Issue 16, 2018

Macromolecular diffusion in crowded media beyond the hard-sphere model


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 (Ur). 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, Ur is obtained by fitting the streptavidin experimental long-time diffusion coefficient Dlongversus the macromolecular concentration for D50 (indicating their molecular weight in kg mol−1) dextran obstacles. The obtained Dlong 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 Dlong and the anomalous exponent (α) for streptavidin diffusion among D10, D400 and D700 dextran obstacles. Dlong, the short-time diffusion coefficient (Dshort) 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.

Graphical abstract: Macromolecular diffusion in crowded media beyond the hard-sphere model

Supplementary files

Article information

Article type
27 Jan 2018
20 Mar 2018
First published
20 Mar 2018
This article is Open Access
Creative Commons BY license

Soft Matter, 2018,14, 3105-3114

Macromolecular diffusion in crowded media beyond the hard-sphere model

P. M. Blanco, J. L. Garcés, S. Madurga and F. Mas, Soft Matter, 2018, 14, 3105 DOI: 10.1039/C8SM00201K

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