title: A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements.
abstract: We introduce a nonradial potential term for coarse-grained (CG) molecular simulations of proteins. This term mimics the backbone dipole-dipole interactions and accounts for the needed directionality to form stable folded secondary structure elements. We show that α-helical and β-sheet peptide chains are correctly described in dynamics without the need of introducing any a priori bias potentials or ad hoc parametrizations, which limit broader applicability of CG simulations for proteins. Moreover, our model is able to catch the formation of supersecondary structural motifs, like transitions from long single α-helices to helix-coil-helix or β-hairpin assemblies. This novel scheme requires the structural information of Cα beads only; it does not introduce any additional degrees of freedom to the system and has a general formulation, which allows it to be used in synergy with various CG protocols, leading to an improved description of the structural and dynamic properties of protein assemblies and networks.
authors.affiliation: Laboratory for Biomolecular Modeling, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland and Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
authors.forename: Davide
authors.initials: D
authors.lastname: Alemani
authors.affiliation: Laboratory for Biomolecular Modeling, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland and Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
authors.forename: Francesca
authors.initials: F
authors.lastname: Collu
authors.affiliation: Laboratory for Biomolecular Modeling, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland and Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
authors.forename: Michele
authors.initials: M
authors.lastname: Cascella
authors.affiliation: Laboratory for Biomolecular Modeling, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland and Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
authors.forename: Matteo
authors.initials: M
authors.lastname: Dal Peraro