{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1361975845352928512.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1111/febs.15224"}},{"identifier":{"@type":"URI","@value":"https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Ffebs.15224"}},{"identifier":{"@type":"URI","@value":"https://onlinelibrary.wiley.com/doi/pdf/10.1111/febs.15224"}},{"identifier":{"@type":"URI","@value":"https://onlinelibrary.wiley.com/doi/full-xml/10.1111/febs.15224"}},{"identifier":{"@type":"URI","@value":"https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/febs.15224"}},{"identifier":{"@type":"PMID","@value":"31976609"}},{"identifier":{"@type":"DOI","@value":"10.2210/pdb6jnd/pdb"}}],"resourceType":"学術雑誌論文(journal article)","dc:title":[{"@value":"Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo‐electron microscopy"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:sec><jats:label/><jats:p>Analysis of the conformational changes of protein is important to elucidate the mechanisms of protein motions correlating with their function. Here, we studied the spontaneous domain motion of unliganded glutamate dehydrogenase from <jats:italic>Thermococcus profundus</jats:italic> using cryo‐electron microscopy and proposed a novel method to construct free‐energy landscape of protein conformations. Each subunit of the homo‐hexameric enzyme comprises nucleotide‐binding domain (NAD domain) and hexamer‐forming core domain. A large active‐site cleft is situated between the two domains and varies from open to close according to the motion of a NAD domain. A three‐dimensional map reconstructed from all cryo‐electron microscopy images displayed disordered volumes of NAD domains, suggesting that NAD domains in the collected images adopted various conformations in domain motion. Focused classifications on NAD domain of subunits provided several maps of possible conformations in domain motion. To deduce what kinds of conformations appeared in EM images, we developed a novel analysis method that describe the EM maps as a linear combination of representative conformations appearing in a 200‐ns molecular dynamics simulation as reference. The analysis enabled us to estimate the appearance frequencies of the representative conformations, which illustrated a free‐energy landscape in domain motion. In the open/close domain motion, two free‐energy basins hindered the direct transformation from open to closed state. Structure models constructed for representative EM maps in classifications demonstrated the correlation between the energy landscape and conformations in domain motion. Based on the results, the domain motion in glutamate dehydrogenase and the analysis method to visualize conformational changes and free‐energy landscape were discussed.</jats:p></jats:sec><jats:sec><jats:title>Database</jats:title><jats:p>The EM maps of the four conformations were deposited to Electron Microscopy Data Bank (EMDB) as accession codes EMD‐9845 (open), EMD‐9846 (half‐open1), EMD‐9847 (half‐open2), and EMD‐9848 (closed), respectively. In addition, the structural models built for the four conformations were deposited to the Protein Data Bank (PDB) as accession codes <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6JN9\">6JN9</jats:ext-link> (open), <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6JNA\">6JNA</jats:ext-link> (half‐open1), <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6JNC\">6JNC</jats:ext-link> (half‐open2), and <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6JND\">6JND</jats:ext-link> (closed), respectively.