Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs

被引：20
|
作者：
Stelzer, Andrew C. [2 ,3 ]
Frank, Aaron T. [1 ]
Bailor, Maximillian H. [2 ,3 ]
Andricioaei, Ioan [1 ]
Al-Hashimi, Hashim M. [2 ,3 ]
机构：
[1] Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA
[2] Univ Michigan, Dept Chem, Ann Arbor, MI 48109 USA
[3] Univ Michigan, Dept Biophys, Ann Arbor, MI 48109 USA
来源：
METHODS | 2009年 / 49卷 / 02期
关键词：
RNA dynamics; Adaptive recognition; Collective motions; Non-coding RNA; Movies; RESIDUAL DIPOLAR COUPLINGS; MOLECULAR-DYNAMICS SIMULATIONS; PROTEIN-STRUCTURE; CHEMICAL-SHIFTS; MG2+ BINDING; ALIGNMENT; RELAXATION; FIELD; MACROMOLECULES; BIOMOLECULES;
D O I：
10.1016/j.ymeth.2009.08.006
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
A broad structural landscape often needs to be characterized in order to fully understand how regulatory RNAs perform their biological functions at the atomic level. We present a protocol for visualizing thermally accessible RNA conformations at atomic-resolution and with timescales extending up to milliseconds. The protocol combines molecular dynamics (MD) simulations with experimental residual dipolar couplings (RDCs) measured in partially aligned C-13/N-15 isotopically enriched elongated RNA samples. The structural ensembles generated in this manner provide insights into RNA dynamics and its role in functionally important transitions. Published by Elsevier Inc.
引用
收藏
页码：167 / 173
页数：7
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