Modelling protein docking using shape complementarity, electrostatics and biochemical information

Journal of Molecular Biology

Volumn 272, Issue 1, 1997, Pages 106-120

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

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

Fast Fourier transform; Molecular recognition; Predictive docking algorithm; Protein protein complex; Protein protein docking

Indexed keywords

DOCKING PROTEIN; ENZYME INHIBITOR; PROTEIN SUBUNIT;

ALGORITHM; ANTIGEN ANTIBODY COMPLEX; ARTICLE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME INHIBITION; FOURIER TRANSFORMATION; MOLECULAR MODEL; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

RUMEX;

EID: 0031565730     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1203     Document Type: Article

References (58)

1. Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F., Brice M. D., Rodgers J. R., Kennard O., Shimanovichi T., Tasumi M. The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
2. Blevins R. A., Tulinsky A. The refinement and the structure of the dimer of alpha-chymotrypsin at 1.67-Å resolution. J. Biol. Chem. 260:1985;4264-4275.
3. Bode W., Chen Z., Bartels K., Kutzbach C., Schmidt-Kastner G., Bartunik H. Refined 2 ångstrom X-ray crystal structure of porcine pancreatic kallikrein a and a specific trypsin-like proteinase, crystallization and structure determination and crystallographic refinement and structure and its comparison with bovine trypsin. J. Mol. Biol. 164:1983;237-282.
4. Bode W., Epp O., Huber R., Laskowski M. Jr, Ardelt W. The crystal and molecular structure of the third domain of silver pheasant ovomucoid (OMSVP3). Eur. J. Biochem. 147:1985;387-395.
5. Bracewell R. N. Numerical transforms. Science. 248:1990;697-704.
6. ab. J. Mol. Biol. 243:1994;767-781.
7. Chen Z., Bode W. Refined 2.5 Å X-ray crystal structure of the complex formed by porcine kallikrein a and the crystallization, patterson search, structure comparison with its components and with the bovine trypsin-pancreatic trypsin inhibitor complex. J. Mol. Biol. 164:1983;283-311.
8. Cherfils J., Duquerroy S., Janin J. Protein protein recognition analyzed by docking simulation. Proteins. 11:1991;271-280.
9. DesJarlais R. L., Sheridan R. P., Seibel G. L., Dixon J. S., Kuntz I. D., Venkataraghavan R. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three dimensional structure. J. Med. Chem. 31:1988;722-729.
10. Dunbrack R. L. Jr., Gerloff D. L., Bower M., Chen X., Lichtarge O., Cohen F. E. Meeting review; the second meeting on the critical assessment of techniques for protein structure prediction (CASP2), Asilomar, California, December 13-16, 1996. Folding & Design. 2:1997;R27-R42.
11. Edmonds D. T., Rogers N. K., Sternberg M. J. E. Regular representation of irregular charge distributions: Application to the electrostatic potentials of globular proteins. Mol. Phys. 52:1984;1487-1494.
12. Fehlhemmer H., Bode W., Huber R. Chrystal structure of bovine trypsinogen at 1.8 Å resolution. II crystallographic refinement, refined crystal structure and comparison with bovine trypsin. J. Mol. Biol. 111:1977;415-438.
13. 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.
14. Freer S. T., Kraut J., Robertus J. D., Wright H. T., Xuong N. H. Chymotrypsinogen, 2.5 angstroms crystal structure, comparison with alpha-chymotrypsin, and implications for zymogen activation. Biochemistry. 9:1970;1997-2009.
15. Fujinaga M., Sielecki A. R., Read R. J., Ardelt W., Laskowski M. Jr, James M. N. G. Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 Å resolution. J. Mol. Biol. 195:1987;397-418.
16. Gilson M. K., Honig B. Calculation of electrostatic potentials in an enzyme active site. Nature. 330:1987;84-86.
17. Gilson M. K., Honig B. Calculation of the total electrostatic energy of a macro-molecyular system: solvation energies, binding energies, and conformational analysis. Proteins. 4:1988;7-18.
18. Hecht H. J., Szardenings M., Collins J., Schomburg D. Three-dimensional structure of the complexes between bovine chymotrypsinogen a and two recombinant variants of human pancreatic secretory trypsin inhibitor (Kazal type). J. Mol. Biol. 220:1991;711-722.
19. 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.
20. Helmer-Citterich M., Tramontano A. Puzzle: a new method for automated protein docking based on surface shape complementarity. J. Mol. Biol. 235:1994;1021-1031.
21. Hingerty B. E., Ritchie R. H., Ferrell T. L., Turner J. E. Biopolymers. 24:1985;427.
22. 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.
