Exploring the Complex Dynamics of an Ion Channel Voltage Sensor Domain via Computation

Abstract

Voltage-gated ion channels are ubiquitous proteins that orchestrate electrical signaling across excitable membranes. Key to their function is activation of the voltage sensor domain (VSD), a transmembrane four alpha-helix bundle that triggers channel opening. Modeling of currents from electrophysiology experiments yields a set of kinetic parameters for a given channel, but no direct molecular insight. Here we use molecular dynamics (MD) simulations to determine the free energy landscape of VSD activation and to, ultimately, predict the time evolution of the resulting gating currents. Our study provides the long-sought-for bridge between electrophysiology and microscopic molecular dynamics and confirms, as already suggested on the basis of experiments, that rate-limiting barriers play a critical role in activation kinetics. IntroductionDespite the complexity of the molecular processes underpinning electrical excitability of cells, the macroscopic currents measured in a typical electrophysiology experiment obey remarkably simple mathematical laws expressed in terms of few state variables. This observation, originating from the pioneering work of Hodgkin and Huxley, is replete with deep consequences: voltage gated ion channels (VGCs), the membrane proteins responsible for such currents, ought to cycle through a small number of distinct structural states. Accordingly, electrophysiology experiments are usually interpreted using the discrete state Markov (DSM) models approach, whereby a set of parameters characterizes each VGC under given conditions (1, 2). This kinetic "discreteness" has been traditionally interpreted as the consequence of few well-defined free energy basins separated by rate-limiting free energy barriers. Identifying the structure associated to each of these minima is a long-standing scientific endeavor that has benefitted from the contribution of various approaches such as mutagenesis experiments (e.g. charge reversal and disulfide locking) (3-6), X-ray crystallography (7,8) and MD simulations (9-12). The significance of these studies that relate the electrical properties of VGCs to their physico-chemical determinants (4,9,(12)(13)(14)(15)) is clear: a molecular level picture is key to understand the modulatory role of a myriad of physiological factors and to develop novel modulators.

Challenges and advances in atomistic simulations of potassium and sodium ion channel gating and permeation

“…; Delemotte et al . ). Interestingly, the same work demonstrated a nearly 0 kcal mol −1 end‐point free energy difference when considering Δ Q as a reaction coordinate (Delemotte et al .…”

Molecular Insights from Conformational Ensembles via Machine Learning

“…In a previous study, we reported five conformational states of the Kv1.2 VSD called E (resting), A (activated), and Δ , Γ , and B (intermediate states) ( 49 , 50 ). Here, we followed the provided checklist ( Box 1 ) and trained an RF classifier to compare these states and elucidate their defining structural elements using more than 12,000 frames from an enhanced sampling trajectory (see Methods ).…”

“…Snapshots corresponding to configurations making up five metastable states were extracted from a metadynamics trajectory taken from our previous study (48,49). The five states were previously identified using the network of salt bridges between the S4 positive residues and their negative counterparts as a collective variable (50).…”

Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport

“…Instead, enhanced sampling was used, in the form of metadynamics simulations [148]. The set of collective variables that was used to enhance the sampling combined breaking and forming of salt bridges and the displacement of the voltage sensor’s charged residue along the pathway defined by binding partners [236]. When projected onto the gating charge reaction coordinate, the free energy landscape reveals that the activation sequence involves five metastable states that are organized in an early activation sequence with three low free energy barriers (~5 kcal/mol) and a late activation sequence involving a single high free energy barrier (~12 kcal/mol) (Figure 4.C).…”

“…Note the three low free energy barriers in the early activation sequence (~5 kcal/mol) and the single high free energy barrier in the late activation sequence (~12 kcal/mol) (D) Comparison between gating currents obtained from kinetic modeling using the free energy landscape calculated by molecular dynamics simulations (black) and inferred from electrophysiology recordings (green). From [236], licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). …”