PittsburghV1, France, Analysis, bibRecord, 000215

Structure guided simulations illuminate the mechanism of ATP transport through VDAC1

Identifieur interne : 000215 ( France/Analysis ); précédent : 000214; suivant : 000216

Structure guided simulations illuminate the mechanism of ATP transport through VDAC1

Auteurs : O. P. Choudhary [États-Unis] ; A. Paz [États-Unis] ; J. L. Adelman [États-Unis] ; J. P. Colletier [France] ; J. Abramson [États-Unis, Inde] ; M. Grabe [États-Unis]

Source :

Nature structural & molecular biology [ 1545-9993 ] ; 2014.

RBID : PMC:4157756

Descripteurs français

English descriptors

KwdEn :
- Adenosine Triphosphate (chemistry), Adenosine Triphosphate (metabolism), Animals, Binding Sites, Computer Simulation, Crystallography, X-Ray, Markov Chains, Mice, Mitochondrial Membranes (metabolism), Models, Molecular, Protein Structure, Tertiary, Voltage-Dependent Anion Channel 1 (chemistry), Voltage-Dependent Anion Channel 1 (metabolism), Voltage-Dependent Anion Channel 1 (physiology).
MESH :
- chemical , chemistry : Adenosine Triphosphate, Voltage-Dependent Anion Channel 1.
- chemical , metabolism : Adenosine Triphosphate, Voltage-Dependent Anion Channel 1.
- metabolism : Mitochondrial Membranes.
- chemical , physiology : Voltage-Dependent Anion Channel 1.
- Animals, Binding Sites, Computer Simulation, Crystallography, X-Ray, Markov Chains, Mice, Models, Molecular, Protein Structure, Tertiary.

Abstract

The voltage-dependent anion channel (VDAC) mediates metabolite and ion flow across the outer mitochondrial membrane of all eukaryotic cells. The open channel passes millions of ATP molecules per second, while the closed state exhibits no detectable ATP flux. High-resolution structures of VDAC1 revealed a 19-stranded β-barrel with an α-helix partially occupying the central pore. To understand ATP permeation through VDAC, we solved the crystal structure of mouse VDAC1 (mVDAC1) in the presence of ATP, revealing a low-affinity binding site. Guided by these coordinates, we initiated hundreds of molecular dynamics (MD) simulations to construct a Markov State Model (MSM) of ATP permeation. These simulations indicate that ATP flows through VDAC using multiple pathways, consistent with our structural data and experimentally determined physiological rates.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157756

DOI: 10.1038/nsmb.2841
PubMed: 24908397
PubMed Central: 4157756

Affiliations:

Links to Exploration step

PMC:4157756

Le document en format XML

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<front><div type="abstract" xml:lang="en"><p id="P1">The voltage-dependent anion channel (VDAC) mediates metabolite and ion flow across the outer mitochondrial membrane of all eukaryotic cells. The open channel passes millions of ATP molecules per second, while the closed state exhibits no detectable ATP flux. High-resolution structures of VDAC1 revealed a 19-stranded β-barrel with an α-helix partially occupying the central pore. To understand ATP permeation through VDAC, we solved the crystal structure of mouse VDAC1 (mVDAC1) in the presence of ATP, revealing a low-affinity binding site. Guided by these coordinates, we initiated hundreds of molecular dynamics (MD) simulations to construct a Markov State Model (MSM) of ATP permeation. These simulations indicate that ATP flows through VDAC using multiple pathways, consistent with our structural data and experimentally determined physiological rates.</p>
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Structure guided simulations illuminate the mechanism of ATP transport through VDAC1

Structure guided simulations illuminate the mechanism of ATP transport through VDAC1

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