Publication: Subsets of slow dynamic modes reveal global information sources as allosteric sites
dc.contributor.coauthor | Altıntel, Bengi | |
dc.contributor.coauthor | Acar, Burçin | |
dc.contributor.coauthor | Haliloğlu, Türkan | |
dc.contributor.department | Department of Chemical and Biological Engineering | |
dc.contributor.kuauthor | Erman, Burak | |
dc.contributor.schoolcollegeinstitute | College of Engineering | |
dc.date.accessioned | 2024-11-09T23:43:17Z | |
dc.date.issued | 2022 | |
dc.description.abstract | Allostery is a key biological control mechanism, and dynamic information flow provides a perspective to describe allosteric interactions in causal relationships. Here, as a novel implementation of the Gaussian Network Model (GNM) based Transfer Entropy (TE) calculations, we show that the dissection of dynamic information into subsets of slow dynamic modes discloses different layers of multi-directional allosteric pathways inherent in a given protein structure. In these subsets of slow modes, the degree of collectivity (Col) in the information transfer of residues with their TE values (TECol score) identifies distinct residues as powerful effectors, global information sources; showing themselves with a high dynamic capacity to collectively disseminate information to others. As exemplified on aspartate transcarbamoylase (ATCase), Na+/K+-adenosine triphosphatase (Na+/K+-ATPase), and human transient receptor potential melastatin 2 (TRPM2) along with a dataset of 20 proteins, these specific residues are associated with known active and allosteric sites. These information source residues, which collectively control others and lead allos-teric communication pathways, hint at plausible binding sites for structure-based rational drug design. (c) 2022 Elsevier Ltd. All rights reserved. | |
dc.description.indexedby | WOS | |
dc.description.indexedby | Scopus | |
dc.description.indexedby | PubMed | |
dc.description.issue | 17 | |
dc.description.openaccess | NO | |
dc.description.publisherscope | International | |
dc.description.sponsoredbyTubitakEu | N/A | |
dc.description.sponsorship | Scientific Research Project Coordination of Bogazici University | |
dc.description.sponsorship | Scientific and Technological Research Council of Turkey (TUBITAK) | |
dc.description.sponsorship | NATO Science for Peace Program [20A05P3, 119F392, G5685] This study was financed by funds from Scientific Research Project Coordination of Bogazici University, The Scientific and Technological Research Council of Turkey (TUBITAK) and NATO Science for Peace Program with grant numbers 20A05P3, 119F392 and G5685, respectively. | |
dc.description.volume | 434 | |
dc.identifier.doi | 10.1016/j.jmb.2022.167644 | |
dc.identifier.eissn | 1089-8638 | |
dc.identifier.issn | 0022-2836 | |
dc.identifier.quartile | Q1 | |
dc.identifier.scopus | 2-s2.0-85132388673 | |
dc.identifier.uri | https://doi.org/10.1016/j.jmb.2022.167644 | |
dc.identifier.uri | https://hdl.handle.net/20.500.14288/13465 | |
dc.identifier.wos | 848635800007 | |
dc.keywords | Allostery | |
dc.keywords | Information transfer | |
dc.keywords | Causality | |
dc.keywords | Collectivity | |
dc.keywords | Global information sources aspartate transcarbamoylase | |
dc.keywords | Conformational-change | |
dc.keywords | Crystal-structure | |
dc.keywords | Escherichia-coli | |
dc.keywords | Structural basis | |
dc.keywords | Dna-pk | |
dc.keywords | Proteins | |
dc.keywords | Binding | |
dc.keywords | Mechanisms | |
dc.keywords | Communication | |
dc.language.iso | eng | |
dc.publisher | Elsevier | |
dc.relation.ispartof | Journal of Molecular Biology | |
dc.subject | Biochemistry | |
dc.subject | Molecular biology | |
dc.title | Subsets of slow dynamic modes reveal global information sources as allosteric sites | |
dc.type | Journal Article | |
dspace.entity.type | Publication | |
local.contributor.kuauthor | Erman, Burak | |
local.publication.orgunit1 | College of Engineering | |
local.publication.orgunit2 | Department of Chemical and Biological Engineering | |
relation.isOrgUnitOfPublication | c747a256-6e0c-4969-b1bf-3b9f2f674289 | |
relation.isOrgUnitOfPublication.latestForDiscovery | c747a256-6e0c-4969-b1bf-3b9f2f674289 | |
relation.isParentOrgUnitOfPublication | 8e756b23-2d4a-4ce8-b1b3-62c794a8c164 | |
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