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

OmpA: a pore or not a pore? Simulation and modeling studies.

Peter J Bond1, José D Faraldo-Gómez, Mark S P Sansom

  • 1Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.

Biophysical Journal
|July 19, 2002
PubMed
Summary

The bacterial outer membrane protein OmpA(171) exhibits dynamic conformational changes, enabling transient pore formation. Molecular dynamics simulations reveal a gating mechanism involving Arg138, explaining its observed ionic conductances.

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 effect of lateral stretch on the deformation energetics of biological membranes and the lipid dynamics within.

bioRxiv : the preprint server for biology·2026
Same author

Distinct mechanisms of inhibition of Kv2 potassium channels by tetraethylammonium and RY785.

eLife·2026
Same author

Insights from aquaporin structures into drug-resistant sleeping sickness.

eLife·2026
Same author

Molecular basis for the regulation of membrane proteins through preferential lipid solvation.

Nature chemical biology·2025
Same author

Electronic Polarizability Tunes the Function of the Human Bestrophin 1 Cl<sup>-</sup> Channel.

Journal of chemical theory and computation·2025
Same author

Functional dynamics of G protein-coupled receptors reveal new routes for drug discovery.

Nature reviews. Drug discovery·2025

Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • The bacterial outer membrane protein OmpA has a beta-barrel domain (OmpA(171)) with a suggested structural role.
  • Crystal structures of OmpA(171) do not show a continuous central pore, yet experimental data indicate ionic conductances.

Purpose of the Study:

  • To investigate the conformational dynamics of OmpA(171) using molecular dynamics (MD) simulations.
  • To explore the potential for transient pore formation within the OmpA(171) beta-barrel.
  • To reconcile the structural and functional properties of OmpA(171).

Main Methods:

  • Molecular dynamics (MD) simulations of OmpA(171) in various environments.
  • Analysis of residue and water molecule mobility within the beta-barrel.

Related Experiment Videos

  • Simulation of OmpA(171) with altered gate region conformations.

    • Main Results:

    • Significant mobility of residues and water molecules within the OmpA(171) beta-barrel was observed.
    • A simulation with a non-native gate conformation revealed an open pore with conductance matching experimental values.
    • OmpA(171) exhibits more dynamic behavior than its crystal structure suggests.

    Conclusions:

    • The OmpA(171) pore is dynamic and can form transiently, explaining observed ionic conductances.
    • A proposed gating mechanism involves the isomerization of Arg138, switching between closed (Glu52) and open (Glu128) states.