Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer

Journal of Computational Chemistry

Volumn 24, Issue 5, 2003, Pages 531-546

  Król, Marcin ^a  

^a JAGIELLONIAN UNIVERSITY   (Poland)

Author keywords

Explicit solvent; IgG light chain dimer; Implicit solvent; Molecular dynamics; Variable domain

Indexed keywords

COMPUTER SIMULATION; FREE ENERGY; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; PROTEINS; SOLVENTS;

SOLVENT MODELS;

DIMERS;

IMMUNOGLOBULIN G; IMMUNOGLOBULIN LIGHT CHAIN; SOLVENT;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; ELECTRICITY; HYDROGEN BOND; IMMUNOGLOBULIN VARIABLE REGION; PROTEIN CONFORMATION; TIME;

COMPUTER SIMULATION; ELECTROSTATICS; HYDROGEN BONDING; IMMUNOGLOBULIN G; IMMUNOGLOBULIN LIGHT CHAINS; IMMUNOGLOBULIN VARIABLE REGION; MODELS, MOLECULAR; PROTEIN CONFORMATION; SOLVENTS; TIME FACTORS;

EID: 0141677983     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.10186     Document Type: Article

References (48)

1. Becker, O. M.; MacKerell Jr, A. D.; Roux, B.; Watanabe, M. Computational Biochemistry and Biophysics; Marcel Dekker, Inc.: New York, 2001; Chapter 3.
2. Duan, Y.; Kollman, P. A. Science 1998, 282, 740.
3. Goodsell, D. S.; Olson, A. J. Proteins Struct Funct Genet 1990, 8, 195.
4. Jiang, L.; Gao, Y.; Mao, F.; Liu, Z.; Lai, L. Proteins Struct Funct Genet 2002, 46, 190.
5. Karplus, M.; Petsko, G. A. Nature 1990, 347, 631.
6. Brower, R. C.; Kimura, S. R. In Computer Simulation of Biomolecular Systems Vol. 3; van Gunsteren, W. F., Weiner, P. K., Wilkinson, A. J., Eds.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 1997: p 223.
7. Roux, B.; Simonson, T. Biophys Chem 1999, 78, 1.
8. Smart, J. L.; Marrone, T. J.; McCammon, J. A. J Comput Chem 1997, 18, 1750.
9. Eisenberg, D.; McClachlan, A. Nature 1986, 319, 199.
10. Fraternali, F.; Gunsteren, W. F. J Mol Biol 1996, 256, 939.
11. Simonson, T. Curr Opin Struct Biol 2001, 11, 243.
12. Sharp, K.; Honig, B. Annu Rev Biophys Biophys Chem 1991, 19, 301.
13. Still, W. C.; Tempczyk, A.; Hawley, R.; Hendrickson, T. J Am Chem Soc 1990, 112, 6127.
14. Schaefer, M.; Bartels, C.; Karplus, M. J Mol Biol 1998, 284, 835.
15. Jean-Charles, A.; Nichols, A.; Sharp, K.; Honig, B.; Tempczyk, A.; Hendrikson, T.; Still, W. C. J Am Chem Soc 1991, 113, 1454.
16. Nina, M.; Beglov, D.; Roux, B. J Phys Chem 1997, 101, 5239.
17. Sitkoff, D.; Sharp, K. A.; Honig, B. J Phys Chem 1994, 98, 1978.
18. Schaefer, M.; Karplus, M. J Phys Chem 1996, 100, 1578.
19. Srinivasan, J.; Cheatham, T.; Cieplak, P.; Kollman, P. A.; Case, D. J Am Chem Soc 1998, 120, 9401.
20. Misra, V. K.; Honig, B. Biochemistry 1996, 35, 1115.
21. Lazaridis, T.; Karplus, M. Proteins Struct Funct Genet 1999, 35, 133.
22. Lazaridis, T.; Karplus, M. Science 1997, 278, 1928.
23. Lazaridis, T.; Karplus, M. J Mol Biol 1999, 288, 477.
24. David, L.; Luo, R.; Gilson, M. K. J Comp Chem 2000, 21, 295.
25. Dominy, B. N.; Brooks, C. L. J Phys Chem B 1999, 103, 3765.
26. Burusulaya, B.; Brooks III, C. J Phys Chem B 2001, 104, 12378.
27. Calimet, N.; Schaefer, M.; Simonson, T. Proteins Struct Funct Genet 2001, 45, 144.
28. Williams, D.; Hall, K. Biophys J 1999, 76, 3192.
29. Tsui, V.; Case, D. J Am Chem Soc 2000, 122, 2489.
30. Roterman, I.; Rybarska, J.; Konieczny, L.; Skowronek, M.; Stopa, B.; Piekarska, B.; Bakalarski, G. Computers Chem 1998, 22, 61.
31. Konieczny, L.; Piekarska, B.; Rybarska, J.; Skowronek, M.; Stopa, B.; Tabor, B.; Da̧broś, W.; Pawlicki, R.; Roterman, I. Folia Histochem Cytobiol 1997, 35, 203.
32. Piekarska, B.; Konieczny, L.; Rybarska, J.; Stopa, B.; Zemanek, G.; Szneler, E.; Król, M.; Nowak, M.; Roterman, I. Biopolymers 2001, 59, 446.
33. Ward, L. D.; Timashew, S. N. Biochemistry 1994, 33, 11891.
34. Kaszuba, J.; Konieczny, L.; Piekarska, B.; Roterman, I.; Rybarska, J. J Physiol Pharmacol 1993, 44, 233.
35. Spólnik, P.; Piekarska, B.; Stopa, B.; Konieczny, L.; Zemanek, G.; Rybarska, J.; Król, M.; Nowak, M.; Roterman, I. Submitted.
36. Brooks, B.; Bruccoleri, R.; Olafson, B.; States, D.; Swaminathan, S.; Karplus, M. J Comp Chem 1983, 4, 187.
37. MacKerell Jr, A. D.; Bashford, D.; Bellot, M.; Dunbrack Jr, R. L.; Evenseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher III, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
38. Mezei, M. J Comput Chem 1997, 18, 812.
39. Lindahl, E.; Hess, B.; van der Spoel, D. J Mol Mod 2001, 7, 306.
40. Ryckaert, J.; Ciccotti, G.; Berendsen, H. J Comp Phys 1977, 23, 327.
41. Nose, S. J Chem Phys 1984, 81, 511.
42. Hoover, W. G. Phys Rev 1985, 31, 1695.
43. Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R. J Chem Phys 1995, 103, 4613.
44. Copyleft, Eveeny Stambulchik; Grace Home, http://plasma-gate. weizmann.ac.il/Grace/ (accessed Summer 2001).
45. Garemyr, R.; Elofsson, A. Proteins Struct Funct Genet 1999, 37, 417.
46. Fox, T.; Kollman, P. A. Proteins Struct Funct Genet 1996, 25, 320.
47. Arnold, G. E.; Ornstein, R. L. Proteins Struct Funct Genet 1994, 18, 19.
48. Barlow, D. J.; Thornton, J. M. J Mol Biol 1983, 168, 867.