Crystallization and structure of staphylococcus aureus peptide deformylase

Abstract

Staphylococcus aureus peptide deformylase has been crystallized, and the three-dimensional x-ray crystal structure has been solved to 1.9 Å resolution. The x-ray crystal structure is useful for solving the structure of other molecules or molecular complexes, and designing modifiers of peptide deformylase activity.

1 - 8 . (canceled)  
     
     
         9 . A scalable three-dimensional configuration of points, at least a portion of said points derived from structure coordinates of at least a portion of an  S. aureus  peptide deformylase molecule or molecular complex listed in Table 1 and having a root mean square deviation of less than about 1.4 Å from said structure coordinates.  
     
     
         10 . A scalable three-dimensional configuration of points, all of said points derived from structure coordinates of an  S. aureus  peptide deformylase molecule or molecular complex listed in Table 1 and having a root mean square deviation of less than about 1.4 Å from said structure coordinates.  
     
     
         11 . The scalable three-dimensional configuration of points of  claim 9  wherein at least a portion of the points derived from the  S. aureus  peptide deformylase structure coordinates are derived from structure coordinates representing the locations of at least the backbone atoms of a plurality of the amino acids defining at least one  S. aureus  peptide deformylase or  S. aureus  peptide deformylase-like active site, the active site comprising amino acids Gly58, Gly60, Leu61, Gln65, Glu109, Gly110, Cys111, Leu112, Ile150, His154, Glu155, and His158.  
     
     
         12 . The scalable three-dimensional configuration of points of  claim 9  wherein at least a portion of the points derived from the  S. aureus  peptide deformylase structure coordinates are derived from structure coordinates representing the locations of at least the backbone atoms of a plurality of the amino acids defining at least one  S. aureus  peptide deformylase or  S. aureus  peptide deformylase-like active site, the active site comprising amino acids Arg56, Ser57, Gly58, Val59, Gly60, Leu61, Gln65, Leu105, Pro106, Thr107, Gly108, Glu109, Gly110, Cys111, Leu112, Asn117, Tyr147, Ile150, Val151, His154, Glu155, and His158.  
     
     
         13 . The scalable three-dimensional configuration of points of  claim 9  displayed as a holographic image, a stereodiagram, a model or a computer-displayed image.  
     
     
         14 . A scalable three-dimensional configuration of points, at least a portion of the points derived from structure coordinates of at least a portion of a molecule or a molecular complex that is structurally homologous to an  S. aureus  peptide deformylase molecule or molecular complex, wherein the points derived from the structurally homologous molecule or molecular complex have a root mean square deviation of less than about 1.4 Å from the structure coordinates of said structurally homologous complex, and wherein the  S. aureus  peptide deformylase molecule or molecular complex is represented by  S. aureus  peptide deformylase structure coordinates listed in Table 1.  
     
     
         15 . The scalable three-dimensional configuration of points of  claim 14  displayed as a holographic image, a stereodiagram, a model or a computer-displayed image  
     
     
         16 . A machine-readable data storage medium comprising a data storage material encoded with machine readable data which, when using a machine programmed with instructions for using said data, displays a graphical three-dimensional representation of at least one molecule or molecular complex selected from the group consisting of: 
 (i) a molecule or molecular complex comprising at least a portion of an  S. aureus  peptide deformylase or an  S. aureus  peptide deformylase-like active site comprising amino acids Gly58, Gly60, Leu61, Gln65, Glu109, Gly110, Cys111, Leu112, Ile150, His154, Glu155, and His158, the active site being defined by a set of points having a root mean square deviation of less than about 0.35 Å from points representing the backbone atoms of said amino acids as represented by structure coordinates listed in Table 1;    (ii) a molecule or molecular complex comprising at least a portion of an  S. aureus  peptide deformylase or an  S. aureus  peptide deformylase-like active site comprising amino acids Arg56, Ser57, Gly58, Val59, Gly60, Leu61, Gln65, Leu105, Pro106, Thr107, Gly108, Glu109, Gly110, Cys111, Leu112, Asn117, Tyr147, Ile150, Val151, His154, Glu155, and His158, the active site being defined by a set of points having a root mean square deviation of less than about 0.8 Å from points representing the backbone atoms of said amino acids as represented by structure coordinates listed in Table 1; and    (iii) a molecule or molecular complex that is structurally homologous to an  S. aureus  peptide deformylase molecule or molecular complex, wherein the  S. aureus  peptide deformylase molecule or molecular complex is represented by structure coordinates listed in Table 1.    
     
