Unraveling the strokes of ion channel molecular machines in computers.

V oltage-gated ion channels are fascinating micromachines responsible for all electrical signaling in biology. In PNAS, Amaral et al. (1) use molecular simulations to show how the new NavAb sodium channel from Arcobacter Butzleri (2) moves between intermediate states similar to K channels, which means it is likely that these principles are generally valid for activation of voltage-gated ion channels. The story of voltage-gated ion channels during the past decade is a beautiful example of experiments and computational studies working hand in hand to advance the state of science. In contrast to most other membrane proteins that are largely hydrophobic, the voltage-sensing domains of these proteins all have an α-helix (S4) with several charges that are responsible for the gating current that can be measured during activation of the channel (3). There has been vivid discussion about the molecular explanation for this process (4); does the segment rotate to alternate between conformations exposed to the intravs. extracellular side, does it rotate and tilt, or does it simply translate vertically when the electrical field changes? MacKinnon’s determination of an X-ray structure of the open state of the Kv1.2 potassium channel in 2005 (5) made it possible to use Kv1.2 to bootstrap discovery of closed ion channel structures by combining molecular modeling with constraints based on cross-linking and other experiments. In only a couple of years, the first early attempts have converged into a remarkably similar view of the relaxed or closed “down-state” of the Kv1.2 voltage sensor (6–10) without any X-ray structures available yet. Other combined studies (11) have further been able to identify and model intermediate conformations that provide direct information about how this particular channel activates (Fig. 1), and, only a few months ago, Jensen et al. managed to simulate the entire actual gating process (12). All this has been a tremendous success of computational modeling, and the sliding helix is now the dominant model for gating. However, none of it would have been possible without exceptional efforts in electrophysiology to derive the molecular restraints (13–15). Yet, in the middle of this success, it is easy to forget that most of the attention has been focused on a fairly narrow class of potassium channels, in particular Kv1.2 and Shaker. Although the voltage sensors of many channels have similar sequences, there is huge functional divergence that gives them completely different roles in our cells. Amaral et al. (1) explore a structure of a sodium channel, NavAb from the bacterium Arcobacter butzleri, recently determined by Payandeh et al. (2). This structure is particularly interesting because the ion channel pore itself is in a closed conformation whereas the four surrounding voltage sensors are almost in the open state—essentially, it appears to be an intermediate conformation corresponding to preopening. Amaral et al. (1) use this intermediate state as a starting point to drive the entire ion channel toward the open and closed states, based on previous X-ray structures and models for the Kv1.2 potassium channel. It is still difficult to simulate the natural deactivation process, and excess hyperpolarization has to be used (12). However, the pattern of the hydrogen bond (or salt-bridge) network between the S4 helix and the rest of the voltage sensor has been shown to fully characterize the different states in previous studies (16), and, by using steered molecular simulation techniques, it is possible to systematically drive the channel between states without directly using specific target coordinates. Amaral et al. (1) use this to parameterize a reaction path with the fully relaxed and fully open conformations as end states, which results in a reaction coordinate R along which the channel transitions can be steered. The authors identify as many as six intermediate conformations along this pathway, they show that many of these are identified and transiently stable for several of the channels, and they illustrate how NavAb moves between them in sequence during activation. Even for a system as large as an ion channel, techniques like this make it quite straightforward to sample complex conformational transitions—although the scientific Fig. 1. Deactivation process for a voltage sensor from a voltage-gated ion channel (illustrated with data from ref. 11). From top to bottom, the sensor starts in a fully activated state corresponding to a depolarizedmembrane. As hyperpolarization is applied, the voltage sensor domain moves through at least two intermediate states in which the charged arginine side chains in the S4 helix (blue) move one position down for each (leaving the next arginine in the chargetransfer center)before it reachesafully relaxed down state. In the down state, a linker causes the voltage sensordomain topush inwardontheporedomain (not shown), which in turn will close the pore. Author contributions: E.L. wrote the paper.