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 Concept Videos

Directing Proteins to the Rough Endoplasmic Reticulum01:34

Directing Proteins to the Rough Endoplasmic Reticulum

The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview

You might also read

Related Articles

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

Sort by
Same author

AlphaFold-based peptide structure prediction: Opportunities, limitations, and future directions.

Biotechnology advances·2026
Same author

<b>Two new species of <i>Astenus</i> Dejean, 1833 (Coleoptera: Staphylinidae: Paederinae) from Mêdog, China</b>.

Zootaxa·2026
Same author

<b>The genus <i>Pinopellis</i> Assing from Mêdog, China, with a new species (Coleoptera: Staphylinidae: Paederinae)</b>.

Zootaxa·2026
Same author

Joint trajectories of ADHD and autistic traits in preschoolers linked to prenatal phthalate exposure: insights from the cord blood metabolome.

Environment international·2026
Same author

[Mechanistic investigation of a natural compound against tumors via modulation of nuclear receptor RXRα-mediated autophagy pathway].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica·2026
Same author

StruCloze: A Unified Framework for Backmapping and Inpainting Biomolecule Structures.

Journal of chemical theory and computation·2026

Related Experiment Video

Updated: May 7, 2026

Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations.

Wei Ye1, Jingxu Yang, Qingfen Yu

  • 1State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.

Physical Chemistry Chemical Physics : PCCP
|September 28, 2013
PubMed
Summary

Archaea's kink-turn small RNA (sRNA) motif and L7Ae protein interaction suggest an induced fit mechanism for small ribonucleoprotein particle (sRNP) assembly. This finding aids understanding of ribosome function and catalysis.

More Related Videos

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

Related Experiment Videos

Last Updated: May 7, 2026

Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

Area of Science:

  • Molecular biology
  • Biophysics
  • Computational biology

Background:

  • The kink-turn sRNA motif is crucial for assembling small ribonucleoprotein particles (sRNPs) with protein L7Ae in archaea.
  • These sRNPs are essential for ribosome maturation and translation.
  • The precise mechanism of sRNA folding coupled with protein binding remains poorly understood.

Purpose of the Study:

  • To investigate the molecular mechanism of kink-turn sRNA folding and binding with protein L7Ae.
  • To elucidate the role of induced fit in sRNP assembly.
  • To explore the dynamics of sRNA-protein interactions.

Main Methods:

  • Molecular dynamics (MD) simulations at room and high temperatures.
  • Analysis of root-mean-square deviation (RMSD) between bound and apo structures.
  • Kolmogorov-Smirnov P test and principal component analysis (PCA).
  • High-temperature unfolding kinetic analysis.

Main Results:

  • MD simulations and statistical analyses suggest an induced fit mechanism for sRNA binding to L7Ae.
  • Both local and global conformational changes in sRNA occur upon L7Ae binding.
  • PCA revealed dynamic closing and opening motions of the kink-turn sRNA.
  • High-temperature unfolding kinetics support the induced fit model.

Conclusions:

  • The binding of L7Ae to kink-turn sRNA likely follows an induced fit mechanism.
  • The observed sRNA dynamics may be critical for sRNP assembly and methylation catalysis.
  • Computational approaches combining MD, PCA, and kinetic analysis are valuable for studying sRNA-protein recognition.