{"created":"2023-08-02T03:58:06.919867+00:00","id":7265,"links":{},"metadata":{"_buckets":{"deposit":"01584361-bd6a-4406-ad73-a585403fe0dc"},"_deposit":{"created_by":10,"id":"7265","owners":[10],"pid":{"revision_id":0,"type":"depid","value":"7265"},"status":"published"},"_oai":{"id":"oai:repository.lib.tottori-u.ac.jp:00007265","sets":["1:9","2:12"]},"author_link":["4875","26958","96"],"item_10001_biblio_info_7":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicIssueDates":{"bibliographicIssueDate":"2014-06","bibliographicIssueDateType":"Issued"},"bibliographicPageEnd":"167","bibliographicPageStart":"158","bibliographicVolumeNumber":"51","bibliographic_titles":[{"bibliographic_title":"Journal of molecular graphics and modelling"},{"bibliographic_title":"Journal of molecular graphics and modelling","bibliographic_titleLang":"en"}]}]},"item_10001_description_5":{"attribute_name":"抄録","attribute_value_mlt":[{"subitem_description":"The modified nucleotide base 7,8-dihydro-8-oxo-guanine (8-oxo-G) is one of the major sources of spontaneous mutagenesis. Nucleotide-sanitizing enzymes, such as the MutT homolog-1 (MTH1) and nudix-type motif 5 (NUDT5), selectively remove 8-oxo-G from the cellular pool of nucleotides. Previous studies showed that, although the syn conformation generally predominates in purine nucleotides with a bulky substituent at the 8-position, 8-oxo-dGMP binds to both MTH1 and NUDT5 in the anti conformation. This study was initiated to investigate the possibility that 8-oxo-dGMP itself may adopt the anti conformation. Molecular dynamics simulations of mononucleotides (dGMP, 8-oxo-dGMP) in aqueous solution were performed. 8-oxo-dGMP adopted the anti conformation as well as the syn conformation, and the proportion of adopting the anti conformation increased in the presence of metal ions. When 8-oxo-dGMP was in the anti conformation, a metal ion was located between the oxygen atom of phosphate and the oxygen atom at the 8-position of 8-oxo-G. The types of stable anti conformations of 8-oxo-dGMP differed, depending on the ionic radii and charges of coexisting ions. These data suggested a role for metal ions, other than as cofactors for the hydrolysis of the di- and tri-phosphate forms of mononucleotides; that the metal ions help retain the anti conformation of the N-glycosidic torsion angle of 8-oxo-dGMP to promote the binding between the 8-oxo-G deoxynucleotide and the nucleotide-sanitizing enzymes.","subitem_description_type":"Other"}]},"item_10001_publisher_8":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"Elsevier Inc."}]},"item_10001_relation_14":{"attribute_name":"DOI","attribute_value_mlt":[{"subitem_relation_type":"isVersionOf","subitem_relation_type_id":{"subitem_relation_type_id_text":"10.1016/j.jmgm.2014.05.007","subitem_relation_type_select":"DOI"}}]},"item_10001_relation_16":{"attribute_name":"情報源","attribute_value_mlt":[{"subitem_relation_name":[{"subitem_relation_name_text":"Shin-ichi Fujiwara, Kenichiro Sawada, Takashi Amisaki.. Molecular dynamics study on conformational differences between dGMP and 8-oxo-dGMP: Effects of metal ions. Journal of molecular graphics and modelling. 2014, 51, 158-167"}]}]},"item_10001_relation_17":{"attribute_name":"関連サイト","attribute_value_mlt":[{"subitem_relation_name":[{"subitem_relation_name_text":"https://www.sciencedirect.com/science/article/pii/S1093326314000801"}],"subitem_relation_type_id":{"subitem_relation_type_id_text":"https://www.sciencedirect.com/science/article/pii/S1093326314000801","subitem_relation_type_select":"URI"}}]},"item_10001_rights_15":{"attribute_name":"権利","attribute_value_mlt":[{"subitem_rights":"Copyright © 2014 Elsevier Inc. All rights reserved. