Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

Area of Science:

• Biophysics
• Computational Chemistry
• Protein Folding Dynamics

Background:

• Understanding protein folding mechanisms is crucial for molecular biology and drug design.
• The Trp-cage miniprotein serves as a model system for studying folding kinetics.
• Previous studies using implicit solvent models yielded different folding pathway predictions.

Purpose of the Study:

• To elucidate the kinetic pathways of Trp-cage folding and unfolding in explicit solvent.
• To compare folding mechanisms predicted by different simulation methods.
• To gain a deeper understanding of the role of solvent in protein folding.

Main Methods:

• Transition Path Sampling (TPS) simulations in explicit solvent.
• Molecular Dynamics (MD) and Replica Exchange MD (REMD) for comparison.
• Committor analysis to identify reaction coordinates.

Main Results:

• TPS successfully sampled unbiased folding/unfolding pathways, overcoming convergence issues of MD and REMD.
• Trp-cage predominantly folds via tertiary contact and salt bridge formation before helix formation (80% of pathways).
• The remaining 20% of pathways involve initial helix formation.
• Transition states feature solvated, native-like structures, with water expulsion as the final folding step.
• Specific water molecules exhibit strong binding and structural roles during the folding transition.

Conclusions:

• Explicit solvent simulations reveal distinct folding pathways for Trp-cage compared to implicit solvent models.
• Solvent dynamics are not the primary reaction coordinate, but specific water interactions are structurally important.
• The study provides a detailed mechanistic insight into miniprotein folding dynamics.