Protonation-dependent base flipping in the catalytic triad of a small RNA

被引：25
|
作者：
Sun, Zhaoxi [1 ]
Wang, Xiaohui [1 ]
Zhang, John Z. H. [2 ,3 ,4 ]
机构：
[1] East China Normal Univ, Inst Theoret & Computat Sci, State Key Lab Precis Spect, Shanghai 200062, Peoples R China
[2] East China Normal Univ, Coll Chem & Mol Engn, Dept Phys, Shanghai 200062, Peoples R China
[3] NYU Shanghai, NYU ECNU Ctr Computat Chem, Shanghai 200062, Peoples R China
[4] NYU, Dept Chem, New York, NY 10003 USA
来源：
CHEMICAL PHYSICS LETTERS | 2017年 / 684卷
基金：
中国国家自然科学基金;
关键词：
GROUP-II INTRON; MOLECULAR-DYNAMICS SIMULATIONS; INTRAMOLECULAR STEM-LOOP; FREE-ENERGY CALCULATIONS; CRYSTAL-STRUCTURE; DNA; EWALD; WATER;
D O I：
10.1016/j.cplett.2017.07.003
中图分类号：
O64 [物理化学（理论化学）、化学物理学];
学科分类号：
070304 ; 081704 ;
摘要：
Protonation dependent base flipping in RNA has never been studied theoretically. In this work we studied protonation-dependent behavior of the base flipping in the catalytic triad of a single-stranded RNA which was previously characterized by NMR experiment. Molecular dynamics simulation reveals that the GA mismatch in this region accounts for this behavior. Free energy profiles show that the stable point for flipping dihedral shifts about 35 and the free energy barrier along the flipping pathway is elevated upon protonation. The orientation of Guanine from syn to anti conformation is coupled with protonation-dependent base flipping and G-HA(+) base pair is formed under acidic condition. (C) 2017 Elsevier B.V. All rights reserved.
引用
收藏
页码：239 / 244
页数：6
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