Hierarchy of RNA Functional Dynamics

Mustoe, Anthony M.; Brooks, Charles L.; Al‐Hashimi, Hashim M.

doi:10.1146/annurev-biochem-060713-035524

Cited by 180 publications

(174 citation statements)

References 185 publications

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“…5A). This mechanism is very similar to that described for RNA helicases, in which a first binding event allows the adjacent base pairs to be destabilized, thereby increasing their fraying (Woodson 2010;Jankowsky 2011;Mustoe et al 2014). We suggest that the UCU bulge and the apical loop constitute binding sites of moderate or low .…”

Section: Discussionsupporting

confidence: 78%

Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein

Belfetmi¹,

Zargarian²,

Tisné³

et al. 2016

RNA

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The mature HIV-1 nucleocapsid protein NCp7 (NC) plays a key role in reverse transcription facilitating the two obligatory strand transfers. Several properties contribute to its efficient chaperon activity: preferential binding to single-stranded regions, nucleic acid aggregation, helix destabilization, and rapid dissociation from nucleic acids. However, little is known about the relationships between these different properties, which are complicated by the ability of the protein to recognize particular HIV-1 stem-loops, such as SL1, SL2, and SL3, with high affinity and without destabilizing them. These latter properties are important in the context of genome packaging, during which NC is part of the Gag precursor. We used NMR to investigate destabilization of the full-length TAR (trans activating response element) RNA by NC, which is involved in the first strand transfer step of reverse transcription. NC was used at a low protein:nucleotide (nt) ratio of 1:59 in these experiments. NMR data for the imino protons of TAR identified most of the base pairs destabilized by NC. These base pairs were adjacent to the loops in the upper part of the TAR hairpin rather than randomly distributed. Gel retardation assays showed that conversion from the initial TAR-cTAR complex to the fully annealed form occurred much more slowly at the 1:59 ratio than at the higher ratios classically used. Nevertheless, NC significantly accelerated the formation of the initial complex at a ratio of 1:59.

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Section: Discussionsupporting

confidence: 78%

Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein

Belfetmi¹,

Zargarian²,

Tisné³

et al. 2016

RNA

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“…In this review, we classify these excited states of RNA based on the nature of the dynamic processes in which they are involved. To simplify the description of complex RNA dynamics, Al-Hashimi and co-workers have recently introduced a general framework that is based on the highly hierarchical and rugged RNA free-energy landscape [33]. In this framework, RNA dynamics are classified as distinct motional modes that represent transitions between different states located within three hierarchical free-energy tiers — Tiers 0, 1 and 2 (Figure 1a).…”

Section: A Hierarchical Free-energy Landscape Of Rna Conformational Tmentioning

confidence: 99%

Characterizing excited conformational states of RNA by NMR spectroscopy

Zhao

Zhang

2015

Current Opinion in Structural Biology

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Conformational dynamics is a hallmark of diverse non-coding RNA functions. During these functional processes, RNA molecules almost ubiquitously undergo conformational transitions that are tuned to meet distinct structural and kinetic requirements for proper function. A complete mechanistic understanding of RNA function requires comprehensive structural and dynamic knowledge of these complex transitions, which often involve alternative higher-energy conformational states that pose a major challenge for high-resolution structural study by conventional methods. In this review, we describe recent progress in RNA NMR that has started to unveil detailed structural, thermodynamic and kinetic insights into some of these excited conformational states of RNA and their functional roles in biology.

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“…For example, riboswitches can adopt different conformations in response to specific conditions of the cellular environment (7,8). Understanding the kinetics, such as the rate and pathways for the conformational changes, is critical for deciphering the mechanism of RNA function (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). Extensive experimental and theoretical studies on RNA folding kinetics have provided significant insights into the kinetic mechanism of RNA functions (19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36).…”

mentioning

confidence: 99%

Understanding the kinetic mechanism of RNA single base pair formation

Chen

2015

Proc. Natl. Acad. Sci. U.S.A.

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RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/ dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model. RNAs perform critical cellular functions at the level of gene expression and regulation (1-4). RNA functions are determined not only by RNA structure or structure motifs [e.g., tetraloop hairpins (5, 6)] but also by conformational distributions and dynamics and kinetics of conformational changes. For example, riboswitches can adopt different conformations in response to specific conditions of the cellular environment (7,8). Understanding the kinetics, such as the rate and pathways for the conformational changes, is critical for deciphering the mechanism of RNA function (9-19). Extensive experimental and theoretical studies on RNA folding kinetics have provided significant insights into the kinetic mechanism of RNA functions (19-36). However, due to the complexity of the RNA folding energy landscape (37-46) and the limitations of experimental tools (47-55), many fundamental problems, including single base flipping and base pair formation and fraying, remain unresolved. These unsolved fundamental problems have hampered our ability to resolve other important issues, such as RNA hairpin and larger structure folding kinetics. Several key questions remain unanswered, such as whether the hairpin folding is rate-limited by the conformational search of the native base pairs, whose formation leads to fast downhill folding of the whole structure, or by the breaking of misfolded base pairs before refolding to the native structure (18,19,(54)(55)(56)(57)(58)(59)(60)(61)(62)(63)(64)(65)(66)(67)(68)(69)(70)(71)(72)(73).Motivated by the need to understand the basic steps of nucleic acids folding, Hagan et al. (74) performed forty-three 200-ps unfolding trajectories at 400 K and identified both on-and offpathway intermediates and two dominant unfolding pathways for a terminal C-G base pair in a DNA duplex. In one of the pathways, bas...

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Hierarchy of RNA Functional Dynamics

Cited by 180 publications

References 185 publications

Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein

Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein

Characterizing excited conformational states of RNA by NMR spectroscopy

Understanding the kinetic mechanism of RNA single base pair formation

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