Claims
- 1. A crystal of pantothenate synthetase (PS).
- 2. A crystal of PS according to claim 1 having unit cell dimensions of a=66.0 ű5%, b=78.1 ű5%, c=77.1 ű5% and β=103.7°±5%.
- 3. A crystal of PS having the monoclinic point group 2.
- 4. A crystal of PS having the space group P21.
- 5. A crystal of PS which diffracts X-rays for the determination of atomic coordinates of PS to a resolution of better than 2 Å.
- 6. A crystal of PS having the three dimensional atomic coordinates of Table 1.
- 7. A method for crystallizing a selenium atom PS derivative which comprises producing PS by recombinant production in a bacterial host in the presence of selenomethionine, recovering a selenium atom PS derivative from the host and growing crystals from the recovered selenium atom PS derivative.
- 8. A method for growing a crystal of PS, which method comprises growing the crystal by vapour diffusion from a solution comprising a 1:1 mixture of a reservoir buffer with PS at a concentration of 20 mg/ml, wherein the reservoir buffer contains 4-7 weight % Polyethylene Glycol 4000 and 50 mM Tris/HCl buffer at pH 8.
- 9. A method for growing a crystal of PS selenium atom derivative, which method comprises growing the crystal by vapour diffusion from a solution comprising a 1:1 mixture of a reservoir buffer with PS selenium atom derivative at a concentration of 20 mg/ml, wherein the reservoir buffer contains 4-7 weight % Polyethylene Glycol 4000, 2 mM DTT and 50 mM Tris/HCl buffer at pH 8.
- 10. A computer-based method of rational drug design which comprises:
providing the structure of the PS as defined by the coordinates of Table 1; providing the structure of a candidate modulator molecule; and fitting the structure of the candidate modulator molecule to the structure of the PS of Table 1.
- 11. A computer-based method of rational drug design which comprises:
providing the coordinates of at least two atoms of the PS of Table 1; providing the structure of a candidate modulator molecule; and fitting the structure of the candidate modulator molecule to the provided coordinates of the PS.
- 12. The method of claim 10, wherein at least one of said atoms is provided by a residue selected from the group consisting of Pro28, Met30, Gly31, His34, Asp35, Gly36, His37, Leu40, Asn58, Gln61, Phe62, Tyr71, Arg123, His126, Ile133, Val134, Leu137, Gly149, Lys151, Asp152, Gln155, Val175, Ile177, Met178, Ala185, Leu186, Ser187, Ser188, and Arg189.
- 13. A computer-based method of rational drug design which comprises:
providing the coordinates of at least a sub-domain of the PS; providing the structure of a candidate modulator molecule; and fitting the structure of the candidate modulator molecule to the coordinates of the PS sub-domain provided.
- 14. The method of any one of claims 10, 11 or 13 which further comprises the steps of:
obtaining or synthesising the candidate modulator; and contacting the candidate modulator with PS to determine the ability of the candidate modulator to interact with PS.
- 15. The method of any one of claims 10, 11 or 13 which further comprises the steps of:
obtaining or synthesising said candidate modulator; forming a complex of PS and said candidate modulator; and analysing said complex by X-ray crystallography to determine the ability of said candidate modulator to interact with PS.
- 16. A compound having a chemical structure selected using the method of any one of claims 10, 11 or 13, said compound being an inhibitor of PS.
- 17. A method of determining three dimensional structures of PS homologues or analogues of unknown structure, the method comprises the steps of:
aligning a representation of an amino acid sequence of a PS homologue or analogue of unknown structure with the amino acid sequence of PS to match homologous regions of the amino acid sequences; modelling the structure of the matched homologous regions of the PS homologue or analogue of unknown structure on the structure as defined by Table 1 of the corresponding regions of PS; and determining a conformation for the PS homologue or analogue of unknown structure which substantially preserves the structure of said matched homologous regions.
- 18. A chimaeric protein having one or more binding pockets for respective ligands selected from the group consisting of Mg2+, ATP, pantoate and β-alanine, the binding pockets providing a plurality of atoms which interact with the respective ligands and which correspond to selected PS atoms in the PS binding pockets for said respective ligands, the relative positions of said plurality of atoms corresponding to the relative positions, as defined by Table 1, of said selected PS atoms.
- 19. A method for determining the structure of a protein, which method comprises;
providing the co-ordinates of Table 1, and either (a) positioning said co-ordinates in the crystal unit cell of said protein so as to provide a structure for said protein, or (b) assigning NMR spectra peaks of said protein by manipulating said co-ordinates.
- 20. A method for determining the structure of a compound bound to PS, said method comprising:
providing a crystal of PS; soaking the crystal with the compound to form a complex; and determining the structure of the complex by employing the data of Table 1.
- 21. A method for determining the structure of a compound bound to PS, said method comprising:
mixing PS with the compound; crystallizing a PS-compound complex; and determining the structure of the complex by reference to the data of Table 1.
