Ribosome structure and protein synthesis inhibitors

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 - 75 . (canceled)  
     
     
         76 . A method of identifying a candidate molecule, the method comprising the steps of: 
 (a) providing a molecular model of a ribofunctional locus of a large subunit of a ribosome, wherein the molecular model is based on atoms derived from an electron density map having a resolution of at least about 4.5 Å; and    (b) using the model to identify a candidate molecule having a surface complementary to the ribofunctional locus.    
     
     
         77 . The method of  claim 76 , wherein the candidate molecule binds the ribofunctional locus of the large subunit of the ribosome.  
     
     
         78 . The method of  claim 76 , comprising the additional step of producing the candidate molecule identified in step (b).  
     
     
         79 . The method of  claim 76 , comprising the additional step of determining whether the candidate molecule modulates ribosomal activity.  
     
     
         80 . The method of  claim 79 , comprising the additional step of identifying a modified molecule.  
     
     
         81 . The method of  claim 80 , comprising the additional step of producing the modified molecule.  
     
     
         82 . The method of  claim 81 , comprising the additional step of determining whether the modified molecule modulates ribosomal activity.  
     
     
         83 . The method of  claim 82 , comprising the additional step of producing the modified molecule.  
     
     
         84 . The method of  claim 76 , wherein the candidate molecule is an antibiotic or an antibiotic analogue.  
     
     
         85 . The method of  claim 80 , wherein the modified molecule is an antibiotic or an antibiotic analogue.  
     
     
         86 . The method of  claim 84 , wherein the antibiotic or antibiotic analogue is a macrolide.  
     
     
         87 . The method of  claim 76 , wherein the ribofunctional locus comprises at least a portion of an active site.  
     
     
         88 . The method of  claim 87 , wherein the active site comprises at least a portion of a peptidyl transferase site.  
     
     
         89 . The method of  claim 87 , wherein the peptidyl transferase site is defined by a plurality of residues set forth in Table 5.  
     
     
         90 . The method of  claim 76 , wherein the ribofunctional locus comprises at least a portion of an A-site.  
     
     
         91 . The method of  claim 90 , wherein the A-site is defined by a plurality of residues set forth in Table 6.  
     
     
         92 . The method of  claim 76  or  90 , wherein the ribofunctional locus comprises a least a portion of a P-site.  
     
     
         93 . The method of  claim 92 , wherein the P-site is defined by a plurality of residues set forth in Table 7.  
     
     
         94 . The method of  claim 76 , wherein the ribofunctional locus comprises at least a portion of a polypeptide exit tunnel.  
     
     
         95 . The method of  claim 94 , wherein the exit tunnel is defined by a plurality of residues set forth in Table 8, Table 9 or Table 10.  
     
     
         96 . The method of  claim 92 , wherein the ribofunctional locus comprises at least a portion of a polypeptide exit tunnel.  
     
     
         97 . The method of  claim 96 , wherein the exit tunnel is defined by a plurality of residues set forth in Table 8, Table 9 or Table 10.  
     
     
         98 . The method of  claim 76 , 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.  
     
     
         99 . The method of  claim 76 , wherein the molecular model is in an electronic form.  
     
     
         100 . The method of  claim 76 , wherein the molecular model is generated from atomic co-ordinates produced by molecular modeling.  
     
     
         101 . The method of  claim 76 , wherein the molecular model is generated from atomic co-ordinates 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.  
     
     
         102 . The method of  claim 76 , wherein the molecular model is generated from atomic co-ordinates 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.  
     
     
         103 . The method of  claim 76 , wherein the molecular model comprises residues that are conserved among prokaryotic organisms.  
     
     
         104 . The method of  claim 76 , wherein the molecular model comprises a residue that is present in a prokaryotic ribosome but is absent from a eukaryotic ribosome.  
     
     
         105 . The method of  claim 104 , wherein the eukaryotic ribosome is a mammalian ribosome.  
     
     
         106 - 112 . (canceled)