Molecular Dynamic Simulation of the Kv1.2 Voltage-Gated Potassium Channel in Open and Closed State Conformations

Photoaffinity Ligand for the Inhalational Anesthetic Sevoflurane Allows Mechanistic Insight into Potassium Channel Modulation

Sevoflurane is a commonly used inhaled general anesthetic. Despite this, its mechanism of action remains largely elusive. Compared to other anesthetics, sevoflurane exhibits distinct functional activity. In particular, sevoflurane is a positive modulator of voltage-gated Shaker-related potassium channels (K_v1.x), which are key regulators of action potentials. Here, we report the synthesis and validation of azisevoflurane, a photoaffinity ligand for the direct identification of sevoflurane binding sites in the K_v1.2 channel. Azisevoflurane retains major sevoflurane protein binding interactions and pharmacological properties within in vivo models. Photoactivation of azisevoflurane induces adduction to amino acid residues that accurately reported sevoflurane protein binding sites in model proteins. Pharmacologically relevant concentrations of azisevoflurane analogously potentiated wild-type K_v1.2 and the established mutant K_v1.2 G329T. In wild-type K_v1.2 channels, azisevoflurane photolabeled Leu317 within the internal S4-S5 linker, a vital helix that couples the voltage sensor to the pore region. A residue lining the same binding cavity was photolabeled by azisevoflurane and protected by sevoflurane in the K_v1.2 G329T. Mutagenesis of Leu317 in WT K_v1.2 abolished sevoflurane voltage-dependent positive modulation. Azisevoflurane additionally photolabeled a second distinct site at Thr384 near the external selectivity filter in the K_v1.2 G329T mutant. The identified sevoflurane binding sites are located in critical regions involved in gating of K_v channels and related ion channels. Azisevoflurane has thus emerged as a new tool to discover inhaled anesthetic targets and binding sites and investigate contributions of these targets to general anesthesia.

Conservation analysis of residues in the S4-S5 linker and the terminal part of the S5-P-S6 pore modulus in Kv and HCN channels: flexible determinants for the electromechanical coupling

Protein mobility is important to achieve protein function. Intrinsic flexibility associated with motion underlies this important issue and the analysis of side chain flexibility gives insights to understand it. In this work, the S5-P-S6 pore modulus (PM) of members of Kv and HCN channels was examined by a combination of sequence alignment, residue composition analysis, and intrinsic side chain flexibility. The PM sequences were organized as a database that was used to reveal and correlate the functional diversity of each analyzed family. Specifically, we focused our attention on the crucial role of the S4-S5 linker and its well-described interaction with the S6 T during the electromechanical coupling. Our analysis suggests the presence of a Gly-hinge in the middle of the S4-S5 linkers. This apparent Gly-hinge links a flexible N-terminal segment with a rigid C-terminal one, although in Kv7 channels, the latter segment is even more flexible. Instead, HCN channels exhibit a putative Thr-hinge and is rich in aromatic residues, in consequence, their linker is more rigid. Concerning S6, we confirm the presence of the two flexible kinks previously described and we provide the complete segmental flexibility profiles for the different families. Our results are discussed in terms of the relation between residue composition, conservation, and local conformational flexibility. This provides important insights to understand and differentiate the characteristic gating properties of these channels as well as their implications in cell physiology.

Insight into the modulation of Shaw2 Kv channels by general anesthetics: structural and functional studies of S4-S5 linker and S6 C-terminal peptides in micelles by NMR

The modulation of the Drosophila Shaw2 Kv channel by 1-alkanols and inhaled anesthetics is correlated with the involvement of the S4-S5 linker and C-terminus of S6, and consistent with stabilization of the channel's closed state. Structural analysis of peptides from S4-S5 (L45) and S6 (S6c), by nuclear magnetic resonance and circular dichroism spectroscopy supports that an α-helical conformation was adopted by L45, while S6c was only in an unstable/dynamic partially folded α-helix in dodecylphosphocholine micelles. Solvent accessibility and paramagnetic probing of L45 revealed that L45 lies parallel to the surface of micelles with charged and polar residues pointing towards the solution while hydrophobic residues are buried inside the micelles. Chemical shift perturbation introduced by 1-butanol on residues Gln320, Thr321, Phe322 and Arg323 of L45, as well as Thr423 and Gln424 of S6c indicates possible anesthetic binding sites on these two important components in the channel activation apparatus. Diffusion measurements confirmed the association of L45, S6c and 1-butanol with micelles which suggests the capability of 1-butanol to influence a possible interaction of L45 and S6c in the micelle environment.

