Internal protein motion in a rough model potential

Area of Science:

• Biophysics
• Statistical Mechanics
• Computational Biology

Background:

• Proteins exhibit complex internal motions influencing biochemical functions.
• Subdiffusive behavior is common in protein dynamics within rugged free energy landscapes.

Purpose of the Study:

• Investigate anomalous diffusion in rough confining potentials, inspired by protein internal dynamics.
• Analyze the impact of potential roughness on particle motion and ergodicity.

Main Methods:

• Employed fractional Fokker-Planck equation and continuous-time random walk models.
• Derived approximate expressions for mean displacement and mean squared displacement.
• Examined ergodic properties and mean maximal excursion.

Main Results:

• Identified three distinct dynamic regimes: free subdiffusion, roughness-impacted motion, and confinement-driven thermal plateau.
• Demonstrated enhanced weak ergodicity breaking in high-roughness systems.
• Showed time-averaged mean squared displacement increases as a power-law over time.

Conclusions:

• Mean maximal excursion quantifies confinement extent, serving as a robust measure for subdiffusive dynamics.
• Protein internal dynamics can be effectively modeled using anomalous diffusion frameworks.
• Roughness significantly alters protein dynamics and ergodicity, impacting functional mechanisms.