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Macromolecular diffusion in crowded media beyond the hard-sphere model

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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 (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 Dlong versus 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

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Publication details

The article was received on 27 Jan 2018, accepted on 20 Mar 2018 and first published on 20 Mar 2018


Article type: Paper
DOI: 10.1039/C8SM00201K
Citation: Soft Matter, 2018, Advance Article
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    Macromolecular diffusion in crowded media beyond the hard-sphere model

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

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