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

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.