Publication:
Subsets of slow dynamic modes reveal global information sources as allosteric sites

dc.contributor.coauthorAltıntel, Bengi
dc.contributor.coauthorAcar, Burçin
dc.contributor.coauthorHaliloğlu, Türkan
dc.contributor.departmentDepartment of Chemical and Biological Engineering
dc.contributor.kuauthorErman, Burak
dc.contributor.schoolcollegeinstituteCollege of Engineering
dc.date.accessioned2024-11-09T23:43:17Z
dc.date.issued2022
dc.description.abstractAllostery 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.indexedbyWOS
dc.description.indexedbyScopus
dc.description.indexedbyPubMed
dc.description.issue17
dc.description.openaccessNO
dc.description.publisherscopeInternational
dc.description.sponsoredbyTubitakEuN/A
dc.description.sponsorshipScientific Research Project Coordination of Bogazici University
dc.description.sponsorshipScientific and Technological Research Council of Turkey (TUBITAK)
dc.description.sponsorshipNATO 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.volume434
dc.identifier.doi10.1016/j.jmb.2022.167644
dc.identifier.eissn1089-8638
dc.identifier.issn0022-2836
dc.identifier.quartileQ1
dc.identifier.scopus2-s2.0-85132388673
dc.identifier.urihttps://doi.org/10.1016/j.jmb.2022.167644
dc.identifier.urihttps://hdl.handle.net/20.500.14288/13465
dc.identifier.wos848635800007
dc.keywordsAllostery
dc.keywordsInformation transfer
dc.keywordsCausality
dc.keywordsCollectivity
dc.keywordsGlobal information sources aspartate transcarbamoylase
dc.keywordsConformational-change
dc.keywordsCrystal-structure
dc.keywordsEscherichia-coli
dc.keywordsStructural basis
dc.keywordsDna-pk
dc.keywordsProteins
dc.keywordsBinding
dc.keywordsMechanisms
dc.keywordsCommunication
dc.language.isoeng
dc.publisherElsevier
dc.relation.ispartofJournal of Molecular Biology
dc.subjectBiochemistry
dc.subjectMolecular biology
dc.titleSubsets of slow dynamic modes reveal global information sources as allosteric sites
dc.typeJournal Article
dspace.entity.typePublication
local.contributor.kuauthorErman, Burak
local.publication.orgunit1College of Engineering
local.publication.orgunit2Department of Chemical and Biological Engineering
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relation.isOrgUnitOfPublication.latestForDiscoveryc747a256-6e0c-4969-b1bf-3b9f2f674289
relation.isParentOrgUnitOfPublication8e756b23-2d4a-4ce8-b1b3-62c794a8c164
relation.isParentOrgUnitOfPublication.latestForDiscovery8e756b23-2d4a-4ce8-b1b3-62c794a8c164

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