     
         17 . A machine-readable data storage medium comprising a data storage material encoded with a first set of machine readable data which, when combined with a second set of machine readable data, using a machine programmed with instructions for using said first set of data and said second set of data, determines at least a portion of the structure coordinates corresponding to the second set of machine readable data, wherein said first set of data comprises a Fourier transform of at least a portion of the structural coordinates for  S. aureus  peptide deformylase listed in Table 1; and said second set of data comprises an x-ray diffraction pattern of a molecule or molecular complex of unknown structure.  
     
     
         18 . A computer-assisted method for obtaining structural information about a molecule or a molecular complex of unknown structure comprising: 
 crystallizing the molecule or molecular complex;    generating an x-ray diffraction pattern from the crystallized molecule or molecular complex;    applying at least a portion of the structure coordinates set forth in Table 1 to the x-ray diffraction pattern to generate a three-dimensional electron density map of at least a portion of the molecule or molecular complex whose structure is unknown.    
     
     
         19 . A computer-assisted method for homology modeling an  S. aureus  peptide deformylase homolog comprising: 
 aligning the amino acid sequence of an  S. aureus  peptide deformylase homolog with the amino acid sequence of  S. aureus  peptide deformylase SEQ ID NO:1 and incorporating the sequence of the  S. aureus  peptide deformylase homolog into a model of  S. aureus  peptide deformylase derived from structure coordinates set forth in Table 1 to yield a preliminary model of the  S. aureus  peptide deformylase homolog;    subjecting the preliminary model to energy minimization to yield an energy minimized model;    remodeling regions of the energy minimized model where stereochemistry restraints are violated to yield a final model of the  S. aureus  peptide deformylase homolog.    
     
     
         20 . A computer-assisted method for identifying a potential modifier of  S. aureus  peptide deformylase activity comprising: 
 supplying a computer modeling application with a set of structure coordinates of a molecule or molecular complex, the molecule or molecular complex comprising at least a portion of at least one  S. aureus  peptide deformylase or  S. aureus  peptide deformylase-like active site, the active site comprising amino acids Gly58, Gly60, Leu61, Gln65, Glu109, Gly110, Cys111, Leu112, Ile150, His154, Glu155, and His158;    supplying the computer modeling application with a set of structure coordinates of a chemical entity; and    determining whether the chemical entity is expected to bind to the molecule or molecular complex, wherein binding to the molecule or molecular complex is indicative of potential modification of  S. aureus  peptide deformylase activity.    
     
     
         21 . The method of  claim 20  further comprising assaying the potential modifier to determine whether it modifies  S. aureus  peptide deformylase activity.  
     
     
         22 . The method of  claim 20  wherein the active site comprises amino acids Gly58, Gly60, Leu61, Gln65, Glu109, Gly110, Cys111, Leu112, Ile150, His154, Glu155, and His158, the active site being defined by a set of points having a root mean square deviation of less than about 0.35 Å from points representing the backbone atoms of said amino acids as represented by structure coordinates listed in Table 1.  
     
     
         23 . The method of  claim 20  wherein determining whether the chemical entity is expected to bind to the molecule or molecular complex comprises performing a fitting operation between the chemical entity and at least one active site of the molecule or molecular complex, followed by computationally analyzing the results of the fitting operation to quantify the association between the chemical entity and the active site.  
     
     
         24 . The method of  claim 20  further comprising screening a library of chemical entities.  
     
     
         25 . A computer-assisted method for identifying a potential modifier of  S. aureus  peptide deformylase activity comprising: 
 supplying a computer modeling application with a set of structure coordinates of a molecule or molecular complex, the molecule or molecular complex comprising at least a portion of at least one  S. aureus  peptide deformylase or  S. aureus  peptide deformylase-like active site, the active site comprising amino acids Arg56, Ser57, Gly58, Val59, Gly60, Leu61, Gln65, Leu105, Pro106, Thr107, Gly108, Glu109, Gly110, Cys111, Leu112, Asn117, Tyr147, Ile150, Val151, His154, Glu155, and His158;    supplying the computer modeling application with a set of structure coordinates of a chemical entity; and    determining whether the chemical entity is expected to bind to the molecule or molecular complex, wherein binding to the molecule or molecular complex is indicative of potential modification of  S. aureus  peptide deformylase activity.    
     
