Solvated docking: Introducing water into the modelling of biomolecular complexes

Bioinformatics

Volumn 22, Issue 19, 2006, Pages 2340-2347

  van Dijk, Aalt D J ^a   Bonvin, Alexandre M J J ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

WATER;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; FEASIBILITY STUDY; MOLECULAR MODEL; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; QUALITY CONTROL; SOLVATION; STRUCTURE ANALYSIS; WATER ANALYSIS;

EID: 33750014560     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl395     Document Type: Article

References (55)

1. Babor,M. et al. (2002) Conserved positions for ribose recognition: importance of water bridging interactions among ATP, ADP and FAD-protein complexes. J. Mol. Biol., 323, 523-532.
2. Bode,W. et al. (1989) The refined 2.0 a X-ray crystal-structure of the complex formed between bovine beta-trypsin and Cmti-I, a trypsin-inhibitor from Squash seeds (Cucurbita-Maxima) - topological similarity of the Squash seed inhibitors with the carboxypeptidase a inhibitor from potatoes. FEBS Lett., 242, 285-292.
3. Bompard Gilles,C. et al. (1996) Substrate mimicry in the active center of a mammalian alpha-amylase: Structural analysis of an enzyme-inhibitor complex. Structure, 4, 1441-1452.
4. Boobbyer,D.N.A. et al. (1989) New hydrogen-bond potentials for use in determining energetically favorable binding-sites on molecules of known structure. J. Med. Chem., 32, 1083-1094.
5. Brunger,A.T. et al. (1998) Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D, 54, 905-921.
6. Buckle,A.M. et al. (1994) Protein-protein recognition - crystal structural-analysis of a Barnase Barstar complex at 2.0-Angstrom resolution. Biochemistry, 33, 8878-8889.
7. Carugo,O. (1999) Correlation between occupancy and B factor of water molecules in protein crystal structures. Protein Eng., 12, 1021-1024.
8. Carugo,O. and Bordo,D. (1999) How many water molecules can be detected by protein crystallography? Acta Crystallogr. D, 55, 479-483.
9. Carvalho,A.L. et al. (2003) Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex. Proc. Natl Acad. Sci. USA, 100, 13809-13814.
10. Chandler,D. (2005) Interfaces and the driving force of hydrophobic assembly. Nature, 437, 640-647.
11. Daura,X. et al. (1999) Peptide folding: When simulation meets experiment. Angew. Chem. Int. Ed., 38, 236-240.
12. Dominguez,C. et al. (2003) HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc., 125, 1731-1737.
13. Fernandez-Recio,J. et al. (2004) Identification of protein-protein interaction sites from docking energy landscapes. J. Mol. Biol., 335, 843-865.
14. Halperin,I. et al. (2002) Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins, 47, 409-43.
15. Houborg,K. et al. (2003) Impact of the physical and chemical environment on the molecular structure of Coprinus cinereus peroxidase. Acta Crystallogr. D, 59, 989-996.
16. Hubbard,S.J. and Thornton,J.M. (1993) NACCESS. Department of Biochemistry and Molecular Biology, University College, London.
17. Hubbard,S.J. et al. (1994) Intramolecular cavities in globular-proteins. Protein Eng., 7, 613-626.
18. Jiang,L. et al. (2005) A 'solvated rotainer' approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins, 58, 893-904.
19. Jorgensen,W.L. and Tirado-rives,J. (1988) The OPLS Potential functions for proteins. Energy minimizations for crystals of cyclin peptides and crambin. J. Am. Chem. Soc., 110, 1657-1666.
20. Jorgensen,W.L. et al. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79, 926-935.
21. Kalodimos,C.G. et al. (2004) Structure and flexibility adaptation in nonspecific and specific protein - DNA complexes. Science, 305, 386-389.
22. Keskin,O. et al. (2004) A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci., 13, 1043-1055.
23. Ko,T.P. et al. (1999) The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein. Structure, 7, 91-102.
24. Lima,C.D. et al. (1997) Structure-based analysis of catalysis and substrate definition in the HIT protein family. Science, 278, 286-290.
25. Lindahl,E. et al. (2001) GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model, 7, 306-317.
26. Linge,J.P. et al. (2003a) ARIA: Automated NOE assignment and NMR structure calculation. Bioinformatics, 19, 315-316.
