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

Simulation of enzyme-substrate interactions: the diffusional encounter step

R C Wade1

  • 1European Molecular Biology Laboratory, Heidelberg, Germany.

Acta Biochimica Polonica
|January 1, 1995
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

On the determinants of electron transfer reorganization energy in a cytochrome P450: cytochrome b5 complex. A combined quantum mechanics and molecular dynamics simulation study.

The Journal of chemical physics·2025
Same author

Graphene BioFET sensors for SARS-CoV-2 detection: a multiscale simulation approach.

Nanoscale advances·2022
Same author

Pulmonary Arterial Pruning and Longitudinal Change in Percent Emphysema and Lung Function: The Genetic Epidemiology of COPD Study.

Chest·2021
Same author

Protein conformational flexibility modulates kinetics and thermodynamics of drug binding.

Nature communications·2017
Same author

Three steps to gold: mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations.

Physical chemistry chemical physics : PCCP·2016
Same author

Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding.

Molecular bioSystems·2015
Same journal

Elemental changes in tooth hard tissues during demineralization and fluoride-induced remineralization: an SEM-EDX study.

Acta biochimica Polonica·2026
Same journal

Precise genome modification of agrobacterium based on one-step homologous recombination via endogenous transfer DNA.

Acta biochimica Polonica·2026
Same journal

Recommendations of the Polish Zebrafish Society on the use of the zebrafish (<i>Danio rerio</i>) model in biomedical research.

Acta biochimica Polonica·2026
Same journal

Pilot analysis of protein profile alterations in plasma and aortic tissue of spontaneously hypertensive rats.

Acta biochimica Polonica·2026
Same journal

Skin examination in extreme conditions.

Acta biochimica Polonica·2026
Same journal

Genetic architecture of obesity and advances in precision pharmacotherapy: a comprehensive review.

Acta biochimica Polonica·2026
See all related articles

This study explores how Brownian dynamics simulations can predict enzyme and ligand encounter rates. Understanding these diffusion-influenced properties is key for designing new enzymes and drugs.

Area of Science:

  • Biochemistry
  • Computational Biology
  • Drug Design

Background:

  • Enzymes are crucial targets for structure-based redesign and drug discovery.
  • Controlling molecular encounter properties is a key strategy for enzyme and ligand design.
  • Understanding diffusion-influenced reaction rates is essential for optimizing molecular interactions.

Purpose of the Study:

  • To describe Brownian dynamics simulation methodology for calculating diffusive bimolecular encounter rates.
  • To apply this methodology to investigate factors affecting diffusion-influenced enzyme rates.
  • To provide a framework for designing molecules with desired diffusional encounter properties.

Main Methods:

  • Brownian dynamics (BD) simulations were employed to calculate rates of diffusive bimolecular encounters.

Related Experiment Videos

  • The methodology was applied to study enzymes and their ligands.
  • Analysis focused on factors influencing the speed of diffusion-influenced enzymatic reactions.

    • Main Results:

    • Brownian dynamics simulations accurately calculate diffusive bimolecular encounter rates.
    • Key factors influencing diffusion-influenced enzyme kinetics were identified.
    • The study demonstrates the utility of BD simulations in enzyme and ligand design.

    Conclusions:

    • Brownian dynamics simulation is a valuable tool for predicting molecular encounter properties.
    • This approach aids in the structure-based design of enzymes and ligands with tailored diffusion characteristics.
    • Understanding diffusional encounters is critical for advancing drug design and enzyme engineering.