{"_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": ["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", "download_preview_message": "", "file_order": 0, "filename": "25802_3_merged_1475679896.pdf", "filesize": [{"value": "10.2 MB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_note", "mimetype": "application/pdf", "size": 10200000.0, "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"], "permalink_uri": "http://hdl.handle.net/2237/25575", "pubdate": {"attribute_name": "PubDate", "attribute_value": "2017-02-15"}, "publish_date": "2017-02-15", "publish_status": "0", "recid": "23380", "relation": {}, "relation_version_is_last": true, "title": ["Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics"], "weko_shared_id": -1}