{"created":"2023-07-27T06:54:17.620941+00:00","id":49555,"links":{},"metadata":{"_buckets":{"deposit":"de4e659d-0959-4018-9450-50f3728c059b"},"_deposit":{"created_by":3,"id":"49555","owners":[3],"pid":{"revision_id":0,"type":"depid","value":"49555"},"status":"published"},"_oai":{"id":"oai:kanazawa-u.repo.nii.ac.jp:00049555","sets":["934:941:943:3790"]},"author_link":["89092","9908","2594","18827","62401","89089","2595"],"item_7_biblio_info_8":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicIssueDates":{"bibliographicIssueDate":"2019","bibliographicIssueDateType":"Issued"},"bibliographicPageEnd":"28","bibliographicPageStart":"15","bibliographicVolumeNumber":"63","bibliographic_titles":[{"bibliographic_title":"The Science Reports of Kanazawa University"},{"bibliographic_title":"The Science Reports of Kanazawa University","bibliographic_titleLang":"en"}]}]},"item_7_creator_34":{"attribute_name":"著者別表示","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"川口, 一朋"}],"nameIdentifiers":[{},{},{}]},{"creatorNames":[{"creatorName":"長尾, 秀実"}],"nameIdentifiers":[{},{}]}]},"item_7_description_21":{"attribute_name":"抄録","attribute_value_mlt":[{"subitem_description":"We investigate the binding/dissociation process of ligand molecule from carbonic\nanhydrase (CA) I carbonic anhydrase (CA) I enzyme by using all-atom molecular\ndynamics simulation. The force field parameters of zinc ion in the CA I active site are estimated\nby quantum chemical calculations and are summarized in this paper. The free energy\nprofile for binding/dissociation process of ligand from CA I active site is calculated by the\nthermodynamic integration combined with the all-atom molecular dynamics simulation. The\nbinding free energy as a function of the distance between the center of mass positions of CA\nI active site and the ligand molecule is estimated. The radial distribution function of the\nCA I-ligand complex is calculated from the trajectory of all-atom molecular dynamics (MD)\nsimulation. We estimate the free energy surface from the radial distribution function. We\ncan obtain the bond constant of the equilibrium state from the value of the free energy surface.\nWe discuss the binding/dissociation process of ligand molecule by calculating the free\nenergy profile to know the stability of the CA I-ligand complex with some thermodynamic\nproperties such as the binding free energy, the equilibrium state of the free energy surface\nand so on.","subitem_description_type":"Abstract"}]},"item_7_identifier_registration":{"attribute_name":"ID登録","attribute_value_mlt":[{"subitem_identifier_reg_text":"10.24517/00055867","subitem_identifier_reg_type":"JaLC"}]},"item_7_publisher_17":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"Institute of Science and Engineering, Kanazawa University"}]},"item_7_relation_28":{"attribute_name":"関連URI","attribute_value_mlt":[{"subitem_relation_name":[{"subitem_relation_name_text":"http://scirep.w3.kanazawa-u.ac.jp/"}],"subitem_relation_type_id":{"subitem_relation_type_id_text":"http://scirep.w3.kanazawa-u.ac.jp/","subitem_relation_type_select":"URI"}}]},"item_7_source_id_9":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"2433-040X","subitem_source_identifier_type":"ISSN"}]},"item_7_version_type_25":{"attribute_name":"著者版フラグ","attribute_value_mlt":[{"subitem_version_resource":"http://purl.org/coar/version/c_970fb48d4fbd8a85","subitem_version_type":"VoR"}]},"item_creator":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Arwansyah, MS"}],"nameIdentifiers":[{"nameIdentifier":"89089","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Kodama, Koichi"}],"nameIdentifiers":[{"nameIdentifier":"62401","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Kurniawan, Isman"}],"nameIdentifiers":[{"nameIdentifier":"18827","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Kataoka, Tatsuki"}],"nameIdentifiers":[{"nameIdentifier":"89092","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Kawaguchi, Kazutomo"}],"nameIdentifiers":[{"nameIdentifier":"2595","nameIdentifierScheme":"WEKO"},{"nameIdentifier":"90402429","nameIdentifierScheme":"e-Rad","nameIdentifierURI":"https://kaken.nii.ac.jp/ja/search/?qm=90402429"},{"nameIdentifier":"90402429","nameIdentifierScheme":"研究者番号","nameIdentifierURI":"https://nrid.nii.ac.jp/nrid/1000090402429"}]},{"creatorNames":[{"creatorName":"Nagao, Hidemi"}],"nameIdentifiers":[{"nameIdentifier":"9908","nameIdentifierScheme":"WEKO"},{"nameIdentifier":"30291892","nameIdentifierScheme":"e-Rad","nameIdentifierURI":"https://kaken.nii.ac.jp/ja/search/?qm=30291892"},{"nameIdentifier":"30291892","nameIdentifierScheme":"金沢大学研究者情報","nameIdentifierURI":"http://ridb.kanazawa-u.ac.jp/public/detail.php?kaken=30291892"},{"nameIdentifier":"30291892","nameIdentifierScheme":"研究者番号","nameIdentifierURI":"https://nrid.nii.ac.jp/nrid/1000030291892"}]}]},"item_files":{"attribute_name":"ファイル情報","attribute_type":"file","attribute_value_mlt":[{"accessrole":"open_date","date":[{"dateType":"Available","dateValue":"2019-10-21"}],"displaytype":"detail","filename":"Sci_Rep63-002.pdf","filesize":[{"value":"1.9 MB"}],"format":"application/pdf","licensetype":"license_11","mimetype":"application/pdf","url":{"label":"Sci_Rep63-002.pdf","url":"https://kanazawa-u.repo.nii.ac.jp/record/49555/files/Sci_Rep63-002.pdf"},"version_id":"a7a3a030-c44f-460f-a730-020bbb9af6c1"}]},"item_keyword":{"attribute_name":"キーワード","attribute_value_mlt":[{"subitem_subject":"CA I active site","subitem_subject_language":"en","subitem_subject_scheme":"Other"},{"subitem_subject":"ligand molecule","subitem_subject_language":"en","subitem_subject_scheme":"Other"},{"subitem_subject":"force field parameters","subitem_subject_language":"en","subitem_subject_scheme":"Other"},{"subitem_subject":"free energy profile","subitem_subject_language":"en","subitem_subject_scheme":"Other"},{"subitem_subject":"free energy surface","subitem_subject_language":"en","subitem_subject_scheme":"Other"}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"eng"}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourcetype":"departmental bulletin paper","resourceuri":"http://purl.org/coar/resource_type/c_6501"}]},"item_title":"Molecular dynamics study of free energy profile for dissociation of ligand from CA I active site","item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"Molecular dynamics study of free energy profile for dissociation of ligand from CA I active site"},{"subitem_title":"Molecular dynamics study of free energy profile for dissociation of ligand from CA I active site","subitem_title_language":"en"}]},"item_type_id":"7","owner":"3","path":["3790"],"pubdate":{"attribute_name":"公開日","attribute_value":"2019-10-21"},"publish_date":"2019-10-21","publish_status":"0","recid":"49555","relation_version_is_last":true,"title":["Molecular dynamics study of free energy profile for dissociation of ligand from CA I active site"],"weko_creator_id":"3","weko_shared_id":3},"updated":"2024-03-06T00:49:35.315287+00:00"}