Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations

Area of Science:

• Protein dynamics
• Biophysics
• Computational biology

Background:

• Unimolecular protein folding reactions are key to understanding protein structure.
• Direct mechanistic comparison between experimental and simulation data is crucial.
• The engineered WW domain FiP35 serves as a model system for beta-sheet folding.

Purpose of the Study:

• To compare microsecond pressure and temperature jump refolding kinetics of FiP35.
• To provide a direct mechanistic comparison between experiment and simulation.
• To investigate the folding mechanism of FiP35 at the boundary of activated and downhill folding.

Main Methods:

• Microsecond pressure and temperature jump refolding kinetics experiments.
• All-atom molecular dynamics simulations in explicit solvent.
• Kinetic modeling of pressure jump simulations.

Main Results:

• Both experimental perturbations revealed fast and slow kinetic phases for FiP35 refolding.
• The slow phase was found to be activated.
• Molecular dynamics simulations showed FiP35 folding in five of six trajectories.
• Kinetic modeling suggested a 4-state mechanism consistent with pressure jump experiments and simulations.

Conclusions:

• FiP35 exists at the boundary between activated intermediates and downhill folding.
• Experimental and computational data highlight the complex folding landscape of FiP35.
• FiP35 is an excellent model for future pressure jump molecular dynamics studies to compare experiment and modeling at the folding mechanism level.