The effect of the neglect of electronic polarization in peptide folding simulations

Journal of Physical Chemistry B

Volumn 106, Issue 49, 2002, Pages 12830-12833

  Soto, Patricia ^a   Mark, Alan E ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTRONIC POLARIZATION;

COMPUTER SIMULATION; ELECTRIC FIELDS; POLARIZATION; PROTEINS; SOLVENTS;

MOLECULAR DYNAMICS;

EID: 0037069843     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp026526i     Document Type: Article

References (33)

1. Cornell, W.D.; Cieplak, P.; Bayly, C.I.; Gould, I.R.; Merz, K.M., Jr.; Ferguson, D.M.; Spellmeyer, D.C.; Fox, T.; Caldwell, J.W.; Kollman, P.A. J. Am. Chem. Soc. 1995, 117, 5179.
2. Jorgensen, W.L.; Maxwell, D.S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225.
3. van Gunsteren, W.F.; Billeter, S.R.; Eising, A.A.; Hunenberger, P.H.; Kruger, P.; Mark, A.E.; Scott, W.R.P.; Tironi, I.G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; Vdf Hochschul-verlang: ETH Zurich, Switzerland, 1996. van Gunsteren, W.F.; Daura, X.; Mark, A.E. In Encyclopedia of Computational Chemistry; von Rague Schleyer, P., Allinger, N.L., Clark, T., Gasteiger, J., Kollman, P.A., Schaefer H.F., III, Schreiner, P.R., Eds.; Wiley & Sons: Chichester, 1998; Vol. 2, p 1211.
4. van Gunsteren, W.F.; Billeter, S.R.; Eising, A.A.; Hunenberger, P.H.; Kruger, P.; Mark, A.E.; Scott, W.R.P.; Tironi, I.G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; Vdf Hochschul-verlang: ETH Zurich, Switzerland, 1996. van Gunsteren, W.F.; Daura, X.; Mark, A.E. In Encyclopedia of Computational Chemistry; von Rague Schleyer, P., Allinger, N.L., Clark, T., Gasteiger, J., Kollman, P.A., Schaefer H.F., III, Schreiner, P.R., Eds.; Wiley & Sons: Chichester, 1998; Vol. 2, p 1211.
5. MacKerell, A.D., Jr.; Bashford, D.; Bellot, M.; Dunbrack, R.L., Jr.; Evanseck, 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, W.E., III; 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.
6. van Belle, D.; Froeyen, M.; Lippens, G.; Wodak, S. J. Mol. Phys. 1992, 77, 239.
7. Rick, S.W.; Stuart, S.J.; Berne, B.J. J. Chem. Phys, 1994, 101, 6141.
8. Saint-Martin, H.; Medina-Llanos, C.; Ortega-Blake, I. J. Chem. Phys. 1990, 93, 6448.
9. Jorgensen, W.L.; McDonald, N.A.; Selmi, M.; Rablen, P.R. J. Am. Chem. Soc. 1995, 117, 11809.
10. Saint-Martin, H.; Hernández-Cobos, J.; Bernal-Uruchurtu, M.I.; Ortega-Blake, I.; Berendsen, H.J.C. J. Chem. Phys. 2000, 113, 10899.
11. Berendsen, H.J.C.; Grigera, J.R.; Straatsma, T.P. J. Phys. Chem. 1987, 91, 6269.
12. Linssen, A.B.M., Ph.D. Thesis, University of Groningen, Groningen, The Netherlands, 1998.
13. Hol, W.G.J.; van Duijnen, P.T.; Berendsen, H.J.C. Nature 1978, 273, 443.
14. Smith, P.E.; van Gunsteren, W.F. J. Chem. Phys. 1994, 100, 3169.
15. van der Spoel, D.; van Maaren, P.J.; Berendsen, H.J.C. J. Chem. Phys. 1998, 108, 10220.
16. Walser, R.; Mark, A.E.; van Gunsteren, W.F. J. Chem. Phys. 2000, 1129 10450.
17. Fioroni, M.; Bruger, K.; Mark, A.E.; Roccatano, D. J. Phys. Chem. B 2000, 104, 12347.
18. Mattos, C.; Ringer, D. Curr. Opin. Struct. Biol. 2001, 11, 761.
19. Daura, X.; van Gunsteren, W.F.; Mark, A.E. Proteins 1999, 34, 269.
20. Chipot, C.; Maigret, B.; Pohorille, A. Proteins 1999, 36, 383.
21. Vriend, G. J. Mol. Graph. 1990, 8, 52.
22. Berendsen, H.J.C.; Postma, J.P.M.; van Gunsteren, W.F.; Di Nola, A.; Haak, J.R. J. Chem. Phys. 1984, 81, 3684.
23. Hess, B.; Bekker, H.; Berendsen, H.J.C.; Fraaije, J.G.E.M. J. Comput. Chem. 1997, 18, 1463.
24. Berendsen, H.J.C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43.
25. van der Spoel, D.; van Buuren, A.R.; Apol, E.; Meulenhoff, P.J.; Tieleman, D.P.; Sijbers, A.L.T.M.; Hess, B.; Feenstra, K.A.; Lindahl, E.; van Drunen, R.; Berendsen, H.J.C. GROMACS User Manual, version 3.1; University of Groningen: Groningen, 2002.
26. Pikkemaat, M.G.; Linssen, A.B.M.; Berendsen, H.J.C.; Janssen, D.B. Protein Eng. 2002, 15, 185.
27. Straatsma, T.P.; McCammon, J.A. Chem. Phys. Lett. 1991, 177, 433.
28. Bottcher C.J.F. Theory of Electric Polarization: Dielectrics in Static Fields; Elsevier: Amsterdam, 1973; Vol. 1.
29. Applequist, J.; Carl, J.R.; Fuug, K.K. J. Am. Chem. Soc. 1972, 94, 2952.
30. van Duijnen, P.T.; Swart, M. J. Phys. Chem. A 1998 102, 2399.
31. CRC Handbook of Chemistry and Physics, 72nd ed.; CRC Press: Boca Raton, 1991-1992.
32. Scholtz, J.M.; Marqusee, S.; Baldwin, R.L.; York, E.J.; Stewart, J.M.; Santoro, M.; Bolen, D.W. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 2854.
33. Villa, A.; Mark, A.E. J. Comput. Chem 2002, 23, 548.