Protein Folding: Molecular Dynamics Simulations
Molecular dynamics simulations are iterative calculations performed using Newton’s equations of motion to predict the movement of atoms or particles over time.
In vivo protein folding is fast and efficient; to study this process experimentally at atomic detail presents a difficult task (Bartlett and Radford 2009). In contrast, molecular dynamics (MD) simulations can access spatial and temporal resolution beyond the capabilities of experimental methods but is hindered in its ability to acquire data over biological timescales (Daggett 2006). There were notable studies paving the way for atomistic MD studies of protein folding and unfolding. For example, the first folding simulation of a globular protein was reported in 1975 using a coarse-grained model of bovine pancreatic trypsin inhibitor (BPTI) (Levitt and Warshel 1975). Further advancement in computer hardware led to the first united-atom simulation of the same protein in 1977...