Interface surfaces for protein-protein complexes

Journal of the ACM

Volumn 53, Issue 3, 2006, Pages 361-378

  Ban, Yih En Andrew ^a   Edelsbrunner, Herbert ^a,b,c   Rudolph, Johannes ^a  

^a DUKE UNIVERSITY   (United States)

^b Raindrop Geomagic   (United States)

^c Duke University   (United States)

Author keywords

Filtrations; Geometric and topological algorithms; Interface surfaces; Protein interaction; Voronoi diagrams

Indexed keywords

GEOMETRIC AND TOPOLOGICAL ALGORITHMS; INTERFACE SURFACES; PROTEIN INTERACTION; VORONOI DIAGRAMS;

ALGORITHMS; CELL CULTURE; MOLECULAR STRUCTURE; NUMERICAL METHODS; PROBLEM SOLVING; PROTEINS; SURFACE STRUCTURE;

INTERFACES (MATERIALS);

EID: 33746828615     PISSN: 00045411     EISSN: 00045411     Source Type: Journal    
DOI: 10.1145/1147954.1147957     Document Type: Article

References (34)

1. BOGAN, A. A., AND THORN, K. S. 1998. Anatomy of hot spots in protein interfaces. J. Molec. Biol. 280, 1-9.
2. CASTRO, M. M., AND ANDERSON, S. 1996. Alanine point-mutations in the reactive region of bovine pancreatic trypsin inhibitor: Effects on the kinetics and thermodynamics of binding to η-trypsin and α-chymotrypsin. Biochemistry 35, 11435-11446.
3. CHAKRABARTI, P., AND JANIN, J. 2002. Dissecting protein-protein recognition sites. Proteins: Struct. Funct. Bioinfo. 47, 334-343.
4. CLACKSON, T., ULTSCH, M. H., WELLS, J. A., AND DE VOS, A. M. 1998. Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity. J. Molec. Biol. 277, 1111-1128.
5. CORNELL, W. D., CIEPLAK, P., BAYLY, C. I., GOULD, I. R., MERZ, K. M., FERGUSON, D. M., SPELLMEYER, D. C., FOX, T., CALDWELL, J. W., AND KOLLMAN, P. A. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Amer. Chem. Soc. 117, 5179-5197.
6. DELANO, W. L., ULTSCH, M. H., DE VOS, A. M., AND WELLS, J. A. 2000. Convergent solutions to binding at a protein-protein interface. Science 287, 1279-1283.
7. EDELSBRUNNER, H. 2001. Geometry and Topology for Mesh Generation. Cambridge University Press, Cambridge, England.
8. EDELSBRUNNER, H. 2003. Surface reconstruction by wrapping finite sets in space, Discrete and Computational Geometry: The Goodman-Pollack Festschrift. Springer-Verlag, Berlin, Germany, 379-404.
9. EDELSBRUNNER, H., FACELLO, M. A., AND LIANG, J. 1998. On the definition and the construction of pockets in macromolecules. Disc. Appl. Math. 88, 83-102.
10. EDELSBRUNNER, H., HARER, J., NATARAJAN, V., AND PASCUCCI, V. 2004. Local and global comparison of continuous functions. In Proceedings of IEEE Visualization 2004, IEEE Computer Society Press, Los Alamitos, CA, 275-280.
11. EDELSBRUNNER, H., HARER, J., AND ZOMORODIAN, A. 2003. Hierarchical Morse complexes for piecewise linear 2-manifolds. Disc. Comput. Geom. 30, 87-107.
12. EDELSBRUNNER, H., LETSCHER, D., AND ZOMORODIAN, A. 2002. Topological persistence and simplification. Disc. Comput. Geom. 28, 511-533.
13. EDELSBRUNNER, H., AND MÜCKE, E. P. 1994. Three-dimensional alpha shapes. ACM Trans. Graph. 13, 43-72.
14. FERNÁNDEZ, A., AND SCHERAGA, H. A. 2003. Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proce. Nati. Acad. Sci., USA 100, 113-118.
15. GABDOULLINE, R. R., AND WADE, R. C. 1996. Analytically defined surfaces to analyze molecular interaction properties. J. Molec. Graph. 14, 374-375.
16. HOPF, H. 1983. Differential Geometry in the Large. Springer-Verlag, Berlin, Germany.
17. JONES, S., AND THORNTON, J. M. 1997. Analysis of protein-protein interaction sites using surface patches. J. Molec. Biol. 272, 121-132.
18. KEIL, M., EXNER, T., AND BRICKMAN, J. 1998. Characterisation of protein-ligand interfaces: Separating surfaces. J. Molec. Model. 4, 335-339.
19. KORTEMME, T., AND BAKER, D. 2002. A simple physical model for binding energy hot-spots in protein-protein complexes. Proce. Nati. Acad. Sci. USA 99, 14116-14121.
20. LEE, B., AND RICHARDS, F. M. 1971. The interpretation of protein structures: Estimation of Static accessibility. J. Molecu. Biol. 55, 379-400.
21. LEE, L. P., AND TIDOR, B. 2001. Barstar is electrostatically optimized for tight binding to barnase. Nature Struc. Biol. 8, 73-76.
22. LO CONTE, L., CHOTHIA, C., AND JANIN, J. 1999. The atomic structure of protein-protein recognition sites. J. Molec. Biol. 285, 2177-2198.
23. MA, B., ELKAYAM, T., WOLFSON., H., AND NUSSINOV, R. 2003. Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proce. Nati. Acad. Sci. USA 100, 5772-5777.
24. MASSEY, W. S. 1967. Algebraic Topology: an Introduction. Springer-Verlag, New York.
25. MASSOVA, I., AND KOLLMAN, P. A. 1999. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J. Ameri. Chem. Soc. 121, 8133-8143.
26. MATSUMOTO, Y. 2002. An Introduction to Morse Theory. American Mathematical Society.
27. RICHARDS. F. M. 1977. Areas volumes, packing and protein structures. Ann. Rev. Biophys. Bioeng. 6, 151-176.
28. SCHREIBER, G., AND FERSHT, A. R. 1995. Energetics of protein-protein interactions: Analysis of the barnase-barstar interface by single mutations and double mutant cycles. J. Mole. Bio. 248, 478-486.
29. SELZER, T., ALBECK, S., AND SCHREIBER, G. 2000. Rational design of faster associating and tighter binding protein complexes. Nature Struct. Bio. 7, 537-541.
30. SHAPIRO, R., RUIZ-GUTIERREZ, M., AND CHEN, C.-Z. 2000. Analysis of the interactions of human ribonuclease inhibitor with angiogenin and ribonuclease a by mutagenesis: Importance of inhibitor residues inside versus outside the C-terminal "hot-spot". J. Mole. Bio. 302, 497-519.
31. SHEINERMAN, F. B., AND HONIG, B. 2002. On the role of electrostatic interactions in the design of protein-protein interfaces. J. Mole. Bio. 318, 161-177.
32. VARSHNEY, A., BROOKS, JR., F. P., RICHARDSON, D. C., WRIGHT, W. V., AND MANOCHA, D. 1995. Definition, computing, and visualizing molecular interfaces. In Proceedings of IEEE Visualization 1995. IEEE Computer Society Press, Los Alamitos, CA, 36-43.
33. WELLS, J. A. 1996. Binding in the growth hormone receptor complex. Proc. Nati. Acad. Sci. USA 93, 1-6.
34. XU, D., TSAI, C. J., AND NUSSINOV, R. 1997. Hydrogen bonds and salt bridges across protein-protein interfaces. Prot. Eng. 10, 999-1012.