Intermediate Rate Atomic Trajectories of RNA by Solid-State NMR Spectroscopy

Olsen, Gregory L.; Bardaro, Michael F.; Echodu, Dorothy C.; Drobny, Gary P.; Varani, Gabriele

doi:10.1021/ja907515s

Cited by 42 publications

(116 citation statements)

References 38 publications

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“…To determine the transient structures with a lifetime of few micro-to-milliseconds, a method to measure RDCs of the transient states has been developed. 78 Paramagnetic relaxation enhancement 79 and the solid-state NMR 80,81 can be also utilized to characterize the transient structures of RNA. All the NMR experiments including the ones described in this review, and additional NMR parameters can complement each other to improve the temporal and spatial resolution of RNA behavior.…”

Section: Perspectivesmentioning

confidence: 99%

NMR Tools to Decipher Dynamic Structure of RNA

Lee¹,

Choi²

2017

Journal of the Korean Magnetic Resonance Society

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It is now well established that RNAs exhibit fundamental roles in regulating cellular processes. Many of these RNAs do not exist in a single conformation. Rather, they undergo dynamic transitions among many different conformations to mediate critical interactions with other biomolecules such as proteins, RNAs, DNAs, or small molecules. Here, we briefly review NMR techniques that describe the dynamic behavior of RNA by determining structural, kinetic, and thermodynamic properties. This conformational flexibility provides the insights into the functional complexity of RNA. A well-known example of dynamic regulatory RNAs is riboswitches. 10,16 Riboswitches are composed of an aptamer domain where a metabolite binds and an expression platform which regulates transcription or translation. Binding of the metabolite to the aptamer domain ultimately induces the changes in the secondary structure of the expression platform that facilitates or inhibits the transcription or the translation, thus controlling gene expression through modulation of RNA dynamics (Fig. 1A). The interaction between RNA and proteins to form RNA-protein complexes (RNP) is also a dynamic process that often induces sequential changes in RNA structure upon binding of proteins. These conformational changes of RNA induced by proteins can direct the order of assembly of RNP. This event is prominent in the hierarchical assembly of a ribosome, a ribozyme composed of RNA and proteins. 21 For example, the binding of ribosomal protein S15 to 16S ribosomal RNA re-orients the helices of 16S RNA that favors the subsequent binding of ribosomal protein S6 and S18. Keywords 22A global conformational change in the secondary structure of RNA is not always a pre-requisite for the function of RNA. A flipping of local bases can regulate the biological processes. For example, 16S ribosomal A-site RNA selects an appropriate

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Section: Perspectivesmentioning

confidence: 99%

NMR Tools to Decipher Dynamic Structure of RNA

Lee¹,

Choi²

2017

Journal of the Korean Magnetic Resonance Society

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“…In a subsequent study [167], detailed models of the dynamics of the three deuterated sites, on the ns-μs timescale, were derived from analysis of 2 H lineshapes and R 1 , R 1Q relaxation data. It was found that U23 and U25 (Fig.…”

Section: Nmr Studies Of the Dynamics Of Biomolecular Conformationamentioning

confidence: 99%

NMR studies of dynamic biomolecular conformational ensembles

Torchia

2015

Progress in Nuclear Magnetic Resonance Spectroscopy

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Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: “Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?” This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA.

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“…Solidstate 2 H NMR spectroscopy was used to describe motion of selected residues in TAR RNA from HIV-1 during protein recognition. [16] NH···N hydrogen bonds in (CUG) 97 RNA were detected by 15 N MAS NMR spectroscopy. [17] 1 H correlation was combined with high-resolution spectral dimensions in NHHN, CHHC, and NHHC experiments.…”

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confidence: 99%