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

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About: Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot
Creator	Lee, Ji Bakhom, Mona Gomez, Yessica La, Phuc Radcliffe, Amethyst Rochelle, Dakota Sorin, Eric Nguyen, Khai
Source	PMC
abstract	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.
has issue date	2017-05-05(xsd:dateTime)
bibo:doi	10.1093/nar/gkx012
bibo:pmid	28115636
has license	cc-by-nc
sha1sum (hex)	1cb717149782a475d885e32ccc68794c9d91a410
schema:url	https://doi.org/10.1093/nar/gkx012
resource representing a document's title	Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot
has PubMed Central identifier	PMC5416846
has PubMed identifier	28115636
schema:publication	Nucleic Acids Res
resource representing a document's body	covid:1cb717149782a475d885e32ccc68794c9d91a410#body_text
is schema:about of	named entity 'folding' named entity 'unfolding' named entity 'sampling' named entity 'transitions' named entity 'model' named entity 'contradict' named entity 'plasticity' named entity 'misfolding' named entity 'SUPPORT' named entity 'CUMULATIVE' named entity 'DETAILED' named entity 'ALL-ATOM MOLECULAR DYNAMICS SIMULATIONS' named entity 'OBSERVATIONS' named entity 'MECHANICAL' named entity 'NATIVE' named entity 'MECHANISM' named entity 'THERMODYNAMICS' named entity 'RESULTS' named entity 'FORMATION' named entity 'frameshifting' named entity 'determining' named entity 'pseudoknot' named entity 'stem' named entity 'plasticity' named entity 'mechanical' named entity 'resistance' named entity 'serve' named entity 'folding' named entity 'identified' named entity 'pseudoknot' named entity 'misfolding' named entity 'frameshifting' named entity 'free energy' named entity 'RMSD' named entity 'pseudoknot' named entity 'native structure' named entity '10.0' named entity 'RMSD' named entity 'helical' named entity 'pseudoknot' named entity 'GROMACS' named entity 'paired stem' named entity 'nucleotides' named entity 'RNA' named entity 'Loop 1' named entity 'secondary structure' named entity 'molecular folding' named entity 'Thirumalai' named entity 'A24' named entity 'conformational states' named entity 'A20' named entity 'macrostate' named entity 'annealing' named entity 'helical' named entity 'solute' named entity '7.2' named entity 'native structure' named entity 'A19' named entity 'misfolding' named entity 'RNAs' named entity 'RNA' named entity 'free energy' named entity 'RMSD' named entity 'metastable' named entity 'Frameshifting' named entity 'folding pathway' named entity 'PLRV' named entity 'statistical mechanical' named entity 'Luteoviridae' named entity 'motif' named entity 'PRF' named entity 'virus' named entity 'crystal structure' named entity 'frameshifting'

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