Multiple solvent crystal structures: Probing binding sites, plasticity and hydration

Journal of Molecular Biology

Volumn 357, Issue 5, 2006, Pages 1471-1482

  Mattos, Carla ^a   Bellamacina, Cornelia R ^b   Peisach, Ezra ^b   Pereira, Antonio ^b   Vitkup, Dennis ^b   Petsko, Gregory A ^b   Ringe, Dagmar ^b  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b BRANDEIS UNIVERSITY   (United States)

Author keywords

Elastase; Multiple solvent crystal structures; Organic solvents; Protein binding sites; Solvent mapping

Indexed keywords

2 PROPANOL; ACETONE; ACETONITRILE; ALCOHOL; BENZENE; CYCLOHEXANE; LIGAND; N,N DIMETHYLFORMAMIDE; ORGANIC SOLVENT; PANCREATIC ELASTASE; SOLVENT; TRIFLUOROETHANOL; WATER;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; DATA BASE; HYDRATION; LIGAND BINDING; MOLECULAR PROBE; NONHUMAN; PLASTICITY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION;

SUIDAE;

EID: 33645067372     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.01.039     Document Type: Article

References (52)

1. S. Vajda, and C.J. Camacho Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol. 22 2004 110 116
2. T. Selzer, S. Albeck, and G. Schreiber Rational design of faster associating and tighter binding protein complexes Nature Struct. Biol. 7 2000 537 541
3. D. Rajamani, S. Thiel, S. Vajda, and C.J. Camacho Anchor residues in protein-protein interactions Proc. Natl Acad. Sci. USA 101 2004 11287 11292
4. O. Keskin, B. Ma, and R. Nussinov Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues J. Mol. Biol. 345 2005 1281 1294
5. D. Ringe What makes a binding site a binding site? Curr. Opin. Struct. Biol. 5 1995 825 829
6. S. Jones, and J.M. Thornton Principles of protein-protein interactions Proc. Natl Acad. Sci. USA 93 1996 13 20
7. R. Najmanovich, J. Kuttner, V. Sobolev, and M. Edelman Side chain flexibility in proteins upon ligand binding Proteins: Struct. Funct. Genet. 39 2000 261 268
8. B. Ma, H.J. Wolfson, and R. Nussinov Protein functional epitopes: hot spots, dynamics and combinatorial libraries Curr. Opin. Struct. Biol. 11 2001 364 369
9. G.A. Papoian, J. Ulander, and P.G. Wolynes Role of water mediated interactions in protein-protein recognition landscapes J. Am. Chem. Soc. 125 2003 9170 9178
10. D. Reichmann, O. Rahat, S. Albeck, R. Meged, O. Dym, and G. Schreiber The modular architecture of protein-protein binding interfaces Proc. Natl Acad. Sci. USA 102 2005 57 62
11. T. Kortvelyesi, S. Dennis, M. Silberstein, L. Brown 3rd, and S. Vajda Algorithms for computational solvent mapping of proteins Proteins: Struct. Funct. Genet. 51 2003 340 351
12. M.D. Cummings, R.L. DesJarlais, A.C. Gibbs, V. Mohan, and E.P. Jaeger Comparison of automated docking programs as virtual screening tools J. Med. Chem. 48 2005 962 976
13. C. Mattos, and D. Ringe Locating and characterizing binding sites on proteins Nature Biotechnol. 14 1996 595 599
14. C. Mattos, and D. Ringe Proteins in organic solvents Curr. Opin. Struct. Biol. 11 2001 761 764
15. P.A. Fitzpatrick, D. Ringe, and A.M. Klibanov X-ray crystal structure of cross-linked subtilisin Carlsberg in water vs. acetonitrile Biochem. Biophys. Res. Commun. 198 1994 675 681
16. N.H. Yennawar, H.P. Yennawar, and G.K. Farber X-ray crystal structure of gamma-chymotrypsin in hexane Biochemistry 33 1994 7326 7336
17. K.N. Allen, C.R. Bellamacina, X. Ding, C.J. Jeffery, C. Mattos, G.A. Petsko, and D. Ringe An experimental approach to mapping the binding surfaces of crystalline proteins J. Phys. Chem. 100 1996 2605 2611
18. J.L. Schmitke, L.J. Stern, and A.M. Klibanov The crystal structure of subtilisin Carlsberg in anhydrous dioxane and its comparison with those in water and acetonitrile Proc. Natl Acad. Sci. USA 94 1997 4250 4255
19. T. Wang, and J. Zhou 3DFS: a new 3D flexible searching system for use in drug design J. Chem. Inf. Comput. Sci. 38 1998 71 77
20. A.C. English, S.H. Done, L.S. Caves, C.R. Groom, and R.E. Hubbard Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol Proteins: Struct. Funct. Genet. 37 1999 628 640
21. A.C. English, C.R. Groom, and R.E. Hubbard Experimental and computational mapping of the binding surface of a crystalline protein Protein Eng. 14 2001 47 59
22. A. Miranker, and M. Karplus Functionality maps of binding sites: a multiple copy simultaneous search method (MCSS) Proteins: Struct. Funct. Genet. 11 1991 29 34
23. P.J. Goodford A computational procedure for determining energetically favorable binding sites on biologically important macromolecules J. Med. Chem. 28 1985 849 857
24. G.R. Smith, and M.J.E. Sternberg Prediction of protein-protein interactions by docking methods Curr. Opin. Struct. Biol. 12 2002 28 35
