Electrostatic complementarity at protein/protein interfaces

Journal of Molecular Biology

Volumn 268, Issue 2, 1997, Pages 570-584

  McCoy, Airlie J ^a   Chandana Epa, V ^a   Colman, Peter M ^a  

^a CSIRO   (Australia)

Author keywords

Charge complementarity; Continuum electrostatics model; Electrostatic complementarity; Protein interaction; Protein interfaces

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL BOND; CRYSTAL STRUCTURE; ELECTRICITY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION;

INFLUENZA VIRUS;

EID: 0031547966     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.0987     Document Type: Article

References (53)

1. Baker E. N., Hubbard R. E. Hydrogen bonding in globular proteins. Prog. Biophys. Mol. Biol. 44:1984;97-109.
2. Barlow D. J., Thornton J. M. Ion-pairs in proteins. J. Mol. Biol. 168:1983;867-885.
3. Bhat T. N., Bentley T. G., Fischmann T. O., Boulot G., Poljak R. J. Small rearrangements in structures of Fv and Fab fragments of antibody D1.3 on antigen binding. Nature. 347:1990;483-485.
4. Bhat T. N., Bentley T. G., Boulot G., Greene M. I., Tello D., Dall'Acqua W., Souchon H., Schwatrz F. P., Mariuzza R. A., Poljak R. J. Bound water molecules and conformational stabilization help mediate an antigen-antibody association. Proc. Natl Acad. Sci. USA. 91:1994;1089-1093.
5. Bondi A. Molecular Crystals, Liquids and Glasses. 1968;John Wiley & Sons, Inc. New York.
6. Braden B. C., Poljak R. J. Structural features of the reactions between antibodies and protein antigens. FASEB J. 9:1995;9-16.
7. Braun P. J., Dennis S., Hofsteenge J., Stone S. R. Use of site-directed mutagenesis to investigate the basis for the specificity of hirudin. Biochemistry. 27:1988;6517-6522.
8. Brooks B. R., Bruccoleri R. E., Olafson B. D., States D. J., Swaminathan S., Karplus M. CHARMM: A program for macromolecular energy, minimisation, and dynamics calculations. J. Comp. Chem. 4:1983;187-217.
9. Brünger A. T. X-PLOR version 3.1: A system for X-ray Crystallography and NMR. 1992;Yale University Press.
10. Chau P.-L., Dean P. M. Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects. J. Comput.-Aided Mol. Des. 8:1994;513-525.
11. Clackson T., Wells J. A. A hot spot of binding energy in a hormone-receptor interface. Science. 267:1995;383-386.
12. Connolly M. L. Analytical molecular surface recognition. J. Appl. Crystallog. 16:1983;548-558.
13. Cunningham B. C., Ultsch M., de Vos A. M., Mulkerrin M. G., Clausen K. C., Wells J. A. Dimerisation of the extracellular domain of the human growth hormone receptor by a single hormone molecule. Science. 254:1991;821-825.
14. Dauber-Osguthorpe P., Roberts V. A., Osguthorpe D. J., Wolff J., Genest M., Hagler A. T. Structure and function of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug receptor system. Proteins: Struct. Funct. Genet. 4:1988;31-47.
15. Demchuck E., Mueller T., Oschkinat H., Sebald W., Wade R. C. Receptor binding properties of four-helix bundle growth factors deduced from electrostatic analysis. Protein Sci. 3:1994;920-935.
16. de Vos A. M., Ultsch M., Kossiakoff A. A. Human growth hormone and extracellular domain of its receptor: crystal structure of the complex. Science. 255:1992;306-312.
17. Folkers P. J. M., Clore G. M., Driscoll P. C., Dodt J., Kohler S., Gronenborn A. M. Solution structure of recombinant hirudin and the Lys47-Glu mutant: a nuclear magnetic resonance and hybrid geometry-dynamical simulated annealing study. Biochemistry. 28:1989;2601-2617.
18. Fujinaga M., Sielecki R., Read R. J., Ardelt W., Laskawski M. Jr, James M. N. G. Crystal and molecular structure of α-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 Å resolution. J. Mol. Biol. 195:1987;397-418.
19. Getzoff E. D., Tainer J. A., Weiner P. K., Kollman P. A., Richardson J. S., Richardson D. C. Electrostatic recognition between superoxide and copper, zinc superoxide dismutase. Nature. 306:1983;287-290.
20. Gilson M. K., Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins: Struct. Funct. Genet. 4:1988;7-18.
21. Haruyama H., Wüthrich K. Conformation of recombinant desulfato-hirudin in aqueous solution determined by nuclear magnetic resonance. Biochemistry. 28:1989;4301-4312.
22. Hawkins R. E., Russell S. J., Baier M., Winter G. The contribution of contact and non-contact residues of antibody in the affinity of binding to antigen: the interaction of mutant D1.3 antibodies with lysozyme. J. Mol. Biol. 234:1993;958-964.
23. Honig B., Nicholls A. Classical electrostatics in biology and chemistry. Science. 268:1995;1144-1149.
24. Hendsch Z. S., Tidor B. Do salt bridges stabilise proteins? A continuum electrostatics analysis. Protein Sci. 3:1994;211-226.
