Twister核酶产生的机制性碎片
Mechanistic Debris Generated by Twister Ribozymes.
作者信息
Breaker Ronald R
机构信息
Department of Molecular, Cellular and Developmental Biology, ‡Department of Molecular Biophysics and Biochemistry, §Howard Hughes Medical Institute, Yale University , New Haven, Connecticut 06520, United States.
出版信息
ACS Chem Biol. 2017 Apr 21;12(4):886-891. doi: 10.1021/acschembio.7b00010. Epub 2017 Feb 21.
Abstract
Twister RNAs represent a recently discovered class of natural ribozymes that promote rapid cleaving of RNA backbones. Although an abundance of theoretical, biochemical, and structural data exist for several members of the twister class, disagreements about the architecture and mechanism of its active site have emerged. Historically, such storms regarding mechanistic details typically occur soon after each new self-cleaving ribozyme class is reported, but paths forward exist to quickly reach calmer conditions.
摘要
Twister RNA代表了一类最近发现的天然核酶，可促进RNA主链的快速切割。尽管针对Twister类的几个成员已有大量的理论、生化和结构数据，但关于其活性位点的结构和机制仍存在分歧。从历史上看，每当报道一种新的自我切割核酶类时，关于其机制细节的这类争议通常很快就会出现，但也有办法能迅速达成更稳定的局面。
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本文引用的文献
1
The structure of a nucleolytic ribozyme that employs a catalytic metal ion.一种利用催化金属离子的核酸裂解核酶的结构。
Nat Chem Biol. 2017 May;13(5):508-513. doi: 10.1038/nchembio.2333. Epub 2017 Mar 6.
2
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Wiley Interdiscip Rev RNA. 2017 May;8(3). doi: 10.1002/wrna.1402. Epub 2016 Nov 14.
3
Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage.手枪状核酶采用假结折叠结构，有利于位点特异性的线性切割。
Nat Chem Biol. 2016 Sep;12(9):702-8. doi: 10.1038/nchembio.2125. Epub 2016 Jul 11.
4
Molecular Dynamics Study of Twister Ribozyme: Role of Mg(2+) Ions and the Hydrogen-Bonding Network in the Active Site.扭曲核酶的分子动力学研究：镁离子和活性位点氢键网络的作用
Biochemistry. 2016 Jul 12;55(27):3834-46. doi: 10.1021/acs.biochem.6b00203. Epub 2016 Jun 27.
5
The Novel Chemical Mechanism of the Twister Ribozyme.扭体酶的新化学机制。
J Am Chem Soc. 2016 May 18;138(19):6151-62. doi: 10.1021/jacs.5b11791. Epub 2016 May 6.
6
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7
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8
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