title: Effect of including torsional parameters for histidine-metal interactions in classical force fields for metalloproteins.
abstract: Classical force-field parameters of the metal site of metalloproteins usually comprise only the partial charges of the involved atoms, as well as the bond-stretching and bending parameters of the metal-ligand interactions. Although for certain metal ligands such as histidine residues, the torsional motions at the metal site play an important role for the dynamics of the protein, no such terms have been considered to be crucial in the parametrization of the force fields, and they have therefore been omitted in the parametrization. In this work, we have optimized AMBER-compatible force-field parameters for the reduced state of the metal site of copper, zinc superoxide dismutase (SOD1) and assessed the effect of including torsional parameters for the histidine-metal interactions in molecular dynamics simulations. On the basis of the obtained results, we recommend that torsion parameters of the metal site are included when processes at the metal site are investigated or when free-energy calculations are performed. As the torsion parameters mainly affect the structure of the metal site, other kinds of structural studies can be performed without considering the torsional parameters of the metal site.
authors.affiliation: Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , München 80539, Germany.
authors.forename: Raúl
authors.initials: R
authors.lastname: Mera-Adasme
authors.forename: Keyarash
authors.initials: K
authors.lastname: Sadeghian
authors.forename: Dage
authors.initials: D
authors.lastname: Sundholm
authors.forename: Christian
authors.initials: C
authors.lastname: Ochsenfeld
mesh_terms: D001665:Binding Sites; D006639:Histidine / Q000737:chemistry / Q000378:metabolism; D008667:Metalloproteins / Q000737:chemistry / Q000378:metabolism*; D008670:Metals / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D013482:Superoxide Dismutase / Q000737:chemistry / Q000378:metabolism
chemical_list: D008667:Metalloproteins; D008670:Metals; D006639:Histidine; D013482:Superoxide Dismutase