{"created":"2021-03-01T06:25:57.189265+00:00","id":18535,"links":{},"metadata":{"_buckets":{"deposit":"34d80e12-30c3-41a2-8c0d-a76ad5926383"},"_deposit":{"id":"18535","owners":[],"pid":{"revision_id":0,"type":"depid","value":"18535"},"status":"published"},"_oai":{"id":"oai:nagoya.repo.nii.ac.jp:00018535"},"item_10_biblio_info_6":{"attribute_name":"\u66f8\u8a8c\u60c5\u5831","attribute_value_mlt":[{"bibliographicIssueDates":{"bibliographicIssueDate":"2011-03","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"12","bibliographicPageEnd":"125102","bibliographicPageStart":"125102","bibliographicVolumeNumber":"134","bibliographic_titles":[{"bibliographic_title":"The Journal of Chemical Physics"}]}]},"item_10_description_4":{"attribute_name":"\u6284\u9332","attribute_value_mlt":[{"subitem_description":"A statistical mechanical model of allosteric transition of proteins is developed by extending the structure-basedmodel of protein folding to cases that a protein has two different native conformations. Partition function is calculated exactly within the model and free-energysurfaces associated with allostery are derived. In this paper, the model of allosteric transition proposed in a previous paper [Proc. Natl. Acad. Sci. U.S.A134, 7775 (2010)] is reformulated to describe both fluctuation in side-chain configurations and that in backbone structures in a balanced way. The model is applied to example proteins, Ras, calmodulin, and CheY: Ras undergoes the allosteric transition between guanosine diphosphate (GDP)-bound and guanosine triphosphate (GTP)-bound forms, and the model results show that the GDP-bound form is stabilized enough to prevent unnecessary signal transmission, but the conformation in the GTP-bound state bears large fluctuation in side-chain configurations, which may help to bind multiple target proteins for multiple pathways of signaling. The calculated results of calmodulin show the scenario of sequential ordering in Ca^2+ binding and the associated allosteric conformational change, which are realized though the sequential appearing of pre-existing structural fluctuations, i.e., fluctuations to show structures suitable to bind Ca^2+ before its binding. Here, the pre-existing fluctuations to accept the second and third Ca^2+ ions are dominated by the side-chain fluctuation. In CheY, the calculated side-chain fluctuation of Tyr106 is coordinated with the backbone structural change in the \u03b24\u2013\u03b14 loop, which explains the pre-existing Y\u2013T coupling process in this protein. Ability of the model to explain allosteric transitions of example proteins supports the view that the large entropic effects lower the free-energy barrier of allosteric transition.","subitem_description_type":"Abstract"}]},"item_10_identifier_60":{"attribute_name":"URI","attribute_value_mlt":[{"subitem_identifier_type":"DOI","subitem_identifier_uri":"http://dx.doi.org/10.1063/1.3565025"},{"subitem_identifier_type":"HDL","subitem_identifier_uri":"http://hdl.handle.net/2237/20621"}]},"item_10_publisher_32":{"attribute_name":"\u51fa\u7248\u8005","attribute_value_mlt":[{"subitem_publisher":"AIP"}]},"item_10_rights_12":{"attribute_name":"\u6a29\u5229","attribute_value_mlt":[{"subitem_rights":"\u00a9 2011 American Institute of Physics"}]},"item_10_select_15":{"attribute_name":"\u8457\u8005\u7248\u30d5\u30e9\u30b0","attribute_value_mlt":[{"subitem_select_item":"author"}]},"item_10_source_id_7":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"0021-9606","subitem_source_identifier_type":"ISSN"}]},"item_creator":{"attribute_name":"\u8457\u8005","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Itoh, Kazuhito"}],"nameIdentifiers":[{"nameIdentifier":"53844","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Sasai, Masaki"}],"nameIdentifiers":[{"nameIdentifier":"53845","nameIdentifierScheme":"WEKO"}]}]},"item_files":{"attribute_name":"\u30d5\u30a1\u30a4\u30eb\u60c5\u5831","attribute_type":"file","attribute_value_mlt":[{"accessrole":"open_date","date":[{"dateType":"Available","dateValue":"2018-02-21"}],"displaytype":"detail","filename":"ItohSasaiJCP2011.pdf","filesize":[{"value":"3.0 MB"}],"format":"application/pdf","licensetype":"license_note","mimetype":"application/pdf","url":{"label":"ItohSasaiJCP2011.pdf","url":"https://nagoya.repo.nii.ac.jp/record/18535/files/ItohSasaiJCP2011.pdf"},"version_id":"b6f7ab06-d823-4d13-9af4-3cc4352484f3"}]},"item_language":{"attribute_name":"\u8a00\u8a9e","attribute_value_mlt":[{"subitem_language":"eng"}]},"item_resource_type":{"attribute_name":"\u8cc7\u6e90\u30bf\u30a4\u30d7","attribute_value_mlt":[{"resourcetype":"journal article","resourceuri":"http://purl.org/coar/resource_type/c_6501"}]},"item_title":"Statistical mechanics of protein allostery: Roles of backbone and side-chain structural fluctuations","item_titles":{"attribute_name":"\u30bf\u30a4\u30c8\u30eb","attribute_value_mlt":[{"subitem_title":"Statistical mechanics of protein allostery: Roles of backbone and side-chain structural fluctuations"}]},"item_type_id":"10","owner":"1","path":["320/321/322"],"pubdate":{"attribute_name":"\u516c\u958b\u65e5","attribute_value":"2014-10-30"},"publish_date":"2014-10-30","publish_status":"0","recid":"18535","relation_version_is_last":true,"title":["Statistical mechanics of protein allostery: Roles of backbone and side-chain structural fluctuations"],"weko_creator_id":"1","weko_shared_id":null},"updated":"2021-03-01T16:38:05.475908+00:00"}