</jats:p></jats:sec>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1381975845352928514","@type":"Researcher","foaf:name":[{"@value":"Mao Oide"}],"jpcoar:affiliationName":[{"@value":"Department of Physics Faculty of Science and Technology Keio University Yokohama Japan"},{"@value":"RIKEN SPring‐8 Center Sayo‐gun Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1381975845352928128","@type":"Researcher","foaf:name":[{"@value":"Takayuki Kato"}],"jpcoar:affiliationName":[{"@value":"Graduate School of Frontier Biosciences Osaka University Suita Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1420001326215241984","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"90589821"},{"@type":"NRID","@value":"1000090589821"},{"@type":"NRID","@value":"9000258296988"},{"@type":"NRID","@value":"9000002742289"},{"@type":"NRID","@value":"9000264244527"},{"@type":"NRID","@value":"9000405638378"},{"@type":"NRID","@value":"9000258297138"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/7000003079"}],"foaf:name":[{"@value":"Tomotaka Oroguchi"}],"jpcoar:affiliationName":[{"@value":"Department of Physics Faculty of Science and Technology Keio University Yokohama Japan"},{"@value":"RIKEN SPring‐8 Center Sayo‐gun Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1381975845352928512","@type":"Researcher","foaf:name":[{"@value":"Masayoshi Nakasako"}],"jpcoar:affiliationName":[{"@value":"Department of Physics Faculty of Science and Technology Keio University Yokohama Japan"},{"@value":"RIKEN SPring‐8 Center Sayo‐gun Japan"}]}],"publication":{"publicationIdentifier":[{"@type":"PISSN","@value":"1742464X"},{"@type":"EISSN","@value":"17424658"}],"prism:publicationName":[{"@value":"The FEBS Journal"}],"dc:publisher":[{"@value":"Wiley"}],"prism:publicationDate":"2020-02-05","prism:volume":"287","prism:number":"16","prism:startingPage":"3472","prism:endingPage":"3493"},"reviewed":"false","dc:rights":["http://onlinelibrary.wiley.com/termsAndConditions#vor"],"url":[{"@id":"https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Ffebs.15224"},{"@id":"https://onlinelibrary.wiley.com/doi/pdf/10.1111/febs.15224"},{"@id":"https://onlinelibrary.wiley.com/doi/full-xml/10.1111/febs.15224"},{"@id":"https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/febs.15224"}],"createdAt":"2020-01-24","modifiedAt":"2023-09-04","foaf:topic":[{"@id":"https://cir.nii.ac.jp/all?q=Thermococcus","dc:title":"Thermococcus"},{"@id":"https://cir.nii.ac.jp/all?q=Motion","dc:title":"Motion"},{"@id":"https://cir.nii.ac.jp/all?q=Energy%20Transfer","dc:title":"Energy Transfer"},{"@id":"https://cir.nii.ac.jp/all?q=Glutamate%20Dehydrogenase","dc:title":"Glutamate Dehydrogenase"},{"@id":"https://cir.nii.ac.jp/all?q=Protein%20Domains","dc:title":"Protein Domains"},{"@id":"https://cir.nii.ac.jp/all?q=Archaeal%20Proteins","dc:title":"Archaeal Proteins"},{"@id":"https://cir.nii.ac.jp/all?q=Cryoelectron%20Microscopy","dc:title":"Cryoelectron Microscopy"},{"@id":"https://cir.nii.ac.jp/all?q=Thermodynamics","dc:title":"Thermodynamics"},{"@id":"https://cir.nii.ac.jp/all?q=Molecular%20Dynamics%20Simulation","dc:title":"Molecular Dynamics Simulation"},{"@id":"https://cir.nii.ac.jp/all?q=Algorithms","dc:title":"Algorithms"}],"project":[{"@id":"https://cir.nii.ac.jp/crid/1040000781958269056","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"17H04854"},{"@type":"JGN","@value":"JP17H04854"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-17H04854/"}],"notation":[{"@language":"ja","@value":"生体分子の機能発揮機構における水和構造の役割の解明"},{"@language":"en","@value":"Elucidation of thermodynamic roles of hydration structure in protein functions"}]},{"@id":"https://cir.nii.ac.jp/crid/1040000781994786688","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"18H05229"},{"@type":"JGN","@value":"JP18H05229"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-18H05229/"}],"notation":[{"@language":"ja","@value":"新世代中性子構造生物学の開拓"},{"@language":"en","@value":"Neutron Structural Biology for New 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Small-Angle X-ray Scattering<sup>,</sup>"}]},{"@id":"https://cir.nii.ac.jp/crid/1362544419156075008","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules"}]},{"@id":"https://cir.nii.ac.jp/crid/1362544419885318016","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Comparison of simple potential functions for simulating liquid water"}]},{"@id":"https://cir.nii.ac.jp/crid/1362825893359135104","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"New tools for automated high-resolution cryo-EM structure determination in RELION-3"}]},{"@id":"https://cir.nii.ac.jp/crid/1362825895934062208","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Disentangling conformational states of macromolecules in 3D-EM through likelihood 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