Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions.
Journal
Biophysical journal
ISSN: 1542-0086
Titre abrégé: Biophys J
Pays: United States
ID NLM: 0370626
Informations de publication
Date de publication:
18 04 2023
18 04 2023
Historique:
received:
24
10
2022
revised:
05
03
2023
accepted:
10
03
2023
pmc-release:
18
04
2024
medline:
21
4
2023
pubmed:
17
3
2023
entrez:
16
3
2023
Statut:
ppublish
Résumé
RNA pseudoknots are a kind of important tertiary motif, and the structures and stabilities of pseudoknots are generally critical to the biological functions of RNAs with the motifs. In this work, we have carefully refined our previously developed coarse-grained model with salt effect through involving a new coarse-grained force field and a replica-exchange Monte Carlo algorithm, and employed the model to predict structures and stabilities of complex RNA pseudoknots in ion solutions beyond minimal H-type pseudoknots. Compared with available experimental data, the newly refined model can successfully predict 3D structures from sequences for the complex RNA pseudoknots including SARS-CoV-2 programming-1 ribosomal frameshifting element and Zika virus xrRNA, and can reliably predict the thermal stabilities of RNA pseudoknots with various sequences and lengths over broad ranges of monovalent/divalent salts. In addition, for complex pseudoknots including SARS-CoV-2 frameshifting element, our analyses show that their thermally unfolding pathways are mainly dependent on the relative stabilities of unfolded intermediate states, in analogy to those of minimal H-type pseudoknots.
Identifiants
pubmed: 36924021
pii: S0006-3495(23)00170-4
doi: 10.1016/j.bpj.2023.03.017
pmc: PMC10147842
pii:
doi:
Substances chimiques
RNA
63231-63-0
Sodium Chloride
451W47IQ8X
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1503-1516Informations de copyright
Copyright © 2023 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests The authors declare no competing interests.
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