Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem

Journal of Molecular Biology

Volumn 276, Issue 1, 1998, Pages 265-285

  Jackson, Richard M ^a   Gabb, Henry A ^a   Sternberg, Michael J E ^a  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

Langevin dipole; Protein docking; Side chain optimisation; Solvation energy

Indexed keywords

CHYMOTRYPSIN; CHYMOTRYPSINOGEN; KALLIKREIN; OVOMUCOID; PROTEIN SUBUNIT; PROTEINASE; PROTEINASE INHIBITOR; SUBTILISIN; TRYPSIN;

ANTIGEN ANTIBODY COMPLEX; ARTICLE; COMPUTER PROGRAM; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; HYDRATION; HYDROPHOBICITY; LYSOSOME; MATHEMATICAL MODEL; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; SOLVATION; THERMODYNAMICS;

EID: 0032512619     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1519     Document Type: Article

References (56)

1. Bacon D.J., Moult J. Docking by least-squares fitting of molecular surface patterns. J. Mol. Biol. 225:1992;849-858
2. Bhat T.N., Bentley G.A., Fischmann T.O., Boulot G., Poljak R.J. Small rearrangements in strucutres of Fv and Fab fragments of antibody D1. 3 on antigen binding. Nature. 347:1990;483-485
3. Blevins R.A., Tulinsky A. The refinement and the structure of the dimer of α-chymotrypsin at 1.67 Å resolution. J. Biol. Chem. 260:1985;4264-4270
4. Bode W., Chen Z., Bartels K., Kutzbach C., Schmidt-Kastner G., Bartunik H. Refined 2 Å X-ray crystal structure of porcine pancreatic kallikrein a and a specific trypsion-like serine proteinase. Crystallization and structure determination and crystallographic refinement and structure and its comparison with bovine trypsin. J. Mol. Biol. 164:1983;237-283
5. Bode W., Epp O., Huber R., Laskowski M. The crystal and molecular structure of the third domain of silver pheasant ovomucoid. Eur. J. Biochem. 147:1985;387-395
6. Braden B.C., Souchon H., Eisele J.-L., Bentley G.A., Bhat T.N., Navaza J., Poljak R.J. Three-dimensional structures of the free and the antigen-complexed Fab form monoclonal anti-lysozyme antibody D44. 1. J. Mol. Biol. 243:1994;767-781
7. Bruccoleri R.E., Karplus M. Prediction of the folding of short peptide segments by uniform conformational sampling. Biopolymers. 26:1987;137-168
8. Chen Z., Bode W. Refined 2.5 Å X-ray crystal structure of the complex formed by porcine kallikrein a and the the crystallization, Patterson search, structure comparison with its components and with bovine trypsin-pancreatic trypsin inhibitor complex. J. Mol. Biol. 164:1983;283-311
9. Cherfils J., Janin J. Protein docking algorithms simulating molecular recognition. Curr. Opin. Struct. Biol. 3:1993;265-269
10. Cherfils J., Duquerroy S., Janin J. Protein-protein recognition analysed by docking simulation. Proteins: Struct. Funct. Genet. 11:1991;271-280
11. Cummings M.D., Hart T.N., Read R.J. Atomic solvation parameters in the analysis of protein-protein docking results. Protein Sci. 4:1995;2087-2099
12. Desmet J., Wilson I.A., Joniau M., Demaeyer M., Lasters I. Computation of the binding of fully flexible peptides to proteins with flexible side-chains. FASEB. J. 11:1997;164-172
13. Fischer D., Lin S.L., Wolfson H.L., Nussinov R. A Geometry-based suite of molecular docking processes. J. Mol. Biol. 248:1995;459-477
14. Fischmann T.O., Bentley G.A., Bhat T.N., Boulot G., Mariuzza R.A., Phillips S.E.V., Tello D., Poljak R.J. Crystallographic refinement of the three-dimensional structure of the D1. 3-lysozyme complex at 2.5 Å resolution. J. Biol. Chem. 266:1991;12915-12920
15. Freer S.T., Kraut J., Robertus J.D., Wright H.T., Xuong N.H. Chymotrypsinogen, 2.5 Å crystal structure, comparison with alpha-chymotrypsin, and implications for zymogen activation. Biochemistry. 9:1970;1997-2009
16. Fujinaga M., Sielecki A.F., Read R.J., Ardelt W., Laskowski M.J., James M.N.G. Refined structure of α-lytic protease at 1.7 Å resolution. J. Mol. Biol. 195:1987;397-418
17. Gabb H.A., Jackson R.M., Sternberg M.J.E. Modelling protein docking using shape complementarity, electrostatics, and biochemical information. J. Mol. Biol. 272:1997;106-120
18. Harrison P. Analysis and prediction of protein structure: disulphide bridges. PhD dissertation. 1996;University of London
19. Harvey S.C. Treatment of electrostatic effects in macromolecular modelling. Proteins: Struct. Funct. Genet. 5:1989;78-92
20. Hecht H.J., Szardenings M., Collins J., Schomburg D. Three-dimensional structure of the complex between bovine chymotrypsinogen a and two recombinant variants of human pancreatic secretory trypsin inhibitor (Kazal type). J. Mol. Biol. 220:1991;711-722
21. Hecht H.J., Szardenings M., Collins J., Schomburg D. Three-dimensional structure of a recombinant variant of human pancreatic secretory trypsin inhibitor (Kazal type). J. Mol. Biol. 225:1992;1095-1103
22. Hill T.L. Statistical Mechanics. 1956;McGraw Hill, New York
23. Islam S.A. Computer aided molecular modelling of DNA-drug interactions. PhD dissertation. 1986;University of London
24. Jackson R.M., Sternberg M.J.E. Application of scaled particle theory to model the hydrophobic effect implications for molecular association and protein stability. Protein Eng. 7:1994;371-383
