Macromolecular diffusion in crowded media beyond the hard-sphere model

Abstract

The effect of macromolecular crowding on diffusion beyond the hard-core sphere model is studied. A new coarse-grained model is presented, the Chain Entanglement Softened Potential (CESP) model, which takes into account the macromolecular flexibility and chain entanglement. The CESP model uses a shoulder-shaped interaction potential that is implemented in the Brownian Dynamics (BD) computations. The interaction potential contains only one parameter associated with the chain entanglement energetic cost (U_r). The hydrodynamic interactions are included in the BD computations via Tokuyama mean-field equations. The model is used to analyze the diffusion of a streptavidin protein among different sized dextran obstacles. For this system, U_r is obtained by fitting the streptavidin experimental long-time diffusion coefficient D^longversus the macromolecular concentration for D50 (indicating their molecular weight in kg mol⁻¹) dextran obstacles. The obtained D^long values show better quantitative agreement with experiments than those obtained with hard-core spheres. Moreover, once parametrized, the CESP model is also able to quantitatively predict D^long and the anomalous exponent (α) for streptavidin diffusion among D10, D400 and D700 dextran obstacles. D^long, the short-time diffusion coefficient (D^short) and α are obtained from the BD simulations by using a new empirical expression, able to describe the full temporal evolution of the diffusion coefficient.