Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA
Open accessPublished version of a preprint
Abstract
Significance: Ribosomes are complexes between ribosomal RNA (rRNA) and a number of proteins. Because ribosome assembly begins with rRNA folding, we simulated the molecular details of Mg 2+ -driven folding of the central domain of the bacterial rRNA. Good agreement with experiments on the folding of the three-way junction in the center of the rRNA validates the model. Coupling of rRNA folding and Mg 2+ binding shows that ions interact with rRNA segments in a coordinated manner. The shape of rRNA changes from a sphere in the unfolded state to a prolate ellipsoid at high Mg 2+ concentration, which is the opposite of what transpires when a globular protein folds. Our study provides the needed framework for undertaking ion-driven folding of large RNA molecules.
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The changes added by human players tend to agree with the 16S structural model, especially in regions linked to important functional sites, such as S8 and S15 binding sites, and a region that undergoes conformational readjustment during 30S assembly.
“In Fig. 4, we show that the changes added by human players tend to agree with the 16S structural model, especially in regions linked to important functional sites, such as S8 and S15 binding sites, and a region that undergoes conformational readjustment during 30S assembly44–49.”
From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [45]
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References 67 · Cited by 31
- Authors
- Hori, N., Denesyuk, N. A., & Thirumalai, D.
- Affiliations
- University of Nottingham (GB)
- The University of Texas at Austin (US)
- Corresponding author
- Thirumalai, D.
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2021-03-03
- Volume
- 118
- Issue
- 10
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC7958424
- OpenAlex
- W3135083938
- Cited by
- 31
- References
- 67
- Citations by year
- 2026: 5 · 2025: 6 · 2024: 5 · 2023: 5 · 2022: 4 · 2021: 6
- FWCI
- 1.57
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Repository@Nottingham (University of Nottingham) (acceptedVersion, other-oa)
- Repository@Nottingham (University of Nottingham) (submittedVersion, cc-by)
- Funders
- National Science Foundation (CHE 19-00093)
- Welch Foundation (F-0019)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- 16S rRNA, rRNA folding, magnesium binding, three-way junction, cooperativity, ribosome assembly, RNA conformational change
- MeSH terms
- Magnesium, Models, Chemical, RNA, Bacterial, RNA, Ribosomal, 16S, RNA Folding
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