Simulated Force Quench Dynamics Shows GB1 Protein Is Not a Two State Folder

Area of Science:

• Biophysics
• Computational Biology
• Protein Dynamics

Background:

• Single molecule force spectroscopy investigates protein unfolding/refolding.
• Traditional analysis often uses a simplified two-state model.
• This model assumes end-to-end distance is the sole reaction coordinate.

Purpose of the Study:

• To determine the free energy surface (PMF) of GB1 protein.
• To investigate protein folding using multiple collective variables.
• To challenge the conventional two-state model interpretation.

Main Methods:

• Atomistic simulations in explicit solvent.
• Calculation of 2D free energy surfaces using end-to-end distance and native contact fraction (ρ).
• Brownian dynamics simulations on the computed free energy landscape.

Main Results:

• Free energy surfaces revealed distinct states, primarily along the ρ coordinate.
• Identification of a metastable molten globule state.
• Evidence supporting GB1 as a three-state folder, not a two-state folder.

Conclusions:

• The end-to-end distance alone is insufficient to describe GB1 protein folding.
• GB1 protein exhibits a three-state folding mechanism.
• Findings align with recent experimental data questioning the two-state model for GB1.