ログイン
言語:

WEKO3

  • トップ
  • ランキング
To
lat lon distance
To

Field does not validate



インデックスリンク

インデックスツリー

メールアドレスを入力してください。

WEKO

One fine body…

WEKO

One fine body…

アイテム

{"_buckets": {"deposit": "ed57b0e0-7655-444d-8a03-da56e36b5a39"}, "_deposit": {"id": "26927", "owners": [], "pid": {"revision_id": 0, "type": "depid", "value": "26927"}, "status": "published"}, "_oai": {"id": "oai:nagoya.repo.nii.ac.jp:00026927", "sets": ["696"]}, "author_link": ["88227", "88228"], "item_10_biblio_info_6": {"attribute_name": "書誌情報", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2015-12-21", "bibliographicIssueDateType": "Issued"}, "bibliographicIssueNumber": "23", "bibliographicPageStart": "235101", "bibliographicVolumeNumber": "143", "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": "We applied a newly proposed prediction method for membrane protein structures to bacteriorhodopsin that has distorted transmembrane helices in the native structure. This method uses an implicit membrane model, which restricts sampling space during folding in a membrane region, and includes helix bending. Replica-exchange simulations were performed with seven transmembrane helices only without a retinal molecule. Obtained structures were classified into clusters of similar structures, which correspond to local-minimum free energy states. The two lowest free energy states corresponded to a native-like structure with the correct empty space for retinal and a structure with this empty space filled with a helix. Previous experiments of bacteriorhodopsin suggested that association of transmembrane helices enables them to make a room for insertion of a retinal. Our results are consistent with these results. Moreover, distortions of helices in the native-like structures were successfully reproduced. In the distortions, whereas the locations of kinks for all helices were similar to those of Protein Data Bank’s data, the amount of bends was more similar for helices away from the retinal than for those close to the retinal in the native structure. This suggests a hypothesis that the amino-acid sequence specifies the location of kinks in transmembrane helices and that the amount of distortions depends on the interactions with the surrounding molecules such as neighboring helices, lipids, and retinal.", "subitem_description_language": "en", "subitem_description_type": "Abstract"}]}, "item_10_publisher_32": {"attribute_name": "出版者", "attribute_value_mlt": [{"subitem_publisher": "AIP Publishing", "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/10.1063/1.4935964", "subitem_relation_type_select": "DOI"}}]}, "item_10_rights_12": {"attribute_name": "権利", "attribute_value_mlt": [{"subitem_rights": "Copyright 2015 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.143, n.23, 2015, p.235101) and may be found at (http://dx.doi.org/10.1063/1.4935964).", "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_61": {"attribute_name": "ISSN(print)", "attribute_value_mlt": [{"subitem_source_identifier": "0021-9606", "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_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": "Urano, Ryo", "creatorNameLang": "en"}], "nameIdentifiers": [{"nameIdentifier": "88227", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Okamoto, Yuko", "creatorNameLang": "en"}], "nameIdentifiers": [{"nameIdentifier": "88228", "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": "2018-12-21"}], "displaytype": "detail", "download_preview_message": "", "file_order": 0, "filename": "1_4935964.pdf", "filesize": [{"value": "6.5 MB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_note", "mimetype": "application/pdf", "size": 6500000.0, "url": {"label": "1_4935964", "objectType": "fulltext", "url": "https://nagoya.repo.nii.ac.jp/record/26927/files/1_4935964.pdf"}, "version_id": "12720a6c-88bb-40d3-b92c-b6240f2b59e9"}]}, "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": "Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin", "item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin", "subitem_title_language": "en"}]}, "item_type_id": "10", "owner": "1", "path": ["696"], "permalink_uri": "http://hdl.handle.net/2237/00029130", "pubdate": {"attribute_name": "PubDate", "attribute_value": "2018-12-21"}, "publish_date": "2018-12-21", "publish_status": "0", "recid": "26927", "relation": {}, "relation_version_is_last": true, "title": ["Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin"], "weko_shared_id": -1}
  1. B100 理学部/理学研究科
  2. B100a 雑誌掲載論文
  3. 学術雑誌

Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin

http://hdl.handle.net/2237/00029130
http://hdl.handle.net/2237/00029130
004417f6-be76-4b89-9fe9-577f6b30dcc1
名前 / ファイル ライセンス アクション
1_4935964.pdf 1_4935964 (6.5 MB)
Item type 学術雑誌論文 / Journal Article(1)
公開日 2018-12-21
タイトル
タイトル Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin
言語 en
著者 Urano, Ryo

× Urano, Ryo

WEKO 88227

en Urano, Ryo

Search repository
Okamoto, Yuko

× Okamoto, Yuko

WEKO 88228

en Okamoto, Yuko

Search repository
アクセス権
アクセス権 open access
アクセス権URI http://purl.org/coar/access_right/c_abf2
権利
言語 en
権利情報 Copyright 2015 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.143, n.23, 2015, p.235101) and may be found at (http://dx.doi.org/10.1063/1.4935964).
抄録
内容記述 We applied a newly proposed prediction method for membrane protein structures to bacteriorhodopsin that has distorted transmembrane helices in the native structure. This method uses an implicit membrane model, which restricts sampling space during folding in a membrane region, and includes helix bending. Replica-exchange simulations were performed with seven transmembrane helices only without a retinal molecule. Obtained structures were classified into clusters of similar structures, which correspond to local-minimum free energy states. The two lowest free energy states corresponded to a native-like structure with the correct empty space for retinal and a structure with this empty space filled with a helix. Previous experiments of bacteriorhodopsin suggested that association of transmembrane helices enables them to make a room for insertion of a retinal. Our results are consistent with these results. Moreover, distortions of helices in the native-like structures were successfully reproduced. In the distortions, whereas the locations of kinks for all helices were similar to those of Protein Data Bank’s data, the amount of bends was more similar for helices away from the retinal than for those close to the retinal in the native structure. This suggests a hypothesis that the amino-acid sequence specifies the location of kinks in transmembrane helices and that the amount of distortions depends on the interactions with the surrounding molecules such as neighboring helices, lipids, and retinal.
言語 en
内容記述タイプ Abstract
出版者
言語 en
出版者 AIP Publishing
言語
言語 eng
資源タイプ
資源タイプresource http://purl.org/coar/resource_type/c_6501
タイプ journal article
出版タイプ
出版タイプ VoR
出版タイプResource http://purl.org/coar/version/c_970fb48d4fbd8a85
DOI
関連タイプ isVersionOf
識別子タイプ DOI
関連識別子 https://doi.org/10.1063/1.4935964
ISSN(print)
収録物識別子タイプ PISSN
収録物識別子 0021-9606
書誌情報 en : The Journal of Chemical Physics

巻 143, 号 23, p. 235101, 発行日 2015-12-21
著者版フラグ
値 publisher
戻る
0
views
See details
Views

Versions

Ver.1 2021-03-01 10:48:47.154567
Show All versions

Share

Mendeley Twitter Facebook Print Addthis

Cite as

エクスポート

OAI-PMH
  • OAI-PMH JPCOAR
  • OAI-PMH DublinCore
  • OAI-PMH DDI
Other Formats
  • JSON
  • BIBTEX

Confirm


Powered by WEKO3


Powered by WEKO3