In silico characterization of the gating and selectivity mechanism of the human TPC2 cation channel

Membrane proteins and ion channels are essential components of the cellular machinery, playing crucial roles in signal transduction, ion transport, and many other biological processes. Amongst ion channels, human two-pore channels (TPCs) are of significant interest due to their unique ligand-dependent ion selectivity, enigmatic voltage sensing mechanism, and biomedical relevance, especially in viral infection. However, despite their importance in the field, ligand and voltage-depending activation and the molecular mechanisms underlying their ion selectivity are still insufficiently understood. Here, we set out to elucidate the mechanistic basis for the ion selectivity of human TPC2 (hTPC2) and the molecular mechanism of ligand-induced channel activation by the lipid PIP2. We performed all-atom in silico electrophysiology simulations and analyzed the data using AI-based and in-house-built scripts to study Na+ and Ca2+ permeation across hTPC2 in real-time and to investigate the conformational changes induced by the presence or absence of bound PIP2.
Our findings reveal that hTPC2 adopts distinct structures depending on the presence of PIP2 and elucidate the conformational transition pathways between these structures. Additionally, we extensively examined the permeation mechanism, solvation states, and binding sites of ions during ion permeation through the pore. Our simulations confirm the experimental observation that hTPC2 is more selective for Na+ over Ca2+ ions in the presence of PIP2. Our results shed light on the multilayered selectivity mechanism of ion selectivity, elucidate the distant communication between the ligand-binding site and the selectivity filter, and reveal how lysosomal pH can affect the mechanism of action of hTPC2.
Overall, our research provides a good understanding of the structural mechanisms and ion conductance properties of human TPCs, paving the way for further investigations into their physiological functions and potential therapeutic applications. The findings of my work also highlight the power of computational structural biology approaches for investigating biomedically important, complex biological systems on the molecular level.