Depletion-induced interactions modulate nanoscale protein diffusion in polymeric crowder solutions

Area of Science:

• Biophysics
• Soft Matter Physics
• Structural Biology

Background:

• Macromolecular crowding influences protein dynamics in biological and experimental settings.
• Polymeric crowders like dextran and Ficoll create entropic forces, but their nanoscale effects on protein motion are not fully understood.

Purpose of the Study:

• To investigate the nanoscale consequences of macromolecular crowding on protein dynamics.
• To probe the collective dynamics of ferritin in solutions with different crowders using advanced spectroscopy.

Main Methods:

• Utilized megahertz X-ray photon correlation spectroscopy (MHz-XPCS) at the European X-ray Free Electron Laser (XFEL).
• Studied the dynamics of the protein ferritin in solutions containing sucrose, dextran, and Ficoll.

Main Results:

• Observed significant changes in collective protein dynamics within polymeric crowders.
• Identified depletion-driven short-range attractions and long-range repulsions leading to intermediate-range protein organization.
• Resolved collective relaxation on microsecond to millisecond timescales via ferritin density fluctuations.
• Found ferritin self-diffusion exhibits scaling behavior with a crossover near 2c*, indicating a transition in mobility.

Conclusions:

• Bulk properties are insufficient to fully describe protein dynamics in crowded environments.
• Polymer-specific interactions and depletion theory are crucial for accurate modeling of crowded systems.
• Crowder type and molecular weight critically influence mesoscale correlations and protein dynamics.