Orchestrating ribosomal RNA folding during ribosome assembly
Sign Up to like & getrecommendations! Published in 2022 at "BioEssays"
DOI: 10.1002/bies.202200066
Abstract: Construction of the eukaryotic ribosome is a complex process in which a nascent ribosomal RNA (rRNA) emerging from RNA Polymerase I hierarchically folds into a native three‐dimensional structure. Modular assembly of individual RNA domains through… read more here.
Keywords: folding ribosome; ribosomal rna; rna folding; rna ... See more keywords
A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints.
Sign Up to like & getrecommendations! Published in 2019 at "Methods"
DOI: 10.1016/j.ymeth.2019.05.001
Abstract: We present a 2D replica exchange protocol incorporating secondary structure information to dramatically improve 3D RNA folding using molecular dynamics simulations. We show that incorporating base-pairing restraints into all-atom, explicit solvent simulations enables the accurate… read more here.
Keywords: molecular dynamics; replica exchange; rna; rna folding ... See more keywords
Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization.
Sign Up to like & getrecommendations! Published in 2017 at "Biochemistry"
DOI: 10.1021/acs.biochem.7b00325
Abstract: RNA folding has been studied extensively in vitro, typically under dilute solution conditions and abiologically high salt concentrations of 1 M Na+ or 10 mM Mg2+. The cellular environment is very different, with 20-40% crowding… read more here.
Keywords: rna; secondary structure; cellular conditions; rna folding ... See more keywords
Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs.
Sign Up to like & getrecommendations! Published in 2019 at "Biochemistry"
DOI: 10.1021/acs.biochem.9b00122
Abstract: Noncanonical base pairs play important roles in assembling the three-dimensional structures critical to the diverse functions of RNA. These associations contribute to the looped segments that intersperse the canonical double-helical elements within folded, globular RNA… read more here.
Keywords: noncanonical base; rna folding; base; effects noncanonical ... See more keywords
Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.1c01233
Abstract: RNA molecules fold as they are transcribed. Cotranscriptional folding of RNA plays a critical role in RNA functions in vivo. Present computational strategies focus on simulations where large structural changes may not be completely sampled.… read more here.
Keywords: folding landscape; rna folding; cotranscriptional folding; rna ... See more keywords
RNA folding and functions of RNA helicases in ribosome biogenesis
Sign Up to like & getrecommendations! Published in 2022 at "RNA Biology"
DOI: 10.1080/15476286.2022.2079890
Abstract: ABSTRACT Eukaryotic ribosome biogenesis involves the synthesis of ribosomal RNA (rRNA) and its stepwise folding into the unique structure present in mature ribosomes. rRNA folding starts already co-transcriptionally in the nucleolus and continues when pre-ribosomal… read more here.
Keywords: rna folding; ribosome biogenesis; rna; rna helicases ... See more keywords
A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding.
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbad110
Abstract: Riboswitches are conserved structural ribonucleic acid (RNA) sensors that are mainly found to regulate a large number of genes/operons in bacteria. Presently, >50 bacterial riboswitch classes have been discovered, but only the thiamine pyrophosphate riboswitch… read more here.
Keywords: rna folding; inverse rna; rna; bacterial riboswitches ... See more keywords
DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btad034
Abstract: Background Folding during transcription can have an important influence on the structure and function of ℝNA molecules, as regions closer to the 5’ end can fold into metastable structures before potentially stronger interactions with the… read more here.
Keywords: folding using; heuristic cotranscriptional; rna folding; transcription ... See more keywords
Distributed biotin–streptavidin transcription roadblocks for mapping cotranscriptional RNA folding
Sign Up to like & getrecommendations! Published in 2017 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkx233
Abstract: Abstract RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods… read more here.
Keywords: transcription; biotin streptavidin; rna; rna folding ... See more keywords
Learning the Fastest RNA Folding Path Based on Reinforcement Learning and Monte Carlo Tree Search
Sign Up to like & getrecommendations! Published in 2021 at "Molecules"
DOI: 10.3390/molecules26154420
Abstract: RNA molecules participate in many important biological processes, and they need to fold into well-defined secondary and tertiary structures to realize their functions. Like the well-known protein folding problem, there is also an RNA folding… read more here.
Keywords: carlo tree; monte carlo; rna; reinforcement learning ... See more keywords