Molecular Dynamics Simulation of Kv Channel Voltage Sensor Helix in a Lipid Membrane with Applied Electric Field

Abstract

In this article, we present the results of the molecular dynamics simulations of amphiphilic helix peptides of 13 amino-acid residues, placed at the lipid-water interface of dipalmitoylphosphatidylcholine bilayers. The peptides are identical with, or are derivatives of, the N-terminal segment of the S4 helix of voltage-dependent K channel KvAP, containing four voltage-sensing arginine residues (R1-R4). Upon changing the direction of the externally applied electric field, the tilt angle of the wild-type peptide changes relative to the lipid-water interface, with the N-terminus heading up with an outward electric field. These movements were not observed using an octane membrane in place of the dipalmitoylphosphatidylcholine membrane, and were markedly suppressed by 1), substituting Phe located one residue before the first arginine (R1) with a hydrophilic residue (Ser, Thr); or 2), changing the periodicity rule of Rs from at-every-third to at-every-fourth position; or 3), replacing R1 with a lysine residue (K). These and other findings suggest that the voltage-dependent movement requires deep positioning of Rs when the resting (inward) electric field is present. Later, we performed simulations of the voltage sensor domain (S1-S4) of Kv1.2 channel. In simulations with a strong electric field (0.1 V/nm or above) and positional restraints on the S1 and S2 helices, S4 movement was observed consisting of displacement along the S4 helix axis and a screwlike axial rotation. Gating-charge-carrying Rs were observed to make serial interactions with E183 in S1 and E226 in S2, in the outer water crevice. A 30-ns-backward simulation started from the open-state model gave rise to a structure similar to the recent resting-state model, with S4 moving vertically approximately 6.7 A. The energy landscape around the movement of S4 appears very ragged due to salt bridges formed between gating-charge-carrying residues and negatively charged residues of S1, S2, and S3 helices. Overall, features of S3 and S4 movements are consistent with the recent helical-screw model. Both forward and backward simulations show the presence of at least two stable intermediate structures in which R2 and R3 form salt bridges with E183 or E226, respectively. These structures are the candidates for the states postulated in previous gating kinetic models, such as the Zagotta-Hoshi-Aldrich model, to account for more than one transition step per subunit for activation.

Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations

“…During the first QðtÞ drop, the four VSDs relaxed from the initial α-state toward a metastable β-state. The latter bears a strong similarity with the intermediate kinetic state previously identified in independent work (22)(23)(24). In the subsequent QðtÞ drop (II), the VSD of subunit 1 underwent further salt-bridge rearrangements, which led to yet another state, called here γ, lasting for over 0.5 μs.…”

From the gating charge response to pore domain movement: Initial motions of Kv1.2 dynamics under physiological voltage changes

“…This Figure shows how the electric field is focused near the S4 domain. Similar behaviour has also been observed in other studies and it has been hypothesized that such a focusing effect contributes to an increased switching sensitivity of the channel as the voltage drop changes [27,28,30,31]. …”

“…In particular, the atomic interactions of the gating charges, Arg 294 , Arg 297 , Arg 300 , and Arg 303 located on the S4 domain, are of interest because their movements are considered to be the driving force for voltage sensor domain motions [11,14,27,28,30–41]. As no constraints were used during these simulations, the arginine positions are influenced by their interactions with lipid and water molecules and thus contribute to changes within the local electrical field of the membrane [11,14,27,28,30,31]. Note that our understanding of their response to voltage depends on convergence of sampling and thus we are limited to what is seen within the 10 ns simulations at each voltage level.…”

“…Note that our understanding of their response to voltage depends on convergence of sampling and thus we are limited to what is seen within the 10 ns simulations at each voltage level. Previous studies of smaller systems, involving only the helix-turn-helix motif of the voltage sensor domain, observed fluctuations in the total number of lipid and water hydrogen-bonds around the gating charges for all proteins when varying the voltage from the resting potential to a depolarized potential [14,30]. Due to the unconstrained nature of our MD simulations, environmental effects such as lipid or water molecule coordination influence arginine sidechain behavior (e.g., flexibility and position within the bilayer).…”

Computer Simulations of Voltage-Gated Cation Channels

“…In these MD simulations, ΔV was generated either by applying an external electric field 30,31 or by employing approaches in which the voltage is imposed via a charge imbalance protocol. 32–34 The latter based on an ionic-charge imbalance between two disconnected aqueous baths of explicit electrolytes, is able to induce a drop in the electrostatic potential across the lipid bilayer in an almost physiologically relevant range of values, without introducing artificial external fields to the system.…”