Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin

• Published in: PLoS computational biology 2017-01, Vol.13 (1), p.e1005319
• Main Authors: Hacisuleyman, Aysima, Erman, Burak
• Format: Article
• Language: English
• Subjects: Allometry; Allosteric Site; Amino Acids - chemistry; Binding Sites; Bioengineering; Biology and Life Sciences; Causality; Communication; Entropy; Funding; Methods; Models, Chemical; Molecular Dynamics Simulation; Physical Sciences; Physiological aspects; Protein Binding; Protein Conformation; Proteins; Research and analysis methods; Social Sciences; Standard deviation; Structure-Activity Relationship; Ubiquitin; Ubiquitin - chemistry; Ubiquitin - ultrastructure; Ubiquitination
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1005319

It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.