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

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
Protein Folding01:22

Protein Folding

Overview
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
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

Constructing smooth potential functions for protein folding.

Journal of molecular graphics & modelling·2001
Same author

Evaluation of ligand overlap by atomic parameters.

Journal of chemical information and computer sciences·2001
Same author

A Gaussian statistical mechanical model for the equilibrium thermodynamics of barnase folding.

Journal of molecular biology·2001
Same author

Disulfide recognition in an optimized threading potential.

Protein engineering·2000
Same author

Potential energy function for continuous state models of globular proteins.

Journal of computational biology : a journal of computational molecular cell biology·2000
Same author

The measurement of molecular diversity by receptor site interaction simulation.

Journal of computer-aided molecular design·1998
Same journal

Multiscale frameworks for exploring protein energy landscapes: advances in theory and simulation.

Journal of biological physics·2026
Same journal

Mapping increased flexibility and conformational divergence via N-terminal helix-to-coil transition in USP12 mutant Y49N: a comprehensive in-detail normal mode simulation study.

Journal of biological physics·2026
Same journal

A thermodynamically consistent approach to modeling epithelial solute and water transport in the proximal convoluted tubule.

Journal of biological physics·2026
Same journal

Exploring the conformational space of the NorA efflux pump of Staphylococcus aureus: a microscale conventional molecular dynamics and metadynamics simulation approach.

Journal of biological physics·2026
Same journal

Coupled optical-thermal-chemical modeling of pulsed 808-nm ICG phototherapy using Monte Carlo photon transport.

Journal of biological physics·2026
Same journal

An innovative combinatorial coordination ratio perturbation approach for decoupled period-amplitude modulation.

Journal of biological physics·2026
See all related articles

Related Experiment Video

Updated: May 14, 2026

Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy
10:09

Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy

Published on: April 28, 2011

Toward correct protein folding potentials.

M Chhajer1, G M Crippen

  • 1Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599 U.S.A.

Journal of Biological Physics
|January 25, 2013
PubMed
Summary
This summary is machine-generated.

Developing a robust protein folding potential is crucial for accurately predicting protein stability. This study introduces a novel representation of the denatured state to improve potential function accuracy, showing good agreement with experimental data for barnase mutants.

Keywords:
barnasedecoysdenatured stateprotein foldingthermodynamic stability

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Related Experiment Videos

Last Updated: May 14, 2026

Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy
10:09

Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy

Published on: April 28, 2011

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Computational Biology
  • Protein Folding
  • Biophysics

Background:

  • Empirical protein folding potential functions are essential for predicting protein structure and stability.
  • Existing potentials often fail to accurately locate the native protein conformation or estimate folding free energy.
  • Current methods for assessing thermodynamic stability can be overly sensitive to minor changes in atomic coordinates.

Purpose of the Study:

  • To develop a robust protein folding potential function that accurately predicts the native conformation and folding free energy.
  • To address limitations in current potential functions by introducing a novel representation of the denatured state.
  • To validate the improved potential function against experimental data for a set of protein mutants.

Main Methods:

  • Devised a novel representation of the denatured state for protein folding.
  • Developed and tested a new empirical potential function for predicting protein folding.
  • Calculated predicted free energies of unfolding for 25 barnase mutants.
  • Compared predicted values with experimentally determined free energies of unfolding.

Main Results:

  • The developed potential function successfully identifies a minimum near the native conformation for a limited set of proteins.
  • Predicted free energies of unfolding for 25 barnase mutants closely matched experimental values.
  • Substantial discrepancies were observed for 17 barnase mutants, indicating areas for further refinement.

Conclusions:

  • A novel representation of the denatured state can lead to more robust protein folding potential functions.
  • The new potential function shows promise in accurately predicting protein stability and folding free energies.
  • Further development is needed to address discrepancies observed in certain mutant cases.