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Literature DB >> 19699798

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

Andrew C Stelzer¹, Aaron T Frank, Maximillian H Bailor, Ioan Andricioaei, Hashim M Al-Hashimi.

Abstract

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 (13)C/(15)N isotopically enriched elongated RNA samples. The structural ensembles generated in this manner provide insights into RNA dynamics and its role in functionally important transitions.

Entities: Chemical

Mesh：

Substances：

Year: 2009 PMID： 19699798 PMCID： PMC3320149 DOI： 10.1016/j.ymeth.2009.08.006

Source DB: PubMed Journal: Methods ISSN： 1046-2023 Impact factor: 3.608

63 in total

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Journal: J Mol Biol Date: 2001-10-12 Impact factor: 5.469

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Authors: Homayoun Valafar; James H Prestegard
Journal: J Magn Reson Date: 2004-04 Impact factor: 2.229

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Authors: Qi Zhang; Andrew C Stelzer; Charles K Fisher; Hashim M Al-Hashimi
Journal: Nature Date: 2007-12-20 Impact factor: 49.962

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Authors: Qi Zhang; Rachel Throolin; Stephen W Pitt; Alexander Serganov; Hashim M Al-Hashimi
Journal: J Am Chem Soc Date: 2003-09-03 Impact factor: 15.419

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Authors: Hashim M Al-Hashimi; Nils G Walter
Journal: Curr Opin Struct Biol Date: 2008-06-09 Impact factor: 6.809

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Authors: Kathleen B Hall
Journal: Curr Opin Chem Biol Date: 2008-10-26 Impact factor: 8.822

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15 in total

Review 1. Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.

Authors: Maximillian H Bailor; Anthony M Mustoe; Charles L Brooks; Hashim M Al-Hashimi
Journal: Curr Opin Struct Biol Date: 2011-04-14 Impact factor: 6.809

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

Review 1. Recent advances in RNA-protein recognition.

2. A standard reference frame for the description of nucleic acid base-pair geometry.

3. REDCAT: a residual dipolar coupling analysis tool.

4. Visualizing spatially correlated dynamics that directs RNA conformational transitions.

5. Probing motions between equivalent RNA domains using magnetic field induced residual dipolar couplings: accounting for correlations between motions and alignment.

6. RNA dynamics: it is about time.

7. Synthesis of small RNAs using T7 RNA polymerase.

8. Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution.

Review 9. RNA in motion.

10. Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions.

Review 1. Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.

2. Information content of long-range NMR data for the characterization of conformational heterogeneity.

3. Natural-abundance ¹⁷O NMR spectroscopy of magnetically aligned lipid nanodiscs.

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