{"_buckets": {"deposit": "176bf72c-6e69-4762-82dd-aad221cc5696"}, "_deposit": {"id": "26929", "owners": [], "pid": {"revision_id": 0, "type": "depid", "value": "26929"}, "status": "published"}, "_oai": {"id": "oai:nagoya.repo.nii.ac.jp:00026929"}, "item_10_biblio_info_6": {"attribute_name": "\u66f8\u8a8c\u60c5\u5831", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2018-03-28", "bibliographicIssueDateType": "Issued"}, "bibliographicIssueNumber": "12", "bibliographicPageStart": "125102", "bibliographicVolumeNumber": "148", "bibliographic_titles": [{"bibliographic_title": "The Journal of Chemical Physics"}]}]}, "item_10_description_4": {"attribute_name": "\u6284\u9332", "attribute_value_mlt": [{"subitem_description": "We performed protein-ligand docking simulations with a ligand T247, which has been reported as a selective inhibitor of a histone deacetylase HDAC3, by the replica-exchange umbrella sampling method in order to estimate the free energy profiles along ligand docking pathways of HDAC3-T247 and HDAC2-T247 systems. The simulation results showed that the docked state of the HDAC3-T247 system is more stable than that of the HDAC2-T247 system although the amino-acid sequences and structures of HDAC3 and HDAC2 are very similar. By comparing structures obtained from the simulations of both systems, we found the difference between structures of hydrophobic residues at the entrance of the catalytic site. Moreover, we performed conventional molecular dynamics simulations of HDAC3 and HDAC2 systems without T247, and the results also showed the same difference of the hydrophobic structures. Therefore, we consider that this hydrophobic structure contributes to the stabilization of the docked state of the HDAC3-T247 system. Furthermore, we show that Tyr209, which is one of the hydrophobic residues in HDAC2, plays a key role in the instability from the simulation results of a mutated-HDAC2 system.", "subitem_description_type": "Abstract"}]}, "item_10_publisher_32": {"attribute_name": "\u51fa\u7248\u8005", "attribute_value_mlt": [{"subitem_publisher": "AIP Publishing"}]}, "item_10_relation_11": {"attribute_name": "DOI", "attribute_value_mlt": [{"subitem_relation_type_id": {"subitem_relation_type_id_text": "https://doi.org/10.1063/1.5019209", "subitem_relation_type_select": "DOI"}}]}, "item_10_rights_12": {"attribute_name": "\u6a29\u5229", "attribute_value_mlt": [{"subitem_rights": "Copyright 2018 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing.The following article appeared in (The Journal of Chemical Physics. v.148, n.12, 2018, p.125102) and may be found at (http://dx.doi.org/10.1063/1.5019209)."}]}, "item_10_select_15": {"attribute_name": "\u8457\u8005\u7248\u30d5\u30e9\u30b0", "attribute_value_mlt": [{"subitem_select_item": "publisher"}]}, "item_10_source_id_61": {"attribute_name": "ISSN\uff08print\uff09", "attribute_value_mlt": [{"subitem_source_identifier": "0021-9606", "subitem_source_identifier_type": "ISSN"}]}, "item_creator": {"attribute_name": "\u8457\u8005", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "Tsukamoto, Shuichiro"}], "nameIdentifiers": [{"nameIdentifier": "88234", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Sakae, Yoshitake"}], "nameIdentifiers": [{"nameIdentifier": "88235", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Itoh, Yukihiro"}], "nameIdentifiers": [{"nameIdentifier": "88236", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Suzuki, Takayoshi"}], "nameIdentifiers": [{"nameIdentifier": "88237", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Okamoto, Yuko"}], "nameIdentifiers": [{"nameIdentifier": "88238", "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": "2018-12-21"}], "displaytype": "detail", "download_preview_message": "", "file_order": 0, "filename": "1_5019209.pdf", "filesize": [{"value": "2.5 MB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_free", "mimetype": "application/pdf", "size": 2500000.0, "url": {"label": "1_5019209", "url": "https://nagoya.repo.nii.ac.jp/record/26929/files/1_5019209.pdf"}, "version_id": "e8178329-32d6-49f2-921b-738d07ef8658"}]}, "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": "Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations", "item_titles": {"attribute_name": "\u30bf\u30a4\u30c8\u30eb", "attribute_value_mlt": [{"subitem_title": "Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations"}]}, "item_type_id": "10", "owner": "1", "path": ["336/695/696"], "permalink_uri": "http://hdl.handle.net/2237/00029132", "pubdate": {"attribute_name": "\u516c\u958b\u65e5", "attribute_value": "2018-12-21"}, "publish_date": "2018-12-21", "publish_status": "0", "recid": "26929", "relation": {}, "relation_version_is_last": true, "title": ["Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations"], "weko_shared_id": null}