BROWNIAN DYNAMICS SIMULATION OF MACROMOLECULE DIFFUSION IN A PROTOCELL.

Area of Science:

• Biophysics
• Computational Biology
• Cellular Biology

Background:

• Cellular interiors are densely packed with macromolecules, impacting reaction thermodynamics and kinetics compared to dilute conditions.
• Macromolecule diffusion, such as green fluorescent protein (GFP) in E. coli, is significantly slower in vivo than in vitro.

Purpose of the Study:

• To investigate macromolecule motion in a crowded cellular environment using Brownian dynamics (BD) simulations.
• To compare simulation results with in vivo experimental data and identify discrepancies.

Main Methods:

• Performed BD simulations of rigid macromolecules (ribosomes, enzymes, GFPs, tRNAs) in a crowded E. coli cytosol model.
• Used bead-per-amino acid or nucleotide models for macromolecules and Stokes radius approximations.
• Incorporated hydrodynamic theory to account for diffusion anisotropy in dilute solutions.

Main Results:

• Excluded volume effects substantially reduce molecular mobility in crowded environments for both molecular-shaped and sphere models.
• No significant difference in diffusivity reduction was observed between molecular-shaped and sphere systems across various molecular sizes.
• Simulated GFP diffusion reduction was still 4-5 times greater than experimentally observed in vivo values.

Conclusions:

• Crowded cellular environments significantly impede macromolecule diffusion due to excluded volume effects.
• Current simulation models, even when accounting for excluded volume, do not fully replicate the experimentally observed diffusion rates of macromolecules in vivo.
• Further investigation into other contributing factors influencing in vivo macromolecule diffusion is warranted.