title: Deriving Coarse-Grained Charges from All-Atom Systems: An Analytic Solution.
abstract: An analytic method to assign optimal coarse-grained charges based on electrostatic potential matching is presented. This solution is the infinite size and density limit of grid-integration charge-fitting and is computationally more efficient by several orders of magnitude. The solution is also minimized with respect to coarse-grained positions which proves to be an extremely important step in reproducing the all-atom electrostatic potential. The joint optimal-charge optimal-position coarse-graining procedure is applied to a number of aggregating proteins using single-site per amino acid resolution. These models provide a good estimate of both the vacuum and Debye-Hückel screened all-atom electrostatic potentials in the vicinity and in the far-field of the protein. Additionally, these coarse-grained models are shown to approximate the all-atom dimerization electrostatic potential energy of 10 aggregating proteins with good accuracy.
authors.affiliation: Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States.
authors.forename: Peter
authors.initials: P
authors.lastname: McCullagh
authors.affiliation: Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523, United States.
authors.forename: Peter T
authors.initials: PT
authors.lastname: Lake
authors.affiliation: Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523, United States.
authors.forename: Martin
authors.initials: M
authors.lastname: McCullagh
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D036022:Capsid Proteins / Q000737:chemistry / Q000378:metabolism; D019281:Dimerization; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D055672:Static Electricity; D014764:Viral Proteins / Q000737:chemistry; D014902:West Nile virus / Q000378:metabolism
chemical_list: D000596:Amino Acids; D036022:Capsid Proteins; D011506:Proteins; D014764:Viral Proteins