Paper Citing NAMD - Abstract
Wirth, Anna Jean; Liu, Yaxin; Prigozhin, Maxim B.; Schulten, Klaus; Gruebele, Martin
Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:7152-7159, JUN 10 2015
The unimolecular folding reaction of small proteins, is now amenable to a very direct mechanistic comparison between experiment and simulation. We present such a comparison of microsecond pressure and temperature jump refolding kinetics Of the engineered WW domain FiP35, a model system for beta-sheet folding. Both perturbations produce experimentally a faster and a slower kinetic phase, and the "slow" microsecond phase is activated. The fast phase shows differences between perturbation methods and is Closer to the downhill limit by temperature jump, but closer to the transiently populated intermediate limit by pressure jump. These observations, make more demands on simulations of the folding process than just a rough comparison of time scales. To complement experiments, we carried out several pressure jump and temperature jump all-atom molecular dynamics trajectories in explicit solvent, where FiP35 folded in five of the six simulations. We analyzed our pressure rump simulations by kinetic modeling and found that the pressure jump experiments and MD simulations are most consistent with a 4-state kinetic mechanism. Together, our experimental and computational data highlight FiP35's position at the boundary where activated inter-Mediates and downhill folding meet, and we Show that this model protein is an excellent candidate for further pressure jump molecular dynamics studies to compare experiment and modeling at the folding mechanism level.