25. S. Dennis, T. Kortvelyesi, and S. Vajda Computational mapping identifies the binding sites of organic solvents on proteins Proc. Natl Acad. Sci. USA 99 2002 4290 4295
26. M. Silberstein, S. Dennis, L. Brown, T. Kortvelyesi, K. Clodfelter, and S. Vajda Identification of substrate binding sites in enzymes by computational solvent mapping J. Mol. Biol. 332 2003 1095 1113
27. M.B. Eisen, D.C. Wiley, M. Karplus, and R.E. Hubbard HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site Proteins: Struct. Funct. Genet. 19 1994 199 221
28. C.L. Verlinde, G. Rudenko, and W.G. Hol In search of new lead compounds for trypanosomiasis drug design: a protein structure-based linked-fragment approach J. Comput. Aided Mol. Des. 6 1992 131 147
29. I. Huc, and J.M. Lehn Virtual combinatorial libraries: dynamic generation of molecular and supramolecular diversity by self-assembly [published erratum appears in Proc Natl Acad Sci U S A 1997 Jul 22;94(15):8272] Proc. Natl Acad. Sci. USA 94 1997 2106 2110
30. S.B. Shuker, P.J. Hajduk, R.P. Meadows, and S.W. Fesik Discovering high-affinity ligands for proteins: SAR by NMR Science 274 1996 1531 1534
31. C. Mattos Protein-water interactions in a dynamic world Trends Biochem. Sci. 27 2002 203208
32. C. Mattos, D.A. Giammona, G.A. Petsko, and D. Ringe Structural analysis of the active site of porcine pancreatic elastase based on the X-ray crystal structures of complexes with trifluoroacetyl-dipeptide-anilide inhibitors Biochemistry 34 1995 3193 3203
33. C. Mattos, and D. Ringe Solvent structure M.G. Rossman E. Arnold International Tables for Crystallography vol. F 2001 Kluwer Academic Publishers Dordrecht 623 640
34. E. Meyer, G. Cole, R. Radhakrishnan, and O. Epp Structure of native porcine pancreatic elastase at 1.65 Å resolutions Acta Crystallog. sect. B 44 1988 26 38
35. D. Atlas The active site of porcine elastase J. Mol. Biol. 93 1975 39 53
36. D.M. Shotton, N.J. White, and H.C. Watson Conformational changes and inhibitor binding at the active site of elastase Cold Spring Harbor Symp. Quant. Biol. 36 1972 91 105
37. E.F. Meyer Jr, R. Radhakrishnan, G.M. Cole, and L.G. Presta Structure of the product complex of acetyl-Ala-Pro-Ala with porcine pancreatic elastase at 1.65 Å resolution J. Mol. Biol. 189 1986 533 539
38. L.H. Takahashi, R. Radhakrishnan, R.E. Rosenfield Jr, E.F. Meyer Jr, D.A. Trainor, and M. Stein X-ray diffraction analysis of the inhibition of porcine pancreatic elastase by a peptidyl trifluoromethylketone J. Mol. Biol. 201 1988 423 428
39. L.H. Takahashi, R. Radhakrishnan, R.E. Rosenfield Jr, and E.F. Meyer Jr Crystallographic analysis of the inhibition of porcine pancreatic elastase by a peptidyl boronic acid: structure of a reaction intermediate Biochemistry 28 1989 7610 7617
40. S. Atwell, M. Ultsch, A.M. De Vos, and J.A. Wells Structural plasticity in a remodeled protein-protein interface Science 278 1997 1125 1128
41. G. Buhrman, V. de Serrano, and C. Mattos Organic solvents order the dynamic switch II in Ras crystals Structure (Camb) 11 2003 747 751
42. A.T. Brunger Crystallographic refinement by simulated annealing. Application to a 2.8 Å resolution structure of aspartate aminotransferase J. Mol. Biol. 203 1988 803 816
43. W. Kabsch Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants J. Appl. Crystallog. 26 1993 795 800
44. A.J. Howard, G.L. Gilliland, B.C. Finzel, T.L. Poulos, D.H. Ohlendorf, and F.R. Selemme Use of an imaging proportional counter in macromolecular crystallography J. Appl. Crystallog. 20 1987 383 387
45. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode C.W. Carter R.M. Sweet Methods in Enzymology: Macromolecular Crystallography, Part A vol. 276 1997 Academic Press New York 307 326
46. A.T. Brunger X-PLOR: A System for X-ray Crystallography and NMR 1992 Yale University Press Hew Haven, CT
47. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallog. sect. A 47 1991 110 119
48. W.L. Jorgensen, and C.J. Swenson Optimized intermolecular potential functions for amides and peptides. Structure and properties of liquid amides J. Am. Chem. Soc. 107 1985 569 578
49. A.D. MacKerell Jr, D. Bashford, M. Bellott, R.L. Dunbrack Jr, J. Evanseck, and M.J. Field All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
50. A.T. Brünger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, and W.L. DeLano Crystallographic & NMR system (CNS): a new software system for macromolecular structure determination Acta Crystallog. sect. D 54 1998 905 921
51. G.J. Kleywegt, and A.T. Brunger Checking your imagination: applications of the free R value Structure 4 1996 897 904
52. P.G. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950