title: Analysis on long-range residue-residue communication using molecular dynamics.
abstract: We investigated the possibility of inter-residue communication of side chains in barstar, an 89 residue protein, using mutual information theory. The normalized mutual information (NMI) of the dihedral angles of the side chains was obtained from all-atom molecular dynamics simulations. The accumulated NMI from an explicit solvent equilibrated trajectory (600 ns) with free backbone exhibits a parabola-shaped distribution over the inter-residue distances (0-36 Å): smaller at the end regimes but larger in the middle regime. This analysis, plus several other measures, does not find unusual long-range communication for free backbone in explicit solvent simulations.
authors.affiliation: Department of Chemistry, University of North Carolina at Chapel Hill.
authors.forename: Sangwook
authors.initials: S
authors.lastname: Wu
authors.affiliation: Department of Chemistry, University of North Carolina at Chapel Hill.
authors.forename: Chang Jun
authors.initials: CJ
authors.lastname: Lee
authors.affiliation: Department of Chemistry, University of North Carolina at Chapel Hill.
authors.forename: Lee G
authors.initials: LG
authors.lastname: Pedersen
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D012997:Solvents; C057438:barstar protein, Bacillus amyloliquefaciens
keywords: explicit/implicit solvent model; information theory; long-range residue communication; molecular dynamics simulation; mutual information