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Entropy 2017, 19(3), 105; doi:10.3390/e19030105

Brownian Dynamics Computational Model of Protein Diffusion in Crowded Media with Dextran Macromolecules as Obstacles

1
Department of Material Science and Physical Chemistry, Barcelona University, 08028 Barcelona, Spain
2
Institute of Theoretical and Computational Chemistry (IQTC), Barcelona University, 08028 Barcelona, Spain
3
Department of Chemistry, University of Lleida (UdL), 25003 Lleida, Spain
*
Authors to whom correspondence should be addressed.
Academic Editor: Antonio M. Scarfone
Received: 22 December 2016 / Revised: 1 March 2017 / Accepted: 3 March 2017 / Published: 9 March 2017
(This article belongs to the Special Issue Nonequilibrium Phenomena in Confined Systems)
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Abstract

The high concentration of macromolecules (i.e., macromolecular crowding) in cellular environments leads to large quantitative effects on the dynamic and equilibrium biological properties. These effects have been experimentally studied using inert macromolecules to mimic a realistic cellular medium. In this paper, two different experimental in vitro systems of diffusing proteins which use dextran macromolecules as obstacles are computationally analyzed. A new model for dextran macromolecules based on effective radii accounting for macromolecular compression induced by crowding is proposed. The obtained results for the diffusion coefficient and the anomalous diffusion exponent exhibit good qualitative and generally good quantitative agreement with experiments. Volume fraction and hydrodynamic interactions are found to be crucial to describe the diffusion coefficient decrease in crowded media. However, no significant influence of the hydrodynamic interactions in the anomalous diffusion exponent is found. View Full-Text
Keywords: macromolecular crowding; Brownian dynamics; dextran modelling; macromolecule diffusion; hydrodynamic interactions macromolecular crowding; Brownian dynamics; dextran modelling; macromolecule diffusion; hydrodynamic interactions
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Blanco, P.M.; Via, M.; Garcés, J.L.; Madurga, S.; Mas, F. Brownian Dynamics Computational Model of Protein Diffusion in Crowded Media with Dextran Macromolecules as Obstacles. Entropy 2017, 19, 105.

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