On the protein-protein diffusional encounter complex

Journal of Molecular Recognition

Volumn 12, Issue 4, 1999, Pages 226-234

  Gabdoulline, Razif R ^a   Wade, Rebecca C ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Association rate; Barnase barstar; Brownian dynamics; Encounter complex; Ionic strength; Protein diffusion; Protein mutation; Protein protein binding; Viscosity

Indexed keywords

DIFFUSION; IONIC STRENGTH; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; VISCOSITY;

EID: 0033167137     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1099-1352(199907/08)12:4<226::AID-JMR462>3.0.CO;2-P     Document Type: Article

References (33)

1. Berg, O. G. and von Hippel, P. H. (1985). Diffusion-controlled macromolecular interactions. Ann. Rev. Biophys. Biophys. Chem. 14, 131-160.
2. Buckle, A. M., Schreiber, G. and Fersht, A. R. (1994). Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0 Å resolution. Biochemistry 33, 8878-8889.
3. Camacho, C. J., Weng, Z., Vajda, S. and DeLisi, C. (1999). Free energy landscapes of encounter complexes in protein-protein association. Biophys. J. 76, 1166-1178.
4. Debye, P. (1942). Reaction rates in ionic solutions. Trans. Electrochem. Soc. 82, 265-272.
5. Gabdoulline, R. R. and Wade, R. C. (1996). Effective charges for macromolecules in solvent. J. Phys. Chem. 100, 3868-3878.
6. Gabdoulline, R. R. and Wade, R. C. (1997). Simulation of diffusional association of barnase and barstar. Biophys. J. 72, 1917-1929.
7. Gabdoulline, R. R. and Wade, R. C. (1998). Brownian dynamics simulation of protein-protein diffusional encounter. Methods 14, 329-341.
8. Goldberg, J. M. and Baldwin, R. L. (1998). Kinetic mechanism of a partial folding reaction. 2. Nature of the transition state. Biochemistry 37, 2556-2563.
9. Hasinoff, B. B. (1982). Kinetics of acetylcholine binding to electric eel acetylcholinesterase in glycerol/water solvents of increased viscosity: evidence for a diffusion-controlled reaction. Biochim. Biophys. Acta 704, 52-58.
10. Hubbard, S. J. and Thornton, J. M. (1993). 'NACCESS', Computer Program, Department of Biochemistry and Molecular Biology, University College London.
11. Janin, J. (1997). The kinetics of protein-protein recognition. Proteins: Struct. Funct. Genet. 28, 153-161.
12. Kramers, H. A. (1940). Brownian motion in a field of force and the diffusion model of chemical reactions. Physica 7, 284-304.
13. Lo Conte, L. L., Chothia, C. and Janin, J. (1999). The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285, 2177-2198.
14. Lounnas, V. and Wade, R. C. (1997). Exceptionally stable salt bridges in cytochrome P450cam have functional roles. Biochemistry 36, 5402-5417.
15. Madura, J. D., Briggs, J. M., Wade, R. C., Davis, M. E., Luty, B. A., Ilin, A., Antosiewicz, J., Gilson, M. K., Bagheri, B., Scott, L. R. and McCammon, J. A. (1995). Electrostatic and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics Program. Comp. Phys. Commun. 91, 57-95.
16. Medina-Noyola, M. and McQuarrie, D. A. (1980). On the interaction of spherical double layers. J. Chem. Phys. 73, 6279-6283.
17. Miller, D. and Dill, K. (1997). Ligand binding to proteins: the binding landscape model. Protein Sci. 6, 2166-2179.
18. Northrup, S. H. and Erickson, H. P. (1992). Kinetics of protein-protein association explained by Brownian dynamics computer simulations. Proc. Natl Acad. Sci. USA 89, 3338-3342.
19. Raman, C. S., Jemmerson, R. J., Nall, B. T. and Allen, M. J. (1992). Diffusion-limited rates for monoclonal antibody binding to cytochrome c. Biochemistry 31, 10370-10379.
20. 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. Mol. Biol. 248, 478-486.
21. Schreiber, G. and Fersht, A. R. (1996). Rapid, electrostatically assisted association of proteins. Nature Struct. Biol. 3, 427-431.
22. Selzer, T. and Schreiber, G. (1999). Predicting the rate enhancement of protein complex formation from the electrostatic energy of interaction. J. Mol. Biol. 287, 409-419.
23. Shoemaker, B. A., Wang, J. and Wolynes, P. G. (1997). Structural correlations in protein folding funnels. PNAS 94, 777-782.
24. Shoup, D. and Szabo, A. (1982). Role of diffusion in ligand binding to macromolecules and cell-bound receptors. Biophys. J. 40, 33-39.
25. Stone, S. R., Dennis, S. and Hofsteenge, J. (1989). Quantitative evaluation of the contribution of ionic interactions to the formation of the thrombin-hirudin complex. Biochemistry 28, 6857-6863.
26. Verwey, E. J. W. and Overbeek, J. T. G. (1948). Theory of the Stability of Lyophillic Colloids. Elsevier, Amsterdam.
27. Vijayakumar, M., Wong, K. -Y., Schreiber, G., Fersht, A. R., Szabo, A. and Zhou, H. -X. (1998). Electrostatic enhancement of diffusion-controlled protein-protein association: comparison of theory and experiment on barnase and barstar. J. Mol. Biol. 278, 1015-1024.
28. Wade, R. C., Gabdoulline, R. R. and Luty, B. (1998). Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases. Proteins: Struct. Funct. Genet. 31, 406-416.
29. Wang, Y., Shen, B. -J. and Sebald, W. (1997). A mixed-charge pair in human interleukin 4 dominates high-affinity interaction with the receptor a chain. Proc. Natl Acad. Sci. USA 94, 1657-1662.
30. Wendt, H., Leder, L., Harma, H., Jelesarov, I., Baici, A. and Bosshard, H. R. (1997). Very rapid, ionic strength-dependent association and folding of a heterodimeric leucine zipper. Biochemistry 36, 204-213.
31. Xavier, K. A. and Willson, R. C. (1998). Association and dissociation kinetics of anti-hen egg lysozyme monoclonal antibodies HyHEL-5 and HyHel-10. Biophys. J. 74, 2036-2045.
32. Xu, D., Lin, S. L. and Nussinov, R. (1997). Protein binding versus protein folding: the role of hydrophilic bridges in protein association. J. Mol. Biol. 265, 68-84.
33. Zhou, H. -X., Briggs, J. M. and McCammon, J. A. (1996). A 240-fold electrostatic rate enhancement for acetylcholinesterase-substrate binding can be predicted by the potential within the the active site. J. Am. Chem. Soc. 118, 13069-13070.