Gating Charge Calculations: Probing Voltage-Sensing Proteins through Computational Electrophysiology

Sensitivity to voltage stimuli is a defining property of electrical excitability and is found in ion channels with dedicated voltage sensors, but also in other channels, transporters and even metabotropic receptors. Voltage dependence is conferred by an effective transmembrane charge transfer that can be attributed to global or localized conformational changes, ion or ligand binding, protonation or changes in water accessibility that reshape the electric field.The Computational Electrophysiology protocol, CompEl, (Kutzner et al., Biophys J. 2011), introduced into GROMACS (Abraham et al., 2015, SoftwareX), allows for simulations of realistic transmembrane potentials by all-atom MD. CompEl generates well-defined ion driving forces by maintaining slight ion number differences between two aqueous compartments in a two-bilayer simulation system and has proven successful in the investigation of ion conduction and selectivity of various ion channels (Kopfer et al., Science 2014; Machtens et al., Cell 2015).Gating charge calculations provide insights into molecular bases of voltage sensing and the comparison with experiments furthermore allows refining models of protein structures. We here present an efficient protocol for gating charge calculations using CompEl. Using an antiparallel, symmetric system and considering the bilayer as a capacitor, we simulate the process of membrane charging by ions to investigate the resulting V-Δq relationship. Thereby we directly determine the gating charge and the change in capacitance associated with any conformational change, taking all possible causes of voltage sensitivity explicitly into account. The decomposition of the gating charges into additive contributions from, e.g., protein, water or solutes, permits direct mechanistic insights into the utilized mechanisms of voltage sensing. The contribution of individual side chains to the total gating charge can be easily determined. We illustrate the method on the K+ channel Kv1.2 and the voltage sensor of the voltage-sensitive phosphate Ci-VSP.