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Principles of protein-protein interactions.
Abstract
This review examines protein complexes in the Brookhaven Protein Databank to gain a better understanding of the principles governing the interactions involved in protein-protein recognition. The factors that influence the formation of protein-protein complexes are explored in four different types of protein-protein complexes--homodimeric proteins, heterodimeric proteins, enzyme-inhibitor complexes, and antibody-protein complexes. The comparison between the complexes highlights differences that reflect their biological roles.
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- Finzel BC, Weber PC, Hardman KD, Salemme FR. Structure of ferricytochrome c' from Rhodospirillum molischianum at 1.67 A resolution. J Mol Biol. 1985 Dec 5;186(3):627–643. [PubMed] [Google Scholar]
- Tsunogae Y, Tanaka I, Yamane T, Kikkawa J, Ashida T, Ishikawa C, Watanabe K, Nakamura S, Takahashi K. Structure of the trypsin-binding domain of Bowman-Birk type protease inhibitor and its interaction with trypsin. J Biochem. 1986 Dec;100(6):1637–1646. [PubMed] [Google Scholar]
- Sheriff S, Silverton EW, Padlan EA, Cohen GH, Smith-Gill SJ, Finzel BC, Davies DR. Three-dimensional structure of an antibody-antigen complex. Proc Natl Acad Sci U S A. 1987 Nov;84(22):8075–8079. [PMC free article] [PubMed] [Google Scholar]
- Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. [PubMed] [Google Scholar]
- Johnson JE. Functional implications of protein-protein interactions in icosahedral viruses. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):27–33. [PMC free article] [PubMed] [Google Scholar]
- Walls PH, Sternberg MJ. New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking. J Mol Biol. 1992 Nov 5;228(1):277–297. [PubMed] [Google Scholar]
- Helmer-Citterich M, Tramontano A. PUZZLE: a new method for automated protein docking based on surface shape complementarity. J Mol Biol. 1994 Jan 21;235(3):1021–1031. [PubMed] [Google Scholar]
- Zielenkiewicz P, Rabczenko A. Methods of molecular modelling of protein-protein interactions. Biophys Chem. 1988 Apr;29(3):219–224. [PubMed] [Google Scholar]
- Janin J, Miller S, Chothia C. Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol. 1988 Nov 5;204(1):155–164. [PubMed] [Google Scholar]
- Miller S. The structure of interfaces between subunits of dimeric and tetrameric proteins. Protein Eng. 1989 Nov;3(2):77–83. [PubMed] [Google Scholar]
- Argos P. An investigation of protein subunit and domain interfaces. Protein Eng. 1988 Jul;2(2):101–113. [PubMed] [Google Scholar]
- Jones S, Thornton JM. Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol. 1995;63(1):31–65. [PubMed] [Google Scholar]
- Janin J, Chothia C. The structure of protein-protein recognition sites. J Biol Chem. 1990 Sep 25;265(27):16027–16030. [PubMed] [Google Scholar]
- Duquerroy S, Cherfils J, Janin J. Protein-protein interaction: an analysis by computer simulation. Ciba Found Symp. 1991;161:237–252. [PubMed] [Google Scholar]
- Korn AP, Burnett RM. Distribution and complementarity of hydropathy in multisubunit proteins. Proteins. 1991;9(1):37–55. [PubMed] [Google Scholar]
- Young L, Jernigan RL, Covell DG. A role for surface hydrophobicity in protein-protein recognition. Protein Sci. 1994 May;3(5):717–729. [PMC free article] [PubMed] [Google Scholar]
- Laskowski M, Jr, Kato I. Protein inhibitors of proteinases. Annu Rev Biochem. 1980;49:593–626. [PubMed] [Google Scholar]
- Taylor WR, Orengo CA. Protein structure alignment. J Mol Biol. 1989 Jul 5;208(1):1–22. [PubMed] [Google Scholar]
- Wells JA. Binding in the growth hormone receptor complex. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):1–6. [PMC free article] [PubMed] [Google Scholar]
- Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971 Feb 14;55(3):379–400. [PubMed] [Google Scholar]
- Chothia C. Hydrophobic bonding and accessible surface area in proteins. Nature. 1974 Mar 22;248(446):338–339. [PubMed] [Google Scholar]
