Brownian Dynamics Computational Model of Protein Diffusion in Crowded Media with Dextran Macromolecules as Obstacles
MetadataShow full item record
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.
Is part ofEntropy, 2017, vol. 19, núm. 3, article 105
European research projects
Except where otherwise noted, this item's license is described as cc-by (c) Blanco, Pablo M. et al., 2017
Showing items related by title, author, creator and subject.
Blanco, Pablo M.; Garcés, Josep Lluís; Madurga, Sergio; Mas i Pujadas, Francesc (Royal Society of Chemistry, 2018-03-20)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 ...
Model-independent link between the macroscopic and microscopic descriptions of multidentate macromolecular binding: Relationship between stepwise, intrinsic, and microscopic equilibrium constants Garcés, Josep Lluís; Rey Castro, Carlos; David, Calin; Madurga, Sergio; Mas i Pujadas, Francesc; Pastor, Isabel; Puy Llorens, Jaume (American Chemical Society, 2009)The binding of ions or other small molecules to macromolecules and surfaces can be macroscopically characterized by means of the stepwise (or stoichiometric) equilibrium constants, which can be obtained experimentally ...
Role of charge regulation and fluctuations in the conformational and mechanical properties of weak flexible polyelectrolytes Blanco, Pablo M.; Madurga, Sergio; Narambuena, Claudio F.; Mas i Pujadas, Francesc; Garcés, Josep Lluís (MDPI, 2019-11-29)This work addresses the role of charge regulation (CR) and the associated fluctuations in the conformational and mechanical properties of weak polyelectrolytes. Due to CR, changes in the pH-value modifies the average ...