New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: from ab initio to molecular dynamics.
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. (Brooks BR et al. J Comput Chem 1983, 4, 1987.1).
Fuchs
Jean-Francois
JF
Laboratoire de Biophysique Moléculaire et Cellulaire, (CEA-CNRS-UJF, UMR 5090), DRDC/BMC CEA, Grenoble, 17 rue des martyrs, Bat K pièce 110, 38054 Grenoble, France.
Nedev
Hristo
H
Poger
David
D
Ferrand
Michel
M
Brenner
Valérie
V
Dognon
Jean-Pierre
JP
Crouzy
Serge
S
D003198:Computer Simulation; D003300:Copper / Q000737:chemistry*; D030562:Databases, Protein; D007477:Ions / Q000737:chemistry; D008628:Mercury / Q000737:chemistry*; D008954:Models, Biological; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity; D013455:Sulfur / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D007477:Ions; D011506:Proteins; D014867:Water; D013455:Sulfur; D003300:Copper; D008628:Mercury