Classical force field parameters for the heme prosthetic group of cytochrome c

Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zaida Luthey-Schulten

Research output: Contribution to journalArticlepeer-review

Abstract

Accurate force fields are essential for describing biological systems in a molecular dynamics simulation. To analyze the docking of the small redox protein cytochrome c (cyt c) requires simulation parameters for the heme in both the reduced and oxidized states. This work presents parameters for the partial charges and geometries for the heme in both redox states with ligands appropriate to cyt c. The parameters are based on both protein X-ray structures and ab initio density functional theory (DFT) geometry optimizations at the B3LYP/6-31G* level. The simulations with the new parameter set reproduce the geometries of the X-ray structures and the interaction energies between water and heme prosthetic group obtained from B3LYP/6-31G* calculations. The parameter set developed here will provide new insights into docking processes of heme containing redox proteins.

Original languageEnglish (US)
Pages (from-to)1613-1622
Number of pages10
JournalJournal of Computational Chemistry
Volume25
Issue number13
DOIs
StatePublished - Oct 2004

Keywords

  • AMBER
  • CHARMM
  • Charges
  • DFT
  • Fe ligation

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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