27. Linge,J.P. et al. (2003b) Refinement of protein structures in explicit solvent. Proteins, 50, 496-506.
28. Lo Conte,L. et al. (1999) The atomic structure of protein-protein recognition sites. J. Mol. Biol., 285, 2177-2198.
29. Loris,R. et al. (1999) Conserved water molecules in a large family of microbial ribonucleases. Proteins, 36, 117-134.
30. Mendez,R. et al. (2005) Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins, 60, 150-169.
31. Mintseris,J. et al. (2005) Protein-protein docking benchmark 2.0: An update. Proteins, 60, 214-216.
32. Moitessier,N. et al. (2006) Docking of Aminoglycosides to hydrated and flexible RNA. J. Med. Chem., 49, 1023-1033.
33. Mustata,G. and Briggs,J.M. (2004) Cluster analysis of water molecules in alanine racemase and their putative structural role. Protein Eng., 17, 223-234.
34. Nishida,M. et al. (2001) Novel recognition mode between Vav and Grb2 SH3 domains. EMBO J., 20, 2995-3007.
35. Osterberg,F. et al. (2002) Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins, 46, 34-40.
36. Rarey,M. et al. (1999) The particle concept: Placing discrete water molecules during protein-ligand docking predictions. Proteins, 34, 17-28.
37. Raschke,T.M. (2006) Water structure and interactions with protein surfaces. Curr. Opin. Struct. Biol., 16, 152-159.
38. Rashin,A.A. et al. (1986) Internal cavities and buried waters in globular proteins. Biochemistry, 25, 3619-3625.
39. Rejto,P.A. and Verkhivker,G.M. (1997) Mean field analysis of FKBP12 complexes with FK506 and rapamycin: Implications for a role of crystallographic water molecules in molecular recognition and specificity. Proteins, 28, 313-324.
40. Robert,C.H. and Ho,P.S. (1995) Significance of bound water to local chain conformations in protein crystals. Proc. Natl Acad. Sci. USA, 92, 7600-7604.
41. Rodier,F. et al. (2005) Hydration of protein-protein interfaces. Proteins, 60, 36-45.
42. Schymkowitz,J.W.H. et al. (2005) Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc. Natl Acad. Sci. USA, 102, 10147-10152.
43. Song,H.K. and Suh,S.W. (1998) Kunitz-type soybean trypsin inhibitor revisited: Refined structure of its complex with porcine trypsin reveals an insight into the interaction between a homologous inhibitor from Erythrina caffra and tissue-type plasminogen activator. J. Mol. Biol., 275, 347-363.
44. Sreenivasan,U. and Axelsen,P.H. (1992) Buried water in homologous serine proteases. Biochemistry, 31, 12785-12791.
45. Takeuchi,Y. et al. (1991) Refined crystal-structure of the complex of subtilisin Bpn' and Streptomyces Subtilisin inhibitor at 1.8 A-resolution.. J. Mol. Biol., 221, 309-325.
46. Tame,J.R.H. et al. (1996) The role of water in sequence-independent ligand binding by an oligopeptide transporter protein. Nat. Struct. Biol., 3, 998-1001.
47. van Dijk,A.D.J. et al. (2005a) Data-driven docking for the study of biomolecular complexes. FEBS J., 272, 293-312.
48. van Dijk,A.D.J. et al. (2005b) Data-driven docking: HADDOCK's adventures in CAPRI. Proteins, 60, 232-238.
49. van Dijk et al. (2006) Information-driven protein-DNA docking using HADDOCK: It is a matter of flexibility. Nucleic Acids Res., 34, 3317-3325.
50. Verdonk,M.L. et al. (2005) Modeling water molecules in protein-ligand docking using GOLD. J. Med. Chem., 48, 6504-6515.
51. Wade,R.C. and Goodford,P.J. (1993) Further development of hydrogen-bond functions for use in determining energetically favorable binding-sites on molecules of known structure.2. Ligand probe groups with the ability to form more than 2 hydrogenbonds. J. Med. Chem., 36, 148-156.
52. Wade,R.C. et al. (1993) Further development of hydrogen-bond functions for use in determining energetically favorable binding-sites on molecules of known structure. 1. Ligand probe groups with the ability to form 2 hydrogen-bonds. J. Med. Chem., 36, 140-147.
53. Wang,G. et al. (2000) Solution structure of the phosphoryl transfer complex between the signal transducing proteins HPr and IIA(glucose) of the Escherichia coli phosphoenolpyruvate: Sugar phosphotransferase system. EMBO J., 19, 5635-5649.
54. Yang,J.M. and Chen,C.C. (2004) GEMDOCK: A generic evolutionary method for molecular docking. Proteins, 55, 288-304.
55. Zhang,X.J. and Matthews,B.W. (1994) Conservation of solvent-binding sites in 10 crystal forms of T4-Lysozyme. Protein Sci., 3, 1031-1039.