Qingfeng Zhong

The M2 channel of influenza A virus: a molecular dynamics study

Molecular dynamics simulations have been performed on a tetramer of the 25‐residue (SSDPLVVAASIIGILHLILWILDRL) synthetic peptide [1] which contains the transmembrane domain of the influenza A virus M2 coat protein. The peptide bundle was initially assembled as a parallel α‐helix bundle in the octane portion of a phase separated water/octane system, which provided a membrane‐mimetic environment. A 4‐ns dynamics trajectory identified a left‐handed coiled coil state of the neutral bundle, with a water filled funnel‐like structural motif at the N‐terminus involving the long hydrophobic sequence. The neck of the funnel begins at V27 and terminates at H37, which blocks the channel. The C‐terminus is held together by inter‐helix hydrogen bonds and contains water below H37. Solvation of the S23 and D24 residues, located at the rim of the funnel, appears to be important for stability of the structure. The calculated average tilt of the helices in the neutral bundle is 27±5°, which agrees well with recent NMR data.

Molecular Dynamics Simulation of a Synthetic Ion Channel

A molecular dynamics simulation has been performed on a synthetic membrane-spanning ion channel, consisting of four alpha-helical peptides, each of which is composed of the amino acids leucine (L) and serine (S), with the sequence Ac-(LSLLLSL)3-CONH2. This four-helix bundle has been shown experimentally to act as a proton-conducting channel in a membrane environment. In the present simulation, the channel was initially assembled as a parallel bundle in the octane portion of a phase-separated water/octane system, which provided a membrane-mimetic environment. An explicit reversible multiple-time-step integrator was used to generate a dynamical trajectory, a few nanoseconds in duration for this composite system on a parallel computer, under ambient conditions. After more than 1 ns, the four helices were found to adopt an associated dimer state with twofold symmetry, which evolved into a coiled-coil tetrameric structure with a left-handed twist. In the coiled-coil state, the polar serine side chains interact to form a layered structure with the core of the bundle filled with H2O. The dipoles of these H2O molecules tended to align opposite the net dipole of the peptide bundle. The calculated dipole relaxation function of the pore H2O molecules exhibits two reorientation times. One is approximately 3.2 ps, and the other is approximately 100 times longer. The diffusion coefficient of the pore H2O is about one-third of the bulk H2O value. The total dipole moment and the inertia tensor of the peptide bundle have been calculated and reveal slow (300 ps) collective oscillatory motions. Our results, which are based on a simple united atom force-field model, suggest that the function of this synthetic ion channel is likely inextricably coupled to its dynamical behavior.

SIMULATION OF THE HIV-1 VPU TRANSMEMBRANE DOMAIN AS A PENTAMERIC BUNDLE

The transmembrane domain of oligomeric protein Vpu encoded by HIV‐1 has been studied by means of a molecular dynamics simulation. A pentameric bundle of unconstrained helices (residues 6–28 of Vpu) with a water filled pore was initially assembled in a membrane mimetic octane/water system. This system was simulated, using the CHARMm19 and OPLS united atom force fields with no constraints at a temperature of 300 K and a pressure of 1 atm. For these forcefields and the initial conditions tested, the oligomeric bundle expelled most of the pore water molecules. The resulting bundle and residual waters adopt a conical structural motif with some resemblance to a potassium channel.

Exploration of the Structural Features Defining the Conduction Properties of a Synthetic Ion Channel

The finite-difference Poisson-Boltzmann methodology was applied to a series of parallel, alpha-helical bundle models of the designed ion channel peptide Ac-(LSSLLSL)3-CONH2. This method is able to fully describe the current-voltage curves for this channel and quantitatively explains their cation selectivity and rectification. We examined a series of energy-minimized models representing different aggregation states, side-chain rotamers, and helical rotations, as well as an ensemble of structures from a molecular dynamics trajectory. Potential energies were computed for single, permeating K+ and Cl- ions at a series of positions along a central pathway through the models. A variable-electric-field Nernst-Planck electrodiffusion model was used, with two adjustable parameters representing the diffusion coefficients of K+ and Cl- to scale the individual ion current magnitudes. The ability of a given DelPhi potential profile to fit the experimental data depended strongly on the magnitude of the desolvation of the permeating ion. Below a pore radius of 3.8 A, the predicted profiles showed large energy barriers, and the experimental data could be fit only with unrealistically high values for the K+ and Cl- diffusion coefficients. For pore radii above 3.8 A, the desolvation energies were 2kT or less. The electrostatic calculations were sensitive to positioning of the Ser side chains, with the best fits associated with maximum exposure of the Ser side-chain hydroxyls to the pore. The backbone component was shown to be the major source of asymmetry in the DelPhi potential profiles. Only two of the energy-minimized structures were able to explain the experimental data, whereas an average of the dynamics structures gave excellent agreement with experimental results. Thus this method provides a promising approach to prediction of current-voltage curves from three-dimensional structures of ion channel proteins.

