Crystallization and structure of Staphylococcus aureus peptide deformylase
AssigneePharmacia & Upjohn Company
InventorsEric T. Baldwin, Melissa S. Harris
Life of this patent
Estimating the term…
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.
Claims69
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.
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.
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 Table 1.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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-ike 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.
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.
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 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.
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.
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.
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.
A method for crystallizing an S. aureus peptide deformylase molecule or molecular complex comprising:
- preparing a stock solution of purified S. aureus peptide deformylase at a concentration of about 1 mg/ml to about 50 mg/ml;
- contacting the stock solution with a precipitating solution containing about 1% by weight to about 35% by weight PEG having a number average molecular weight between about 300 and about 20,000;
- about 0 M to about 0.2 M MgCl2;
- and about 0% by weight to about 25% by weight DMSO;
- the precipitating solution being buffered to a pH of about 5 to about 9;
- and
- allowing S. aureus peptide deformylase to crystallize from the resulting solution.
A method for crystallizing an S. aureus peptide deformylase molecule or molecular complex comprising:
- preparing a stock solution of purified S. aureus peptide deformylase at a concentration of about 1 mg/ml to about 50 mg/ml;
- contacting the stock solution with a precipitating solution containing about 1% by weight to about 40% by weight PEG having a number average molecular weight between about 300 and about 20,000;
- about 0.005 M to about 0.5 M citric acid;
- about 0% by weight to about 25% by weight DMSO;
- and sufficient base to adjust the pH of the precipitating solution to about 5.0 to about 6.5;
- and
- allowing S. aureus peptide deformylase to crystallize from the resulting solution.
A method for crystallizing an S. aureus peptide deformylase molecule or molecular complex comprising:
- preparing a stock solution of purified S. aureus peptide deformylase at a concentration of about 1 mg/ml to about 50 mg/ml;
- contacting the stock solution with a precipitating solution containing about 0.2 M to about 1.5 M sodium citrate;
- about 0.005 M to about 0.5 M Hepes;
- about 0% by weight to about 25% by weight DMSO;
- and sufficient base to adjust the pH of the precipitating solution to about 7.0 to about 8.5;
- and
- allowing S. aureus peptide deformylase to crystallize from the resulting solution.
A method for crystallizing an S. aureus peptide deformylase molecule or molecular complex comprising:
- preparing a stock solution of purified S. aureus peptide deformylase at a concentration of about 1 mg/ml to about 50 mg/ml;
- contacting the stock solution with a precipitating solution containing about 1% by weight to about 40% by weight PEG having a number average molecular weight between about 300 and about 20,000;
- about 0 M to about 0.4 M MgCl2;
- and about 0% by weight to about 25% by weight DMSO;
- the precipitating solution being buffered to a pH of about 7 to about 9;
- and
- allowing S. aureus peptide deformylase to crystallize from the resulting solution.
Crystalline S. aureus peptide deformylase.
A crystal of S. aureus peptide deformylase having the orthorhombic space group symmetry C2221.
A crystal of S. aureus peptide deformylase comprising a unit cell having dimensions a, b, and c;
- wherein a is about 90 Å to about 100 Å, b is about 116 Å to about 128 Å, and c is about 45 Å to about 50 Å;
- and wherein α=β=γ=90°.
A crystal of S. aureus peptide deformylase having the orthorhombic space group symmetry C2221 and comprising a unit cell having dimensions a, b, and c;
- wherein a is about 90 Å to about 100 Å, b is about 116 Å to about 128 Å, and c is about 45 Å to about 50 Å;
- and wherein α=β=γ=90°.
A crystal of S. aureus peptide deformylase having the space group symmetry C2 and comprising a unit cell having dimensions a, b, and c;
- wherein a is about 85 Å to about 100 Å, b is about 35 Å to about 50 Å, and c is about 90 Å to about 110 Å;
- and wherein α=γ=90° and β is about 90° to about 95°.
A crystal of S. aureus peptide deformylase having the tetragonal space group symmetry P41 or P42212 and comprising a unit cell having dimensions a, b, and c;
- wherein a and b are about 130 Å to about 190 Å, and c is about 30 Å to about 70 Å;
- and wherein α=β=γ=90°.
A crystal of S. aureus peptide deformylase comprising atoms arranged in a spatial relationship represented by the structure coordinates listed in Table 1.
A crystal of S. aureus peptide deformylase having a single S. aureus peptide deformylase molecule as the asymmetric unit.
A crystal of S. aureus peptide deformylase having an S. aureus peptide deformylase amino acid SEQ ID NO:
- 1.
A crystal of S. aureus peptide deformylase having a S. aureus peptide deformylase amino acid SEQ ID NO:
- 1, except that at least one methionine is replaced with selenomethionine.
A crystal of S. aureus peptide deformylase having a coordinated metal ion selected from the group of metals consisting of Fe, Zn, Ni and combinations thereof.
Dependencies are inferred from the claim text.