In search of a consensus model of the resting state of a voltage-sensing domain

Abstract

Voltage-sensing domains (VSDs) undergo conformational changes in response to the membrane potential and are the critical structural modules responsible for the activation of voltage-gated channels. Structural information about the key conformational states underlying voltage activation is currently incomplete. Through the use of experimentally determined residue-residue interactions as structural constraints, we determine and refine a model of the Kv channel VSD in the resting conformation. The resulting structural model is in broad agreement with results that originate from various labs using different techniques, indicating the emergence of a consensus for the structural basis of voltage sensing.

Figure 1

Instantaneous configuration of the VSD of the Kv1.2 channel before and after restrained MD simulations. In each panel, the transparent helices show the initial coordinates while the final coordinates are represented in solid colors. (A) Bridge I: residues I177C and R294C form a Cd²⁺-cysteine bridge between the S1 and S4 helices. (B) Bridge II: residues I230C and R294C form a Cd²⁺-cysteine bridge between the S2 and S4 helices. (C) Bridge III: residues I230D and F267D form a Mg²⁺-aspartate bridge between the S3 and S4 helices. (D) Bridge IV: residues E236 and R294K in S2 and S4 interact to stabilize the resting state.

Figure 2

Overlay of simulated VSD structures of the Kv1.2 channel after imposing harmonic restraints. Color scheme is as follows: TM helix S1 is gray, TM helix S2 is yellow, TM helix S3 is red, and TM helix S4 is blue. The Cα shown in the figure correspond to the residues that have been subjected to harmonic restraints. RMSD values given in parenthesis indicate the deviation of the Cα atoms among the four restrained simulations. The overall RMSD of each structure relative to the average consensus model does not exceed 2.2 Å.

Figure 3

Side-by-side comparison of the active (left) and consensus model resting (right) states for a single VSD of the Kv1.2 channel. The Cα of R294 is displaced 7-10 Å vertically. RMS fluctuation values were obtained from Khalili-Araghi's extended simulations and reflect the spread of vertical z coordinates for the backbone Cα atom. Coordinates for the two models are provided as supplementary information.

Figure 4

Model of Kv1.2 VSD bound to avidin via biotin with 10 Å IPEO linker. The coordinates correspond to the consensus model of the resting state. The biotin linker was attached via a disulfide bond to L298C (in Kv1.2). The corresponding residue in KvAP was experimentally shown to be accessible to intracellular avidin (Ruta et al., 2005). The docking was performed while keeping the VSD fixed to ensure that the biotin-avidin did not perturb the protein.