41 research outputs found
A Hydrophobic Gate in an Ion Channel: The Closed State of the Nicotinic Acetylcholine Receptor
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,
gamma-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 A.
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 ca. 10 kT to the permeation of sodium ions,
placing an upper bound on the closed channel conductance of 0.3 pS. Thus, a 3 A
radius hydrophobic pore can form a functional barrier to the permeation of a 1
A 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.Comment: Accepted by Physical Biology; includes a supplement and a
supplementary mpeg movie can be found at
http://sbcb.bioch.ox.ac.uk/oliver/download/Movies/watergate.mp
Concentration Dependent Ion Selectivity in VDAC: A Molecular Dynamics Simulation Study
The voltage-dependent anion channel (VDAC) forms the major pore in the outer mitochondrial membrane. Its high conducting open state features a moderate anion selectivity. There is some evidence indicating that the electrophysiological properties of VDAC vary with the salt concentration. Using a theoretical approach the molecular basis for this concentration dependence was investigated. Molecular dynamics simulations and continuum electrostatic calculations performed on the mouse VDAC1 isoform clearly demonstrate that the distribution of fixed charges in the channel creates an electric field, which determines the anion preference of VDAC at low salt concentration. Increasing the salt concentration in the bulk results in a higher concentration of ions in the VDAC wide pore. This event induces a large electrostatic screening of the charged residues promoting a less anion selective channel. Residues that are responsible for the electrostatic pattern of the channel were identified using the molecular dynamics trajectories. Some of these residues are found to be conserved suggesting that ion permeation between different VDAC species occurs through a common mechanism. This inference is buttressed by electrophysiological experiments performed on bean VDAC32 protein akin to mouse VDAC
APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane
Electrostatic forces are one of the primary determinants of molecular interactions. They help guide the folding of proteins, increase the binding of one protein to another and facilitate protein-DNA and protein-ligand binding. A popular method for computing the electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation, and there are several easy-to-use software packages available that solve the PB equation for soluble proteins. Here we present a freely available program, called APBSmem, for carrying out these calculations in the presence of a membrane. The Adaptive Poisson-Boltzmann Solver (APBS) is used as a back-end for solving the PB equation, and a Java-based graphical user interface (GUI) coordinates a set of routines that introduce the influence of the membrane, determine its placement relative to the protein, and set the membrane potential. The software Jmol is embedded in the GUI to visualize the protein inserted in the membrane before the calculation and the electrostatic potential after completing the computation. We expect that the ease with which the GUI allows one to carry out these calculations will make this software a useful resource for experimenters and computational researchers alike. Three examples of membrane protein electrostatic calculations are carried out to illustrate how to use APBSmem and to highlight the different quantities of interest that can be calculated
Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel
Structure and dynamics of voltage-gated ion channels, in particular the motion of
the S4 helix, is a highly interesting and hotly debated topic in current
membrane protein research. It has critical implications for insertion and
stabilization of membrane proteins as well as for finding how transitions occur
in membrane proteins—not to mention numerous applications in drug
design. Here, we present a full 1 µs atomic-detail molecular dynamics
simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By
applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements,
including up to 120° rotation of the S4 segment, changes in
hydrogen-bonding patterns, but only low amounts of translation. A smaller
rotation (∼35°) of the extracellular end of all S4 segments is
present also in a reference 0.5 µs simulation without applied field,
which indicates that the crystal structure might be slightly different from the
natural state of the voltage sensor. The conformation change upon
hyperpolarization is closely coupled to an increase in 310 helix
contents in S4, starting from the intracellular side. This could support a model
for transition from the crystal structure where the hyperpolarization
destabilizes S4–lipid hydrogen bonds, which leads to the helix
rotating to keep the arginine side chains away from the hydrophobic phase, and
the driving force for final relaxation by downward translation is partly
entropic, which would explain the slow process. The coordinates of the
transmembrane part of the simulated channel actually stay closer to the recently
determined higher-resolution Kv1.2 chimera channel than the starting structure
for the entire second half of the simulation (0.5–1 µs).
Together with lipids binding in matching positions and significant thinning of
the membrane also observed in experiments, this provides additional support for
the predictive power of microsecond-scale membrane protein simulations
PIP2-Binding Site in Kir Channels: Definition by Multiscale Biomolecular Simulations†
Phosphatidylinositol bisphosphate (PIP(2)) is an activator of mammalian inwardly rectifying potassium (Kir) channels. Multiscale simulations, via a sequential combination of coarse-grained and atomistic molecular dynamics, enabled exploration of the interactions of PIP(2) molecules within the inner leaflet of a lipid bilayer membrane with possible binding sites on Kir channels. Three Kir channel structures were investigated: X-ray structures of KirBac1.1 and of a Kir3.1-KirBac1.3 chimera and a homology model of Kir6.2. Coarse-grained simulations of the Kir channels in PIP(2)-containing lipid bilayers identified the PIP(2)-binding site on each channel. These models of the PIP(2)-channel complexes were refined by conversion to an atomistic representation followed by molecular dynamics simulation in a lipid bilayer. All three channels were revealed to contain a conserved binding site at the N-terminal end of the slide (M0) helix, at the interface between adjacent subunits of the channel. This binding site agrees with mutagenesis data and is in the proximity of the site occupied by a detergent molecule in the Kir chimera channel crystal. Polar contacts in the coarse-grained simulations corresponded to long-lived electrostatic and H-bonding interactions between the channel and PIP(2) in the atomistic simulations, enabling identification of key side chains
Voltage-Dependent Gating in a “Voltage Sensor-Less” Ion Channel
An unusual mechanism of ion channel regulation generates voltage-dependent gating in the absence of a canonical voltage-sensing domain
Structure, Function, and Modification of the Voltage Sensor in Voltage-Gated Ion Channels
Membrane-Perturbing Properties of Two Arg-Rich Paddle Domains from Voltage-Gated Sensors in the KvAP and HsapBK K +
Energetics of insertion of soluble proteins into membrane
A number of soluble proteins that insert into membranes show a characteristic hairpin bent helix-helix pair, which is presumed to play an important role in insertion into the lipid membrane. However, little is known about the energetics of membrane insertion of such proteins. It is predicted that the spontaneous insertion of hydrophobic helical proteins into lipid bilayers is mainly driven by a hydrophobic free-energy and interaction of polar and charged side chains of protein with the solvent. With a consideration of hairpin bent a helix as an 'elliptical frustrum' we have demonstrated that insertion of such bent alpha-helices into the lipid bilayers is an outcome of various free energies like solvation, lipid perturbation, protein immobilization in lipid and packing energy. Different physical origins and different magnitudes of various free energies satisfy this model for insertion into the membranes