✦ LIBER ✦

Parameterization of Ca+2–protein interactions for molecular dynamics simulations

✍ Scribed by Elad Project; Esther Nachliel; Menachem Gutman

Publisher: John Wiley and Sons
Year: 2008
Tongue: English
Weight: 448 KB
Volume: 29
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.20876

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✦ Synopsis

Abstract

Molecular dynamics simulations of Ca^+2^ ions near protein were performed with three force fields: GROMOS96, OPLS‐AA, and CHARMM22. The simulations reveal major, force‐field dependent, inconsistencies in the interaction between the Ca^+2^ ions with the protein. The variations are attributed to the nonbonded parameterizations of the Ca^+2^‐carboxylates interactions. The simulations results were compared to experimental data, using the Ca^+2^‐HCOO^−^ equilibrium as a model. The OPLS‐AA force field grossly overestimates the binding affinity of the Ca^+2^ ions to the carboxylate whereas the GROMOS96 and CHARMM22 force fields underestimate the stability of the complex. Optimization of the Lennard‐Jones parameters for the Ca^+2^‐carboxylate interactions were carried out, yielding new parameters which reproduce experimental data. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

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