ArticleNucleic acids research2018
Translocation kinetics and structural dynamics of ribosomes are modulated by the conformational plasticity of downstream pseudoknots.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- Detection of Myoglobin Gene Polymorphism Associated With Pigeons' Growth Traits.Animal genetics · 2026Article
- Synthetic rational design of live-attenuated Zika viruses based on a computational model.Nucleic acids research · 2025Article
- Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot.PLoS computational biology · 2024Article
- Structural and Functional Insights into Viral Programmed Ribosomal Frameshifting.Annual review of virology · 2023Review
- Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor.Nature communications · 2023Article
- Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot.PLoS computational biology · 2023Article
- Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation.Nature communications · 2022Article
- Thinking Outside the Frame: Impacting Genomes Capacity by Programmed Ribosomal Frameshifting.Frontiers in molecular biosciences · 2022Review
- The SARS-CoV-2 Programmed -1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 Å Using Chaperone-Assisted RNA Crystallography.ACS chemical biology · 2021Article
- Formation of frameshift-stimulating RNA pseudoknots is facilitated by remodeling of their folding intermediates.Nucleic acids research · 2021Article
- Modulation of Viral Programmed Ribosomal Frameshifting and Stop Codon Readthrough by the Host Restriction Factor Shiftless.Viruses · 2021Article
- Programmed -1 ribosomal frameshifting from the perspective of the conformational dynamics of mRNA and ribosomes.Computational and structural biotechnology journal · 2021Review
- Regulators of Viral Frameshifting: More Than RNA Influences Translation Events.Annual review of virology · 2020Review
- Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- High-throughput interrogation of programmed ribosomal frameshifting in human cells.Nature communications · 2020Article
- An RNA pseudoknot stimulates HTLV-1RNA (New York, N.Y.) · 2020Article
- High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life.Genome biology · 2020Article
- Complex dynamics under tension in a high-efficiency frameshift stimulatory structure.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Slippery ribosomes prefer shapeshifting mRNAs.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Downstream stable mRNA secondary structures can stall elongating ribosomes by impeding the concerted movements of tRNAs and mRNA on the ribosome during translocation. The addition of a downstream mRNA structure, such as a stem-loop or a pseudoknot, is essential to induce -1 programmed ribosomal frameshifting (-1 PRF). Interestingly, previous studies revealed that -1 PRF efficiencies correlate with conformational plasticity of pseudoknots, defined as their propensity to form incompletely folded structures, rather than with the mechanical properties of pseudoknots. To elucidate the detailed molecular mechanisms of translocation and -1 PRF, we applied several smFRET assays to systematically examine how translocation rates and conformational dynamics of ribosomes were affected by different pseudoknots. Our results show that initial pseudoknot-unwinding significantly inhibits late-stage translocation and modulates conformational dynamics of ribosomal post-translocation complexes. The effects of pseudoknots on the structural dynamics of ribosomes strongly correlate with their abilities to induce -1 PRF. Our results lead us to propose a kinetic scheme for translocation which includes an initial power-stroke step and a following thermal-ratcheting step. This scheme provides mechanistic insights on how selective modulation of late-stage translocation by pseudoknots affects -1 PRF. Overall our findings advance current understanding of translocation and ribosome-induced mRNA structure unwinding.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.