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 Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

You might also read

Related Articles

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

Sort by
Same author

Quantifying the Peripheral Surface Information Entropy from Conformational Ensembles of Globular Protein-Peptide Complexes.

Biophysical journal·2026
Same author

<i>Ab initio</i> gene prediction for protein-coding regions.

Bioinformatics advances·2023
Same author

Protein Function Analysis through Machine Learning.

Biomolecules·2022
Same author

Functional Dynamics of Substrate Recognition in TEM Beta-Lactamase.

Entropy (Basel, Switzerland)·2022
Same author

Victory Tax: A Holistic Income Tax System.

Entropy (Basel, Switzerland)·2021
Same author

JEDi: java essential dynamics inspector - a molecular trajectory analysis toolkit.

BMC bioinformatics·2021

Related Experiment Video

Updated: May 24, 2026

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the &#181;s-ms Timescale
08:09

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale

Published on: April 19, 2021

Calculating ensemble averaged descriptions of protein rigidity without sampling.

Luis C González1, Hui Wang, Dennis R Livesay

  • 1Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America.

Plos One
|March 3, 2012
PubMed
Summary

We developed the Virtual Pebble Game (VPG) to efficiently calculate protein rigidity and thermodynamic stability by averaging network properties. This method accurately reflects ensemble-averaged characteristics, offering insights into protein mechanical stability.

More Related Videos

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
12:26

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

Related Experiment Videos

Last Updated: May 24, 2026

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the &#181;s-ms Timescale
08:09

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale

Published on: April 19, 2021

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
12:26

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Protein rigidity is linked to thermodynamic stability, particularly in native structures.
  • Traditional methods for calculating mechanical network rigidity, like the Pebble Game (PG), require sampling conformational ensembles.
  • Accounting for topological fluctuations is crucial for accurate thermodynamic property assessment.

Purpose of the Study:

  • To develop an efficient computational method for assessing protein rigidity and thermodynamic stability.
  • To represent the ensemble of protein network topologies with a single effective network.
  • To eliminate the need for extensive conformational sampling in rigidity calculations.

Main Methods:

  • Developed the mean-field Virtual Pebble Game (VPG) algorithm.
  • Represented conformational ensembles by an effective network with weighted edges.
  • Interpreted the VPG as a flow problem on the effective network, avoiding sampling.

Main Results:

  • Applied the VPG to a dataset of 272 protein structures.
  • Demonstrated that VPG rigidity characterizations numerically and visually match ensemble-averaged thermodynamic properties.
  • Validated the VPG's accuracy in reflecting protein mechanical behavior.

Conclusions:

  • The Virtual Pebble Game (VPG) provides an efficient alternative for calculating protein rigidity and stability.
  • VPG accurately captures ensemble-averaged properties, reflecting the mechanical role of interactions in protein stability.
  • This method facilitates a deeper understanding of the relationship between protein mechanics and stability.