WEKO3
インデックスリンク
アイテム
{"_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": ["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": [{"nameIdentifier": "84158", "nameIdentifierScheme": "WEKO"}, {"nameIdentifier": "30579412", "nameIdentifierScheme": "e-Rad", "nameIdentifierURI": "https://kaken.nii.ac.jp/ja/search/?qm=30579412"}]}]}, "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": [{"nameIdentifier": "101342", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Sumikama, Takashi"}], "nameIdentifiers": [{"nameIdentifier": "84157", "nameIdentifierScheme": "WEKO"}, {"nameIdentifier": "30579412", "nameIdentifierScheme": "e-Rad", "nameIdentifierURI": "https://kaken.nii.ac.jp/ja/search/?qm=30579412"}]}, {"creatorNames": [{"creatorName": "Oiki, Shigetoshi"}], "nameIdentifiers": [{"nameIdentifier": "87401", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Saito, Shinji"}], "nameIdentifiers": [{"nameIdentifier": "101343", "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": "2022-11-03"}], "displaytype": "detail", "download_preview_message": "", "file_order": 0, "filename": "NA-PR-SUMIKAMA-T-4786.pdf", "filesize": [{"value": "1.3 MB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_11", "mimetype": "application/pdf", "size": 1300000.0, "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"], "permalink_uri": "https://doi.org/10.24517/00064337", "pubdate": {"attribute_name": "公開日", "attribute_value": "2021-11-04"}, "publish_date": "2021-11-04", "publish_status": "0", "recid": "58067", "relation": {}, "relation_version_is_last": true, "title": ["Vectorial insertion of a β-helical peptide into membrane: a theoretical study on polytheonamide B"], "weko_shared_id": -1}
Vectorial insertion of a β-helical peptide into membrane: a theoretical study on polytheonamide B
https://doi.org/10.24517/00064337
https://doi.org/10.24517/0006433711ff680f-58c1-4acd-a032-d17ed012d625
名前 / ファイル | ライセンス | アクション |
---|---|---|
NA-PR-SUMIKAMA-T-4786.pdf (1.3 MB)
|
Item type | 学術雑誌論文 / Journal Article(1) | |||||
---|---|---|---|---|---|---|
公開日 | 2021-11-04 | |||||
タイトル | ||||||
タイトル | Vectorial insertion of a β-helical peptide into membrane: a theoretical study on polytheonamide B | |||||
言語 | ||||||
言語 | eng | |||||
資源タイプ | ||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
資源タイプ | journal article | |||||
ID登録 | ||||||
ID登録 | 10.24517/00064337 | |||||
ID登録タイプ | JaLC | |||||
著者 |
Kalathinga, Mahroof
× Kalathinga, Mahroof× Sumikama, Takashi× Oiki, Shigetoshi× Saito, Shinji |
|||||
著者別表示 |
炭竈, 享司
× 炭竈, 享司 |
|||||
提供者所属 | ||||||
内容記述タイプ | Other | |||||
内容記述 | 金沢大学ナノ生命科学研究所 | |||||
書誌情報 |
Biophysical Journal 巻 120, 号 21, p. 4786-4797, 発行日 2021-11-02 |
|||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 0006-3495 | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 1542-0086 | |||||
NCID | ||||||
収録物識別子タイプ | NCID | |||||
収録物識別子 | AA00566095 | |||||
DOI | ||||||
関連タイプ | isVersionOf | |||||
識別子タイプ | DOI | |||||
関連識別子 | 10.1016/j.bpj.2021.09.028 | |||||
出版者 | ||||||
出版者 | Biophysical Society / Elsevier | |||||
抄録 | ||||||
内容記述タイプ | Abstract | |||||
内容記述 | 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. | |||||
内容記述 | ||||||
内容記述タイプ | Other | |||||
内容記述 | Embargo Period 12 months | |||||
権利 | ||||||
権利情報 | Copyright © 2021 Biophysical Society. | |||||
著者版フラグ | ||||||
出版タイプ | AM | |||||
出版タイプResource | http://purl.org/coar/version/c_ab4af688f83e57aa | |||||
関連URI | ||||||
識別子タイプ | URI | |||||
関連識別子 | http://www.elsevier.com/locate/issn/ | |||||
関連名称 | http://www.elsevier.com/locate/issn/00063495 | |||||
関連URI | ||||||
識別子タイプ | URI | |||||
関連識別子 | http://www.cell.com/biophysj/ | |||||
関連名称 | http://www.cell.com/biophysj/ | |||||
関連URI | ||||||
識別子タイプ | URI | |||||
関連識別子 | https://www.sciencedirect.com/science/article/abs/pii/S0006349521007906?via%3Dihub | |||||
関連名称 | https://www.sciencedirect.com/science/article/abs/pii/S0006349521007906?via%3Dihub |