Brownian dynamics simulation of the competitive reactions: Binase dimerization and the association of binase and barstar

Biophysical Chemistry

Volumn 130, Issue 1-2, 2007, Pages 26-31

  Ermakova, E ^a  

^a KAZAN INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Russian Federation)

Author keywords

Barstar; Binase; Brownian dynamics simulation; Dimer; Electrostatic interactions

Indexed keywords

ARTICLE; CHEMICAL REACTION; COMPETITIVE INHIBITION; DIMERIZATION; IONIC STRENGTH; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; PH MEASUREMENT; PRIORITY JOURNAL; REACTION ANALYSIS; SIMULATION;

BACTERIAL PROTEINS; DIMERIZATION; ENDORIBONUCLEASES; HYDROGEN-ION CONCENTRATION; OSMOLAR CONCENTRATION; PROTEIN CONFORMATION; SOLUTIONS;

EID: 34548766009     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2007.06.012     Document Type: Article

References (34)

1. Elcock A.H., Sept D., and McCammon J.A. Computer simulation of protein-protein interactions. J. Phys. Chem., B 105 (2001) 1504-1518
2. Sinha N., and Smith-Gill S.J. Electrostatics in protein binding and function. Curr. Protein Pept. Sci. 3 (2002) 601-614
3. May A., and Zacharias M. Accounting for global protein deformability during protein-protein and protein-ligand docking. Biochem. Biophys. Acta 1754 (2005) 225-231
4. Spaar A., Dammer Ch., Gabdoulline R.R., Wade R.C., and Helms V. Diffusional encounter of barnase and barstar. Biophys. J. 90 (2006) 1913-1924
5. Gabdoulline R.R., and Wade R.C. Simulation of the diffusional association of barnase and barstar. Biophys. J. 72 (1997) 1917-1929
6. Gabdoulline R.R., and Wade R.C. Biomolecular duffusional association. Curr. Opin. Struct. Biol. 12 (2002) 204-213
7. Gabdoulline R.R., and Wade R.C. On the protein-protein diffusional encounter complex. J. Mol. Recognit. 12 (1999) 226-234
8. Gross E.L. A Brownian dynamics study of the interaction of Phormidium laminosum Plastocyanin with Phormidium laminosum Cytochrome f. Biophys. J. 87 (2004) 2043-2059
9. Ouporov I.V., Knull H.R., and Thomasson K.A. Brownian dynamics simulations of interactions between Aldolase and G- or F-Actin. Biophys. J. 76 (1999) 17-27
10. Ermakova E. Lysozyme dimerization: brownian dynamics simulation. J. Mol. Model. 12 (2005) 34-41
11. Altobelli G., and Subramaniam Sh. Kinetics of association of anti-lysozyme monoclonal antibody D44.1 and hen-egg lysozyme. Biophys. J. 79 (2000) 2954-2965
12. Camacho C.J., Weng Z., Vajda S., and DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophys. J. 76 (1999) 1166-1178
13. Wang T., Tomic S., Gabdoulline R.R., and Wade R.C. How optimal are the binding energetics of barnase and barstar?. Biophys. J. 87 (2004) 1618-1630
14. Buckle A.M., Schreiber G., and Fersht A.R. Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0 Å resolution. Biochemistry 33 (1994) 8878-8889
15. Ababou A., van der Vaart A., Gogonea V., and Merz Jr. K.M. Interaction energy decomposition in protein-protein association: a quantum mechanical study of barnase-barstar complex. Biophys. Chemist. 125 (2007) 221-236
16. Yakovlev G.I., Struminskaya N.K., Znamenskaya L.V., Kipenskaya L.V., Leshinskaya I.B., and Hartley R.W. Contribution of arginine-82 and arginine-86 to catalysis of RNases from Bacillus intermedius (binase). FEBS Lett. 428 (1998) 57-58
17. Yakovlev G.I., Moiseyev G.P., Protasevich I.I., Ranjbar B., Kirpichnikov M.P., Gilli R.M., Briand C.M., Hartley R., and Makarov A.A. Dissociation constants and thermal stability of complexes of Bacillus intermedius RNase and the protein inhibitor of Bacillus amiloliquefaciens RNase. FEBS Lett. 366 (1995) 156-158
18. Protasevich I.I., Schulga A.A., Vasilieva L.I., Polyakov K.M., Lobachov V.M., Hartley R.W., Kirpichnikov M.P., and Makarov A.A. Key role of barstar Cys-40 residue in the mechanism of heat denaturation of bacterial ribonuclease complexes with barstar. FEBS Lett. 445 (1999) 384-388
19. Mitkevich V.A., Schulga A.A., Ermolyuk Y.S., Lobachov V.M., Chekhov V.O., Yakovlev G.I., Hartley R.W., Pace C.N., Kirpichnikov M.P., and Makarov A.A. Thermodynamics of denaturation of complexes of barnase and binase with barstar. Biophys. Chemist. 105 (2003) 383-390
20. Ermakova E.A. A comparative study of the interaction of Bacillus amyloliquefaciens ribonuclease (barnase) and Bacillus intermedius ribonuclease (binase) with barstar by brownian dynamics simulation. Biophysics (Russia) 51 (2006) 202-208
21. Northrup S.H., Boles J.O., and Reynolds J.C.L. Electrostatic effects in the Brownian dynamics of association and orientation of heme proteins. J. Phys. Chem. 91 (1987) 5991-5998
22. Northrup S.H., Laughen T., and Stevenson G. MacroDox. Macromolecular Simulation program (1997), Tennessee Technological University, Cookeville, TN
23. Northrup S.H., Boles J.O., and Reynolds J.C.L. Brownian dynamics of cytochrome c and cytochrome c peroxidase association. Science 241 (1988) 67-70
24. Tanford C., and Kirkwood J.G. Theory of protein titration curves. I. General equations for impenetrable spheres. J. Am. Chem. Soc. 79 (1957) 5333-5339
25. Matthew J.B., and Gurd F.R.N. Calculation of electrostatic interactions in proteins. Methods Enzymol. 130 (1986) 413-436
26. Warwicker J., and Watson H.C. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. J. Mol. Biol. 157 (1982) 671-679
27. Ermak D.L., and McCammon J.A. Brownian dynamics with hydrodynamic interactions. J. Chem. Phys. 69 (1978) 1353-1360
28. Smoluchowski M.V. Drei vortäge über diffusion, brownsche molekularbewegung und koagulation von kolloidteilchen. Phys. Z. 17 (1916) 557-571
29. Spaar A., and Helms V. Free energy landscape of protein-protein encounter resulting from brownian dynamics simulations of barnase:barstar. J. Chem. Theory Comput. 1 (2005) 723-736
30. Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F., Brice M.D., Rogers J.R., Kennard O., Shimanouchi T., and Tatsumi M. The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112 (1977) 535-542
31. Faizullin D.A., Stupishina E.A., Krushelnitsky A.G., and Fedotov V.D. Studies of dynamic features of binase in solution using hydrogen exchange and H-NMR relaxation techniques. Mol. Biol. (Russia) 29 (1995) 563-573
32. Pavlovskiy A.G., Sanishvily R.G., Borisova S.N., Strokopytov B.V., Vagin A.A., Chepurnova N.K., and Vainshtein B.K. Structure of the two crystal modification of ribonuclease Bacillius intermedius. Kristallografia 34 (1989) 137-142
33. Dong F., Vijayakumar M., and Zhou H.-X. Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar. Biophys. J. 85 (2003) 49-60
34. Koradi R., Billeter M., and Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14 (1996) 51-55