     
         26 . The method of  claim 25  further comprising assaying the potential modifier to determine whether it modifies  S. aureus  peptide deformylase activity.  
     
     
         27 . The method of  claim 25  wherein the active site comprises amino acids Arg56, Ser57, Gly58, Val59, Gly60, Leu61, Gln65, Leu105, Pro106, Thr107, Gly108, Glu109, Gly110, Cys111, Leu112, Asn117, Tyr147, Ile150, Val151, His154, Glu155, and His158, the active site being defined by a set of points having a root mean square deviation of less than about 0.8 Å from points representing the backbone atoms of said amino acids as represented by structure coordinates listed in Table 1.  
     
     
         28 . The method of  claim 25  wherein determining whether the chemical entity is expected to bind to the molecule or molecular complex comprises performing a fitting operation between the chemical entity and at least one active site of the molecule or molecular complex, followed by computationally analyzing the results of the fitting operation to quantify the association between the chemical entity and the active site.  
     
     
         29 . The method of  claim 25  further comprising screening a library of chemical entities.  
     
     
         30 . A computer-assisted method for designing a potential modifier of  S. aureus  peptide deformylase activity comprising: 
 supplying a computer modeling application with a set of structure coordinates of a molecule or molecular complex, the molecule or molecular complex comprising at least a portion of at least one  S. aureus  peptide deformylase or  S. aureus  peptide deformylase-like active site, the active site comprising amino acids Gly58, Gly60, Leu61, Gln65, Glu109, Gly110, Cys111, Leu112, Ile150, His154, Glu155, and His158;    supplying the computer modeling application with a set of structure coordinates for a chemical entity;    evaluating the potential binding interactions between the chemical entity and active site of the molecule or molecular complex;    structurally modifying the chemical entity to yield a set of structure coordinates for a modified chemical entity; and    determining whether the modified chemical entity is expected to bind to the molecule or molecular complex, wherein binding to the molecule or molecular complex is indicative of potential modification of  S. aureus  peptide deformylase activity.    
     
     
         31 . The method of  claim 30  further comprising assaying the potential modifier to determine whether it modifies  S. aureus  peptide deformylase activity.  
     
     
         32 . The method of  claim 30  wherein the active site comprises amino acids Gly58, Gly60, Leu61, Gln65, Glu109, Gly110, Cys111, Leu112, Ile150, His154, Glu155, and His158, the active site being defined by a set of points having a root mean square deviation of less than about 0.35 Å from points representing the backbone atoms of said amino acids as represented by structure coordinates listed in Table 1.  
     
     
         33 . The method of  claim 30  wherein determining whether the modified chemical entity is expected to bind to the molecule or molecular complex comprises performing a fitting operation between the chemical entity and the active site of the molecule or molecular complex, followed by computationally analyzing the results of the fitting operation to quantify the association between the chemical entity and the active site.  
     
     
         34 . The method of  claim 30  wherein the set of structure coordinates for the chemical entity is obtained from a chemical fragment library.  
     
     
         35 . A computer-assisted method for designing a potential modifier of  S. aureus  peptide deformylase activity comprising: 
 supplying a computer modeling application with a set of structure coordinates of a molecule or molecular complex., the molecule or molecular complex comprising at least a portion of at least one  S. aureus  peptide deformylase or  S. aureus  peptide deformylase-like active site, the active site comprising amino acids Arg56, Ser57, Gly58, Val59, Gly60, Leu61, Gln65, Leu105, Pro106, Thr107, Gly108, Glu109, Gly110, Cys111, Leu112, Asn117, Tyr147, Ile150, Val151, His154, Glu155, and His158;    supplying the computer modeling application with a set of structure coordinates for a chemical entity;    evaluating the potential binding interactions between the chemical entity and active site of the molecule or molecular complex;    structurally modifying the chemical entity to yield a set of structure coordinates for a modified chemical entity; and    determining whether the modified chemical entity is expected to bind to the molecule or molecular complex, wherein binding to the molecule or molecular complex is indicative of potential modification of  S. aureus  peptide deformylase activity.    
     
