title: Timing Correlations in Proteins Predict Functional Modules and Dynamic Allostery.
abstract: How protein structure encodes functionality is not fully understood. For example, long-range intraprotein communication can occur without measurable conformational change and is often not captured by existing structural correlation functions. It is shown here that important functional information is encoded in the timing of protein motions, rather than motion itself. I introduce the conditional activity function to quantify such timing correlations among the degrees of freedom within proteins. For three proteins, the conditional activities between side-chain dihedral angles were computed using the output of microseconds-long atomistic simulations. The new approach demonstrates that a sparse fraction of side-chain pairs are dynamically correlated over long distances (spanning protein lengths up to 7 nm), in sharp contrast to structural correlations, which are short-ranged (<1 nm). Regions of high self- and inter-side-chain dynamical correlations are found, corresponding to experimentally determined functional modules and allosteric connections, respectively.
authors.affiliation: Green Center for Molecular, Computational, and Systems Biology, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States.|Department of Biophyics, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States.|Pitzer Center for Theoretical Chemistry, University of California , Berkeley, California 94720, United States.
authors.forename: Milo M
authors.initials: MM
authors.lastname: Lin
mesh_terms: D026923:Amino Acid Transport Systems, Basic / Q000737:chemistry; D019277:Entropy; D029968:Escherichia coli Proteins / Q000737:chemistry; D006801:Humans; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D021281:Quantitative Structure-Activity Relationship
chemical_list: D026923:Amino Acid Transport Systems, Basic; D029968:Escherichia coli Proteins; D011506:Proteins; C430024:lysP protein, E coli