Homology-modelling protein-ligand interactions: Allowing for ligand-induced conformational change

Journal of Molecular Biology

Volumn 399, Issue 4, 2010, Pages 645-661

  Dalton, James A R ^a   Jackson, Richard M ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

Conformational change; Homology modelling; Induced fit; Protein ligand; Structural alignment

Indexed keywords

ANGIOTENSIN CONVERTING ENZYME 2; CYCLIN DEPENDENT KINASE 2; CYCLIN DEPENDENT KINASE 5; DIHYDROFOLATE REDUCTASE; FLUINDOSTATIN; LIGAND; PROTEIN; THYMIDINE PHOSPHORYLASE;

ACCURACY; ALGORITHM; ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS);

EID: 77954758781     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.04.047     Document Type: Article

References (45)

1. Martin A.C., MacArthur M.W., Thornton J.M. Assessment of comparative modeling in CASP2. Proteins 1997, 29:14-28.
2. Moult J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr. Opin. Struct. Biol. 2005, 15:285-289.
3. Moult J., Fidelis K., Kryshtafovych A., Rost B., Hubbard T., Tramontano A. Critical assessment of methods of protein structure prediction-round VII. Proteins 2007, 69:3-9.
4. Guy J.L., Jackson R.M., Acharya K.R., Sturrock E.D., Hooper N.M., Turner A.J. Angiotensin-converting enzyme-2 (ACE2): comparative modelling of the active site, specificity requirements, and chloride dependence. Biochemistry 2003, 42:13185-13192.
5. Kneissl B., Leonhardt B., Hildebrandt A., Tautermann C.S. Revisiting automated G-protein coupled receptor modeling: the benefit of additional template structures for a neurokinin-1 receptor model. J. Med. Chem. 2009, 52:3166-3173.
6. Evers A., Gohlke H., Klebe G. Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials. J. Mol. Biol. 2003, 334:327-345.
7. Hare B.J., Walters W.P., Caron P.R., Bemis G.W. CORES: an automated method for generating three-dimensional models of protein/ligand complexes. J. Med. Chem. 2004, 47:4731-4740.
8. Martin L., Catherinot V., Labesse G. KinDOCK: a tool for comparative docking of protein kinase ligands. Nucleic Acids Res. 2006, 34:W325-329.
9. Brylinski M., Skolnick J. FINDSITE: a threading-based approach to ligand homology modeling. PLoS Comput. Biol. 2009, 5:e1000405.
10. Mitchell J.B. The relationship between the sequence identities of alpha helical proteins in the PDB and the molecular similarities of their ligands. J. Chem. Inf. Comput. Sci. 2001, 41:1617-1622.
11. Nobeli I., Spriggs R.V., George R.A., Thornton J.M. A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E. coli. J. Mol. Biol. 2005, 347:415-436.
12. Kalinina O.V., Gelfand M.S., Russell R.B. Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinformatics 2009, 10:174.
13. Koshland D.E. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl Acad. Sci. USA 1958, 44:98-104.
14. Tuffery P., Etchebest C., Hazout S., Lavery R. A new approach to the rapid determination of protein side chain conformations. J. Biomol. Struct. Dyn. 1991, 8:1267-1289.
15. Jackson R.M., Gabb H.A., Sternberg M.J. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J. Mol. Biol. 1998, 276:265-285.
16. O'Sullivan O., Suhre K., Abergel C., Higgins D.G., Notredame C. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol. 2004, 340:385-395.
17. Sali A., Blundell T.L. Comparative modelling by satisfaction of spatial restraints. J. Mol. Biol. 1993, 234:779-815.
18. Omega, OpenEye Science Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508.
19. Dalton J.A., Jackson R.M. An evaluation of automated homology modelling methods at low target template sequence similarity. Bioinformatics 2007, 23:1901-1908.
20. Loferer M.J., Kolossváry I., Aszódi A. Analyzing the performance of conformational search programs on compound databases. J. Mol. Graphics Modell. 2007, 25:700-710.
21. Boström J. Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools. J. Comput.-Aided Mol. Des. 2001, 15:1137-1152.
22. Boström J., Greenwood J.R., Gottfries J. Assessing the performance of Omega with respect to retrieving bioactive conformations. J. Mol. Graphics Modell. 2003, 21:449-462.
23. Brakoulias A., Jackson R.M. Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching. Proteins 2004, 56:250-260.
24. Kinnings S.L., Jackson R.M. LigMatch: a multiple structure-based ligand matching method for 3D virtual screening. J. Chem. Inf. Model. 2009, 49:2056-2066.
25. Nicholls A., MacCuish N.E., MacCuish J.D. Variable selection and model validation of 2D and 3D molecular descriptors. J. Comput.-Aided Mol. Des. 2004, 18:451-474.
26. Dunbrack R.L. Rotamer libraries in the 21st century. Curr. Opin. Struct. Biol. 2002, 12:431-440.
27. Hartshorn M.J., Verdonk M.L., Chessari G., Brewerton S.C., Mooij W.T.M., Mortenson P.N., Murray C.W. Diverse, high-quality test set for the validation of protein-ligand docking performance. J. Med. Chem. 2007, 50:726-741.
28. McGann M.R., Almond H.R., Nicholls A., Grant J.A., Brown F.K. Gaussian docking functions. Biopolymers 2003, 68:76-90.
29. Kairys V., Fernandes M.X., Gilson M.K. Screening drug-like compounds by docking to homology models: a systematic study. J. Chem. Inf. Model. 2006, 46:365-379.
30. McGovern S.L., Shoichet B.K. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J. Med. Chem. 2003, 46:2895-2907.
31. DeWeese-Scott C., Moult J. Molecular modeling of protein function regions. Proteins 2004, 55:942-961.
32. Kopp J., Schwede T. Automated protein structure homology modeling: a progress report. Pharmacogenomics 2004, 5:405-416.
33. Grigoryan G., Ochoa A., Keating A.E. Computing van der Waals energies in the context of the rotamer approximation. Proteins 2007, 68:863-878.
34. Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117:5179-5197.
35. Wang J., Wolf R.M., Caldwell J.W., Kollman P.A., Case D.A. Development and testing of a general amber force field. J. Comput. Chem. 2004, 25:1157-1174.
36. Spellmeyer D.C., Wong A.K., Bower M.J., Blaney J.M. Conformational analysis using distance geometry methods. J. Mol. Graphics Modell. 1997, 15:18-36.
37. Jakalian A., Bush B.L., Jack D.B., Bayly C.I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method. J. Comput. Chem. 2000, 21:132-146.
38. Wang J., Wang W., Kollman P.A., Case D.A. Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graphics Modell. 2006, 25:247-260.
39. QuacPac, OpenEye Science Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508.
40. OpenBabel, http://openbabel.org/wiki/Main_Page.
41. Gold N.D., Jackson R.M. SitesBase: a database for structure-based protein-ligand binding site comparisons. Nucleic Acids Res. 2006, 34:D231-234.
42. Davies J.R., Jackson R.M., Mardia K.V., Taylor C.C. The Poisson Index: a new probabilistic model for protein-ligand binding site similarity. Bioinformatics 2007, 23:3001-3008.
43. Halgren T.A. The representation of van der Waals (vdW) interactions in molecular mechanics force fields: potential form, combination rules and vdW parameters. J. Am. Chem. Soc. 1992, 114:7827-7843.
44. Szybki, OpenEye Science Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508.
45. Chen W., Huang J., Gilson M.K. Identification of symmetries in molecules and complexes. J. Chem. Inf. Comput. Sci. 2004, 44:1301-1313.