Parameterization of Ca+2-Protein Interactions for Molecular Dynamics Simulations

Elad Project, Esther Nachliel, Menachem Gutman

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)1163-1169
Number of pages7
JournalJournal of Computational Chemistry
Volume29
Issue number7
DOIs
StatePublished - May 2008

Keywords

  • Ca
  • Force field
  • Lennard-Jones
  • Molecular dynamics
  • Residence time

Fingerprint

Dive into the research topics of 'Parameterization of Ca+2-Protein Interactions for Molecular Dynamics Simulations'. Together they form a unique fingerprint.

Cite this