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

IF 0.4 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Chem-Bio Informatics Journal Pub Date : 2022-05-12 DOI:10.1273/cbij.22.21
Kyohei Imai, Daichi Takimoto, Ryosuke Saito, C. Watanabe, Kaori Fukuzawa, Kurita Noriyuki
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引用次数: 0

摘要

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