title: Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations.
abstract: 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 β-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 jump 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 intermediates 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.
authors.affiliation: Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States.
authors.forename: Anna Jean
authors.initials: AJ
authors.lastname: Wirth
authors.affiliation: Department of Physics, and Beckman Institute, University of Illinois, Urbana, Illinois 61801, United States.
authors.forename: Yanxin
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States.
authors.forename: Maxim B
authors.initials: MB
authors.lastname: Prigozhin
authors.affiliation: Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States.|Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, United States.|Department of Physics, and Beckman Institute, University of Illinois, Urbana, Illinois 61801, United States.
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten
authors.affiliation: Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States.|Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, United States.|Department of Physics, and Beckman Institute, University of Illinois, Urbana, Illinois 61801, United States.
authors.forename: Martin
authors.initials: M
authors.lastname: Gruebele
mesh_terms: D029968:Escherichia coli Proteins / Q000737:chemistry; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D011312:Pressure; D017510:Protein Folding; D013696:Temperature
chemical_list: D029968:Escherichia coli Proteins