UCSF

The molecular actions of proteins occur along reaction coordinates. Current computer methods have limited ability to explore them. We describe a fast protocol called MELD-path that (1) efficiently samples relevant conformational states via MELD, an accelerator of Molecular Dynamics (MD), (2) seeds multiple short MD trajectories from MELD states, and then (3) constructs Markov State Models (MSM) that give the routes and kinetics. We tested the method against extensive (multi μs) MD simulations of the right-handed- to left-handed-helix transition of a 9-mer peptide of AIB, the symmetry of which allows us to establish convergence. MELD-path finds all the metastable states, their correct relative populations, and the full ensemble of routes, not just a single assumed route. For this transition, we find a very broad route structure. MELD-path is highly parallelizable and efficient, yielding the full route map in a few days of computation. We believe MELD-path could be a general and rapid way to explore mechanistic processes in biomolecules on the computer.