New model potentials for sulfur–copper(I) and sulfur–mercury(II) interactions in proteins: From ab initio to molecular dynamics
✍ Scribed by Jean-Francois Fuchs; Hristo Nedev; David Poger; Michel Ferrand; Valérie Brenner; Jean-Pierre Dognon; Serge Crouzy
- Publisher
- John Wiley and Sons
- Year
- 2006
- Tongue
- English
- Weight
- 591 KB
- Volume
- 27
- Category
- Article
- ISSN
- 0192-8651
No coin nor oath required. For personal study only.
✦ Synopsis
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 (r^3^) 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. (Brooks BR et al. J Comput Chem 1983, 4, 1987.1) © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 837–856, 2006