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

页码：167 / 173

页数：7

共 5 条

[1] Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition
Frank, Aaron T.
Stelzer, Andrew C.
Al-Hashimi, Hashim M.
Andricioaei, Ioan
NUCLEIC ACIDS RESEARCH, 2009, 37 (11) : 3670 - 3679
[2] A General Method for Constructing Atomic-Resolution RNA Ensembles using NMR Residual Dipolar Couplings: The Basis for Interhelical Motions Revealed
Salmon, Loic
Bascom, Gavin
Andricioaei, Ioan
Al-Hashimi, Hashim M.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2013, 135 (14) : 5457 - 5466
[3] Atomic-Resolution Structural Dynamics in Crystalline Proteins from NMR and Molecular Simulation
Mollica, Luca
Baias, Maria
Lewandowski, Jozef R.
Wylie, Benjamin J.
Sperling, Lindsay J.
Rienstra, Chad M.
Emsley, Lyndon
Blackledge, Martin
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2012, 3 (23): : 3657 - 3662
[4] Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings
Salmon, Loic
Giambasu, George M.
Nikolova, Evgenia N.
Petzold, Katja
Bhattacharya, Akash
Case, David A.
Al-Hashimi, Hashim M.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2015, 137 (40) : 12954 - 12965
[5] Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy
Bothe, Jameson R.
Nikolova, Evgenia N.
Eichhorn, Catherine D.
Chugh, Jeetender
Hansen, Alexandar L.
Al-Hashimi, Hashim M.
NATURE METHODS, 2011, 8 (11) : 919 - 931

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