A Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Binary Complex of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase with MgATP
文献类型：期刊论文
| 作者 | Gao, Kaifu1,2; Jia, Ya1,2; Yang, Minghui3 |
| 刊名 | BIOCHEMISTRY
 |
| 出版日期 | 2016-12-13 |
| 卷号 | 55期号:49页码:6931-6939 |
| 英文摘要 | 6-Hydroxymethy1-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the first reaction in the folate biosynthetic pathway. Comparison of its X-ray and nuclear magnetic resonance structures suggests that the enzyme undergoes significant conformational change upon binding to its substrates, especially in three catalytic loops. Experimental research has shown that, in its binary form, even bound by analogues of MgATP, loops 2 and 3 remain rather flexible; this raises questions about the putative large-scale induced-fit conformational change of the HPPK MgATP binary complex. In this work, long-time all-atomic molecular dynamics simulations were conducted to investigate the loop dynamics in this complex. Our simulations show that, with loop 3 closed, multiple conformations of loop 2, including the open, semiopen, and closed forms, are all accessible to the binary complex. These results provide valuable structural insights into the details of conformational changes upon 6-hydroxymethy1-7,8-dihydropterin (HP) binding and biological activities of HPPK. Conformational network analysis and principal component analysis related to the loops are also discussed. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 类目[WOS] | Biochemistry & Molecular Biology |
| 研究领域[WOS] | Biochemistry & Molecular Biology |
| 关键词[WOS] | NORMAL-MODE ANALYSIS ; INDUCED-FIT ; PROTEIN DYNAMICS ; PRINCIPAL COMPONENT ; CRYSTAL-STRUCTURE ; ADENYLATE KINASE ; HPPK APOENZYME ; CHEMICAL STEP ; ENZYME ; SELECTION |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000389866400018 |
| 源URL | [http://ir.wipm.ac.cn/handle/112942/9987]  |
| 专题 | 武汉物理与数学研究所_理论与交叉研究部 |
| 作者单位 | 1.Cent China Normal Univ, Inst Biophys, Wuhan 430079, Peoples R China 2.Cent China Normal Univ, Dept Phys, Wuhan 430079, Peoples R China 3.Chinese Acad Sci, Key Lab Magnet Resonance Biol Syst, State Key Lab Magnet Resonance & Atom & Mol Phys, Wuhan Ctr Magnet Resonance,Wuhan Inst Phys & Math, Wuhan 430071, Peoples R China |
| 推荐引用方式 GB/T 7714 | Gao, Kaifu,Jia, Ya,Yang, Minghui. A Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Binary Complex of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase with MgATP[J]. BIOCHEMISTRY,2016,55(49):6931-6939. |
| APA | Gao, Kaifu,Jia, Ya,&Yang, Minghui.(2016).A Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Binary Complex of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase with MgATP.BIOCHEMISTRY,55(49),6931-6939. |
| MLA | Gao, Kaifu,et al."A Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Binary Complex of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase with MgATP".BIOCHEMISTRY 55.49(2016):6931-6939. |
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来源：武汉物理与数学研究所
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