Literature DB >> 18957331

RNA in motion.

Kathleen B Hall1.   

Abstract

Although RNA duplex regions are highly structured and inflexible, other elements of an RNA molecule are capable of dynamic motions. These flexible regions are the sites of interactions with small molecules, proteins, and other RNAs, yet there are few descriptions of these regions that include the timescale and amplitude of their motions. No one technique is sufficient to accurately describe these motions, but the combination of in vitro methods, particularly NMR relaxation methods, and more robust in silico methods, is beginning to yield the type of data that can be used to understand RNA function. Very few RNAs have been described by both techniques, and here one such RNA and one RNA:protein complex are reviewed.

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Year:  2008        PMID: 18957331      PMCID: PMC2646008          DOI: 10.1016/j.cbpa.2008.09.033

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.822


  27 in total

1.  The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes.

Authors:  Donghan Lee; Joseph D Walsh; Ping Yu; Michelle A Markus; Theodora Choli-Papadopoulou; Charles D Schwieters; Susan Krueger; David E Draper; Yun-Xing Wang
Journal:  J Mol Biol       Date:  2007-01-10       Impact factor: 5.469

2.  Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

Authors:  Alberto Pérez; Iván Marchán; Daniel Svozil; Jiri Sponer; Thomas E Cheatham; Charles A Laughton; Modesto Orozco
Journal:  Biophys J       Date:  2007-03-09       Impact factor: 4.033

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

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

4.  iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge.

Authors:  Catherine Musselman; Hashim M Al-Hashimi; Ioan Andricioaei
Journal:  Biophys J       Date:  2007-04-20       Impact factor: 4.033

5.  Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements.

Authors:  Jennifer M Kavran; Thomas A Steitz
Journal:  J Mol Biol       Date:  2007-06-04       Impact factor: 5.469

6.  Molecular dynamics simulation of the structure, dynamics, and thermostability of the RNA hairpins uCACGg and cUUCGg.

Authors:  Alessandra Villa; Elisabeth Widjajakusuma; Gerhard Stock
Journal:  J Phys Chem B       Date:  2007-12-11       Impact factor: 2.991

7.  Dynamics of large elongated RNA by NMR carbon relaxation.

Authors:  Alexandar L Hansen; Hashim M Al-Hashimi
Journal:  J Am Chem Soc       Date:  2007-11-30       Impact factor: 15.419

8.  Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: role in the kissing-duplex structural transition.

Authors:  Xiaoyan Sun; Qi Zhang; Hashim M Al-Hashimi
Journal:  Nucleic Acids Res       Date:  2007-02-20       Impact factor: 16.971

9.  L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy.

Authors:  Hendrik R A Jonker; Serge Ilin; S Kaspar Grimm; Jens Wöhnert; Harald Schwalbe
Journal:  Nucleic Acids Res       Date:  2006-12-14       Impact factor: 16.971

10.  Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA.

Authors:  Filip Rázga; Jaroslav Koca; Ali Mokdad; Jirí Sponer
Journal:  Nucleic Acids Res       Date:  2007-06-06       Impact factor: 16.971

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  18 in total

1.  Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.

Authors:  Pavel Banás; Nils G Walter; Jirí Sponer; Michal Otyepka
Journal:  J Phys Chem B       Date:  2010-07-08       Impact factor: 2.991

2.  Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.

Authors:  Vojtech Mlýnský; Pavel Banás; Daniel Hollas; Kamila Réblová; Nils G Walter; Jirí Sponer; Michal Otyepka
Journal:  J Phys Chem B       Date:  2010-05-20       Impact factor: 2.991

3.  Functional role of ribosomal signatures.

Authors:  Ke Chen; John Eargle; Krishnarjun Sarkar; Martin Gruebele; Zaida Luthey-Schulten
Journal:  Biophys J       Date:  2010-12-15       Impact factor: 4.033

4.  Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.

Authors:  Serdal Kirmizialtin; Scott P Hennelly; Alexander Schug; Jose N Onuchic; Karissa Y Sanbonmatsu
Journal:  Methods Enzymol       Date:  2015-02-07       Impact factor: 1.600

Review 5.  Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition.

Authors:  Qi Zhang; Hashim M Al-Hashimi
Journal:  RNA       Date:  2009-09-23       Impact factor: 4.942

Review 6.  RNA dynamics: perspectives from spin labels.

Authors:  Phuong Nguyen; Peter Z Qin
Journal:  Wiley Interdiscip Rev RNA       Date:  2011-08-22       Impact factor: 9.957

7.  Ultrafast dynamics show that the theophylline and 3-methylxanthine aptamers employ a conformational capture mechanism for binding their ligands.

Authors:  Sang Won Lee; Liang Zhao; Arthur Pardi; Tianbing Xia
Journal:  Biochemistry       Date:  2010-04-06       Impact factor: 3.162

8.  Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

Authors:  Elizabeth J Denning; U Deva Priyakumar; Lennart Nilsson; Alexander D Mackerell
Journal:  J Comput Chem       Date:  2011-04-05       Impact factor: 3.376

9.  Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure.

Authors:  Niel M Henriksen; Darrell R Davis; Thomas E Cheatham
Journal:  J Biomol NMR       Date:  2012-06-20       Impact factor: 2.835

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

Authors:  Andrew C Stelzer; Aaron T Frank; Maximillian H Bailor; Ioan Andricioaei; Hashim M Al-Hashimi
Journal:  Methods       Date:  2009-08-21       Impact factor: 3.608

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