Is the rigid-body assumption reasonable?: Insights into the effects of dynamics on the electrostatic analysis of barnase-barstar

Journal of Non-Crystalline Solids

Volumn 357, Issue 2, 2011, Pages 707-716

  Kieslich, Chris A ^a   Gorham Jr , Ronald D ^a   Morikis, Dimitrios ^a  

^a University of California Riverside   (United States)

Author keywords

Barnase barstar; Electrostatic clustering; Molecular dynamics; Poisson Boltzmann electrostatics; Rigid body assumption

Indexed keywords

ALANINE MUTATIONS; AMINO ACID RESIDUES; BARNASE; BARNASE-BARSTAR; BEFORE AND AFTER; BIOLOGICAL FUNCTIONS; CHARGE PERTURBATIONS; CONFORMATIONAL FLUCTUATIONS; ELECTROSTATIC ANALYSIS; ELECTROSTATIC CALCULATIONS; ELECTROSTATIC INTERACTION ENERGY; EXPERIMENTAL DATA; FREE-ENERGY CALCULATIONS; MOLECULAR DYNAMICS SIMULATIONS; POISSON-BOLTZMANN; PROTEIN DESIGN; PROTEIN STRUCTURES; RIGID BODY; THEORETICAL CALCULATIONS;

AMINO ACIDS; ASSOCIATION REACTIONS; CLUSTER ANALYSIS; DISSOCIATION; DYNAMICS; FREE ENERGY; MOLECULAR DYNAMICS; PROTEINS;

ELECTROSTATICS;

EID: 78751566641     PISSN: 00223093     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jnoncrysol.2010.05.087     Document Type: Conference Paper

References (53)

