Simulation of the diffusional association of barnase and barstar

Biophysical Journal

Volumn 72, Issue 5, 1997, Pages 1917-1929

  Gabdoulline, R R ^a   Wade, R C ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CALCULATION; MOLECULAR DYNAMICS; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION;

EID: 0030891436     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78838-6     Document Type: Article

References (56)

1. Allison, S. A., S. H. Northrup, and J. A. McCammon. 1986. Simulation of biomoiecular diffusion and complex formation. Biophys. J. 49:167-175.
2. Antosiewicz, J., J. M. Briggs, and J. A. McCammon. 1996. Orientational steering in enzyme-substrate association: ionic strength dependence of hydrodynamic torque effects. Eur. Biophys. J. 24:137-141.
3. Antosiewicz, J., and J. A. McCammon. 1995. Electrostatic and hydrodynamic orientational steering effects in enzyme-substrate association. Biophys. J. 69:57-65.
4. Berg, O. G., and P. H. von Hippel. 1985. Diffusion-controlled macromolecular interactions. Ann. Rev. Biophys. Biophys. Chem. 14:131-160.
5. Bernstein, F. C., T. F. Koetzle, G. J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi. 1977. The protein data base: a computer-based archival file for macromolecular structure. J. Mol. Biol. 112:535-542.
6. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217.
7. Brune, D., and S. Kim. 1994. Hydrodynamic steering effects in protein association. Proc. Natl. Acad. Sci. U.S.A. 91:2930-2934.
8. Buckle, A. M., K. Henrick, and A. R. Fersht. 1993. Crystal structural analysis of mutations in the hydrophobic cores of barnase. J. Mol. Biol. 234:847.
9. Buckle, A. M., G. Schreiber, and A. R. Fersht. 1994. Protein-protein recognition: crystal structural analysis of a bamase-barstar complex at 2.0 Å resolution. Biochemistry. 33:8878-8889.
10. Bycroft, M., S. Ludvingen, A. R. Fersht, and F. M. Poulsen. 1991. Determination of the solution conformation of barnase using NMR spectroscopy. Biochemistry. 30:8697-8701.
11. Calef, D. F. 1983. Diffusion-controlled reactions. Ann. Rev. Phys. Chem. 34:493-524.
12. Creighton, T. E. 1993. Protein: structures and molecular properties. W. H. Freeman and Co., New York.
13. Davis, M. E., and J. A. McCammon. 1989. Solving the finite difference linearized Poisson-Boltzmann equation: a comparison of relaxation and conjugate gradient methods. J. Comp. Chem. 10:386-391.
14. Davis, M. E., and J. A. McCammon. 1990. Calculating electrostatic forces from grid-calculated potentials. J. Comp. Chem. 11:401-409.
15. DeLisi, C. 1980. The biophysics of ligand-receptor interactions. Q. Rev. Biophys. 13:201-230.
16. Ermak, D. L., and J. A. McCammon. 1978. Brownian dynamics with hydrodynamic interactions. J. Chem. Phys. 69:1352-1360.
17. Gabdoulline, R. R., and R. C. Wade. 1996. Effective charges for macromolecules in solvent. J. Phys. Chem. 100:3868-3878.
18. Gosting, L. J. 1956. Measurement and interpretation of diffusion coefficients of proteins. Adv. Protein Chem. 11:429-554.
19. Hartley, R. W. 1993. Directed mutagenesis and barnase-barstar recognition. Biochemistry. 32:5978-5984.
20. Ito, W., H. Yasui, and Y. Kurosawa. 1995. Mutations in the complimentarity determining regions do not cause differences in free energy during the process of formation of the activated complex between the antibody and the corresponding protein antigen. J. Mol. Biol. 248:729-732.
21. Johnstone, R. W., S. M. Andrew, M. P. Hogarth, G. A. Pietersz, and I. F. C. McKenzie. 1990. The effect of temperature on the binding kinetics and equilibrium constants of monoclonal antibodies to cell surface antigens. Mol. Immunol. 27:327-333.
22. Jorgensen, W., and J. Tirado-Rives. 1988. The OPLS potential functions for proteins. Energy minimization for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1657-1666.
23. Jucovic, M., and R. W. Hartley. 1996. Protein-protein interaction: A genetic selection for compensating mutations at the barnase-barstar interface. Proc. Natl. Acad. Sci. U.S.A. 93:2343-2347.
24. Kozack, R. E., M. J. d'Mello, and S. Subramaniam. 1995. Computer modeling of electrostatic steering and orientational effects in antibody-antigen association. Biophys. J. 68:807-814.
25. Kozack, R. E., and S. Subramaniam. 1993. Brownian dynamics simulations of molecular recognition in an antibody-antigen system. Protein Sci. 2:915-926.
26. Kraulis, P. 1991. MolScript, a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950.
27. Luty, B. A., E. Amrani, and J. A. McCammon. 1993. Simulations of the bimolecular reaction between superoxide and superoxide dismutase: synthesis of the encounter and reaction steps. J. Am. Chem. Soc. 115: 11874-11877.
