Molecular Dynamics-Based Thermodynamic and Kinetic Characterization of Membrane Protein Conformational Transitions.

by Ogden, Dylan; Moradi, Mahmoud

A review. Mol. dynamics (MD) simulations are routinely used to study structural dynamics of membrane proteins. However, conventional MD is often unable to sample functionally important conformational transitions of membrane proteins such as those involved in active membrane transport or channel activation process. Here we describe a combination of multiple MD based techniques that allows for a rigorous characterization of energetics and kinetics of large-scale conformational changes in membrane proteins. The methodol. is based on biased, nonequil, collective-variable based simulations including nonequil pulling, string method with swarms of trajectories, bias-exchange umbrella sampling, and rate estn. techniques.