The response of a membrane-bound Kv1.2 ion channel to an applied transmembrane potential has been studied using molecular dynamics simulations. Channel deactivation is shown to involve three intermediate states of the voltage sensor domain (VSD), and concomitant movement of helix S4 charges 10-15 Å along the bilayer normal; the latter being enabled by zipper-like sequential pairing of S4 basic residues with neighboring VSD acidic residues and membrane-lipid head groups. During the observed sequential transitions S4 basic residues pass through the recently discovered charge transfer center with its conserved phenylalanine residue, F 233 . Analysis indicates that the local electric field within the VSD is focused near the F 233 residue and that it remains essentially unaltered during the entire process. Overall, the present computations provide an atomistic description of VSD response to hyperpolarization, add support to the sliding helix model, and capture essential features inferred from a variety of recent experiments.gating charge | S4 helix | voltage-gated channel V oltage sensor domains (VSDs) are membrane-embedded constructs, which work as electrical devices responding to changes in the transmembrane (TM) voltage. They are ubiquitous to voltage-gated channels (VGCs) in which four of these units are attached to the main pore (1). During channel activation, the displacements of the charges tethered to the VSD give rise to transient "gating" currents, the time integral of which is the "gating charge" (GQR) translocated across the membrane capacitance. Phenomenological kinetic models devised to describe the time course of such currents are very diverse but all indicate that during VGC activation, the VSD undergoes a complex conformational change that encompasses many transitions (2-5).Three main models have been proposed to rationalize the transfer of a large GQR across the low dielectric membrane in VGCs (6, 7). All are associated with the motion of S4, the conserved highly positively charged helix of the VSDs (8). In the sliding helix model (9, 10), the positively charged (basic) residues of the S4 segment form sequential ion pairs with acidic residues on neighboring TM segments and move a large distance perpendicular to the membrane plane. The transporter model derives from measurements of a focused electrical field within the membrane and suggests that during activation, the latter is reshaped. Accordingly, it is posited that S4 does not move its charges physically very far across the membrane (8). A third model was introduced following publication of the KvAP structure (11). Here, the position of the S3-S4 helical hairpin with respect to the pore domain suggested a gating mechanism in which the hairpin moves through the membrane in a paddle-like motion translocating S4 basic residues across the membrane, and reaching a TM position only in the activated state. Crystal structures of the Kv1.2 channel (12) and the Kv1.2-Kv2.1 paddle chimera (13) indicated later that the KvAP structure likely represented a non...

The recent crystal structure of Orai, the pore unit of a calcium release-activated calcium (CRAC) channel, is used as the starting point for molecular dynamics and free-energy calculations designed to probe this channel's conduction properties. In free molecular dynamics simulations, cations localize preferentially at the extracellular channel entrance near the ring of Glu residues identified in the crystal structure, whereas anions localize in the basic intracellular half of the pore. To begin to understand ion permeation, the potential of mean force (PMF) was calculated for displacing a single Na + ion along the pore of the CRAC channel. The computed PMF indicates that the central hydrophobic region provides the major hindrance for ion diffusion along the permeation pathway, thereby illustrating the nonconducting nature of the crystal structure conformation. Strikingly, further PMF calculations demonstrate that the mutation V174A decreases the free energy barrier for conduction, rendering the channel effectively open. This seemingly dramatic effect of mutating a nonpolar residue for a smaller nonpolar residue in the pore hydrophobic region suggests an important role for the latter in conduction. Indeed, our computations show that even without significant channel-gating motions, a subtle change in the number of pore waters is sufficient to reshape the local electrostatic field and modulate the energetics of conduction, a result that rationalizes recent experimental findings. The present work suggests the activation mechanism for the wild-type CRAC channel is likely regulated by the number of pore waters and hence pore hydration governs the conductance.store-operated calcium entry | computer simulation C alcium release-activated calcium (CRAC) channels in the plasma membrane are integral membrane proteins that play a central role in cellular signaling by generating the sustained influx of calcium (1-3). Immune response in cells consists typically of a fall in Ca 2+ content within the endoplasmic reticulum (ER), followed by the opening of the store-operated CRAC channels that leads to the sustained increase in intracellular Ca 2+ concentrations (4). Despite about two decades of research, the molecular components underlying this process of store-operated calcium entry (SOCE) have been unknown until recently, when the stromal interaction molecule (STIM) was determined to be the ER Ca 2+ sensor (5, 6) that activates the channel in response to the depletion of intracellular calcium store content. Later, the Orai protein was identified as the pore subunit of the channel (7-9). CRAC regulator 2A was then discovered to reinforce the binding of the two aforementioned key components at elevated Ca 2+ levels to promote the SOCE, and to inhibit the influx at low Ca 2+ levels by dissociating from the complex (10). The newly published crystal structure of the CRAC channel pore subunit, Orai, from Drosophila melanogaster at 3.35 Å resolution, provides groundbreaking insights into a molecular architecture that is distinct from ...

Accurate modeling of ion transport through synthetic and biological transmembrane channels has been so far a challenging problem. We introduce here a new method that allows one to study such transport under realistic biological conditions. We present results from molecular dynamics simulations of an ion channel formed by a peptide nanotube, embedded in a lipid bilayer, and subject to transmembrane potentials generated by asymmetric distributions of ions on both sides of the membrane. We show that the method is efficient for generating ionic currents and allows us to estimate the intrinsic conductance of the channel.

Recently, the structure of the Shaker channel Kv1.2 has been determined at a 2.9-angstroms resolution. This opens new possibilities in deciphering the mechanism underlying the function of voltage-gated potassium (Kv) channels. Molecular dynamics simulations of the channel, embedded in a membrane environment show that the channel is in its open state and that the gating charges carried by S4 are exposed to the solvent. The hydrated environment of S4 favors a local collapse of the electrostatic potential, which generates high electric-field gradients around the arginine gating charges. Comparison to experiments suggests furthermore that activation of the channel requires mainly a lateral displacement of S4. Overall, the results agree with the transporter model devised for Kv channels from electrophysiology experiments, and provide a possible pathway for the mechanistic response to membrane depolarization.