Mechanism of selectivity filter constriction in potassium channel: Insights from high-throughput steered molecular dynamics simulations.

Potassium channels are essential for regulating cellular excitability by controlling K ion flow. In voltage-gated potassium (Kv) channels, C-type inactivation modulates action potentials and holds significant physiological and clinical importance. The selectivity filter (SF) of potassium channels functions as the C-type inactivation gate by alternating between conductive and non-conductive states. The bacterial KcsA potassium channel, characterized by well-defined structural features, serves as an ideal model for investigating this mechanism through molecular dynamics (MD) simulations. However, limitations in computational power and the time scales of C-type inactivation, which extend up to seconds, have constrained a comprehensive understanding of this process. This study used high-throughput steered molecular dynamics (SMD) simulations, employing a knowledge-based acceleration strategy, to capture spontaneous SF constriction within nanoseconds in KcsA. Over a thousand SMD simulations recorded hundreds of SF constriction events, revealing a common constriction mechanism driven by an ion occupancy switch from state 13 to state 14 within the SF, facilitated by water molecules located behind the SF. Simulations of the E71V-mutated KcsA suggest that this constricted state and mechanism may also extend to Kv-like channels, albeit with reduced water dependence. These findings underscore the essential roles of ions and water molecules in regulating protein dynamics and highlight strategies for high-throughput MD studies to further explore protein dynamics.