1. A.H. Elcock, R.R. Gabdoulline, R.C. Wade, and J.A. McCammon Computer simulation of protein-protein association kinetics: acetylcholinesterase- fasciculin Journal of Molecular Biology 291 1999 149 162
2. T. Selzer, and G. Schreiber Predicting the rate enhancement of protein complex formation from the electrostatic energy of interaction Journal of Molecular Biology 287 1999 409 419
3. L. Zhang, B. Mallik, and D. Morikis Immunophysical exploration of C3d-CR2(CCP1-2) interaction using molecular dynamics and electrostatics Journal of Molecular Biology 369 2007 567 583
4. A.H. Elcock, and J.A. McCammon Electrostatic contributions to the stability of halophilic proteins Journal of Molecular Biology 280 1998 731 748
5. J. Antosiewicz, J.A. McCammon, and M.K. Gilson Prediction of pH-dependent properties of proteins Journal of Molecular Biology 238 1994 415 436
6. D. Morikis, A.H. Elcock, P.A. Jennings, and J.A. McCammon Proton transfer dynamics of GART: The pH-dependent catalytic mechanism examined by electrostatic calculations Protein Science 10 2001 2379 2392
7. J.A. McCammon, S.H. Northrup, and S.A. Allison Diffusional dynamics of ligand receptor association The Journal of Physical Chemistry 90 1986 3901 3905
8. T. Selzer, and G. Schreiber New insights into the mechanism of protein-protein association Proteins 45 2001 190 198
9. C. Kiel, T. Selzer, Y. Shaul, G. Schreiber, and C. Herrmann Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex Proceedings of The National Academy of Sciences (USA) 25 2004 9223 9228
10. J. Janin The kinetics of protein-protein recognition Proteins 28 1997 153 161
11. C. Tang, J. Iwahara, and G.M. Clore Visualization of transient encounter complexes in protein-protein association Nature 444 2006 383 386
12. M.E. Davis, and J.A. McCammon Electrostatics in biomolecular structure and dynamics Chemical Reviews 90 1990 509 521
13. B.Z. Lu, Y.C. Zhou, M.J. Holst, and J.A. McCammon Recent progress in numerical methods for the Poisson-Boltzmann equation in biophysical application Communications in Computational Physics 3 2008 973 1009
14. N.A. Baker, D. Sept, S. Joseph, M.J. Holst, and J.A. McCammon Electrostatics of nanosystems: application to microtubules and the ribosome Proceedings of the National Academy of Sciences of the United States of America 98 2001 10037 10041
15. L. Zhang, and D. Morikis Immunophysical properties and prediction of activities for vaccinia virus complement control protein and smallpox inhibitor of complement enzymes using molecular dynamics and electrostatics Biophysical Journal 90 2006 3106 3119
16. G. Sfyroera, M. Katragadda, D. Morikis, S.N. Isaacs, and J.D. Lambris Electrostatic modeling predicts the activities of orthopoxvirus complement control proteins Journal of Immunology 174 2005 2143 2151
17. K. Pyaram, C.A. Kieslich, V.N. Yadav, D. Morikis, and A. Sahu Influence of electrostatics on the complement regulatory functions of Kaposica, the complement inhibitor of Kaposi's Sarcoma-associated herpesvirus Journal of Immunology 184 2010 1956 1967
18. R. Carbo, L. Leyda, and M. Arnau How similar is a molecule to another? An electron-density measure of similarity between 2 molecular-structures International Journal of Quantum Chemistry 17 1980 1185 1189
19. E.E. Hodgkin, and W.G. Richards Molecular similarity based on electrostatic potential and electric-field International Journal of Quantum Chemistry 1987 105 110
20. C.A. Reynolds, C. Burt, and W.G. Richards A linear molecular similarity index Quantitative Structure-Activity Relationships 11 1992 34 35
21. J.D. Petke Cumulative and discrete similarity analysis of electrostatic potentials and fields Journal of Computational Chemistry 14 1993 928 933
22. R.C. Wade, R.R. Gabdoulline, and F. De Rienzo Protein interaction property similarity analysis International Journal of Quantum Chemistry 83 2001 122 127
23. N. Blomberg, R.R. Gabdoulline, M. Nilges, and R.C. Wade Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity Proteins 37 1999 379 387
24. C. A. Kieslich, J. Yang, D. Gunopulos, D. Morikis, Automated computational protocol for alanine scans and clustering of electrostatic potentials: application to C3d.CR2 association, biotechnology progress, (2010) submitted for publication.
25. G. Schreiber, and A.R. Fersht Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering Biochemistry 32 1993 5145 5150
26. G. Schreiber, and A.R. Fersht Energetics of protein-protein interactions - analysis of the barnase-barstar interface by single mutations and double mutant cycles Journal of Molecular Biology 248 1995 478 486
27. G. Schreiber, and A.R. Fersht Rapid, electrostatically assisted association of proteins Nature Structural Biology 3 1996 427 431
28. G. Schreiber, C. Frisch, and A.R. Fersht The role of Glu73 of barnase in catalysis and the binding of barstar Journal of Molecular Biology 270 1997 111 122
29. A.M. Buckle, G. Schreiber, and A.R. Fersht Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0-Å resolution Biochemistry 1994 8878 8889 (Pubitemid 24257995)
30. F.B. Sheinerman, and B. Honig On the role of electrostatic interactions in the design of protein-protein interfaces Journal of Molecular Biology 318 2002 161 177
31. A. Spaar, C. Dammer, R.R. Gabdoulline, R.C. Wade, and V. Helms Diffusional encounter of barnase and barstar Biophysical Journal 90 2006 1913 1924
32. A. Spaar, and V. Helms Free energy landscape of protein-protein encounter resulting from Brownian dynamics simulations of barnase: barstar Journal of Chemical Theory and Computation 1 2005 723 736
33. A. Spaar, and V. Helms Ionic strength effects on the association funnel of barnase and barstar investigated by Brownian dynamics simulations Journal of Non-Crystalline Solids 352 2006 4437 4444
34. M. Vijayakumar, K.Y. Wong, G. Schreiber, A.R. Fersht, A. Szabo, and H.X. Zhou Electrostatic enhancement of diffusion-controlled protein-protein association: comparison of theory and experiment on barnase and barstar Journal of Molecular Biology 278 1998 1015 1024
35. T. Wang, S. Tomic, R.R. Gabdoulline, and R.C. Wade How optimal are the binding energetics of barnase and barstar? Biophysical Journal 87 2004 1618 1630
36. R.R. Gabdoulline, and R.C. Wade Simulation of the diffusional association of barnase and barstar Biophysical Journal 72 1997 1917 1929
37. R.R. Gabdoulline, and R.C. Wade On the protein-protein diffusional encounter complex Journal of Molecular Recognition 12 1999 226 234
38. C.J. Camacho, Z.P. Weng, S. Vajda, and C. DeLisi Free energy landscapes of encounter complexes in protein-protein association Biophysical Journal 76 1999 1166 1178
39. L.P. Lee, and B. Tidor Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex Protein Science 10 2001 362 377
40. L.P. Lee, and B. Tidor Barstar is electrostatically optimized for tight binding to barnase Nature Structural Biology 8 2001 73 76
41. G. Vriend What if - a molecular modeling and drug design program Journal of Molecular Graphics 8 1990 52 56
42. T.J. Dolinsky, J.E. Nielsen, J.A. McCammon, and N.A. Baker PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations Nucleic Acids Research 32 2004 W665 W667
43. D. Sitkoff, K.A. Sharp, and B. Honig Accurate calculation of hydration free energies using macroscopic solvent models The Journal of Physical Chemistry 98 1994 1978 1988
44. R Development Core Team R: A Language and Environment for Statistical Computing 2009 R Foundation for Statistical Computing Vienna, Austria URL http://www.R-project.org
45. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kale, and K. Schulten Scalable molecular dynamics with NAMD Journal of Computational Chemistry 26 2005 1781 1802
46. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics Journal of Molecular Graphics 14 1996 33 38
47. A.D. MacKerell, D. Bashford, M. Bellott, R.L. Dunbrack, J.D. Evanseck, M.J. Field, S. Fischer, J.M. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins The Journal of Physical Chemistry. B 102 1998 3586 3616
48. W.M. Rand Objective criteria for the evaluation of clustering methods Journal of the American Statistical Association 66 1971 846 850
49. R.W.W. Hooft, G. Vriend, C. Sander, and E.E. Abola Errors in protein structures Nature 381 1996 272-272
50. M.P. Jacobson, R.A. Friesner, Z.X. Xiang, and B. Honig On the role of the crystal environment in determining protein side-chain conformations Journal of Molecular Biology 320 2002 597 608
51. M. Andrec, D.A. Snyder, Z. Zhou, J. Young, G.T. Montelione, and R.M. Levy A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing Proteins 69 2007 449 465
52. D. Morikis, J.T. Sage, A.K. Rizos, and P.M. Champion Resonance Raman studies of myoglobin single-crystals Journal of the American Chemical Society 110 1988 6341 6342
53. A.S. Cheung, C.A. Kieslich, J. Yang, and D. Morikis Solvation effects in calculated electrostatic association free energies for the C3d-CR2 complex and comparison with experimental data Biopolymers 93 2010 509 519