Next Article in Journal
On Quantum Collapse as a Basis for the Second Law of Thermodynamics
Next Article in Special Issue
Fluctuation-Driven Transport in Biological Nanopores. A 3D Poisson–Nernst–Planck Study
Previous Article in Journal
“Over-Learning” Phenomenon of Wavelet Neural Networks in Remote Sensing Image Classifications with Different Entropy Error Functions
Previous Article in Special Issue
Taxis of Artificial Swimmers in a Spatio-Temporally Modulated Activation Medium
Open AccessArticle

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
Entropy 2017, 19(3), 105; https://doi.org/10.3390/e19030105
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)
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
Show Figures

Figure 1

MDPI and ACS Style

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.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop