  claim 62 , where the exit tunnel is defined by a plurality of residues set forth in Table 8, Table 9 or Table 10. 
     
     
         64 . The computer system of  claim 47 , wherein the ribofunctional locus is defined by a plurality of residues set forth in Table 11, Table 12, Table 13, Table 14, Table 15, Table 16 or Table 17. 
     
     
         65 . The computer system of  claim 47 , wherein the atomic co-ordinates are produced by molecular modeling. 
     
     
         66 . The computer system of  claim 47 , wherein 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, or 1JJ2. 
     
     
         67 . The computer system of  claim 47 , wherein 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, or 1JJ2. 
     
     
         68 . The computer system of  claim 47 , wherein the ribofunctional locus is defined by atoms of a ribosomal RNA. 
     
     
         69 . The computer system of  claim 47 , wherein the ribofunctional locus is defined by atoms of a ribosomal protein. 
     
     
         70 . The computer system of  claim 47 , wherein the atomic co-ordinates define a residue that is present in a ribosome of a pathogen but absent from a ribosome of a host organism. 
     
     
         71 . The computer system of  claim 70 , wherein the host organism is a mammal. 
     
     
         72 . The computer system of  claim 71 , wherein the mammal is a human. 
     
     
         73 . The computer system of  claim 47 , wherein the atomic co-ordinates define residues that are conserved among pathogens. 
     
     
         74 . The computer system of  claim 47 , further comprising a program for performing drug design. 
     
     
         75 . A molecular model produced by the computer system of  claim 47 . 
     
     
         76 - 112 . (canceled)