28. Luty, B. A., and J. A. McCammon. 1993. Simulations of bimolecular reactions: synthesis of the encounter and reaction steps. Molecular Simulations. 10:61-65.
29. Madura, J. D., J. M. Briggs, R. C. Wade, M. E. Davis, B. A. Luty, A. Ilin, J. Antosiewicz, M. K. Gilson, B. Bagheri, L. R. Scott, and J. A. McCammon. 1995. Electrostatic and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics Program. Comp. Phys. Comm. 91:57-95.
30. Madura, J. D., M. E. Davis, M. K. Gilson, R. C. Wade, B. A. Luty, and J. A. McCammon. 1994. Biological applications of electrostatic calculations and Brownian dynamics simulations. Rev. Comp. Chem. V:229-267.
31. Malmqvist, M. 1993. Surface plasmon resonance for detection and measurement of antibody-antigen affinity and kinetics. Curr. Opin. Immunol. 5:282-286.
32. McCammon, J. A., S. H. Northrup, and S. A. Allison. 1986. Diffusional dynamics of ligand-receptor association. J. Phys. Chem. 90:3901-3905.
33. Meiering, E. M., L. Serrano, and A. R. Fersht. 1992. Effect of active site residues in barnase on activity and stability. J. Mol. Biol 225:585-589.
34. Nambi, P., A. Wierzbicki, and S. A. Allison. 1991. Intermolecular interaction between bovine pancreatic trypsin inhibitor molecules probed by Brownian dynamics simulation. J. Phys. Chem. 95:9595-9600.
35. Northrup, S. H. 1994. Hydrodynamic motions of large molecules. Curr. Opin. Struct. Biol. 4:269-274.
36. Northrup, S. H., S. A. Allison, and A. A. McCammon. 1983. Brownian dynamics simulations of diffusion influenced bimolecular reactions. J. Chem. Phys. 80:1517-1524.
37. Northrup, S. H., J. O. Boles, and J. C. L. Reynolds. 1987. Electrostatic effects in the Brownian dynamics of association and orientation of heme proteins. J. Phys. Chem. 91:5991-5998.
38. Northrup, S. H., J. O. Boles, and J. C. L. Reynolds. 1988. Brownian dynamics of cytochrome c and cytochrome c peroxidase association. Science. 241:67-70.
39. Northrup, S. H., and H. P. Erickson. 1992. Kinetics of protein-protein association explained by Brownian dynamics computer simulations. Proc. Natl. Acad. Sci. U.S.A. 89:3338-3342.
40. 5. Biochemistry. 32:6613-6623.
41. Northrup, S. H., F. Zarin, and J. A. McCammon. 1982. Rate theory for gated diffusion-influenced ligand binding to proteins. J. Phys. Chem. 86:2314-2321.
42. Pollard, J. H. 1976. A handbook of numerical and statistical techniques. Cambridge University Press, Cambridge, UK.
43. QUANTA molecular modeling software package. 1992. Molecular Simulations, Inc., San Diego, CA.
44. Schreiber, G., and A. R. Fersht. 1993. Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering. Biochemistry. 32:5145-5150.
45. Schreiber, G., and A. R. Fersht. 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.
46. Schreiber, G., and A. R. Fersht. 1996. Rapid, electrostatically assisted association of proteins. Nat. Struct. Biol. 3:427-431.
47. Smoluchowski, M. V. 1917. Versuch einer mathematischen Theorie der Koagulationskinetik kolloider Loeschungen. Z. Phys. Chem. 92: 129-168.
48. Stone, S. R., S. Dennis, and J. Hofsteenge. 1986. Quantitative evaluation of the contribution of ionic interactions to the formation of the thrombinhirudin complex. Biochemistry. 28:6857-6863.
49. Szabo, A., D. Shoup, S. H. Northrup, and J. A. McCammon. 1982. Stochastically gated diffusion-influenced reactions. J. Chem. Phys. 77: 4484-4493.
50. Szabo, A., L. Stolz, and R. Granzow. 1995. Surface plasmon resonance and its use in bimolecular interaction analysis (BIA). Curr. Opin. Struct. Biol. 5:699-705.
51. Wade, R. C. 1996. Brownian dynamics simulations of enzyme-substrate encounter. Biochem. Soc. Trans. 24:254-259.
52. Wade, R. C., B. A. Luty, E. D. Demchuk, J. D. Madura, M. E. Davis, J. M. Briggs, and J. A. McCammon. 1994. Simulation of enzyme-substrate encounter with gated active sites. Nature Struct. Biol. 1:65-69.
53. Ward, E. S., D. Güssow, A. D. Griffiths, P. T. Jones, and G. Winter. 1989. Binding activities of a repertoire of single immunoglobulin variable domains secreted from Escherichia coli. Nature. 341:544-546.
54. Zhou, H.-X. 1990. On the calculation of diffusive reaction rates using Brownian dynamics simulations. J. Phys. Chem. 92:3092-3095.
55. Zhou, H.-X. 1993. Brownian dynamics study of the influences of electrostatic interaction and diffusion on protein-protein association kinetics. Biophys. J. 64:1711-1726.
56. Zhou, H.-X. 1996. Effect of interaction potentials in diffusion-influenced reactions with small reactive regions. J. Chem. Phys. 105:7235-7237.