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

Membrane Asymmetry Regulating Transporters01:19

Membrane Asymmetry Regulating Transporters

Enzymes like flippase, floppase, and scramblase transfer phospholipids from one layer to another in the membrane, thereby affecting membrane asymmetry.
Flippase
Eukaryotic flippases are type-IV P-type ATPases or P4-ATPases belonging to P-type ATPase family proteins that are membrane-bound pumps involved in the ATP-mediated transport of ions and molecules across the membrane. Flippases flip specific phospholipids from the outer to the inner leaflet of a membrane. All P4-ATPases have one...
Multi-pass Transmembrane Proteins and β-barrels01:09

Multi-pass Transmembrane Proteins and β-barrels

In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as G-protein-linked receptors (GPCRs) and...
Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
The Significance of Membrane Transport01:44

The Significance of Membrane Transport

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...
Single-pass Transmembrane Proteins01:25

Single-pass Transmembrane Proteins

Integral membrane proteins are tightly associated with the cell membrane and play a crucial role in cell communication, signaling, adhesion, and transport of the molecules. Some integral membrane proteins are present only in the membrane monolayer. For example, the enzyme fatty acid amide hydrolase is present in the cytoplasmic side of the membrane monolayer. In contrast, another type of integral membrane protein, also known as a transmembrane protein, spans across the membrane. Transmembrane...
Protein Transport into the Inner Mitochondrial Membrane01:34

Protein Transport into the Inner Mitochondrial Membrane

Nuclear encoded mitochondrial precursors are imported to the inner membrane in a multistep process involving two separate translocons, TIM22 and TIM23. TIM23 is a cation-selective pore that remains closed by the N terminal segment of the protein. Negative charges on the TIM23 act as a receptor for the incoming precursor, pulling the positively charged matrix-targeting sequence for peptide insertion and translocation.
Transport of mitochondrial precursors across the TIM23 channel is driven by...

You might also read

Related Articles

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

Sort by
Same author

High-Rate Fingerprinting of Protein Isoforms by Quasi-regulated Enzyme-free Transport Through CytK Nanopores.

Research square·2026
Same author

Improving All-Atom Molecular Dynamics Models for Quantitative Prediction of Nanopore Blockade Current.

bioRxiv : the preprint server for biology·2026
Same author

Engineering a Biological Nanopore for Monitoring Protein Dynamics and Conformational Changes at the Single-Molecule Level.

ACS nano·2026
Same author

RNA-DNA Fusomer Fibers With Customizable Physicochemical, Mechanical, and Biological Properties for Next-Generation Therapeutics.

Small (Weinheim an der Bergstrasse, Germany)·2026
Same author

Intracellular neuronal recordings across DNA tiles.

Nature nanotechnology·2026
Same author

DNA-Lipid Nanodiscs with a Polyethylene Glycol Interface.

Journal of the American Chemical Society·2026

Related Experiment Video

Updated: Jul 11, 2026

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy
10:49

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy

Published on: March 5, 2017

Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics.

David B Wells1, Volha Abramkina, Aleksei Aksimentiev

  • 1Department of Physics, University of Illinois at Urbana--Champaign, Urbana, Illinois 61801, USA. dbwells2@uiuc.edu

The Journal of Chemical Physics
|October 2, 2007
PubMed
Summary

This study introduces a faster computational method for simulating biomolecule transport through membrane channels. The enhanced technique accurately predicts permeation events, aiding in understanding cellular transport mechanisms.

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

High Resolution Physical Characterization of Single Metallic Nanoparticles
09:56

High Resolution Physical Characterization of Single Metallic Nanoparticles

Published on: June 28, 2019

Related Experiment Videos

Last Updated: Jul 11, 2026

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy
10:49

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy

Published on: March 5, 2017

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

High Resolution Physical Characterization of Single Metallic Nanoparticles
09:56

High Resolution Physical Characterization of Single Metallic Nanoparticles

Published on: June 28, 2019

Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Dynamics

Background:

  • Biomolecule transport across cell membranes is crucial for cellular function.
  • Understanding the atomic-level mechanisms of membrane channel permeation is limited.
  • Conventional molecular dynamics (MD) simulations are often too slow to capture these events.

Purpose of the Study:

  • To develop a computationally efficient method for simulating electric field-driven transport of large solutes through membrane channels.
  • To enable realistic simulations of permeation events on nanosecond timescales, which typically require millisecond simulations.
  • To investigate the permeation of DNA and peptides through the alpha-hemolysin channel.

Main Methods:

  • Developed a hybrid simulation approach combining MD with steered molecular dynamics (SMD).
  • Calculated the electrostatic potential distribution within the channel using all-atom MD simulations.
  • Applied the computed potential to guide charged solutes through the channel in G-SMD simulations.
  • Validated the method by comparing computed and experimental relative permeation rates of DNA strands.

Main Results:

  • The G-SMD method accurately simulates electric field-driven transport of DNA and peptides through alpha-hemolysin.
  • Simulations on the nanosecond timescale realistically captured permeation events.
  • Computed relative permeation rates for DNA strands showed good agreement with experimental data.
  • The method significantly accelerates the simulation of permeation events compared to conventional MD.

Conclusions:

  • The developed G-SMD method offers a significant speedup for simulating biomolecule transport through membrane channels.
  • This approach provides a powerful tool for understanding atomic-level transport mechanisms.
  • The findings have implications for designing new nanopores and understanding biological transport processes.