     
         36 . The method of  claim 35  further comprising assaying the potential modifer to determine whether it modifies  S. aureus  peptide deformylase activity.  
     
     
         37 . The method of  claim 35  wherein the active site comprises amino acids Arg56, Ser57, Gly58, Val59, Gly60, Leu61, Gln65, Leu105, Pro106, Thr107, Gly108, Glu109, Gly110, Cys111, Leu112, Asn117, Tyr147, Ile150, Val150, Glu155, and His158, the active site being defined by a set of points having a root mean square deviation of less than about 0.8 Å from points representing the backbone atoms of said amino acids as represented by structure coordinates listed in Table 1.  
     
     
         38 . The method of  claim 35  wherein determining whether the modified chemical entity is expected to bind to the molecule or molecular complex comprises performing a fitting operation between the chemical entity and the active site of the molecule or molecular complex, followed by computationally analyzing the results of the fitting operation to quantify the association between the chemical entity and the active site.  
     
     
         39 . The method of  claim 35  wherein the set of structure coordinates for the chemical entity is obtained from a chemical fragment library.  
     
     
         40 . A computer-assisted method for designing a potential modifier of  S. aureus  peptide deformylase activity de novo comprising: 
 supplying a computer modeling application with a set of structure coordinates of a molecule or molecular complex, the molecule or molecular complex comprising at least a portion of at least one  S. aureus  peptide deformylase or  S. aureus  peptide deformylase-like active site, wherein the active site comprises amino acids Gly58, Gly60, Leu61, Gln65, Glu109, Gly110, Cys111, Leu112, Ile150, His154, Glu155, and His158;    forming a chemical entity represented by set of structure coordinates; and    determining whether the chemical entity is expected to bind to the molecule or molecular complex, wherein binding to the molecule or molecular complex is indicative of potential modification of  S. aureus  peptide deformylase activity.    
     
     
         41 . The method of  claim 40  further comprising assaying the potential modifier to determine whether it modifies  S. aureus  peptide deformylase activity.  
     
     
         42 . The method of  claim 40  wherein the active site comprises amino acids Gly58, Gly60, Leu61, Gln65, Glu109, Gly110, Cys111, Leu112, Ile150, His154, Glu155, and His158, the active site being defined by a set of points having a root mean square deviation of less than about 0.35 Å from points representing the backbone atoms of said amino acids as represented by structure coordinates listed in Table 1.  
     
     
         43 . The method of  claim 40  wherein determining whether the modified chemical entity is expected to bind to the molecule or molecular complex comprises performing a fitting operation between the chemical entity and the active site of the molecule or molecular complex, followed by computationally analyzing the results of the fitting operation to quantify the association between the chemical entity and the active site.  
     
     
         44 . A computer-assisted method for designing a potential modified of  S. aureus  peptide deformylase activity de novo comprising: 
 supplying a computer modeling application with a set of structure coordinates of a molecule or molecular complex, the molecule or molecular complex comprising at least a portion of at least one  S. aureus  peptide deformylase or  S. aureus  peptide deformylase-like active site, wherein the active site comprises amino acids Arg56, Ser57, Gly58, Val59, Gly60, Leu61, Gln65, Leu105, Pro106, Thr107, Gly108, Glu109, Gly110, Cys111, Leu112, Asn117, Tyr147, Ile150, Val151, His154, Glu155, and His158;    forming a chemical entity represented by set of structure coordinates; and    determining whether the chemical entity is expected to bind to the molecule or molecular complex, wherein binding to the molecule or molecular complex is indicative of potential modification of  S. aureus  peptide deformylase activity.    
     
     
         45 . The method of  claim 44  further comprising assaying the potential modifier to determine whether it modifies  S. aureus  peptide deformylase activity.  
     
