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Elliptical β-barrel deformation underlies gating in VDAC1.

L Bergdoll¹, M Elgeti², J Belyaeva²

¹Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS, UMR 7255-Aix Marseille Université, Marseille, France.

Protein Science : a Publication of the Protein Society

|June 19, 2026

Summary

Voltage-dependent anion channels (VDAC) control mitochondrial transport. Pressure-perturbed experiments reveal VDAC gating involves reversible beta-barrel deformation, not a fully closed state.

Keywords:

DEER MD simulations VDAC gating pressure perturbation

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Area of Science:

Biophysics
Structural Biology
Membrane Protein Dynamics

Background:

Voltage-dependent anion channels (VDAC) are crucial for mitochondrial metabolite transport.
The precise structural mechanism of VDAC gating remains poorly understood.

Purpose of the Study:

To elucidate the structural mechanism of VDAC gating.
To investigate the open-to-closed transition of VDAC.

Main Methods:

Atomistic molecular dynamics (MD) simulations.
Double electron-electron resonance (DEER) spectroscopy.
Hydrostatic pressure perturbation.
Lipid nanodisc reconstitution.

Main Results:

MD simulations identified intrinsic flexibility in VDAC beta-strands and loops.
High-pressure DEER confirmed reversible, asymmetric beta-barrel deformation.
An elliptical VDAC conformation was identified as a pressure-stabilized, gating-competent state.
Metabolite permeation simulations showed an energy barrier in the elliptical state.

Conclusions:

VDAC gating is driven by reversible beta-barrel deformation.
The elliptical conformation represents a transient gating state.
Pressure-perturbed DEER combined with MD is a powerful strategy for studying transient membrane channel conformations.