Constant pressure and temperature molecular-dynamics simulation of the hydrated diphytanolphosphatidylcholine lipid bilayer

Diphytanolphosphatidylcholine (DPhPC) is a lipid widely used in the study of membrane channel activity. Herein we report the results of a constant temperature (T=25 °C) and constant pressure (p=1 atm) molecular-dynamics (MD) simulation of a hydrated liquid crystal phase DPhPC bilayer. The simulated system consisted of a periodically replicated cell containing 64 lipid and 1792 water molecules. The system was monitored during a trajectory spanning more than one nanosecond. The resulting unconstrained area density per lipid agreed quantitatively with experimental data. The calculated bilayer profile and acyl chain order parameters also compared favorably with x-ray scattering and nuclear magnetic resonance (NMR) data.

Two possible conducting states of the influenza A virus M2 ion channel

Molecular dynamics simulations have been performed on protonated four‐helix bundles based on the 25‐residue Duff–Ashley transmembrane sequence of the M2 channel of the influenza A virus. Well‐equilibrated tetrameric channels, with one, two and four of the H37 residues protonated, were investigated. The protonated peptide bundles were immersed in the octane portion of a phase‐separated water/octane system, which provided a membrane‐mimetic environment. The simulations suggest that there could be two conducting states of the M2 channel corresponding to tetramers containing one or two protonated histidines. The more open structure of the doubly protonated state suggests it would have the higher conductance.

Molecular dynamics study of the LS3 voltage-gated ion channel

Molecular dynamics calculations have been carried out on a model of the LS3 synthetic ion channel in a membrane mimetic environment. In the absence of an external electrostatic field, the LS3 channel, which consists of a bundle of six α‐helices with sequence Ac‐(LSSLLSL)3‐CONH2, exhibits large structural fluctuations. However, in the presence of the field, the bundle adopts a well defined coiled‐coil structure with an inner pore of water. The observed structural changes induced by the applied field are consistent with the proposed gating mechanism of the ion channel.

Molecular dynamics simulation of four-α-helix bundles that bind the anesthetic halothane

The mutation of a single leucine residue (L38) to methionine (M) is known experimentally to significantly increase the affinity of the synthetic four‐α‐helix bundle (Aα2)2 for the anesthetic halothane. We present a molecular dynamics study of the mutant (Aα2–L38M)2 peptide, which consists of a dimer of 62‐residue U‐shaped di‐α‐helical monomers assembled in an anti topology. A comparison between the simulation results and those obtained for the native (Aα2)2 peptide indicates that the overall secondary structure of the bundle is not affected by the mutation, but that the side chains within the monomers are better packed in the mutant structure. Unlike the native peptide, binding of a single halothane molecule to the hydrophobic core of (Aα2–L38M)2 deforms the helical nature of one monomer in a region close to the mutation site. Increased exposure of the cysteine side chain to the hydrophobic core in the mutant structure leads to the enhancement of the attractive interaction between halothane and this specific residue. Since the mutated residues are located outside the hydrophobic core the observed increased affinity for halothane appears to be an indirect effect of the mutation.

Molecular dynamics study of structure and gating of low molecular weight ion channels

Abstract We implement molecular dynamics (MD) simulations on low molecular weight alpha helix-based functional synthetic and native ion channels. The synthetic channels are the LS2 proton channel and the LS3 voltage-gated channel. The simulation manifests key features of the channels such as the coiled-coil structure of the alpha-helix bundle and the continuous aqueous pore. By implementing simulations with and without an applied voltage, we develop a hypothesis as to the voltage-gating mechanism. The native channel is the M2 proton channel in the influenza A virus, which plays an essential role in the infection process. This channel is pH gated via protonation of one or more imidazole rings in the H37 residues. Simulation of the neutral channel reveals a coiled-coil structure whose pore is penetrated by water, but not threaded by a water column. By means of simulations with different numbers of charged H37 residues, we demonstrate a possible gating action via opening up the channel to a continuous water column, and also provide support for the alternative proton relay gating mechanism.

Molecular Dynamics Simulation of Ion Channels

Although the biological function of ion channels associated with cells has been clarified, an atomic level understanding of these transmembrane proteins is still lacking. Molecular Dynamics (MD) simulations are a well suited tool to gain insight into the function of such proteins in their host environment. First, we give a brief introduction to the field of ion channels by describing the basic properties, structure, and function of an ion channel. We then present specific results for three a-helical bundles: the synthetic LS2 and LS3 channels, and a shortened sequence of the M2 channel protein associated with the influenza virus.