Line-FRAP, a versatile method based on fluorescence recovery after photobleaching to measure diffusion rates in vitro and in vivo

Abstract

A cell is a densely packed conglomerate of macromolecules, where diffusion is essential for their function. The crowded conditions may affect diffusion both through hard (occluded space) and soft (weak, non-specific) interactions. Multiple-methods have been developed to measure diffusion rates at physiological protein concentrations within cells, however, each of them has its limitations. Here, we introduce Line-FRAP, a method based on measuring recovery of photobleaching under a confocal microscope that allows diffusion rate measurements for fast diffusing molecules to be measured in versatile environments using standard equipment. Implementation of Line mode to the classical FRAP technique greatly improves the time resolution in data acquisition, from 20-50 Hz in the classical mode to 800 Hz in the line mode. We also introduce an updated method for data analysis to obtain diffusion coefficients in various environments, with the number of pixels bleached at the first frame after bleaching being a critical parameter. We evaluated the method using different proteins either chemically labelled or by fusion to YFP. The calculated diffusion rates were comparable to literature data as measured in vitro, in HeLa cells and in E.coli. Diffusion coefficients in HeLa was ~2.5-fold slower and in E. coli 15-fold slower than measured in buffer. Moreover, we show that increasing the osmotic pressure on E.coli further decreases diffusion, till a point where proteins stop to move. The method presented here is easy to apply on a standard confocal microscope, fits a large range of molecules with different sizes and provides robust results in any conceivable environment and protein concentration for fast diffusing molecules.