The rate-limiting step for biochemical interactions in cells is often the time it takes for the relevant molecules to get where they need to go. Measurements have shown that the mobility of molecules in cellular cytoplasm is an order of magnitude smaller than their mobility in aqueous solutions, but it is unclear if the slower rate of diffusion is caused by a crowded cytoplasm or if it is due to sticky interactions with cellular constituents.
As reported in Physical Review E, a better understanding may come from comparing experiments that track fluorescent proteins as they diffuse through a cell with computer simulations of the same process. Yoriko Lill from Purdue University, Indiana, and colleagues studied E. coli cells that were genetically modified to express green fluorescent protein. The authors used a microscope to track the path of a single fluorescent protein as it diffused through the cytoplasm. By acquiring images at different rates, from to frames per second, the authors were able to investigate a range of time and length scales that they compared with computer simulations. They also simulated diffusion of proteins in the cytoplasm with different concentrations of small spherical objects, which acted as obstacles.
The authors conclude that the reduced mobility of proteins measured in the cytoplasm could be attributed to the reduced space for movement in a crowded cytoplasm, although they cannot rule out contributions from specific interactions with cellular constituents. – Margaret Foster