Large-scale protein conformational transitions revealed by weighted ensemble simulations and EPR

Large-amplitude protein conformational changes are essential for cellular processes. Electron paramagnetic resonance (EPR) spectroscopy can detect such conformational changes by measuring distances between site-directed spin labels, but lacks atomistic detail. While standard molecular dynamics (MD) simulations provide atomistic details, the relevant timescales are often inaccessible. Here, we combine weighted ensemble path sampling with EPR distances to capture long-timescale protein conformational transitions in an unbiased manner. We simulated hundreds of pathways for a large-scale conformational transition between the closed and open states of the lysine/arginine/ornithine binding protein (LAOBP). Furthermore, we identified key residue-level interactions that distinguish the two states. Selective mutagenesis of these residues leads to stabilization of the open state of the protein. This approach integrates sparse EPR distances with atomistic simulations, revealing hidden protein states that evolve on milliseconds to seconds timescales.