Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution

Journal of Chemical Physics

Volumn 120, Issue 4, 2004, Pages 2056-2068

  Egwolf, Bernhard ^a   Tavan, Paul ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION THEORY; COMPUTER SIMULATION; CONTINUUM MECHANICS; DENSITY (SPECIFIC GRAVITY); ELECTRIC SHIELDING; ELECTROSTATICS; FINITE DIFFERENCE METHOD; IONIC CONDUCTION; ITERATIVE METHODS; LINEAR EQUATIONS; MOLECULAR DYNAMICS; PARAMETER ESTIMATION; POISSON EQUATION; PROBLEM SOLVING; SOLUTIONS; SOLVENTS;

DIELECTRIC SHIELDING; REACTION FIELD FORCES;

PROTEINS;

ELECTROLYTE; ION; PROTEIN; SOLVENT;

ARTICLE; BINDING SITE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ELECTRICITY; ELECTROCHEMISTRY; KINETICS; METHODOLOGY; PROTEIN BINDING; SOLUTION AND SOLUBILITY;

BINDING SITES; CHEMISTRY; COMPUTER SIMULATION; ELECTROCHEMISTRY; ELECTROLYTES; ELECTROSTATICS; IONS; KINETICS; METHODS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEINS; SOLUTIONS; SOLVENTS;

EID: 1242287118     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1636154     Document Type: Article

References (44)

1. H. J. C. Berendsen, Science 271, 954 (1996).
2. H. Grubmüller, B. Heymann, and P. Tavan, Science 271, 997 (1996).
3. S. Spörlein et al., Proc. Natl. Acad. Sci. U.S.A. 99, 7998 (2002).
4. R. Lavery et al., J. Phys.: Condens. Matter 14, R383 (2002).
5. T. Hansson, C. Oostenbrink, and W. F. van Gunsteren, Curr. Opin. Struct. Biol. 12, 190 (2002)
6. M. Levitt, Chem. Scr. 29A, 197 (1989).
7. M. M. Teeter, Annu. Rev. Biophys. Biophys. Chem. 20, 577 (1991).
8. B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003).
9. P. Debye and E. Hückel, Phys. Z. 24, 185 (1923).
10. M. E. Davis and J. A. McCammon, Chem. Rev. 90, 509 (1990).
11. J. Tomasi and M. Persico, Chem. Rev. 94, 2027 (1994).
12. B. Roux and T. Simonson, Biophys. Chem. 78, 1 (1999).
13. G. Mathias, B. Egwolf, M. Nonella, and P. Tavan, J. Chem. Phys. 118, 10847 (2003).
14. C. L. Brooks III, B. M. Pettitt, and M. Karplus, J. Chem. Phys. 83, 5897 (1985).
15. B. A. Luty, M. E. Davis, I. G. Tironi, and W. F. van Gunsteren, Mol. Simul. 14, 11 (1994).
16. B. A. Luty, I. G. Tironi, and W. F. van Gunsteren, J. Chem. Phys. 103, 3014 (1995).
17. C. Sagui and T. A. Darden, Annu. Rev. Biophys. Biomol. Struct. 28, 155 (1999).
18. P. H. Hünenberger and W. F. van Gunsteren, J. Chem. Phys. 108, 6117 (1998).
19. A. Nicholls and B. Honig, J. Comput. Chem. 12, 435 (1991).
20. M. E. Davis, J. D. Madura, B. A. Luty, and J. A. McCammon, Comput. Phys. Commun. 62, 187 (1991).
21. M. K. Gilson, M. E. Davis, B. A. Luty, and J. A. McCammon, J. Phys. Chem. 97, 3591 (1993).
22. C. M. Cortis and R. A. Friesner, J. Comput. Chem. 18, 1570 (1997).
23. C. M. Cortis and R. A. Friesner, J. Comput. Chem. 18, 1591 (1997).
24. M. Holst, N. Baker, and F. Wang, J. Comput. Chem. 21, 1319 (2000).
25. N. Baker, M. Holst, and F. Wang, J. Comput. Chem. 21, 1343 (2000).
26. D. Horvath, D. van Belle, G. Lippens, and S. J. Wodak, J. Chem. Phys. 104, 6679 (1996).
27. A. H. Boschitsch, M. O. Fenley, and H.-X. Zhou, J. Phys. Chem. B 106, 2741 (2002).
28. A. J. Bordner and G. A. Huber, J. Comput. Chem. 24, 353 (2003).
29. C. Niedermeier and K. Schulten, Mol. Simul. 8, 361 (1992).
30. J. G. Kirkwood, J. Chem. Phys. 2, 351 (1934).
31. I. G. Tironi, R. Sperb, P. E. Smith, and W. F. van Gunsteren, J. Chem. Phys. 102, 5451 (1995).
32. H. Sklenar, F. Eisenhaber, M. Poncin, and R. Lavery, in Theoretical Biochemistry and Molecular Biophysics, 2. Proteins, edited by D. L. Beveridge and R. Lavery (Adenine, New York, 1991), pp. 317-335.
33. M. Schaefer and M. Karplus, J. Phys. Chem. 100, 1578 (1996).
34. M. Schaefer, C. Bartels, F. Leclerc, and M. Karplus, J. Comput. Chem. 22, 1857 (2001).
35. J. D. Jackson, Classical Electrodynamics (Wiley, New York, 1975).
36. F. Fogolari, P. Zuccato, G. Esposito, and P. Viglino, Biophys. J. 76, 1 (1999).
37. B. R. Brooks et al., J. Comput. Chem. 4, 187 (1983).
38. J. Richardi, C. Millot, and P. H. Fries, J. Chem. Phys. 110, 1138 (1999).
39. W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson, J. Am. Chem. Soc. 112, 6127 (1990).
40. J. Zhu, Y. Shi, and H. Liu, J. Phys. Chem. B 106, 4844 (2002).
41. P. F. B. Gonçalves and H. Stassen, J. Comput. Chem. 23, 706 (2002).
42. S. C. Harvey, Proteins 5, 78 (1989).
43. H. Alper and R. M. Levy, J. Chem. Phys. 99, 9847 (1993).
44. M. Eichinger, H. Grubmüller, H. Heller, and P. Tavan, J. Comput. Chem. 18, 1729 (1997).