Evidence map›Paper›PMID 38777820›Full record

ArticleNature communications2024

Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution.

Shannon Ward, Alex Childs, Ceri Staley, Christopher Waugh, Julie A Watts, Anna M Kotowska, Rahul Bhosale, Aditi N Borkar

Abstract read
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Mechanistic insights into 50Science advances · 2025
    Article
  3. Article
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Shannon Ward *School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK.ORCID http://orcid.org/0000-0002-0807-3808
Alex Childs *School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK.
Ceri Staley *School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK.
Christopher WaughSchool of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK.
Julie A WattsSchool of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK.ORCID http://orcid.org/0000-0002-5292-0445
Anna M KotowskaSchool of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK.ORCID http://orcid.org/0000-0002-4239-1535
Rahul BhosaleSchool of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.ORCID http://orcid.org/0000-0001-6515-4922
Aditi N BorkarSchool of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK. aditi.borkar@nottingham.ac.uk.ORCID http://orcid.org/0000-0001-9278-1438

Funding

RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) BB/S011102/1RCUK | Engineering and Physical Sciences Research Council (EPSRC) EP/P029868/1RCUK | Medical Research Council (MRC) IMPACT DTPUniversity of Nottingham Anne McLaren Fellowship
6 · The paper itself

Abstract

The 3D architecture of RNAs governs their molecular interactions, chemical reactions, and biological functions. However, a large number of RNAs and their protein complexes remain poorly understood due to the limitations of conventional structural biology techniques in deciphering their complex structures and dynamic interactions. To address this limitation, we have benchmarked an integrated approach that combines cryogenic OrbiSIMS, a state-of-the-art solid-state mass spectrometry technique, with computational methods for modelling RNA structures at atomic resolution with enhanced precision. Furthermore, using 7SK RNP as a test case, we have successfully determined the full 3D structure of a native RNA in its apo, native and disease-remodelled states, which offers insights into the structural interactions and plasticity of the 7SK complex within these states. Overall, our study establishes cryo-OrbiSIMS as a valuable tool in the field of RNA structural biology as it enables the study of challenging, native RNA systems.

Indexed as

Nucleic Acid ConformationRNAMass SpectrometryModels, MolecularMolecular Dynamics SimulationRibonucleoproteinsRibonucleoproteinsRNA

Identifiers

PMID38777820
PMCPMC11111741

What OpenQuestion holds

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Registered trials

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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.