{"_buckets": {"deposit": "3782f354-8842-49bd-8582-eb7d355220ec"}, "_deposit": {"id": "12279", "owners": [], "pid": {"revision_id": 0, "type": "depid", "value": "12279"}, "status": "published"}, "_oai": {"id": "oai:nagoya.repo.nii.ac.jp:00012279", "sets": ["696"]}, "author_link": ["38770", "38771"], "item_10_biblio_info_6": {"attribute_name": "書誌情報", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2009-10", "bibliographicIssueDateType": "Issued"}, "bibliographicIssueNumber": "16", "bibliographicPageEnd": "165103", "bibliographicPageStart": "165103", "bibliographicVolumeNumber": "131", "bibliographic_titles": [{"bibliographic_title": "THE JOURNAL OF CHEMICAL PHYSICS", "bibliographic_titleLang": "en"}]}]}, "item_10_description_4": {"attribute_name": "抄録", "attribute_value_mlt": [{"subitem_description": "Gramicidin A is a linear hydrophobic 15-residue peptide which consists of alternating D- and L-amino acids and forms a unique tertiary structure, called the β^6.3-helix, to act as a cation-selective ion channel in the natural conditions. In order to investigate the intrinsic ability of the gramicidin A monomer to form secondary structures, we performed the folding simulation of gramicidin A using a simulated annealing molecular dynamics (MD) method in vacuum mimicking the low-dielectric, homogeneous membrane environment. The initial conformation was a fully extended one. From the 200 different MD runs, we obtained a right-handed β^4.4-helix as the lowest-potential-energy structure, and left-handed β^4.4-helix, right-handed and left-handed β^6.3-helix as local-minimum energy states. These results are in accord with those of the experiments of gramicidin A in homogeneous organic solvent. Our simulations showed a slight right-hand sense in the lower-energy conformations and a quite β-sheet-forming tendency throughout almost the entire sequence. In order to examine the stability of the obtained right-handed β^6.3-helix and β^4.4-helix structures in more realistic membrane environment, we have also performed all-atom MD simulations in explicit water, ion, and lipid molecules, starting from these β-helix structures. The results suggested that β^6.3-helix is more stable than β^4.4-helix in the inhomogeneous, explicit membrane environment, where the pore water and the hydrogen bonds between Trp side-chains and lipid-head groups have a role to further stabilize the β^6.3-helix conformation.", "subitem_description_language": "en", "subitem_description_type": "Abstract"}]}, "item_10_identifier_60": {"attribute_name": "URI", "attribute_value_mlt": [{"subitem_identifier_type": "HDL", "subitem_identifier_uri": "http://hdl.handle.net/2237/14159"}, {"subitem_identifier_type": "DOI", "subitem_identifier_uri": "http://dx.doi.org/10.1063/1.3247578"}]}, "item_10_publisher_32": {"attribute_name": "出版者", "attribute_value_mlt": [{"subitem_publisher": "American Institute of Physics", "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/10.1063/1.3247578", "subitem_relation_type_select": "DOI"}}]}, "item_10_rights_12": {"attribute_name": "権利", "attribute_value_mlt": [{"subitem_rights": "Copyright (2010) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.", "subitem_rights_language": "en"}]}, "item_10_select_15": {"attribute_name": "著者版フラグ", "attribute_value_mlt": [{"subitem_select_item": "publisher"}]}, "item_10_source_id_7": {"attribute_name": "ISSN", "attribute_value_mlt": [{"subitem_source_identifier": "0021-9606", "subitem_source_identifier_type": "PISSN"}]}, "item_10_text_14": {"attribute_name": "フォーマット", "attribute_value_mlt": [{"subitem_text_value": "application/pdf"}]}, "item_1615787544753": {"attribute_name": "出版タイプ", "attribute_value_mlt": [{"subitem_version_resource": "http://purl.org/coar/version/c_970fb48d4fbd8a85", "subitem_version_type": "VoR"}]}, "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": "Mori, Takaharu", "creatorNameLang": "en"}], "nameIdentifiers": [{"nameIdentifier": "38770", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Okamoto, Yuko", "creatorNameLang": "en"}], "nameIdentifiers": [{"nameIdentifier": "38771", "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": "2018-02-20"}], "displaytype": "detail", "download_preview_message": "", "file_order": 0, "filename": "THE_JOURNAL_OF_CHEMICAL_PHYSICS_131_16_165103.pdf", "filesize": [{"value": "375.9 kB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_note", "mimetype": "application/pdf", "size": 375900.0, "url": {"label": "THE_JOURNAL_OF_CHEMICAL_PHYSICS_131_16_165103.pdf", "objectType": "fulltext", "url": "https://nagoya.repo.nii.ac.jp/record/12279/files/THE_JOURNAL_OF_CHEMICAL_PHYSICS_131_16_165103.pdf"}, "version_id": "070b28fa-4dcd-4bf8-a23e-43d6872a186d"}]}, "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": "Folding simulations of gramicidin A into theβ-helix conformations: Simulated annealing molecular dynamics study", "item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "Folding simulations of gramicidin A into theβ-helix conformations: Simulated annealing molecular dynamics study", "subitem_title_language": "en"}]}, "item_type_id": "10", "owner": "1", "path": ["696"], "permalink_uri": "http://hdl.handle.net/2237/14159", "pubdate": {"attribute_name": "PubDate", "attribute_value": "2010-09-16"}, "publish_date": "2010-09-16", "publish_status": "0", "recid": "12279", "relation": {}, "relation_version_is_last": true, "title": ["Folding simulations of gramicidin A into theβ-helix conformations: Simulated annealing molecular dynamics study"], "weko_shared_id": -1}