{"_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"}, "item_10_biblio_info_6": {"attribute_name": "\u66f8\u8a8c\u60c5\u5831", "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"}]}]}, "item_10_description_4": {"attribute_name": "\u6284\u9332", "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 \u03b2^6.3-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 \u03b2^4.4-helix as the lowest-potential-energy structure, and left-handed \u03b2^4.4-helix, right-handed and left-handed \u03b2^6.3-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 \u03b2-sheet-forming tendency throughout almost the entire sequence. In order to examine the stability of the obtained right-handed \u03b2^6.3-helix and \u03b2^4.4-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 \u03b2-helix structures. The results suggested that \u03b2^6.3-helix is more stable than \u03b2^4.4-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 \u03b2^6.3-helix conformation.", "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": "\u51fa\u7248\u8005", "attribute_value_mlt": [{"subitem_publisher": "American Institute of Physics"}]}, "item_10_rights_12": {"attribute_name": "\u6a29\u5229", "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."}]}, "item_10_select_15": {"attribute_name": "\u8457\u8005\u7248\u30d5\u30e9\u30b0", "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": "ISSN"}]}, "item_10_text_14": {"attribute_name": "\u30d5\u30a9\u30fc\u30de\u30c3\u30c8", "attribute_value_mlt": [{"subitem_text_value": "application/pdf"}]}, "item_creator": {"attribute_name": "\u8457\u8005", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "Mori, Takaharu"}], "nameIdentifiers": [{"nameIdentifier": "38770", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Okamoto, Yuko"}], "nameIdentifiers": [{"nameIdentifier": "38771", "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": "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_free", "mimetype": "application/pdf", "size": 375900.0, "url": {"label": "THE_JOURNAL_OF_CHEMICAL_PHYSICS_131_16_165103.pdf", "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": "\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": "Folding simulations of gramicidin A into the\u03b2-helix conformations: Simulated annealing molecular dynamics study", "item_titles": {"attribute_name": "\u30bf\u30a4\u30c8\u30eb", "attribute_value_mlt": [{"subitem_title": "Folding simulations of gramicidin A into the\u03b2-helix conformations: Simulated annealing molecular dynamics study"}]}, "item_type_id": "10", "owner": "1", "path": ["336/695/696"], "permalink_uri": "http://hdl.handle.net/2237/14159", "pubdate": {"attribute_name": "\u516c\u958b\u65e5", "attribute_name_i18n": "\u516c\u958b\u65e5", "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 the\u03b2-helix conformations: Simulated annealing molecular dynamics study"], "weko_shared_id": 3}