23. Janin J. Protein-protein recognition. Prog. Biophys.Mol. Biol. 64:1995a;145-166.
24. Janin J. Elusive affinities. Proteins. 21:1995b;30-39.
25. Jiang F., Kim S. Soft docking matching of molecular surface cubes. J. Mol. Biol. 219:1991;79-102.
26. Kabsch W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallog. sect. A. 34:1978;827-828.
27. Katchalski-Katzir E., Shariv I., Eisenstein M., Friesen A. A., Aflalo C., Wodak S. J. Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl. Acad. Sci. USA. 89:1992;2195-2199.
28. Kuntz I. D., Blaney J. M., Oatley S. J., Langridge R., Ferrin T. E. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161:1982;269-288.
29. Laskiwski R. A. Surfnet: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph. 13:1995;323-330.
30. Laskowski R. A., Luscombe N. M., Swindells M. B., Thornton J. M. Protein clefts in molecular recognition and function. Protein Sci. 5:1996;2438-2452.
31. Lattman E. E. Optimal sampling of the rotation function. The Molelcular Replacement Method. 1972;Gordon and Breach, New York.
32. Lawrence M. C., Colman P. M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234:1993;946-950.
33. MacCullum R. M., Martin A. C. R., Thornton J. M. Protein-protein recognition. J. Mol. Biol. 262:1996;732-745.
34. 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.
35. Marquart M., Walter J., Deisenhofer J., Bode W., Huber R. The geometry of the reactive site and of the peptide groups in trypsin and trypsinogen and its complexes with inhibitors. Acta Crystallog. 39:1983;480.
36. 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.
37. 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;6582-6589.
38. Meyer M., Wilson P., D. S. Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking. J. Mol. Biol. 264:1996;199-210.
39. Mitsui Y., Satow Y., Watanabe Y., Iitaka Y. Crystal structure of a bacterial protein proteinase inhibitor (streptomyces subtilisin inhibitor) at 2.6 Å resolution. J. Mol. Biol. 131:1979;697-724.
40. Nicholls A., Honig B. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comput. Chem. 12:1991;435-445.
41. Norel R., Lin S. L., Wolfson H. L., Nussinov R. Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed sparse points in docking. J. Mol. Biol. 252:1995;263-273.
42. ab. Proc. Natl Acad. Sci. USA. 86:1989;5938-5942.
43. Press W. H., Teukolsky S. A., Vetterling W. T., Flannery B. P. Numerical Recipes in Fortran, 1986;Cambridge University Press, Cambridge.
44. Ptitsyn O. B. Structures of folding intermediates. Curr. Opin. Struct. Biol. 5:1995;74-78.
45. Rogers N. K., Sternberg M. J. E. Electrostatic interactions in globular proteins: Different dielectric models applied to the packing of α-helices. J. Mol. Biol. 174:1984;527-542.
46. Sharp K., Honig B. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19:1990;301-332.
47. 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.
48. Shoichet B. K., Kuntz I. D. Protein docking and complementarity. J. Mol. Biol. 221:1991;327-346.
49. Shoichet B. K., Kuntz I. D. Predicting the structure of protein complexes: a step in the right direction. Chem. Biol. 3:1996;151-156.
50. Strynadka N. C. J., Eisenstein M., Katchalski-Katzir E., Shoichet B. K., Kuntz I. D., Abagyan R., Totrov M., Janin J., Cherfils J., Zimmerman F., Olson A., Duncan B., Rao M., Jackson R., Sternberg M. J. E., James M. N. G. Molecular docking programs successfully predict the binding of a β-lactamese inhibitory protein to TEM-1 β-lactamese. Nature Struct. Biol. 3:1996;233-239.
51. Takechi Y., Satow Y., Nakamura K. T., Mitsui Y. Refined crystal structure of the complex of subtilisin BPN' and streptomyces subtilisin inhibitor at 1.8 Å resolution. J. Mol. Biol. 221:1991;309-325.
52. Totrov M., Abagyan R. Detailed ab initio prediction of lysozyme-antibody complex with 1.6 Å accuracy. Nature Struct. Biol. 1:1994;259-263.
53. Vakser I. A., Aflao C. Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins. 20:1994;320-329.
54. Wall L., Schwartz R. L. Programming Perl. 1991;O'Reilly & Associates, Inc. Sebastopol.
55. 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.
56. Warwicker J., Watson H. C. Calculation of the electric potential in the active site cleft due to α-helix dipoles. J. Mol. Biol. 157:1982;671-679.
57. Weng Z. P., Vajda S., Delisi C. Prediction of protein complexes using empirical free-energy functions. Protein Sci. 5:1996;614-626.
58. Wlodawer A., Deisenhofer J., Huber R. Comparison of two highly refined structures of bovine pancreatic trypsin inhibitor. J. Mol. Biol. 193:1987;145-156.