Ion channels are pore-forming transmembrane proteins that regulate the salt ion flow across cell membranes. One family of these proteins is the voltage-gated sodium (Na_V) channels that exist in excitable cells. The Na_V channels generate and propagate electrical signals through the excitable cells by controlling the flow of salt ions, therefore mediate life sustaining physiological processes such as heartbeat, muscle contraction, brain activity, etc. The mutations and dysfunctions of Na_V channels are related to various severe diseases. This makes Na_V channels appealing targets for therapeutic drugs. While previous experimental and computational studies have greatly advanced our understanding of ion channel operation mechanism, we still lack the information of why certain residues are indispensable and their role in the permeation process. The connection between residues’ significance and functionality is still missing. On the other hand, the gramicidin A (GA) channel has been well characterized both structurally and functionally. Due to its simplicity, the GA channel has been the system of choice for computational model testing.
Here we present a simulation protocol for investigating the individual components' contributions in the permeation mechanism by analyzing the electric field generated by each component of the system. The GA and Na_V1.7 channels were investigated in our study to demonstrate the feasibility and credibility of using electric field as probing method for study ion channel operation mechanisms. We will show conformational ensemble, molecular dynamics (MD), and umbrella sampling simulations that capture different time scales related to ion permeation. The electric field calculations from the MD trajectories are used to rationalize the molecular origin of the driving force of ion diffusion and channel reorganization. In addition to the key residues that hold specific roles in the ion permeation process of Na_V1.7 from previous research of this protein, our results also identified other residues that may have significant impact on the permeation process, which provides directions and guidance for future experimental studies.

Taoyi Chen

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