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

Protein Folding01:25

Protein Folding

12.6K
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...
12.6K
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

2.8K
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
2.8K

You might also read

Related Articles

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

Sort by
Same author

Impact of running average value of non-fasting serum triglyceride for secondary prevention of coronary artery disease.

Journal of cardiology·2026
Same author

Conformational Remodeling Underlies Activity Loss in Disease-Linked Asparagine Synthetase Variant.

bioRxiv : the preprint server for biology·2026
Same author

Cryo-EM reveals how ASX-173 inhibits human asparagine synthetase to activate the integrated stress response.

bioRxiv : the preprint server for biology·2025
Same author

Correlation between Running Average of Serum Uric Acid Levels and Clinical Course in Secondary Prevention of Coronary Artery Disease.

Internal medicine (Tokyo, Japan)·2025
Same author

Long-Term Exposure to High Low-Density Lipoprotein Cholesterol Levels and Clinical Course in Secondary Prevention After Coronary Artery Disease.

Circulation reports·2025
Same author

3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase.

Nature communications·2024
Same journal

A Video Protocol of a Randomized Controlled Clinical Trial - Electrochemotherapy of Cutaneous Metastases with Reduced Dose Bleomycin (BLESS Trial).

Journal of visualized experiments : JoVE·2026
Same journal

A Standardized Ex Vivo Porcine Oromucosal Model for Evaluating Peptide Fluxes.

Journal of visualized experiments : JoVE·2026
Same journal

Lightweight English Text Classification with Deep Learning Based on Complex System Theory.

Journal of visualized experiments : JoVE·2026
Same journal

Integrating Artificial Intelligence-Assisted Translation Support into English Courses: Effects on Translation Accuracy, Perceived Stress, and Anxiety.

Journal of visualized experiments : JoVE·2026
Same journal

A Toxin-Based Counter-Selection System for Markerless Gene Deletion and High-Density Tn5 Transposon Mutagenesis in Pectobacterium brasiliense.

Journal of visualized experiments : JoVE·2026
Same journal

Seamless Multimodal Human-Robot Communication: Integration Techniques in Human-Computer Interaction.

Journal of visualized experiments : JoVE·2026
See all related articles

Related Experiment Video

Updated: Apr 8, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.2K

A Workflow for Visualizing Protein Conformational Dynamics from Cryo-EM Maps Using Human Asparagine Synthetase.

Yuichiro Takagi1

  • 1Department of Biochemistry, Molecular Biology and Pharmacology, Indiana University School of Medicine; ytakagi@iu.edu.

Journal of Visualized Experiments : Jove
|April 6, 2026
PubMed
Summary
This summary is machine-generated.

This study introduces a workflow for analyzing protein conformational changes in cryo-electron microscopy (cryo-EM) data. It combines 3D variability analysis (3DVA) and model refinement to reveal dynamic structural variations and refine atomic models.

More Related Videos

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion
13:43

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

Published on: January 31, 2022

15.8K
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

10.4K

Related Experiment Videos

Last Updated: Apr 8, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.2K
A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion
13:43

A Robust Single-Particle Cryo-Electron Microscopy cryo-EM Processing Workflow with cryoSPARC, RELION, and Scipion

Published on: January 31, 2022

15.8K
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

10.4K

Area of Science:

  • Structural Biology
  • Biophysics
  • Biochemistry

Background:

  • Conformational heterogeneity in macromolecules presents a challenge for structural determination using cryo-electron microscopy (cryo-EM).
  • Traditional discrete classification methods may not fully capture continuous or complex motions within protein structures.
  • Understanding protein dynamics is crucial for elucidating biological function.

Purpose of the Study:

  • To present a comprehensive workflow for analyzing conformational heterogeneity in cryo-EM data.
  • To enable the visualization and refinement of atomic models representing different structural states.
  • To provide a framework for linking protein dynamics to biochemical and functional hypotheses.

Main Methods:

  • Utilizing 3D variability analysis (3DVA) in CryoSPARC to compute variability maps from particle images.
  • Applying principal component analysis to identify modes of structural variation.
  • Employing variability refinement in Phenix to generate ensembles of atomic models corresponding to different conformational frames.
  • Demonstrating the workflow using human asparagine synthetase (ASNS).

Main Results:

  • Generation of 3D variability maps highlighting principal modes of structural motion.
  • Refinement of multi-model atomic structures representing discrete conformational states.
  • Production of visualization files for comparative analysis and movie generation.
  • Successful application to cryo-EM reconstructions in the 2.0-6.0 Å resolution range.

Conclusions:

  • The presented workflow effectively analyzes conformational heterogeneity in cryo-EM data.
  • It allows for the detailed study of continuous domain motions, hinge-bending, and local rearrangements.
  • The approach facilitates direct comparison of conformational extremes and quantitative dynamic analysis (e.g., RMSF calculations).