RNA folding kinetics control riboswitch sensitivity in vivo [PDF]
Nature CommunicationsRiboswitches are ligand-responsive gene-regulatory RNA elements that perform key roles in maintaining cellular homeostasis. Understanding how riboswitch sensitivity to ligand (EC50) is controlled is critical to explain how highly conserved aptamer ...
David Z. Bushhouse +2 more
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Hidden Structural Modules in a Cooperative RNA Folding Transition
Cell Reports, 2018 Summary: Large-scale, cooperative rearrangements underlie the functions of RNA in RNA-protein machines and gene regulation. To understand how such rearrangements are orchestrated, we used high-throughput chemical footprinting to dissect a seemingly ...
Brant Gracia +5 more
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A Graph Grammar for Modelling RNA Folding [PDF]
Electronic Proceedings in Theoretical Computer Science, 2016 We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the global behaviour ...
Adane Letta Mamuye +2 more
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RAFFT: Efficient prediction of RNA folding pathways using the fast Fourier transform. [PDF]
PLoS Computational Biology, 2022 We propose a novel heuristic to predict RNA secondary structure formation pathways that has two components: (i) a folding algorithm and (ii) a kinetic ansatz.
Vaitea Opuu +3 more
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A simple, practical and complete
Algorithms for Molecular Biology, 2010 Background The problem of computationally predicting the secondary structure (or folding) of RNA molecules was first introduced more than thirty years ago and yet continues to be an area of active research and development.
Gusfield Dan, Frid Yelena
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Transient RNA–protein interactions in RNA folding [PDF]
FEBS Journal, 2011 The RNA folding trajectory features numerous off‐pathway folding traps, which represent conformations that are often equally as stable as the native functional ones. Therefore, the conversion between these off‐pathway structures and the native correctly folded ones is the critical step in RNA folding. This process, referred to as RNA refolding, is slow,
Boris Fürtig
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Perspectives on Viral RNA Genomes and the RNA Folding Problem [PDF]
Viruses, 2020 Viral RNA genomes change shape as virus particles disassemble, form replication complexes, attach to ribosomes for translation, evade host defense mechanisms, and assemble new virus particles.
Susan J. Schroeder
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Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates [PDF]
Molecular Cell, 2021 Angela M Yu, Luyi Cheng, Venkat Gopalan
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Protein solubility and folding enhancement by interaction with RNA. [PDF]
PLoS ONE, 2008 While basic mechanisms of several major molecular chaperones are well understood, this machinery has been known to be involved in folding of only limited number of proteins inside the cells. Here, we report a chaperone type of protein folding facilitated
Seong Il Choi +12 more
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Transient Protein-RNA Interactions Guide Nascent Ribosomal RNA Folding [PDF]
Cell, 2019 Olivier Duss +2 more
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