Instantaneous Normal Modes as an Unforced Reaction Coordinate for Protein Conformational Transitions

re l n el me redu s no pen ion ent conformational fluctuations facilitate the coupling between proton binding and global structural transitions (7). fluctuations can be captured based on collective protein instantaneous low-frequency normal modes generated from an elastic network model, while retaining the underlying We illustrate the approach using equilibrium MD trajecto-taneous normal mode trajectories give rise to common intermediate substates, some of which drive the structura