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Diffusion in macromolecular crowded media: Monte Carlo simulation of obstructed diffusion vs. FRAP experiments

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Abstract

The diffusion of tracer particles in 3D macromolecular crowded media has been studied using two methodologies, simulation and experimental, with the aim of comparing their results. First, the diffusion of a tracer in an obstructed 3D lattice with mobile and big size obstacles has been analyzed through a Monte Carlo (MC) simulation procedure. Secondly, fluorescence recovery after photobleaching (FRAP) experiments have been carried out to study the diffusion of a model protein (alpha-chymotrypsin) in in vitro crowded solution where two type of Dextran molecules are used as crowder agents. To facilitate the comparison, the relative size between the tracer and the crowder is the same in both studies. The results indicate a qualitative agreement between the diffusional behaviors observed in the two studies. The dependence of the anomalous diffusion exponent and the limiting diffusion coefficient on the obstacle size and excluded volume shows, in both cases, a similar tendency. The introduction of a reduced mobility parameter in the simulation model accounting for the short-range tracer–obstacle interactions allows obtaining a quantitative agreement between the limiting diffusion coefficient values yielded by both procedures. The simulation–experiment quantitative agreement for the anomalous diffusion exponent requires further improvements. As far as we know, this is the first reported work where both techniques are used in parallel to study the diffusion in macromolecular crowded media.

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Acknowledgments

We acknowledge the financial support from CNCSIS 551 Romania, Spanish Ministry of Science and Innovation (Projects UNBA05-33-001 and CTM2009-14612) and “Comissionat d’Universitats i Recerca de la Generalitat de Catalunya” (grants 2009SGR465 and XRQTC). IP thanks the Juan de la Cierva Program of the Spanish Ministry of Science.

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Authors and Affiliations

  1. Physical Chemistry Department and Research Institute of Theoretical and Computational Chemistry (IQTCUB) of the University of Barcelona (UB), C/Martí i Franquès, 1, 08028, Barcelona, Catalonia, Spain

    Eudald Vilaseca, Isabel Pastor, Sergio Madurga & Francesc Mas

  2. Department of Chemistry, University of the West Timisoara, Timisoara, Romania

    Adriana Isvoran

  3. Chemistry Department, Lleida University (UdL), Lleida, Catalonia, Spain

    Josep-Lluís Garcés

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  1. Eudald Vilaseca
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  2. Isabel Pastor
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  6. Francesc Mas
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Correspondence to Francesc Mas.

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Published as part of the special issue celebrating theoretical and computational chemistry in Spain.

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Vilaseca, E., Pastor, I., Isvoran, A. et al. Diffusion in macromolecular crowded media: Monte Carlo simulation of obstructed diffusion vs. FRAP experiments. Theor Chem Acc 128, 795–805 (2011). https://doi.org/10.1007/s00214-010-0840-5

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