title: Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins.
abstract: We present a new generation of coarse-grained (CG) potentials that account for a simplified electrostatic description of soluble proteins. The treatment of permanent electrostatic dipoles of the backbone and polar side-chains allows to simulate proteins, preserving an excellent structural and dynamic agreement with respective reference structures and all-atom molecular dynamics simulations. Moreover, multiprotein complexes can be well described maintaining their molecular interfaces thanks to the ability of this scheme to better describe the actual electrostatics at a CG level of resolution. An efficient and robust heuristic algorithm based on particle swarm optimization is used for the derivation of CG parameters via a force-matching procedure. The ability of this protocol to deal with high dimensional search spaces suggests that the extension of this optimization procedure to larger data sets may lead to the generation of a fully transferable CG force field. At the present stage, these electrostatic-consistent CG potentials are easily and efficiently parametrized, show a good degree of transferability, and can be used to simulate soluble proteins or, more interestingly, large macromolecular assemblies for which long all-atom simulations may not be easily affordable.
authors.affiliation: Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne-EPFL , Lausanne, CH-1015, Switzerland.
authors.forename: Enrico
authors.initials: E
authors.lastname: Spiga
authors.affiliation: Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne-EPFL , Lausanne, CH-1015, Switzerland.
authors.forename: Davide
authors.initials: D
authors.lastname: Alemani
authors.affiliation: Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne-EPFL , Lausanne, CH-1015, Switzerland.
authors.forename: Matteo T
authors.initials: MT
authors.lastname: Degiacomi
authors.affiliation: Departement für Chemie und Biochemie, Universität Bern , Freiestrasse 3, Bern, CH-3012, Switzerland.
authors.forename: Michele
authors.initials: M
authors.lastname: Cascella
authors.affiliation: Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne-EPFL , Lausanne, CH-1015, Switzerland.
authors.forename: Matteo Dal
authors.initials: MD
authors.lastname: Peraro