Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Constraining ribosomal RNA conformational space.

Paola Favaretto1, Arjun Bhutkar, Temple F Smith

  • 1BioMolecular Engineering Research Center, Boston University, 36 Cummington Street, Boston, MA 02215, USA.

Nucleic Acids Research
|September 13, 2005
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

LIF-Induced Tumor Plasticity Establishes an Immunosuppressive Myeloid Niche in LKB1-Mutant Lung Cancer.

Cancer discovery·2026
Same author

Intrinsic electrical activity drives small-cell lung cancer progression.

Nature·2025
Same author

Mismatch repair deficiency is not sufficient to elicit tumor immunogenicity.

Nature genetics·2023
Same author

Modeling diverse genetic subtypes of lung adenocarcinoma with a next-generation alveolar type 2 organoid platform.

Genes & development·2022
Same author

Systematic Comparison of Pancreatic Ductal Adenocarcinoma Models Identifies a Conserved Highly Plastic Basal Cell State.

Cancer research·2022
Same author

Publisher Correction: Keap1 mutation renders lung adenocarcinomas dependent on Slc33a1.

Nature cancer·2022
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

Ribosomal RNA (rRNA) achieves its essential core structure through sequence composition and ribosomal proteins. This computational study reveals how these factors limit conformational possibilities, ensuring a stable functional fold for protein synthesis.

Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Biology

Background:

  • Ribosomal RNA (rRNA) adopts a specific, conserved secondary structure essential for its function.
  • The native rRNA sequence navigates a vast conformational landscape to achieve this unique fold.
  • Understanding the constraints on rRNA folding is crucial for deciphering its biological mechanisms.

Purpose of the Study:

  • To computationally investigate the mechanisms constraining rRNA secondary-structure conformational space.
  • To determine the roles of ribosomal proteins and rRNA sequence composition in achieving a stable rRNA fold.
  • To analyze the folding pathways of Escherichia coli 16S rRNA.

Main Methods:

  • Utilized computational analysis and free energy minimization software for secondary structure prediction.

Related Experiment Videos

  • Employed rRNA-ribosomal protein interaction data specific to Escherichia coli 16S rRNA.
  • Simulated folding processes to identify stable conformational states.

    • Main Results:

    • Identified ribosomal proteins and rRNA sequence composition as key factors limiting conformational diversity.
    • Demonstrated that selection pressures on sequence and protein interactions guide rRNA to a single stable structure.
    • Computational predictions align with the universally conserved core fold of rRNA.

    Conclusions:

    • Ribosomal protein-rRNA interactions are critical in constraining rRNA secondary structure.
    • Sequence composition of rRNA, under evolutionary selection, also plays a vital role in stabilizing its fold.
    • These combined mechanisms ensure the fidelity of rRNA folding, essential for ribosome function.