{"created":"2021-03-01T06:31:14.158390+00:00","id":23380,"links":{},"metadata":{"_buckets":{"deposit":"6a5a71ce-d68c-44e1-93e3-c48c71e3426d"},"_deposit":{"id":"23380","owners":[],"pid":{"revision_id":0,"type":"depid","value":"23380"},"status":"published"},"_oai":{"id":"oai:nagoya.repo.nii.ac.jp:00023380","sets":["336:695:696"]},"author_link":["69314","69315","69316"],"item_10_biblio_info_6":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicIssueDates":{"bibliographicIssueDate":"2016-11","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"10","bibliographicPageEnd":"2098","bibliographicPageStart":"2086","bibliographicVolumeNumber":"111","bibliographic_titles":[{"bibliographic_title":"Biophysical Journal","bibliographic_titleLang":"en"}]}]},"item_10_description_4":{"attribute_name":"抄録","attribute_value_mlt":[{"subitem_description":"Developments in atomic force microscopy have opened up a new path toward single-molecular phenomena; in particular, during the process of pulling a membrane protein out of a lipid bilayer. However, the characteristic features of the force-distance (F-D) curve of a bacteriorhodopsin in purple membrane, for instance, have not yet been fully elucidated in terms of physicochemical principles. To address the issue, we performed a computer simulation of bacteriorhodopsin with, to our knowledge, a novel coarse-grained (C-G) model. Peptide planes are represented as rigid spheres, while the surrounding environment consisting of water solvents and lipid bilayers is represented as an implicit continuum. Force-field parameters were determined on the basis of auxiliary simulations and experimental values of transfer free energy of each amino acid from water to membrane. According to Popot’s two-stage model, we separated molecular interactions involving membrane proteins into two parts: I) affinity of each amino acid to the membrane and intrahelical hydrogen bonding between main chain peptide bonds; and II) interhelix interactions. Then, only part I was incorporated into the C-G model because we assumed that the part plays a dominant role in the forced unfolding process. As a result, the C-G simulation has successfully reproduced the key features, including peak positions, of the experimental F-D curves in the literature, indicating that the peak positions are essentially determined by the residue-lipid and intrahelix interactions. Furthermore, we investigated the relationships between the energy barrier formation on the forced unfolding pathways and the force peaks of the F-D curves.","subitem_description_language":"en","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/10.1016/j.bpj.2016.09.051"},{"subitem_identifier_type":"HDL","subitem_identifier_uri":"http://hdl.handle.net/2237/25575"}]},"item_10_publisher_32":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"Elsevier","subitem_publisher_language":"en"}]},"item_10_relation_11":{"attribute_name":"DOI","attribute_value_mlt":[{"subitem_relation_type":"isVersionOf","subitem_relation_type_id":{"subitem_relation_type_id_text":"https://doi.org/10.1016/j.bpj.2016.09.051","subitem_relation_type_select":"DOI"}}]},"item_10_rights_12":{"attribute_name":"権利","attribute_value_mlt":[{"subitem_rights":"© 2016. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/","subitem_rights_language":"en"}]},"item_10_select_15":{"attribute_name":"著者版フラグ","attribute_value_mlt":[{"subitem_select_item":"author"}]},"item_10_source_id_7":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"0006-3495","subitem_source_identifier_type":"PISSN"}]},"item_1615787544753":{"attribute_name":"出版タイプ","attribute_value_mlt":[{"subitem_version_resource":"http://purl.org/coar/version/c_ab4af688f83e57aa","subitem_version_type":"AM"}]},"item_access_right":{"attribute_name":"アクセス権","attribute_value_mlt":[{"subitem_access_right":"open access","subitem_access_right_uri":"http://purl.org/coar/access_right/c_abf2"}]},"item_creator":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Yamada, Tatsuya","creatorNameLang":"en"}],"nameIdentifiers":[{"nameIdentifier":"69314","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Yamato, Takahisa","creatorNameLang":"en"}],"nameIdentifiers":[{"nameIdentifier":"69315","nameIdentifierScheme":"WEKO"}]},{"creatorNames":[{"creatorName":"Mitaku, Shigeki","creatorNameLang":"en"}],"nameIdentifiers":[{"nameIdentifier":"69316","nameIdentifierScheme":"WEKO"}]}]},"item_files":{"attribute_name":"ファイル情報","attribute_type":"file","attribute_value_mlt":[{"accessrole":"open_date","date":[{"dateType":"Available","dateValue":"2017-11-01"}],"displaytype":"detail","filename":"25802_3_merged_1475679896.pdf","filesize":[{"value":"10.2 MB"}],"format":"application/pdf","licensetype":"license_note","mimetype":"application/pdf","url":{"label":"25802_3_merged_1475679896.pdf ファイル公開：2017/11/01","objectType":"fulltext","url":"https://nagoya.repo.nii.ac.jp/record/23380/files/25802_3_merged_1475679896.pdf"},"version_id":"90b9e02a-8283-47ad-b208-91fe1e8d09a0"}]},"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":"journal article","resourceuri":"http://purl.org/coar/resource_type/c_6501"}]},"item_title":"Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics","item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics","subitem_title_language":"en"}]},"item_type_id":"10","owner":"1","path":["696"],"pubdate":{"attribute_name":"PubDate","attribute_value":"2017-02-15"},"publish_date":"2017-02-15","publish_status":"0","recid":"23380","relation_version_is_last":true,"title":["Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics"],"weko_creator_id":"1","weko_shared_id":-1},"updated":"2023-01-16T04:13:01.160908+00:00"}