title: Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions.
abstract: A fast and approximate method of generating allosteric communication landscapes in proteins is presented by using Schreiber's entropy transfer concept in combination with the Gaussian Network Model of proteins. Predictions of the model and the allosteric communication landscapes generated show that information transfer in proteins does not necessarily take place along a single path, but an ensemble of pathways is possible. The model emphasizes that knowledge of entropy only is not sufficient for determining allosteric communication and additional information based on time delayed correlations should be introduced, which leads to the presence of causality in proteins. The model provides a simple tool for mapping entropy sink-source relations into pairs of residues. By this approach, residues that should be manipulated to control protein activity may be determined. This should be of great importance for allosteric drug design and for understanding the effects of mutations on function. The model is applied to determine allosteric communication in three proteins, Ubiquitin, Pyruvate Kinase, and the PDZ domain. Predictions are in agreement with molecular dynamics simulations and experimental evidence. Proteins 2017; 85:1056-1064. © 2017 Wiley Periodicals, Inc.
authors.affiliation: Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey.
authors.forename: Aysima
authors.initials: A
authors.lastname: Hacisuleyman
authors.affiliation: Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey.
authors.forename: Burak
authors.identifier: 0000-0002-2496-6059
authors.initials: B
authors.lastname: Erman
mesh_terms: D000494:Allosteric Regulation; D000495:Allosteric Site; D019277:Entropy; D006801:Humans; D056004:Molecular Dynamics Simulation; D054731:PDZ Domains; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D011770:Pyruvate Kinase / Q000737:chemistry*; D013997:Time Factors; D025801:Ubiquitin / Q000737:chemistry*
chemical_list: D025801:Ubiquitin; D011770:Pyruvate Kinase
keywords: PDZ domain; correlation function; drug design; dynamic Gaussian network model; fluctuations; joint probability of fluctuations; molecular dynamics; mutual entropy; pyruvate kinase; ubiquitin