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/"}]},"item_10001_source_id_11":{"attribute_name":"書誌レコードID","attribute_value_mlt":[{"subitem_source_identifier":"AA11533349","subitem_source_identifier_type":"NCID"}]},"item_10001_source_id_9":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"10933263","subitem_source_identifier_type":"ISSN"}]},"item_10001_text_33":{"attribute_name":"著者所属（英）","attribute_value_mlt":[{"subitem_text_language":"en","subitem_text_value":"Department of Biological Regulation, Faculty of Medicine, Tottori University"},{"subitem_text_language":"en","subitem_text_value":"Department of Biological Regulation, Faculty of Medicine, Tottori University"},{"subitem_text_language":"en","subitem_text_value":"Department of Biological Regulation, Faculty of Medicine, Tottori University"}]},"item_10001_version_type_20":{"attribute_name":"著者版フラグ","attribute_value_mlt":[{"subitem_version_type":"AM"}]},"item_creator":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Fujiwara, Shin-ichi","creatorNameLang":"en"}],"nameIdentifiers":[{},{},{}]},{"creatorNames":[{"creatorName":"Sawada, Kenichiro","creatorNameLang":"en"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Amisaki, Takashi","creatorNameLang":"en"}],"nameIdentifiers":[{},{},{}]}]},"item_files":{"attribute_name":"ファイル情報","attribute_type":"file","attribute_value_mlt":[{"accessrole":"open_date","date":[{"dateType":"Available","dateValue":"2023-03-17"}],"displaytype":"detail","filename":"jmgm51_158.pdf","filesize":[{"value":"542.0 kB"}],"format":"application/pdf","licensefree":"Copyright © 2014 Elsevier Inc. All rights reserved. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/","licensetype":"license_note","mimetype":"application/pdf","url":{"label":"jmgm51_158.pdf","url":"https://repository.lib.tottori-u.ac.jp/record/7265/files/jmgm51_158.pdf"},"version_id":"0ad8a260-6435-458c-bfdc-8010a14896d1"}]},"item_keyword":{"attribute_name":"キーワード","attribute_value_mlt":[{"subitem_subject":"Mononucleotide","subitem_subject_scheme":"Other"},{"subitem_subject":"Molecular dynamics simulations","subitem_subject_scheme":"Other"},{"subitem_subject":"8-oxo-dGTP","subitem_subject_scheme":"Other"},{"subitem_subject":"Divalent ion","subitem_subject_scheme":"Other"},{"subitem_subject":"Nucleotide-sanitizing enzyme","subitem_subject_scheme":"Other"},{"subitem_subject":"Conformation","subitem_subject_scheme":"Other"},{"subitem_subject":"Mononucleotide","subitem_subject_language":"en","subitem_subject_scheme":"Other"},{"subitem_subject":"Molecular dynamics simulations","subitem_subject_language":"en","subitem_subject_scheme":"Other"},{"subitem_subject":"8-oxo-dGTP","subitem_subject_language":"en","subitem_subject_scheme":"Other"},{"subitem_subject":"Divalent ion","subitem_subject_language":"en","subitem_subject_scheme":"Other"},{"subitem_subject":"Nucleotide-sanitizing enzyme","subitem_subject_language":"en","subitem_subject_scheme":"Other"},{"subitem_subject":"Conformation","subitem_subject_language":"en","subitem_subject_scheme":"Other"}]},"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"}]},"item_title":"Molecular dynamics study on conformational differences between dGMP and 8-oxo-dGMP: Effects of metal ions","item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"Molecular dynamics study on conformational differences between dGMP and 8-oxo-dGMP: Effects of metal ions","subitem_title_language":"en"}]},"item_type_id":"10001","owner":"10","path":["12","9"],"pubdate":{"attribute_name":"PubDate","attribute_value":"2019-09-19"},"publish_date":"2019-09-19","publish_status":"0","recid":"7265","relation_version_is_last":true,"title":["Molecular dynamics study on conformational differences between dGMP and 8-oxo-dGMP: Effects of metal ions"],"weko_creator_id":"10","weko_shared_id":-1},"updated":"2023-09-29T00:42:33.556712+00:00"}