25. Huber R., Kukla D., Bode W., Schwager P., Bartels K., Deisenhofer J., Steigemann W. Structure of the complex formed by bovine pancreatic trypsin inhibitor. II Crystallographic refinement at 1.9 Å resolution. J. Mol. Biol. 89:1974;73-101.
26. 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.
27. 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.
28. Janin J. Elusive affinities. Proteins: Struct. Funct. Genet. 21:1995;30-39.
29. Janin J., Chothia C. The structure of protein-protein recognition sites. J. Biol. Chem. 265:1990;16027-16030.
30. Jones S. J., Thornton J. M. Protein-protein interactions: a review of protein dimer structures. Prog. Biophys. Mol. Biol. 63:1995;31-65.
31. Karshikov A., Bode W., Tulinsky A., Stone S. R. Electrostatic interactions in the association of proteins: analysis of the thrombin-hirudin complex. Protein Sci. 1:1992;727-735.
32. Lavoie T. B., Drohan W. N., Smith-Gill S. J. Experimental analysis by site-directed mutagenesis of somatic mutation effects on affinity and fine specificity in antibodies specific for lysozyme. J. Immunol. 148:1992;503-513.
33. Lawrence M. C., Colman P. M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234:1993;946-950.
34. Lescar J., Pellegrini M., Souchon H., Tello D., Poljak R., Peterson N., Greene M., Alzari P. Crystal structure of a cross reaction complex between Fab F9.13.7 and guinea-fowl lysozyme. J. Biol. Chem. 270:1995;18067-18076.
35. Malby R. L., Tulip W. R., Harley V. R., McKimm-Breschkin J. L., Laver W. G., Webster R. G., Colman P. M. The structure of a complex between the NC10 antibody and influenza virus neuraminidase and comparison with the overlapping binding site of the NC41 antibody. Structure. 2:1994;733-746.
36. McDonald N. Q., Lapatto R., Murray-Rust J., Gunning J., Wlodawer A., Blundell T. L. New protein fold revealed by a 2.3 Å resolution crystal structure of nerve growth factor. Nature. 354:1991;411-414.
37. McPhalen C. A., James M. N. G. Crystal and molecular structure of the serine proteinase inhibitor (CI-2) from barley seeds. Biochemistry. 26:1988;261-269.
38. Nicholls A., Honig B. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J Comput. Chem. 12:1991.
39. Novotny J., Sharp K. Electrostatic fields in antibodies and antibody/antigen complexes. Prog. Biophys. Mol. Biol. 58:1992;203-224.
40. Novotny J., Bruccoleri R. E., Saul F. A. On the attribution of binding energy in antigen-antibody complexes MPC603, D1.3, and HyHEL-5. Biochemistry. 28:1989;4735-4749.
41. Nuss J. M., Bossart P. J., Air G. M. Identification of critical contact residues in the NC41 epitope of a subtype N9 influenza neuraminidase. Proteins: Struct. Funct. Genet. 15:1993;121-132.
42. Padlan E. A., Silverton E. W., Sheriff S., Cohen G. H., Smith-Gill S. J., Davies D. R. Structure of an antibody-antigen complex: Crystal structure of the HyHEL10 Fab-lysozyme complex. Proc. Natl. Acad. Sci. USA. 86:1989;5938-5942.
43. Patten P. A., Gray N. S., Yang P. L., Marks C. B., Wedemayer G. J., Bonface J. J., Stevens R. C., Schultz P. G. The immunological evolution of catalysis. Science. 271:1996;1086-1091.
44. Pauling L. The Nature of the Chemical Bond. 1960;Cornell University Press, Ithaca.
45. Ramachandran G. N., Sasisekharan V. Conformation of polypeptides and proteins. Advan. Protein Chem. 23:1968;283-437.
46. Rashin A. A., Honig B. On the environment of ionizable groups in globular proteins. J. Mol. Biol. 173:1984;515-521.
47. Roberts V. A., Freeman H. C., Olson A. J., Tainer J. A., Getzoff E. D. Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c. J. Biol. Chem. 266:1991;13431-13441.
48. Rydel T. J., Tulinsky A., Bode W., Huber R. The refined structure of the hirudin-thrombin complex. J. Mol. Biol. 221:1991;583-601.
49. Sheriff S., Silverton E. W., Padlan E. A., Cohen G. H., Smith-Gill S. J., Finzel B. C., Davies D. R. Three dimensional structure of an antibody-antigen complex. Proc. Natl. Acad. Sci. USA. 84:1987;8075-8079.
50. Sitkoff D., Sharp K. A., Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1994;1978-1988.
51. Slagle S. P., Kozack R. E., Subramaniam S. Role of electrostatics in antibody-antigen association: anti-hen egg lysozyme/lysozyme complex (HyHEL-5/HEL). J. Biomol. Struct. Dynam. 12:1994;439-456.
52. Tulip W. R., Varghese J. N., Laver W. G., Webster R. G., Colman P. M. Refined crystal structure of the influenza virus N9 neuraminidase - NC41 Fab complex. J. Mol. Biol. 227:1992;122-148.
53. Tulip W. R., Harley V. R., Webster R. G., Novotny J. N9 neuraminidase complexes with antibodies NC41 and NC10: empirical free energy calculations capture specificity trends observed with mutant binding data. Biochemistry. 33:1994;7986-7997.