Diffusion and Viscosity in Mixed Protein Solutions

The viscosity and diffusion properties of crowded protein systems were investigated with molecular dynamics simulations of SH3 mixtures with different crowders, and results were compared with experimental data. The simulations accurately reproduced experimental trends across a wide range of protein concentrations, including highly crowded environments up to 300 g/L. Notably, viscosity increased with crowding but varied little between different crowder types, while diffusion rates were significantly reduced depending on protein-protein interaction strength. Analysis using the Stokes-Einstein relation indicated that the reduction in diffusion exceeded what was expected from viscosity changes alone, with the additional slow-down attributable to transient cluster formation driven by weakly attractive interactions. Contact kinetics analysis further revealed that longer-lived interactions contributed more significantly to reduced diffusion rates than short-lived interactions. This study also highlights the accuracy of current computational methodologies for capturing the dynamics of proteins in highly concentrated solutions and provides insights into the molecular mechanisms affecting protein mobility in crowded environments.