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 Concept Videos

The Significance of Membrane Transport01:44

The Significance of Membrane Transport

40.9K
The transport of solutes across the cell membrane is essential for metabolic processes, like maintaining cell size and volume, generating the action potential, exchanging nutrients and gases, etc. Membrane transport can be either passive or active. It can be simple diffusion, facilitated, or mediated transport aided by transport proteins such as transporters and channels.
Transporters facilitate either an active or passive movement of solutes. They can allow a single-molecule transport down its...
40.9K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Molecular Mechanisms of KIT Receptor Dimerization and Oncogenic Activation Revealed by Multiscale Simulations.

Journal of chemical information and modeling·2026
Same author

Correction to "Efficient Protein-Ligand Binding Free Energy Estimation with Coarse-Grained Funnel Metadynamics".

Journal of chemical theory and computation·2026
Same author

The Correlation between Binding and Transport of a Siderophore Complex through Its TonB-Dependent Transporter.

ACS omega·2026
Same author

Coarse-Grained Simulations Reveal Salt- and Length-Dependent Condensation of G4C2 RNA Repeats.

The journal of physical chemistry letters·2026
Same author

Martini 3 Metabolome.

Journal of chemical theory and computation·2026
Same author

Condensates as Conformation Editors of Disordered Client Proteins.

Journal of the American Chemical Society·2026

Related Experiment Video

Updated: Jan 7, 2026

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

9.3K

Unlocking High-Throughput Investigation of Transport Tunnels in Enzymes Using Coarse-Grained Simulation Methods.

Nishita Mandal1,2, Jan A Stevens3, Adolfo B Poma4

  • 1Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań 61-614, Poland.

Journal of Chemical Theory and Computation
|January 2, 2026
PubMed
Summary

Coarse-grained (CG) molecular dynamics methods efficiently characterize enzyme transport tunnels, crucial for substrate access. The Martini-Go̅ model excels at capturing dynamic tunnel changes, aiding enzyme engineering and drug design.

More Related Videos

Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution
11:55

Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution

Published on: August 16, 2016

12.1K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.5K

Related Experiment Videos

Last Updated: Jan 7, 2026

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

Published on: January 16, 2016

9.3K
Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution
11:55

Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution

Published on: August 16, 2016

12.1K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.5K

Area of Science:

  • Biochemistry and Molecular Dynamics
  • Enzymology and Protein Structure

Background:

  • Enzyme transport tunnels are vital for function but difficult to study due to their transient nature.
  • Conventional simulation methods struggle to capture the dynamic behavior of these internal enzyme pathways.

Purpose of the Study:

  • To systematically evaluate coarse-grained (CG) molecular dynamics approaches for characterizing enzyme transport tunnel structure and dynamics.
  • To compare the performance of Martini with Elastic network restraints, Martini with Go̅-model restraints, and SIRAH using haloalkane dehalogenase LinB as a model system.

Main Methods:

  • Systematic evaluation of three CG molecular dynamics methods: Martini with Elastic network restraints, Martini with Go̅-model restraints, and SIRAH.
  • Utilized haloalkane dehalogenase LinB and its engineered variants as model systems.
  • Validated findings across nine enzymes from oxidoreductase, transferase, and hydrolase classes.

Main Results:

  • CG methods accurately reproduced tunnel geometry from all-atom (AA) simulations with significant computational speedups.
  • The Martini-Go̅ model effectively captured mutation-induced tunnel dynamics, including tunnel closure and de novo opening.
  • Martini with Elastic network restraints showed limitations due to structural bias, while SIRAH also demonstrated varying degrees of accuracy in dynamics.

Conclusions:

  • CG simulations are powerful, computationally efficient tools for analyzing enzyme transport tunnels.
  • The Martini-Go̅ model shows particular promise for studying subtle tunnel dynamics.
  • These findings facilitate high-throughput analysis, enzyme engineering, and drug design targeting enzyme tunnels.