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

A structure-based method for derivation of all-atom potentials for protein folding.

Edo Kussell1, Jun Shimada, Eugene I Shakhnovich

  • 1Department of Biophysics, Harvard University, 240 Longwood Avenue, Boston, MA 02115, USA.

Proceedings of the National Academy of Sciences of the United States of America
|April 12, 2002
PubMed
Summary

This study introduces a new method to derive all-atom protein folding potentials. The developed potentials accurately predicted protein structures, achieving C(alpha) root-mean-square deviation below 2 Å for a three-helix bundle.

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

Complete enzyme clustering enhances coenzyme Q biosynthesis via substrate channeling.

Nature communications·2026
Same author

Biophysical fitness landscape design traps viral evolution.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Chaperonin recognition of protein dynamics drives drug resistance.

bioRxiv : the preprint server for biology·2026
Same author

Co-targeting Metabolic Neighbours Constraints Bacterial Adaptive Evolution.

bioRxiv : the preprint server for biology·2026
Same author

CASPULE: A computational tool to study sticker spacer polymer condensates.

PLoS computational biology·2026
Same author

Evolutionary dynamics under phenotypic uncertainty.

bioRxiv : the preprint server for biology·2026

Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Accurate protein structure prediction is crucial for understanding biological function.
  • Developing effective all-atom protein folding potentials remains a significant challenge in computational biophysics.

Purpose of the Study:

  • To present and validate a novel method for deriving all-atom protein folding potentials.
  • To assess the accuracy of these potentials in predicting native protein structures.

Main Methods:

  • The study derived potentials comprising atomic contact and local density terms.
  • All-atom protein folding simulations were performed using the derived potentials.
  • The method was tested on a three-helix bundle, hairpin, and helical sequences.

Related Experiment Videos

Main Results:

  • The derived potentials successfully folded a three-helix bundle, with lowest energy conformations within 2 Å root-mean-square deviation (C(alpha) distance) of the native structure.
  • Similar accuracy was achieved for hairpin and helical sequences using distinct potentials.
  • A high correlation was observed between derived parameters across different proteins.

Conclusions:

  • The developed method provides accurate all-atom protein folding potentials.
  • The findings suggest the potential for a universal potential capable of folding diverse proteins at the atomic level.
  • This work advances the field of computational protein structure prediction.