Force fields including charge transfer and local polarization effects: Application to proteins containing multi/heavy metal ions.
The question whether molecular dynamics (MD) simulations can yield reliable structural and dynamical properties of metalloproteins depend on the accuracy of the force field, i.e., the potential energy function (PEF) and associated parameters modeling the interactions of the metal ion of interest with water and protein ligands. Previously, we had developed a CTPOL PEF for protein simulations of Zn(2+) bound to Cys(-) and/or His(0) that includes charge transfer and local polarization effects as well as metal van der Waals parameters that reproduce the structural and thermodynamical properties of 22 dications. Here, we evaluate if the CTPOL PEF and the new metal parameters (referred to as the CTPOLa force field) can be applied to proteins containing polynuclear metal-binding sites and heavy toxic metal ions, using the CdZn(2)-Cys(9) beta-domain of rat liver metallothionein-2 and the Hg(2+)-bound 18-residue peptide from MerP as test systems. Using the CTPOLa force field, simulations of the beta-domain of rat liver metallothionein-2 totaling 19 ns could preserve the experimentally observed CdZn(2)-Cys(9) complex geometry and overall protein structure, whereas simulations neglecting charge transfer and local polarization effects could not. However, the CTPOLa force field cannot reproduce the experimentally observed linear bicoordination of Hg(2+) in the MerP peptide without adding an angular restraint to the CTPOL PEF to correct the angle distribution about Hg(2+). Thus, the force fields presented herein for the group IIB metal ions can be applied to simulation studies of proteins containing polynuclear metal-binding sites and heavy metal ions in aqueous solution. PEF neglecting charge transfer and local polarization effects in conjunction with vdW parameters adjusted to reproduce the structural and thermodynamical properties of only the metal ion in question could not yield an accurate representation of the metal-binding site and overall protein structure.
Sakharov
Dmitri V
DV
Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
Lim
Carmay
C
D000818:Animals; D001665:Binding Sites; D002104:Cadmium / Q000737:chemistry; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008628:Mercury / Q000737:chemistry; D008667:Metalloproteins / Q000737:chemistry*; D008668:Metallothionein / Q000737:chemistry; D019216:Metals, Heavy / Q000737:chemistry*; D008956:Models, Chemical; D017434:Protein Structure, Tertiary; D051381:Rats; D015032:Zinc / Q000737:chemistry
D008667:Metalloproteins; D019216:Metals, Heavy; D002104:Cadmium; D008668:Metallothionein; D008628:Mercury; D015032:Zinc