{"_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"}, "item_10_biblio_info_6": {"attribute_name": "\u66f8\u8a8c\u60c5\u5831", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2016-11", "bibliographicIssueDateType": "Issued"}, "bibliographicIssueNumber": "10", "bibliographicPageEnd": "2098", "bibliographicPageStart": "2086", "bibliographicVolumeNumber": "111", "bibliographic_titles": [{"bibliographic_title": "Biophysical Journal"}]}]}, "item_10_description_4": {"attribute_name": "\u6284\u9332", "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\u2019s 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_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": "\u51fa\u7248\u8005", "attribute_value_mlt": [{"subitem_publisher": "Elsevier"}]}, "item_10_rights_12": {"attribute_name": "\u6a29\u5229", "attribute_value_mlt": [{"subitem_rights": "\u00a9 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/"}]}, "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": "0006-3495", "subitem_source_identifier_type": "ISSN"}]}, "item_creator": {"attribute_name": "\u8457\u8005", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "Yamada, Tatsuya"}], "nameIdentifiers": [{"nameIdentifier": "69314", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Yamato, Takahisa"}], "nameIdentifiers": [{"nameIdentifier": "69315", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Mitaku, Shigeki"}], "nameIdentifiers": [{"nameIdentifier": "69316", "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": "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_free", "mimetype": "application/pdf", "size": 10200000.0, "url": {"label": "25802_3_merged_1475679896.pdf \u30d5\u30a1\u30a4\u30eb\u516c\u958b\uff1a2017/11/01", "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": "\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": "Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics", "item_titles": {"attribute_name": "\u30bf\u30a4\u30c8\u30eb", "attribute_value_mlt": [{"subitem_title": "Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics"}]}, "item_type_id": "10", "owner": "1", "path": ["336/695/696"], "permalink_uri": "http://hdl.handle.net/2237/25575", "pubdate": {"attribute_name": "\u516c\u958b\u65e5", "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": null}