Brownian Dynamics Computational Model of Protein Diffusion in Crowded Media with Dextran Macromolecules as Obstacles
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....
| Autores: | , , , , |
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| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2017 |
| País: | España |
| Institución: | Universitat de Lleida (UdL) |
| Repositorio: | Repositori Obert UdL |
| OAI Identifier: | oai:repositori.udl.cat:10459.1/69789 |
| Acceso en línea: | https://doi.org/10.3390/e19030105 http://hdl.handle.net/10459.1/69789 |
| Access Level: | acceso abierto |
| Palabra clave: | Macromolecular crowding Brownian dynamics Dextran modelling Macromolecule diffusion Hydrodynamic interactions |
| Sumario: | 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. |
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