Prediction of allosteric communication pathways in proteins

• DOI: 10.1093/bioinformatics/btac380
• Publication Date: 2022-06-08T12:29:48Z
• Authors: Turkan Haliloglu; Aysima Hacisuleyman; Burak Erman
• Keywords: 0303 health sciences; 03 medical and health sciences; Allosteric Regulation; Catalytic Domain; Communication; Humans; Proteins; Allosteric Site

Abstract Motivation Allostery in proteins is an essential phenomenon biological processes. In this article, we present a computational model to predict paths of maximum information transfer between active and allosteric sites. theoretic study, use mutual as the measure transfer, where transition probability from one residue its contacting neighbors proportional magnitude two residues. Starting given using Hidden Markov Model, successively determine neighboring residues that eventually lead path optimum transfer. The Gaussian approximation pairs adopted. limits validity are discussed terms nonlinear theory reduction form. Results Predictions tested on six widely studied cases, CheY Bacterial Chemotaxis, B-cell Lymphoma extra-large (Bcl-xL), Human proline isomerase cyclophilin A (CypA), Dihydrofolate reductase (DHFR), HRas GTPase Caspase-1. communication transmission rendering propagation local fluctuations sites throughout structure multiple correlate well with known experimental data. Distinct originating site may likely represent multi functionality such involving more than and/or pre-existence some other functional states. Our computationally fast simple can give pathways, which crucial for understanding control protein functionality. Supplementary data available at Bioinformatics online.