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

Thermodynamic calculations in biological systems.

L Mario Amzel1, Xavier Siebert, Anthony Armstrong

  • 1Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, United States. mario@neruda.med.jhmi.edu

Biophysical Chemistry
|June 28, 2005
PubMed
Summary

Molecular dynamics (MD) simulations offer atomic-level insights into complex biochemical and biophysical processes. This review highlights how MD calculations illuminate rate acceleration, protein unfolding mechanisms, and molecular binding phenomena.

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

Enhancement of Protein-Protein Interactions by Destabilizing Mutations Revealed by HDX-MS.

Biomolecules·2025
Same author

Enhancing OSA Assessment with Explainable AI<sup></sup>.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference·2023
Same author

Sodium/Iodide Symporter Metastable Intermediates Provide Insights into Conformational Transition between Principal Thermodynamic States.

The journal of physical chemistry. B·2023
Same author

Structural insights into the mechanism of the sodium/iodide symporter.

Nature·2022
Same author

Class I PI3K Biology.

Current topics in microbiology and immunology·2022
Same author

Development of high-affinity nanobodies specific for Na<sub>V</sub>1.4 and Na<sub>V</sub>1.5 voltage-gated sodium channel isoforms.

The Journal of biological chemistry·2022

Area of Science:

  • Biochemistry
  • Biophysics
  • Computational Chemistry

Background:

  • Understanding intra- and inter-molecular interactions is crucial for solving complex problems in biochemistry and biophysics.
  • Molecular dynamics (MD) calculations provide a powerful tool for investigating these interactions at an atomic level.
  • This review focuses on the application of MD simulations to interpret key experimental observations.

Purpose of the Study:

  • To demonstrate the utility of MD calculations in gaining atomic-level insights into biochemical and biophysical phenomena.
  • To review three specific examples where MD simulations elucidated important experimental findings.
  • To highlight the role of computational methods in advancing scientific understanding.

Main Methods:

  • Molecular dynamics (MD) simulations were employed to analyze molecular interactions and behaviors.

Related Experiment Videos

  • The review examines three distinct case studies utilizing MD calculations.
  • These studies focus on conformational constraints, protein unfolding, and molecular binding.

    • Main Results:

    • MD simulations revealed the entropic contribution to rate acceleration due to conformational constraints.
    • The mechanism of force-induced protein unfolding was elucidated at the atomic level.
    • MD calculations quantified the loss of translational entropy during small molecule-protein binding.

    Conclusions:

    • MD calculations provide invaluable atomic detail for understanding complex biochemical and biophysical processes.
    • The reviewed examples showcase the power of MD simulations in explaining experimental observations.
    • Computational approaches like MD are essential for tackling previously intractable problems in molecular sciences.