Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins.

Abstract

A set of geometrical parameters has been determined for single manganese metalloproteins for the AMBER force field, and ultimately to other force fields with a similar philosophy. Twelve (12) models from 9 different single-cluster manganese proteins were optimized and parametrized, using a bonded model approach. Mn-ligand bonds, Mn-ligand angles, and Restrained Electrostatic Potential charges for all the 74 residues in the first metal coordination sphere of each Mn metalloprotein were parametrized. The determined parameters were validated with molecular dynamics simulations and several statistics strategies were used to analyze the results. In addition, to validate the parametrized models, frequency and normal mode calculations were performed and comparisons were obtained for the overall structures both with quantum mechanics and molecular mechanics calculations. Linear and polynomial fittings were performed to estimate Mn-ligand bond force constants for generic manganese centers. Furthermore, averages are proposed for the main Mn-ligand angle interactions of typical manganese coordination centers: axial, square and triangular equatorial planes, and tetrahedral positions, for the different combinations of donor atoms from waters and hard ligands.