{"created":"2023-07-27T06:58:58.216624+00:00","id":58067,"links":{},"metadata":{"_buckets":{"deposit":"829565e2-d752-4074-88bb-6a241e2a0d1a"},"_deposit":{"created_by":18,"id":"58067","owners":[18],"pid":{"revision_id":0,"type":"depid","value":"58067"},"status":"published"},"_oai":{"id":"oai:kanazawa-u.repo.nii.ac.jp:00058067","sets":["4161:3020:3021"]},"author_link":["101342","84158","84157","87401","101343"],"item_4_biblio_info_8":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicIssueDates":{"bibliographicIssueDate":"2021-11-02","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"21","bibliographicPageEnd":"4797","bibliographicPageStart":"4786","bibliographicVolumeNumber":"120","bibliographic_titles":[{"bibliographic_title":"Biophysical Journal"}]}]},"item_4_creator_33":{"attribute_name":"著者別表示","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"炭竈, 享司"}],"nameIdentifiers":[{},{}]}]},"item_4_description_21":{"attribute_name":"抄録","attribute_value_mlt":[{"subitem_description":"Spontaneous unidirectional, or vectorial, insertion of transmembrane peptides is a fundamental biophysical process for toxin and viral actions. Polytheonamide B (pTB) is a potent cytotoxic peptide with a β6.3-helical structure. Previous experimental studies revealed that the pTB inserts into the membrane in a vectorial fashion and forms a channel with its single molecular length long enough to span the membrane. Also, molecular dynamics simulation studies demonstrated that the pTB is prefolded in aqueous solution. These are unique features of pTB because most of the peptide toxins form channels through oligomerization of transmembrane helices. Here, we performed all-atom molecular dynamics simulations to examine the dynamic mechanism of the vectorial insertion of pTB, providing underlying elementary processes of the membrane insertion of a prefolded single transmembrane peptide. We find that the insertion of pTB proceeds with only the local lateral compression of the membrane in three successive phases: “landing,” “penetration,” and “equilibration” phases. The free energy calculations using the replica-exchange umbrella sampling simulations present an energy cost of 4.3 kcal/mol at the membrane surface for the membrane insertion of pTB from bulk water. The trajectories of membrane insertion revealed that the insertion process can occur in two possible pathways, namely “trapped” and “untrapped” insertions; in some cases, pTB is trapped in the upper leaflet during the penetration phase. Our simulations demonstrated the importance of membrane anchoring by the hydrophobic N-terminal blocking group in the landing phase, leading to subsequent vectorial insertion.","subitem_description_type":"Abstract"}]},"item_4_description_22":{"attribute_name":"内容記述","attribute_value_mlt":[{"subitem_description":"Embargo Period 12 months","subitem_description_type":"Other"}]},"item_4_description_5":{"attribute_name":"提供者所属","attribute_value_mlt":[{"subitem_description":"金沢大学ナノ生命科学研究所","subitem_description_type":"Other"}]},"item_4_identifier_registration":{"attribute_name":"ID登録","attribute_value_mlt":[{"subitem_identifier_reg_text":"10.24517/00064337","subitem_identifier_reg_type":"JaLC"}]},"item_4_publisher_17":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":" Biophysical Society / Elsevier"}]},"item_4_relation_12":{"attribute_name":"DOI","attribute_value_mlt":[{"subitem_relation_type":"isVersionOf","subitem_relation_type_id":{"subitem_relation_type_id_text":"10.1016/j.bpj.2021.09.028","subitem_relation_type_select":"DOI"}}]},"item_4_relation_28":{"attribute_name":"関連URI","attribute_value_mlt":[{"subitem_relation_name":[{"subitem_relation_name_text":"http://www.elsevier.com/locate/issn/00063495"}],"subitem_relation_type_id":{"subitem_relation_type_id_text":"http://www.elsevier.com/locate/issn/","subitem_relation_type_select":"URI"}},{"subitem_relation_name":[{"subitem_relation_name_text":"http://www.cell.com/biophysj/"}],"subitem_relation_type_id":{"subitem_relation_type_id_text":"http://www.cell.com/biophysj/","subitem_relation_type_select":"URI"}},{"subitem_relation_name":[{"subitem_relation_name_text":"https://www.sciencedirect.com/science/article/abs/pii/S0006349521007906?via%3Dihub"}],"subitem_relation_type_id":{"subitem_relation_type_id_text":"https://www.sciencedirect.com/science/article/abs/pii/S0006349521007906?via%3Dihub","subitem_relation_type_select":"URI"}}]},"item_4_rights_23":{"attribute_name":"権利","attribute_value_mlt":[{"subitem_rights":"Copyright © 2021 Biophysical Society."}]},"item_4_source_id_11":{"attribute_name":"NCID","attribute_value_mlt":[{"subitem_source_identifier":"AA00566095","subitem_source_identifier_type":"NCID"}]},"item_4_source_id_9":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"0006-3495","subitem_source_identifier_type":"ISSN"},{"subitem_source_identifier":"1542-0086","subitem_source_identifier_type":"ISSN"}]},"item_4_version_type_25":{"attribute_name":"著者版フラグ","attribute_value_mlt":[{"subitem_version_resource":"http://purl.org/coar/version/c_ab4af688f83e57aa","subitem_version_type":"AM"}]},"item_creator":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Kalathinga, Mahroof"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Sumikama, Takashi"}],"nameIdentifiers":[{},{}]},{"creatorNames":[{"creatorName":"Oiki, Shigetoshi"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Saito, Shinji"}],"nameIdentifiers":[{}]}]},"item_files":{"attribute_name":"ファイル情報","attribute_type":"file","attribute_value_mlt":[{"accessrole":"open_date","date":[{"dateType":"Available","dateValue":"2022-11-03"}],"displaytype":"detail","filename":"NA-PR-SUMIKAMA-T-4786.pdf","filesize":[{"value":"1.3 MB"}],"format":"application/pdf","licensetype":"license_11","mimetype":"application/pdf","url":{"label":"NA-PR-SUMIKAMA-T-4786.pdf","url":"https://kanazawa-u.repo.nii.ac.jp/record/58067/files/NA-PR-SUMIKAMA-T-4786.pdf"},"version_id":"57b1c238-3f23-46d0-916a-94bc0fc92dca"}]},"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":"Vectorial insertion of a β-helical peptide into membrane: a theoretical study on polytheonamide B","item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"Vectorial insertion of a β-helical peptide into membrane: a theoretical study on polytheonamide B"}]},"item_type_id":"4","owner":"18","path":["3021"],"pubdate":{"attribute_name":"公開日","attribute_value":"2021-11-04"},"publish_date":"2021-11-04","publish_status":"0","recid":"58067","relation_version_is_last":true,"title":["Vectorial insertion of a β-helical peptide into membrane: a theoretical study on polytheonamide B"],"weko_creator_id":"18","weko_shared_id":-1},"updated":"2023-07-27T10:16:32.219188+00:00"}