- 22. A method of assessing the ability of a candidate modulator to interact with PS which comprises:
obtaining or synthesising said candidate modulator; forming a crystallised complex of PS and said candidate modulator, said complex diffracting X-rays for the determination of atomic coordinates of said complex to a resolution of better than 2 Å; and analysing said complex by X-ray crystallography to determine the ability of said candidate modulator to interact with PS.
- 23. A computer readable medium with at least one of:
(a) atomic coordinate data according to Table 1 recorded thereon, said data defining the three-dimensional structure of PS, at least one sub-domain of the three-dimensional structure of PS, or the coordinates of at least two atoms of PS; (b) structure factor data for PS recorded thereon, the structure factor data being derivable from the atomic coordinate data of Table 1; (c) atomic coordinate data of a target PS homologue or analogue generated by homology modelling of the target based on the data of Table 1; (d) atomic coordinate data of a protein generated by interpreting X-ray crystallographic data or NMR data by reference to the data of Table 1; and (e) structure factor data derivable from the atomic coordinate data of (c) or (d).
- 24. A computer readable medium according to claim 23, wherein said atomic coordinate data is for at least one of the atoms provided by a residue selected from the group consisting of Pro28, Met30, Gly31, His34, Asp35, Gly36, His37, Leu40, Asn58, Gln61, Phe62, Tyr71, Arg123, His126, Ile133, Val134, Leu137, Gly149, Lys151, Asp152, Gln155, Val175, Ile177, Met178, Ala185, Leu186, Ser187, Ser188, and Arg189.
- 25. A computer system, intended to generate structures and/or perform rational drug design for PS, PS homologues or analogues, complexes of PS with a potential modulator, or complexes of PS homologues or analogues with potential modulators,
the system containing computer-readable data comprising at least one of:
(a) atomic coordinate data according to Table 1, said data defining the three-dimensional structure of PS, at least one sub-domain of the three-dimensional structure of PS, or the coordinates of at least two atoms of PS; (b) structure factor data for PS, said structure factor data being derivable from the atomic coordinate data of Table 1; (c) atomic coordinate data of a target PS homologue or analogue generated by homology modelling of the target based on the data of Table 1; (d) atomic coordinate data of a protein generated by interpreting X-ray crystallographic data or NMR data by reference to the data of Table 1; and (e) structure factor data derivable from the atomic coordinate data of (c) or (d).
- 26. A computer system according to claim 25 containing atomic coordinate data according to Table 1, wherein said atomic coordinate data is for at least one of the atoms provided by a residue selected from the group consisting of Pro28, Met30, Gly31, His34, Asp35, Gly36, His37, Leu40, Asn58, Gln61, Phe62, Tyr71, Arg123, His126, Ile133, Val134, Leu137, Gly149, Lys151, Asp152, Gln155, Val175, Ile177, Met178, Ala185, Leu186, Ser187, Ser188, and Arg189.
- 27. A computer system according to claim 25 comprising:
(i) a computer-readable data storage medium comprising data storage material encoded with said computer-readable data; (ii) a working memory for storing instructions for processing said computer-readable data; and (iii) a central-processing unit coupled to said working memory and to said computer-readable data storage medium for processing said computer-readable data and thereby generating structures and/or performing rational drug design.
- 28. A computer system according to claim 27 further comprising a display coupled to said central-processing unit for displaying said structures.
- 29. A method of providing data for generating structures and/or performing rational drug design for PS, PS homologues or analogues, complexes of PS with a potential modulator, or complexes of PS homologues or analogues with potential modulators, the method comprising:
(i) establishing communication with a remote device containing computer-readable data comprising at least one of: (a) atomic coordinate data according to Table 1, said data defining the three-dimensional structure of PS, at least one sub-domain of the three-dimensional structure of PS, or the coordinates of at least two atoms of PS; (b) structure factor data for PS, said structure factor data being derivable from the atomic coordinate data of Table 1; (c) atomic coordinate data of a target PS homologue or analogue generated by homology modelling of the target based on the data of Table 1; (d) atomic coordinate data of a protein generated by interpreting X-ray crystallographic data or NMR data by reference to the data of Table 1; and (e) structure factor data derivable from the atomic coordinate data of (c) or (d); and (ii) receiving said computer-readable data from said remote device.
Priority Claims (1)
Number |
Date |
Country |
Kind |
PCT/GB01/04067 |
Sep 2001 |
WO |
|
RELATED APPLICATIONS
[0001] This application is a continuation-in-part of (i) U.S. Ser. No. 09/659,759 filed Sep. 11, 2000, and (ii) of International Application PCT/GB/04067 filed Sep. 11, 2001 which is a continuation-in-part of U.S. Ser. No. 09/659,759. The contents of each of these applications are incorporated herein in their entirety.
Continuation in Parts (1)
|
Number |
Date |
Country |
Parent |
09659759 |
Sep 2000 |
US |
Child |
10113948 |
Apr 2002 |
US |