Please use this identifier to cite or link to this item: https://hdl.handle.net/20.500.11851/7035
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dc.contributor.authorHeinzelmann, Germano-
dc.contributor.authorBaştuğ, Turgut-
dc.contributor.authorKuyucak, Serdar-
dc.date.accessioned2021-09-11T15:45:03Z-
dc.date.available2021-09-11T15:45:03Z-
dc.date.issued2013en_US
dc.identifier.issn1520-6106-
dc.identifier.urihttps://doi.org/10.1021/jp4010423-
dc.identifier.urihttps://hdl.handle.net/20.500.11851/7035-
dc.description.abstractThe bacterial aspartate transporter Glt(Ph) cotransports three Na+ ions with the substrate. The mechanism and energetics of ligand binding have previously been studied using molecular dynamics simulations on the crystal structure of Glt(Ph) captured in the outward-facing state. Here we use the recent crystal structure of the inward-facing state of Glt(Ph) to study the reverse process of unbinding of ligands. Gating behavior is studied in the presence of different ligands. A detailed characterization of the intracellular gate is given, pointing out the differences from the extracellular gate. We then perform free energy simulations to calculate the binding affinities of all the ligands in different combinations, from which the unbinding order is determined as Na2, (gate opens), Asp, Na1, and Na3. The strong coupling between Asp and Na1 is quantified from several free energy calculations. Na3 has the largest affinity to Glt(Ph), and therefore, its unbinding is proposed as the rate-limiting step in the transport cycle. The release time of Na3, estimated from Kramers' rate theory, is shown to be consistent with the experimental turnover rate of the transporter.en_US
dc.description.sponsorshipAustralian Research CouncilAustralian Research Council; Turkish Scientific and Technical Research CouncilTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK)en_US
dc.description.sponsorshipThis work was supported by grants from the Australian Research Council and Turkish Scientific and Technical Research Council. Calculations were performed using the HPC facilities at the National Computational Infrastructure (Canberra) and ULAKBIM (Ankara). We thank Rob Vandenberg and Renae Ryan for discussions on the structure and function of Glt<INF>Ph</INF>.en_US
dc.language.isoenen_US
dc.publisherAmer Chemical Socen_US
dc.relation.ispartofJournal of Physical Chemistry Ben_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subject[No Keywords]en_US
dc.titleMechanism and Energetics of Ligand Release in the Aspartate Transporter Glt(ph)en_US
dc.typeArticleen_US
dc.departmentFaculties, Faculty of Engineering, Department of Material Science and Nanotechnology Engineeringen_US
dc.departmentFakülteler, Mühendislik Fakültesi, Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümütr_TR
dc.identifier.volume117en_US
dc.identifier.issue18en_US
dc.identifier.startpage5486en_US
dc.identifier.endpage5496en_US
dc.authorid0000-0001-9123-9292-
dc.authorid0000-0001-7168-6941-
dc.authorid0000-0003-4315-9532-
dc.identifier.wosWOS:000318891700009en_US
dc.identifier.scopus2-s2.0-84877702735en_US
dc.institutionauthorBaştuğ, Turgut-
dc.identifier.pmid23590433en_US
dc.identifier.doi10.1021/jp4010423-
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.identifier.scopusqualityQ1-
item.openairetypeArticle-
item.languageiso639-1en-
item.grantfulltextnone-
item.fulltextNo Fulltext-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.cerifentitytypePublications-
crisitem.author.dept02.6. Department of Material Science and Nanotechnology Engineering-
Appears in Collections:Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü / Department of Material Science & Nanotechnology Engineering
PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
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