title: Force field independent metal parameters using a nonbonded dummy model.
abstract: The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn(2+), Zn(2+), Mg(2+), and Ca(2+), as well as providing new parameters for Ni(2+), Co(2+), and Fe(2+). In all the cases, we are able to reproduce both M(2+)-O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase I as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers.
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden.
authors.forename: Fernanda
authors.initials: F
authors.lastname: Duarte
authors.forename: Paul
authors.initials: P
authors.lastname: Bauer
authors.forename: Alexandre
authors.initials: A
authors.lastname: Barrozo
authors.forename: Beat Anton
authors.initials: BA
authors.lastname: Amrein
authors.forename: Miha
authors.initials: M
authors.lastname: Purg
authors.forename: Johan
authors.initials: J
authors.lastname: Aqvist
authors.forename: Shina Caroline Lynn
authors.initials: SC
authors.lastname: Kamerlin
mesh_terms: D020134:Catalytic Domain; D002412:Cations / Q000737:chemistry*; D004926:Escherichia coli; D029968:Escherichia coli Proteins / Q000737:chemistry; D006801:Humans; D007791:Lactoylglutathione Lyase / Q000737:chemistry; D008670:Metals / Q000737:chemistry*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D055672:Static Electricity; D014867:Water / Q000737:chemistry
chemical_list: D002412:Cations; D029968:Escherichia coli Proteins; D008670:Metals; D014867:Water; C000597196:GLO1 protein, human; D007791:Lactoylglutathione Lyase