Deciphering Ca 2+ Permeation and Valence Selectivity in Ca V 1: Molecular Dynamics Simulations Reveal the Three-Ion Knock-on Mechanism

Abstract Voltage-gated calcium (Ca V ) channels are pivotal in cellular signaling due to their selective calcium ion permeation upon membrane depolarization. While previous studies have established the highly selective permeability of Ca V channels, the detailed molecular mechanism remains elusive. Here we use extensive atomistic molecular dynamics simulations to elucidate the mechanisms governing ion permeation and valence selectivity in Ca V 1 channels. Employing the electronic continuum correction method, we simulated a calcium conductance of approximately 9–11 pS, aligning closely with experimental measurement. Our simulations uncovered a three-ion knock-on mechanism critical for efficient calcium ion permeation, necessitating the binding of at least two calcium ions within the selectivity filter (SF) and the subsequent entry of a third ion. In silico mutation simulations further validated the importance of multi-ion coordination in the SF for efficient ion permeation, identifying two critical residues, D706 and E1101, that are essential for the binding of two calcium ions in the SF. Moreover, we explored the competitive permeation of calcium and sodium ions, and obtained a valence selectivity favoring calcium over sodium at a ratio of approximately 35:1 under the bi-cation condition. This selectivity arises from the strong electrostatic interactions of calcium ions in the confined SF and the three-ion knock-on mechanism. Our findings provide novel insights into the molecular underpinnings of Ca V channel function, with implications for understanding calcium-dependent cellular processes.