STIM1 transmembrane helix dimerization captured by AI-guided transition path sampling

Abstract STIM1 is a Ca 2+ -sensing protein in the endoplasmic reticulum (ER) membrane. The depletion of ER Ca 2+ stores induces a large conformational transition of the cytosolic STIM1 C-terminus, initiated by the dimerization of the transmembrane (TM) domain. We use the AI-guided transition path sampling algorithm aimmd to extensively sample the dimerization of STIM1-TM helices in an ER-mimicking lipid bilayer. In nearly 0.5 milliseconds of all-atom molecular dynamics simulations without bias potentials, we harvest over 170 transition paths, each about 1.2 µ s long on average. We find that STIM1 dimerizes into three distinct and coexisting configurations, which reconciles conflicting results from earlier crosslinking studies. The dominant X-shaped bound state centers around contacts supported by the SxxxG TM interfacial motif. Mutating residues in this contact interface allows us to tune the STIM1-dimerization propensity in fluorescence experiments. From the trained model of the committor probability of dimerization, we identify the transition state ensemble for TM-helix dimerization. At the transition state, interhelical contacts in the luminal halves of the two monomers dominate, which likely enables the luminal Ca 2+ -sensing domain in STIM1 to condition the dimerization of the TM helices. Our work demonstrates the unique power of AI-guided simulations to sample rare and slow molecular transitions, and to produce detailed atomistic insight into the mechanism of STIM1 TM-helix dimerization as a key step in ER Ca 2+ -sensing. Significance STIM1 is a protein sensor that signals drops in the Ca 2+ concentration inside the endoplasmic reticulum (ER) to the cytosol. As Ca 2+ levels decrease, the STIM1 transmembrane (TM) helices dimerize. We sample this TM helix dimerization in AI-guided atomistic molecular simulations, revealing two distinct pathways of dimerization. We reconcile conflicting results of earlier crosslinking studies by showing that both reported dimer configurations coexist as the end points of distinct association pathways. The dominance of interhelical contacts on the luminal side at the transition state enables the luminal Ca 2+ -sensing domain to condition helix dimerization. AI-guided path sampling made it possible to sample rare helix dimerization events far outside the current reach of regular molecular simulations.