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

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.