Molecular dynamics simulations of voltage-gated cation channels: insights on voltage-sensor domain function and modulation

Since their discovery in the 1950s, the structure and function of voltage-gated cation channels (VGCC) has been largely understood thanks to results stemming from electrophysiology, pharmacology, spectroscopy, and structural biology. Over the past decade, computational methods such as molecular dynamics (MD) simulations have also contributed, providing molecular level information that can be tested against experimental results, thereby allowing the validation of the models and protocols. Importantly, MD can shed light on elements of VGCC function that cannot be easily accessed through “classical” experiments. Here, we review the results of recent MD simulations addressing key questions that pertain to the function and modulation of the VGCC’s voltage-sensor domain (VSD) highlighting: (1) the movement of the S4-helix basic residues during channel activation, articulating how the electrical driving force acts upon them; (2) the nature of the VSD intermediate states on transitioning between open and closed states of the VGCC; and (3) the molecular level effects on the VSD arising from mutations of specific S4 positively charged residues involved in certain genetic diseases.

Permeation and block of the Kv1.2 channel examined using brownian and molecular dynamics

Using both Brownian and molecular dynamics, we replicate many of the salient features of Kv1.2, including the current-voltage-concentration profiles and the binding affinity and binding mechanisms of charybdotoxin, a scorpion venom. We also elucidate how structural differences in the inner vestibule can give rise to significant differences in its permeation characteristics. Current-voltage-concentration profiles are constructed using Brownian dynamics simulations, based on the crystal structure 2A79. The results are compatible with experimental data, showing similar conductance, rectification, and saturation with current. Unlike KcsA, for example, the inner pore of Kv1.2 is mainly hydrophobic and neutral, and to explore the consequences of this, we investigate the effect of mutating neutral proline residues at the mouth of the inner vestibule to charged aspartate residues. We find an increased conductance, less inward rectification, and quicker saturation of the current-voltage profile. Our simulations use modifications to our Brownian dynamics program that extend the range of channels that can be usefully modeled. Using molecular dynamics, we investigate the binding of the charybdotoxin scorpion venom to the outer vestibule of the channel. A potential of mean force is derived using umbrella sampling, giving a dissociation constant within a factor of ∼2 to experimentally derived constants. The residues involved in the toxin binding are in agreement with experimental mutagenesis studies. We thus show that the experimental observations on the voltage-gated channel, including the toxin-channel interaction, can reliably be replicated by using the two widely used computational tools.

Down-state model of the voltage-sensing domain of a potassium channel

Voltage-sensing domains (VSDs) of voltage-gated potassium (Kv) channels undergo a series of conformational changes upon membrane depolarization, from a down state when the channel is at rest to an up state, all of which lead to the opening of the channel pore. The crystal structures reported to date reveal the pore in an open state and the VSDs in an up state. To gain insights into the structure of the down state, we used a set of experiment-based restraints to generate a model of the down state of the KvAP VSD using molecular-dynamics simulations of the VSD in a lipid bilayer in excess water. The equilibrated VSD configuration is consistent with the biotin-avidin accessibility and internal salt-bridge data used to generate it, and with additional biotin-avidin accessibility data. In the model, both the S3b and S4 segments are displaced approximately 10 A toward the intracellular side with respect to the up-state configuration, but they do not move as a rigid body. Arginine side chains that carry the majority of the gating charge also make large excursions between the up and down states. In both states, arginines interact with water and participate in salt bridges with acidic residues and lipid phosphate groups. An important feature that emerges from the down-state model is that the N-terminal half of the S4 segment adopts a 3(10)-helical conformation, which appears to be necessary to satisfy a complex salt-bridge network.