The SIMDA framework maps PIP2-binding sites regulating the KCNQ1 channel

Abstract

Voltage-gated potassium channel KCNQ1 (Kv7.1) underpins cardiac repolarization, epithelial ion transport, and inner ear function. Its versatility arises from interactions with KCNE proteins, calmodulin (CaM), and the lipid phosphatidylinositol 4,5-bisphosphate (PIP2), yet the molecular basis of PIP2 regulation remains incompletely understood. Here, we present the Stepwise Integrated Multi-scale Dynamics and Advanced Analysis (SIMDA) framework, which integrates coarse-grained and all-atom molecular dynamics, well-tempered metadynamics, and clustering and energy analyses. Over 2,000 µs of simulations across eight functional states find six recurrent PIP2 sites (C0-C5), each complex populating three to four. Sites C1 and C3 agree with experimental densities, whereas C0, C4, and C5 are forward predictions. KCNE3 stabilizes the primary C1 site by amplifying a C-terminal twist motion, while CaM tunes binding at C4 and C5. Interconnected transfer pathways form a dynamic circular route among sites. SIMDA thus provides a generalizable strategy for dissecting lipid-protein dynamics. PIP2 lipid regulates the cardiac potassium channel KCNQ1. Here, the authors use multiscale simulations to map six PIP2 binding sites and show how KCNE3 and calmodulin redistribute lipid binding to tune channel activity.