A quantitative look at protein diffusion in cells and crowded media

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Living systems are highly dynamic. In particular, most cellular processes involve motions of molecules across or between cellular compartments. Thus understanding how cells work will require understanding how proteins move in the cellular environment. In this context, my research focuses on protein diffusion. My goal is to understand how protein diffusion in the cell interior (a crowded and non-equilibrium environment) might differ from diffusion in simple fluids, and how these differences might impact the many cellular processes involving protein diffusion. To do so, we will take advantage of recent developments in microscopy, which presently allow characterizing diffusion, using fluorescence techniques, over a range of length-scales extending from the size of a cell (~ 10 microns) to the characteristic mesh size of the cell cytoskeleton (~50 nm).  One question we will address is that of the length-scale dependence of protein diffusion. There is strong evidence that, in cells, proteins diffuse faster over short length-scales than they do over large length-scales. In order to better understand the origin of this phenomenon, we will perform variable length-scale diffusion measurements in crowded polymer solutions and gels mimicking the cellular environment. Using biomimetic model systems will allow precisely and systematically controlling parameters such as crowding agent concentration or the temperature, that may influence the diffusion. This will be essential in order to test the validity of the different models that have been proposed in recent years to explain diffusion in crowded environments.  Another question we will address is that of the effective temperature of a living cell. Diffusion in simple liquids is caused by thermal collisions with the fluid molecules, resulting in a diffusion coefficient that is proportional to the fluid’s absolute temperature. However, several recent studies have shown that, in cells, non-thermal stochastic processes play a role in the diffusion of probe particles as small as 100 nm in diameter. This results in a diffusion process with a higher than expected diffusion coefficient, i.e. a higher effective temperature. We will test whether this effect extends to the diffusion of small (~5 nm) particles such as proteins. If appropriate, we will work to establish the source of the non-thermal stochastic noise.  Our work will participate in advancing a more quantitative approach to cell biology. We will supply quantitative data that will help discriminate between different models of anomalous diffusion in crowded environments such as the cell interior. In turn, this will help develop better models of the many cellular processes that involve diffusion. Our work will also provide examples of how the laws of statistical mechanics developed for simple physical systems need to be modified in order become relevant in living systems such as the cellular environment.