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

Reaction coordinates and rates from transition paths.

Robert B Best1, Gerhard Hummer

  • 1Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 132, Bethesda, MD 20892-0520, USA.

Proceedings of the National Academy of Sciences of the United States of America
|April 9, 2005
PubMed
Summary
This summary is machine-generated.

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

Molecular architecture of heterochromatin at the nuclear periphery of primary human cells.

Nature communications·2026
Same author

Extrapolating molecular dynamics simulations to zero time step and across thermodynamic space.

The Journal of chemical physics·2026
Same author

Arc mediates intercellular tau transmission via extracellular vesicles.

Cell·2026
Same author

pH-dependent activation of the Na<sup>+</sup>/H<sup>+</sup> antiporter NhaA and conformational dynamics of its N-terminus.

Nature communications·2026
Same author

Structural flexibility of the human vault particle revealed by high-resolution cryo-EM and molecular dynamics simulations.

Nature communications·2026
Same author

Discovery and Development of a Potent LIMK2 Isoform-Specific Degrader.

ACS chemical biology·2026
Same journal

In This Issue.

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

Long-term cultural continuity across the Neanderthal-modern human sequence at Üçağızlı II Cave, northern Levant.

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

Dolphins use names to remember whom to avoid.

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

Retraction for Shaked and Frenkel, Curiouser and curiouser: Meningeal lymphoid structures in the aging brain.

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

Small but mighty: The outsized role of small water bodies in the global carbon cycle.

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

Functional traits produce conditional outcomes in different community contexts.

Proceedings of the National Academy of Sciences of the United States of America·2026
See all related articles

Researchers developed a Bayesian method to understand reaction mechanisms by analyzing transition states and optimizing reaction coordinates. This approach was applied to protein folding, identifying key steps in the process.

Area of Science:

  • Physical Chemistry
  • Computational Biology
  • Biophysics

Background:

  • Understanding molecular reaction mechanisms is crucial for predicting chemical and biological processes.
  • The transition-state ensemble and transition paths are key to elucidating reaction dynamics in solution.

Purpose of the Study:

  • To introduce a novel Bayesian framework for analyzing reaction mechanisms.
  • To develop a variational procedure for optimizing reaction coordinates.
  • To apply the developed theory to complex systems like protein folding and molecular reorientation.

Main Methods:

  • Utilized a Bayesian formula connecting equilibrium and transition-path ensembles.
  • Employed a variational procedure to optimize reaction coordinates.
  • Applied the methods to model protein folding (three-helix bundle) and dipole reorientation in carbon nanotubes.

Related Experiment Videos

Main Results:

  • Successfully identified transition states, ranked reaction coordinates, and estimated rate coefficients.
  • Optimized reaction coordinates for protein folding, revealing the transition state.
  • Identified the formation and packing of helix 2 and 3 as the folding bottleneck for the studied protein model.

Conclusions:

  • The Bayesian approach provides a robust framework for characterizing reaction mechanisms and transition states.
  • Variational optimization of reaction coordinates enhances the accuracy of mechanistic studies.
  • The method offers valuable insights into the molecular dynamics of protein folding and confined molecular systems.