title: Topologically Based Multipolar Reconstruction of Electrostatic Interactions in Multiscale Simulations of Proteins.
abstract: We present a new method to incorporate electrostatic interactions in coarse-grained representations of proteins. The model is based on a topologically reconstructed multipolar expansion of the all-atom centers of charge, specifically of the backbone dipoles and the polar or charged side chains. The reliability of the model is checked by studying different test cases, namely protein-cofactor/substrate interactions, protein large conformational changes, and protein-protein complexes. In all cases, the model quantitatively reproduces the all-atom electrostatic field in both a static and a dynamic framework. The model is of general applicability and can be used to improve both full coarse-grained simulations and hybrid all-atom/coarse-grained multiscale approaches.
authors.affiliation: Laboratory of Computational Chemistry and Biochemistry and Laboratory for Biomolecular Modeling, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland, International School for Advanced Studies (SISSA/ISAS) and CNR-INFM-DEMOCRITOS, I-34014 Trieste, Italy, and Italian Institute of Technology, Italy.
authors.forename: Michele
authors.initials: M
authors.lastname: Cascella
authors.affiliation: Laboratory of Computational Chemistry and Biochemistry and Laboratory for Biomolecular Modeling, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland, International School for Advanced Studies (SISSA/ISAS) and CNR-INFM-DEMOCRITOS, I-34014 Trieste, Italy, and Italian Institute of Technology, Italy.
authors.forename: Marilisa A
authors.initials: MA
authors.lastname: Neri
authors.affiliation: Laboratory of Computational Chemistry and Biochemistry and Laboratory for Biomolecular Modeling, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland, International School for Advanced Studies (SISSA/ISAS) and CNR-INFM-DEMOCRITOS, I-34014 Trieste, Italy, and Italian Institute of Technology, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Carloni
authors.affiliation: Laboratory of Computational Chemistry and Biochemistry and Laboratory for Biomolecular Modeling, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland, International School for Advanced Studies (SISSA/ISAS) and CNR-INFM-DEMOCRITOS, I-34014 Trieste, Italy, and Italian Institute of Technology, Italy.
authors.forename: Matteo Dal
authors.initials: MD
authors.lastname: Peraro