FMO calculations for zinc metalloprotease:Fragmentation of amino-acid residues coordinated to zinc ion

IF 0.4 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Kyohei Imai, Daichi Takimoto, Ryosuke Saito, C. Watanabe, Kaori Fukuzawa, Kurita Noriyuki
{"title":"FMO calculations for zinc metalloprotease:Fragmentation of amino-acid residues coordinated to zinc ion","authors":"Kyohei Imai, Daichi Takimoto, Ryosuke Saito, C. Watanabe, Kaori Fukuzawa, Kurita Noriyuki","doi":"10.1273/cbij.22.21","DOIUrl":null,"url":null,"abstract":"We investigated electronic states of a complex of zinc metalloprotease ubiquitin ligase 2 (UBR2) with its peptide ligand using ab initio fragment molecular orbital (FMO) calculations. UBR2 possesses three Zn ions and several residues of UBR2 are coordinated to each Zn ion to form an active site of UBR2. To provide a precise description of these coordination bonds, we included these residues in the same fragment as Zn ion in FMO calculations. The results revealed that all coordinated residues should be included in the same fragment as Zn ion for obtaining the converged results. This fact can be applicable equally to metalloproteases including other metal ions.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.4000,"publicationDate":"2022-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Chem-Bio Informatics Journal","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1273/cbij.22.21","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

We investigated electronic states of a complex of zinc metalloprotease ubiquitin ligase 2 (UBR2) with its peptide ligand using ab initio fragment molecular orbital (FMO) calculations. UBR2 possesses three Zn ions and several residues of UBR2 are coordinated to each Zn ion to form an active site of UBR2. To provide a precise description of these coordination bonds, we included these residues in the same fragment as Zn ion in FMO calculations. The results revealed that all coordinated residues should be included in the same fragment as Zn ion for obtaining the converged results. This fact can be applicable equally to metalloproteases including other metal ions.
锌金属蛋白酶的FMO计算:与锌离子协调的氨基酸残基的碎片化
我们利用从头算片段分子轨道(FMO)方法研究了锌金属蛋白酶泛素连接酶2 (UBR2)及其肽配体复合物的电子态。UBR2具有三个Zn离子,并且UBR2的几个残基与每个Zn离子配合形成UBR2的一个活性位点。为了提供这些配位键的精确描述,我们在FMO计算中将这些残基与Zn离子包含在同一片段中。结果表明,为了得到收敛的结果,所有配位残基必须包含在与Zn离子相同的片段中。这一事实同样适用于包括其他金属离子在内的金属蛋白酶。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Chem-Bio Informatics Journal
Chem-Bio Informatics Journal BIOCHEMISTRY & MOLECULAR BIOLOGY-
CiteScore
0.60
自引率
0.00%
发文量
8
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信