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A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor

Oliver Beckstein1,2 and Mark S P Sansom2

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The nicotinic acetylcholine receptor (nAChR) is the prototypic member of the 'Cys-loop' superfamily of ligand-gated ion channels which mediate synaptic neurotransmission, and whose other members include receptors for glycine, γ-aminobutyric acid and serotonin. Cryo-electron microscopy has yielded a three-dimensional structure of the nAChR in its closed state. However, the exact nature and location of the channel gate remains uncertain. Although the transmembrane pore is constricted close to its center, it is not completely occluded. Rather, the pore has a central hydrophobic zone of radius about 3 Å. Model calculations suggest that such a constriction may form a hydrophobic gate, preventing movement of ions through a channel. We present a detailed and quantitative simulation study of the hydrophobic gating model of the nicotinic receptor, in order to fully evaluate this hypothesis. We demonstrate that the hydrophobic constriction of the nAChR pore indeed forms a closed gate. Potential of mean force (PMF) calculations reveal that the constriction presents a barrier of height about 10 kT to the permeation of sodium ions, placing an upper bound on the closed channel conductance of 0.3 pS. Thus, a 3 Å radius hydrophobic pore can form a functional barrier to the permeation of a 1 Å radius Na+ ion. Using a united-atom force field for the protein instead of an all-atom one retains the qualitative features but results in differing conductances, showing that the PMF is sensitive to the detailed molecular interactions.


PACS

87.16.Uv Active transport processes

87.15.K- Molecular interactions; membrane-protein interactions

87.15.B- Structure of biomolecules

87.16.A- Theory, modeling, and simulations

Subjects

Biological physics

Dates

Issue 2 (June 2006)

Received 2 February 2006, accepted for publication 14 June 2006

Published 7 July 2006

 
An M2 helix bundle depicted as ribbons, the membrane mimetic slab is made from methane molecules on a fcc lattice, water molecules are represented as sticks, and ions as ice-blue (Na+) or yellow (Cl-) spheres.


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