25. Jackson R.M., Sternberg M.J.E. A continuum model for protein-protein interactions application to the docking problem. J. Mol. Biol. 250:1995;258-275
26. Jiang F., Kim S.-H. "Soft docking" matching of molecular surface cubes. J. Mol. Biol. 219:1991;79-102
27. Katchalski-Katzir E., Shariv I., Eisenstein M., Friesem A.A., Aflalo C., Vakser I.A. Molecular surface recognition determination of geometric fit between proteins and ligands by correlation techniques. Proc. Natl Acad. Sci. USA. 89:1992;2195-2199
28. Koehl P., Delarue M. Application of a self-consitent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol. 239:1994;249-275
29. Lee C. Predicting protein mutant energetics by self-consistent ensemble optimization. J. Mol. Biol. 236:1994;918-939
30. Lee F.S., Chu Z.T., Warshel A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by POLARIS and ENZYMIX programs. J. Comput. Chem. 14:1993;161-185
31. Luzhkov V., Warshel A. Microscopic models for quantum mechanical calculations of chemical processes in solution LD/AMPAC and SCAAS/AMPAC calculations of solvation energies. J. Comput. Chem. 13:1992;199-213
32. Maenaka K., Matsushima M., Song H., Sunada F., Watanabe K., Kumagai I. Dissection of protein-carbohydrate interactions in mutant hen egg-white lysozyme complexes and their hydrolytic activity. J. Mol. Biol. 247:1995;281-293
33. Marquart M., Walter J., Deisenhofer J., Bode W., Huber R. The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors. Acta Crystallog. sect. B. 39:1983;480-490
34. McPhalen C.A., James M.N.G. Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds. Biochemistry. 26:1987;261-269
35. McPhalen C.A., James M.N.G. Structural comparison of two serine proteinase-protein inhibitor complexes eglin-c-subtilisin Carlsberg and CI-2-subtilisin Novo. Biochemistry. 27:1988;6582-6598
36. Momany F.A., McGuire R.F., Burgess A.W., Scheraga H.A. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interations, hydrogen bond interactions and intrisic torsion potentials for the naturally occuring amino acids. J. Phys. Chem. 79:1975;2361-2366
37. Neidhart J.J., Petsko G.A. The refined crystal structure of subtilisin Carlsberg at 2.5 Å resolution. Protein Eng. 2:1988;271-276
38. Padlan E.A., Silverton E.W., Sheriff S., Cohen G.H., Smith-Gill S.J., Davies D.R. Structure of an antibody complex. Crystal strucutre of the HyHEL-10 Fab-lysozyme complex. Proc. Natl Acad. Sci. USA. 86:1989;5938-5942
39. Parkin S., Rubb B., Hope H. Structure of bovine pancreatic trypsin-inhibitor at 125k - definition of carboxyl terminal residues gly57 and ala58. Acta. Crystallog. sect. D. 52:1996;18-29
40. Richards F.M. Areas, volumes, packing, and protein structure. Annu. Rev. Biophys. Bioeng. 6:1977;151-176
41. Richmond T.J. Solvent accessible surface area and excluded volume in proteins analytical equations for overlapping spheres and implications for the hydrophobic effect. J. Mol. Biol. 178:1984;63-89
42. Russell S.T., Warshel A. Calculation of electrostatic energies in proteins the energetics of ionized groups in bovine pancreatic trypsin inhibitor. J. Mol. Biol. 185:1985;389-404
43. Schrauber H., Eisenhaber F., Argos P. Rotamers to be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J. Mol. Biol. 230:1993;592-612
44. Sheriff S., Silverton E.W., Padlan E.A., Cohen G.H., Smith-Gill S.J., Davies D.R. Three-dimensional structure of an antibody-antigen complex. Proc. Natl Acad. Sci. USA. 84:1987;8075-8079
45. Shoichet B.K., Kuntz I.D. Protein docking and complementarity. J. Mol. Biol. 221:1991;327-346
46. Sitkoff D., Sharp K.A., Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1994;1978-1988
47. Totrov M.M., Abagyan R.A. Detailed ab initio prediction of lysozyme-antibody complex with 1.6 Å accuracy. Nature Struct. Biol. 1:1994;259-263
48. Tuffery P., Etchebest C., Hazout S., Lavery R. A new approach to the rapid determination of protein side-chain conformations. J. Biomol. Struct. Dynam. 8:1991;1267-1289
49. Walls P.H., Sternberg M.J.E. New algorithm to model protein-protein recognition based on surface complementarity. J. Mol. Biol. 228:1992;277-297
50. Walter J., Steigemann T.P., Singh H., Bartunik H., Bode W., Huber R. On the disordered activation domain in trypsinogen. Chemical labelling and low temperature crystallography. Acta Crystallog. sect. B. 38:1982;1462-1472
51. Warshel A., Levitt M. Theoretical studies of enzymic reactions dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103:1976;227-249
52. Warshel A., Russell S.T. Electrostatic interactions in biological systems and in solution. Quart. Rev. Biophys. 17:1984;283-422
53. Weiner S.J., Kollman P.A., Case D.A., Singh U.C., Ghio C., Alagona G., Profeta S., Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:1984;765-784
54. Weng Z., Vajda S., Delisi C. Prediction of protein complexes using empirical free energy functions. Protein Sci. 5:1996;614-626
55. Wilson C., Mace J.E., Agard D.A. Computational method for the design of enzymes with altered substrate specificity. J. Mol. Biol. 220:1991;495-506
56. Wilson I.A., Stanfield R.L. Antibody-antigen interactions. Curr. Opin. Struct. Biol. 3:1993;113-118