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

Exploring the energy landscape in proteins

J E Straub1, D Thirumalai

  • 1Department of Chemistry, Boston University, MA 02215.

Proceedings of the National Academy of Sciences of the United States of America
|February 1, 1993
PubMed
Summary

We developed new methods to analyze protein energy landscapes and motions using molecular dynamics simulations. Our findings suggest that protein energy landscapes share universal statistical characteristics across different systems.

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

Connecting multiway enhancer-promoter interactions to changes in gene expression in cancer.

bioRxiv : the preprint server for biology·2026
Same author

Green-Synthesized rGO-CeO<sub>2</sub> Nanocomposites for Enhanced Visible-Light Photodegradation of Eosin Y.

Chemistry, an Asian journal·2026
Same author

Droplet growth, Ostwald's rule, and emergence of order in Fused in Sarcoma.

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

Rotational migration in human pancreatic ductal organoids depends on actin and myosin activity.

Communications biology·2025
Same author

Rotational migration in human pancreatic ductal organoids depends on actin and myosin activity.

ArXiv·2025
Same author

Iterative annealing mechanism for protein and RNA chaperones.

Biophysical journal·2025

Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Dynamics

Background:

  • Understanding protein energy landscapes and conformational dynamics is crucial for deciphering protein function.
  • Molecular dynamics simulations offer a powerful tool to investigate these complex processes at atomic resolution.

Purpose of the Study:

  • To present novel methods for probing protein energy landscapes and motions.
  • To analyze the conformational space sampling and energy barriers in protein systems.

Main Methods:

  • Utilizing generalized ergodic measure to compute the rate of conformational space sampling.
  • Employing nonbonded force dynamics to determine the time scale for ergodicity.
  • Applying instantaneous normal-mode spectra to evaluate the distribution of energy barrier heights.

Main Results:

  • Demonstrated rapid sampling of diverse conformational substrates within short simulation times (< 10 psec).
  • Identified energy barriers of a few kcal/mol governing large-scale protein motions at longer timescales.
  • Showed that the distribution of energy barrier heights for S-peptide follows a Poisson distribution.

Conclusions:

  • The statistical characteristics of protein energy landscapes may be a universal feature.
  • These methods provide insights into protein folding, function, and dynamics.

Related Experiment Videos