     
         46 . The method of  claim 44  wherein the active site comprises amino acids Arg56, Ser57, Gly58, Val59, Gly60, Leu61, Gln65, Leu105, Pro106, Thr107, Gly108, Glu109, Gly110, Cys111, Leu112, Asn117, Tyr147, Ile150, Val151, His154, Glu155, and His158, the active site being defined by a set of points having a root mean square deviation of less than about 0.8 Å from points representing the backbone atoms of said amino acids as represented by structure coordinates listed in Table 1.  
     
     
         47 . The method of  claim 44  wherein determining whether the modified chemical entity is expected to bind to the molecule or molecular complex comprises performing a fitting operation between the chemical entity and the active site of the molecule or molecular complex, followed by computationally analyzing the results of the fitting operation to quantify the association between the chemical entity and the active site.  
     
     
         48 . The method of any of claims  20 , 25, 30, 35, 40, or 44 further comprising supplying or synthesizing the potential modifier, then assaying the potential modifier to determine whether it modifies  S. aureus  peptide deformylase activity.  
     
     
         49 . A method for making a potential modifier of  S. aureus  peptide deformylase activity, the method comprising chemically or enzymatically synthesizing a chemical entity to yield a potential modifier of  S. aureus  peptide deformylase activity, the chemical entity having been identified during a computer-assisted process comprising supplying a computer modeling application with a set of structure coordinates of a molecule or molecular complex, the molecule or molecular complex comprising at least a portion of a  S. aureus  peptide deformylase or  S. aureus  peptide deformylase-like active site; supplying the computer modeling application with a set of structure coordinates of a chemical entity; and determining whether the chemical entity is expected to bind to the molecule or molecular complex at the active site, wherein binding to the molecule or molecular complex is indicative of potential modification of  S. aureus  peptide deformylase activity.  
     
     
         50 . A method for making a potential modifier of  S. aureus  peptide deformylase activity, the method comprising chemically or enzymatically synthesizing a chemical entity to yield a potential modifier of  S. aureus  peptide deformylase activity, the chemical entity having been designed during a computer-assisted process comprising supplying a computer modeling application with a set of structure coordinates of a molecule or molecular complex, the molecule or molecular complex comprising at least a portion of a  S. aureus  peptide deformylase or  S. aureus  peptide deformylase-like active site; supplying the computer modeling application with a set of structure coordinates for a chemical entity; evaluating the potential binding interactions between the chemical entity and the active site of the molecule or molecular complex; structurally modifying the chemical entity to yield a set of structure coordinates for a modified chemical entity; and determining whether the chemical entity is expected to bind to the molecule or molecular complex at the active site, wherein binding to the molecule or molecular complex is indicative of potential modification of  S. aureus  peptide deformylase activity.  
     
     
         51 . A method for making a potential modifier of  S. aureus  peptide deformylase activity, the method comprising chemically or enzymatically synthesizing a chemical entity to yield a potential modifier of  S. aureus  peptide deformylase activity, the chemical entity having been designed during a computer-assisted process comprising supplying a computer modeling application with a set of structure coordinates of a molecule or molecular complex, the molecule or molecular complex comprising at least a portion of a  S. aureus  peptide deformylase or  S. aureus  peptide deformylase-like active site; forming a chemical entity represented by set of structure coordinates; and determining whether the chemical entity is expected to bind to the molecule or molecular complex at the active site, wherein binding to the molecule or molecular complex is indicative of potential modification of  S. aureus  peptide deformylase activity.  
     
     
         52 . A potential modifier of  S. aureus  peptide deformylase activity identified or designed according to the method of claims  20 ,  25 ,  30 ,  35 ,  40 ,  44 ,  49 ,  50 , or  51 .  
     
     
         53 . A composition comprising a potential modifier of  S. aureus  peptide deformylase activity identified or designed according to the method of claims  20 ,  25 ,  30 ,  35 ,  40 ,  44 ,  49 ,  50 , or  51 .  
     
     
         54 . A pharmaceutical composition comprising a potential modifier of  S. aureus  peptide deformylase activity identified or designed according to the method of claims  20 ,  25 ,  30 ,  35 ,  40 ,  44 ,  49 ,  50 , or  51 , or a salt thereof, and pharmaceutically acceptable carrier.  
     
     
         55 - 69 . (canceled)