New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: From ab initio to molecular dynamics

Fuchs, Jean-Francois, Nedev, Hristo, Poger, David, Ferrand, Michel, Brenner, Valérie, Dognon, Jean-Pierre and Crouzy, Serge (2006) New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: From ab initio to molecular dynamics. Journal of Computational Chemistry, 27 7: 837-856. doi:10.1002/jcc.20392


Author Fuchs, Jean-Francois
Nedev, Hristo
Poger, David
Ferrand, Michel
Brenner, Valérie
Dognon, Jean-Pierre
Crouzy, Serge
Title New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: From ab initio to molecular dynamics
Journal name Journal of Computational Chemistry   Check publisher's open access policy
ISSN 1096-987X
0192-8651
Publication date 2006-01-01
Sub-type Article (original research)
DOI 10.1002/jcc.20392
Volume 27
Issue 7
Start page 837
End page 856
Total pages 20
Place of publication New York
Publisher Wiley
Language eng
Subject 029901 Biological Physics
060112 Structural Biology (incl. Macromolecular Modelling)
Abstract We have developed new force field and parameters for copper(I) and mercury(II) to be used in molecular dynamics simulations of metalloproteins. Parameters have been derived from fitting of ab initio interaction potentials calculated at the MP2 level of theory, and results compared to experimental data when available. Nonbonded parameters for the metals have been calculated from ab initio interaction potentials with TIP3P water. Due to high charge transfer between Cu(I) or Hg(II) and their ligands, the model is restricted to a linear coordination of the metal bonded to two sulfur atoms. The experimentally observed asymmetric distribution of metal ligand bond lengths (r) is accounted for by the addition of an anharmonic (r3) term in the potential. Finally, the new parameters and potential, introduced into the CHARMM force field, are tested in short molecular dynamics simulations of two metal thiolates fragments in water.
Keyword Metalloproteins
Hg(II)
Cu(I)
CHARMM force field
Fit from ab initio potential
Molecular dynamics simulation
Q-Index Code C1

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
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