Mechanical Unfolding of the Beet Western Yellow Virus −1 Frameshift Signal

White, Katherine H.; Orzechowski, Marek; Fourmy, Dominique; Visscher, Koen

doi:10.1021/ja111281f

Cited by 33 publications

(50 citation statements)

References 91 publications

(321 reference statements)

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“…Furthermore, the experimental time and spatial resolutions (1–10 ms and ~1 nm) are relatively low compared to those of the smoothed simulation traces (0.3 ns and 0.3 nm). A similar difference between experimental and simulated force-extension profiles was reported previously39. Nevertheless, the SMD simulation results revealed the relative mechanical stabilities of the three major parts of the RNA pseudoknot SF206 and provide insight into the microscopic unfolding mechanism.…”

Section: Resultssupporting

confidence: 83%

“…The single-molecule mechanical unfolding results of SRV-1 pseudoknots suggest that the cooperative mean unfolding force has a positive correlation with −1 frameshifting efficiency when the slippery sequence and the spacer are maintained largely constant, consistent with previous studies3537. However, the possible correlation between mechanical unfolding rate and frameshifting efficiency has not been extensively investigated, due to a limited number of mutants studied or a small number of pulling traces obtained for the native pseudoknots35363739. We showed in this study that the cooperative mechanical unfolding rates of the seven SRV-1 pseudoknots studied are inversely proportional to frameshifting efficiencies in a wide range of stretching forces.…”

Section: Discussionsupporting

confidence: 78%

“…However, the molecular determinants of the downstream mRNA structure stimulating −1 frameshifting efficiency are still unclear. Single-molecule mechanical pulling studies using optical tweezers have provided insight into the possible correlation between frameshifting stimulatory mRNA structures and −1 frameshifting efficiency353637383940. Two studies showed a correlation between the frameshifting efficiency and the mechanical strength of an mRNA pseudoknot3537.…”

mentioning

confidence: 99%

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Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation

Zhong

Yang

Zhang

et al. 2016

Sci Rep

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Minus-one ribosomal frameshifting is a translational recoding mechanism widely utilized by many RNA viruses to generate accurate ratios of structural and catalytic proteins. An RNA pseudoknot structure located in the overlapping region of the gag and pro genes of Simian Retrovirus type 1 (SRV-1) stimulates frameshifting. However, the experimental characterization of SRV-1 pseudoknot (un)folding dynamics and the effect of the base triple formation is lacking. Here, we report the results of our single-molecule nanomanipulation using optical tweezers and theoretical simulation by steered molecular dynamics. Our results directly reveal that the energetic coupling between loop 2 and stem 1 via minor-groove base triple formation enhances the mechanical stability. The terminal base pair in stem 1 (directly in contact with a translating ribosome at the slippery site) also affects the mechanical stability of the pseudoknot. The −1 frameshifting efficiency is positively correlated with the cooperative one-step unfolding force and inversely correlated with the one-step mechanical unfolding rate at zero force. A significantly improved correlation was observed between −1 frameshifting efficiency and unfolding rate at forces of 15–35 pN, consistent with the fact that the ribosome is a force-generating molecular motor with helicase activity. No correlation was observed between thermal stability and −1 frameshifting efficiency.

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Section: Resultssupporting

confidence: 83%

Section: Discussionsupporting

confidence: 78%

mentioning

confidence: 99%

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Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation

Zhong

Yang

Zhang

et al. 2016

Sci Rep

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“…The folding mechanics reported herein are consistent with the unfolding of BWYV described by recent optical tweezer experiments and steered molecular dynamics simulations (46), and add a new level of complexity by accounting for the formation of non-native structure. The presence of multiple misfolded states on the free energy surface is in agreement with the PK5 pseudoknot pathway reported by Cao et al.…”

Section: Resultssupporting

confidence: 84%

Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot

et al. 2017

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Massive all-atom molecular dynamics simulations were conducted across a distributed computing network to study the folding, unfolding, misfolding and conformational plasticity of the high-efficiency frameshifting double mutant of the 26 nt potato leaf roll virus RNA pseudoknot. Our robust sampling, which included over 40 starting structures spanning the spectrum from the extended unfolded state to the native fold, yielded nearly 120 μs of cumulative sampling time. Conformational microstate transitions on the 1.0 ns to 10.0 μs timescales were observed, with post-equilibration sampling providing detailed representations of the conformational free energy landscape and the complex folding mechanism inherent to the pseudoknot motif. Herein, we identify and characterize two alternative native structures, three intermediate states, and numerous misfolded states, the latter of which have not previously been characterized via atomistic simulation techniques. While in line with previous thermodynamics-based models of a general RNA folding mechanism, our observations indicate that stem-strand-sequence-separation may serve as an alternative predictor of the order of stem formation during pseudoknot folding. Our results contradict a model of frameshifting based on structural rigidity and resistance to mechanical unfolding, and instead strongly support more recent studies in which conformational plasticity is identified as a determining factor in frameshifting efficiency.

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“…Reconstructing quantitative energy landscapes should therefore provide insight into how the dynamics and energetics of such RNA structures relate to their biological function, possibly aiding the development of therapeutics. The mechanical unfolding of pseudoknots has been studied previously with SMFS [26][27][28][29][30][31], but the full profile of the energy landscape of a pseudoknot has not yet been experimentally reconstructed.…”

mentioning

confidence: 99%

Reconstructing Folding Energy Landscape Profiles from Nonequilibrium Pulling Curves with an Inverse Weierstrass Integral Transform

et al. 2014

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The energy landscapes that drive structure formation in biopolymers are difficult to measure. Here we validate experimentally a novel method to reconstruct landscape profiles from single-molecule pulling curves using an inverse Weierstrass transform (IWT) of the Jarzysnki free-energy integral. The method was applied to unfolding measurements of a DNA hairpin, replicating the results found by the more-established weighted histogram (WHAM) and inverse Boltzmann methods. Applying both WHAM and IWT methods to reconstruct the folding landscape for a RNA pseudoknot having a stiff energy barrier, we found that landscape features with sharper curvature than the force probe stiffness could not be recovered with the IWT method. The IWT method is thus best for analyzing data from stiff force probes such as atomic force microscopes.

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Mechanical Unfolding of the Beet Western Yellow Virus −1 Frameshift Signal

Cited by 33 publications

References 91 publications

Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation

Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation

Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot

Reconstructing Folding Energy Landscape Profiles from Nonequilibrium Pulling Curves with an Inverse Weierstrass Integral Transform

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