Development of molecular simulation methods to accurately represent protein-surface interactions: Method assessment for the calculation of electrostatic effects

Biointerphases

Volumn 4, Issue 4, 2009, Pages 57-64

  Collier, Galen ^a   Vellore, Nadeem A ^a   Latour, Robert A ^a   Stuart, Steven J ^b  

^a AMRL   (United States)

^b CLEMSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BOLTZMANN EQUATION; IONS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; POISSON DISTRIBUTION; POISSON EQUATION; PROTEINS;

ELECTROSTATIC EFFECT; EMPIRICAL FORCE FIELDS; EQUILIBRIUM DISTRIBUTIONS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SIMULATIONS; NONBONDED INTERACTION; POISSON-BOLTZMANN EQUATIONS; PROTEIN-SURFACE INTERACTIONS;

ELECTROSTATICS;

EID: 76149132366     PISSN: 15594106     EISSN: 19348630     Source Type: Journal    
DOI: 10.1116/1.3266417     Document Type: Article

References (33)

1. Sivaraman, K. P. Fears, and R. A. Latour, Langmuir 25, 3050 (2009)
2. R. A. Latour, Biointerphases 3, FC2 (2008)
3. J. B. Klauda, X. Wu, R. W. Pastor, and B. R. Brooks, J. Phys. Chem. B 111,4393 2007.
4. R. J. Loncharich and B. R. Brooks, Proteins 6, 32 1989
5. H. Schreiber and O. Steinhauser, Biochemistry 6, 32 1992.
6. H. Schreiber and O. Steinhauser, J. Mol. Biol. 228, 909 1992.
7. H. Schreiber and O. Steinhauser, Chem. Phys. 168, 75 1992.
8. T. A. Darden, D. York, and L. G. Pedersen, J. Chem. Phys. 98, 10089 1993
9. R. Garemyr and A. Elofsson, Proteins 37, 417 1999.
10. T. E. Cheatham, J. L. Miller, T. Fox, T. A. Darden, and P. A. Kollman, J. Am. Chem. Soc. 117, 4193 1995.
11. I. Yeh and M. L. Berkowitz, J. Chem. Phys. 111, 3155 1999.
12. M. Kawata, M. Mikami, and U. Nagashima, J. Chem. Phys. 116, 3430 2002.
13. A. Arnold, J. de Joannis, and C. Holm, J. Chem. Phys. 117, 2496 2002.
14. J. de Joannis, A. Arnold, and C. Holm, J. Chem. Phys. 117, 2503 2002
15. A. Brodka and A. Grzybowski, J. Chem. Phys. 117, 8208 2002.
16. D. Bostick and M. L. Berkowitz, Biophys. J. 85, 97 2003.
17. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 1983
18. N. Foloppe and A. D. MacKerell, Jr., J. Comput. Chem. 21, 86 2000.
19. F. Fogolari, A. Brigo, and H. Molinari, J. Mol. Recognit. 15, 377 2002
20. K. P. Fears, S. E. Creager, and R. A. Latour, Langmuir 24, 37 2008
21. J. N. Israelachvili, Intermolecular and Surface Forces, 2nd ed. Academic, New York, 1992
22. J. M. Smith, H. C. Van Ness, and M. Abbott, Introduction to Chemical Engineering Thermodynamics, 6th ed. McGraw-Hill, New York, 2000
23. A. Ulman and N. Tillman, Langmuir 5, 1418 1989.
24. W. L. Jorgensen and C. Jenson, J. Comput. Chem. 19, 1179 1998
25. F. Wang, S. J. Stuart, and R. A. Latour, Biointerphases 3, 9 2008.
26. S. E. Feller, R. W. Pastor, A. Rojnuckarin, S. Bogusz, and B. R. Brooks, J. Phys. Chem. 100, 17011 1996.
27. P. Mark and L. Nilsson, J. Comput. Chem. 23, 1211 2002
28. W. C. Swope, H. C. Andersen, P. H. Berens, and K. R. Wilson, J. Chem. Phys. 76, 637 1982.
29. D. J. Evans and B. L. Holian, J. Chem. Phys. 83, 4069 1985.
30. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 1977
31. M. E. J. Newman and G. T. Barkema, Monte Carlo Methods in Statistical Physics Oxford University Press, Oxford, 1999.
32. B. Jonsson, H. Wennerstrom, and B. Halle, J. Phys. Chem. 84,2179 1980.
33. I. S. Joung and T. E. Cheatham III, J. Phys. Chem. B 112, 9020 2008