- Thornton JM, Edwards MS, Taylor WR, Barlow DJ. Location of 'continuous' antigenic determinants in the protruding regions of proteins. EMBO J. 1986 Feb;5(2):409–413. [PMC free article] [PubMed] [Google Scholar]
- McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J Mol Biol. 1994 May 20;238(5):777–793. [PubMed] [Google Scholar]
- Hurley JH, Thorsness PE, Ramalingam V, Helmers NH, Koshland DE, Jr, Stroud RM. Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase. Proc Natl Acad Sci U S A. 1989 Nov;86(22):8635–8639. [PMC free article] [PubMed] [Google Scholar]
- Weis WI, Kahn R, Fourme R, Drickamer K, Hendrickson WA. Structure of the calcium-dependent lectin domain from a rat mannose-binding protein determined by MAD phasing. Science. 1991 Dec 13;254(5038):1608–1615. [PubMed] [Google Scholar]
- Smith DL, Almo SC, Toney MD, Ringe D. 2.8-A-resolution crystal structure of an active-site mutant of aspartate aminotransferase from Escherichia coli. Biochemistry. 1989 Oct 3;28(20):8161–8167. [PubMed] [Google Scholar]
- Freymann D, Down J, Carrington M, Roditi I, Turner M, Wiley D. 2.9 A resolution structure of the N-terminal domain of a variant surface glycoprotein from Trypanosoma brucei. J Mol Biol. 1990 Nov 5;216(1):141–160. [PubMed] [Google Scholar]
- Chothia C, Janin J. Principles of protein-protein recognition. Nature. 1975 Aug 28;256(5520):705–708. [PubMed] [Google Scholar]
- Morgan RS, Miller SL, McAdon JM. The symmetry of self-complementary surfaces. J Mol Biol. 1979 Jan 5;127(1):31–38. [PubMed] [Google Scholar]
- Connolly ML. Shape complementarity at the hemoglobin alpha 1 beta 1 subunit interface. Biopolymers. 1986 Jul;25(7):1229–1247. [PubMed] [Google Scholar]
- Lawrence MC, Colman PM. Shape complementarity at protein/protein interfaces. J Mol Biol. 1993 Dec 20;234(4):946–950. [PubMed] [Google Scholar]
- Vakser IA, Aflalo C. Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins. 1994 Dec;20(4):320–329. [PubMed] [Google Scholar]
- Eigenbrot C, Randal M, Quan C, Burnier J, O'Connell L, Rinderknecht E, Kossiakoff AA. X-ray structure of human relaxin at 1.5 A. Comparison to insulin and implications for receptor binding determinants. J Mol Biol. 1991 Sep 5;221(1):15–21. [PubMed] [Google Scholar]
- Hubbard SJ, Thornton JM, Campbell SF. Substrate recognition by proteinases. Faraday Discuss. 1992;(93):13–23. [PubMed] [Google Scholar]
- Navia MA, Fitzgerald PM, McKeever BM, Leu CT, Heimbach JC, Herber WK, Sigal IS, Darke PL, Springer JP. Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1. Nature. 1989 Feb 16;337(6208):615–620. [PubMed] [Google Scholar]
- Mitsui Y, Satow Y, Watanabe Y, Hirono S, Iitaka Y. Crystal structures of Streptomyces subtilisin inhibitor and its complex with subtilisin BPN'. Nature. 1979 Feb 8;277(5696):447–452. [PubMed] [Google Scholar]
- Tainer JA, Getzoff ED, Beem KM, Richardson JS, Richardson DC. Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase. J Mol Biol. 1982 Sep 15;160(2):181–217. [PubMed] [Google Scholar]
- Wilson IA, Stanfield RL. Antibody-antigen interactions: new structures and new conformational changes. Curr Opin Struct Biol. 1994 Dec;4(6):857–867. [PubMed] [Google Scholar]
- Gerstein M, Schulz G, Chothia C. Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers. J Mol Biol. 1993 Jan 20;229(2):494–501. [PubMed] [Google Scholar]
- Gerstein M, Anderson BF, Norris GE, Baker EN, Lesk AM, Chothia C. Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces. J Mol Biol. 1993 Nov 20;234(2):357–372. [PubMed] [Google Scholar]
- Davies DR, Cohen GH. Interactions of protein antigens with antibodies. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):7–12. [PMC free article] [PubMed] [Google Scholar]
- Stanfield RL, Takimoto-Kamimura M, Rini JM, Profy AT, Wilson IA. Major antigen-induced domain rearrangements in an antibody. Structure. 1993 Oct 15;1(2):83–93. [PubMed] [Google Scholar]
- Miller S, Lesk AM, Janin J, Chothia C. The accessible surface area and stability of oligomeric proteins. Nature. 328(6133):834–836. [PubMed] [Google Scholar]