A stochastic simulation algorithm for analysis of fluorescence recovery after photobleaching kinetics

Abstract

Fluorescence recovery after photobleaching (FRAP) is a confocal microscopybased technique widely used for in vivo quantification of intracellular molecular movements and interactions. FRAP is very useful for elucidating several fundamental but complicated cellular activities, such as cell membrane diffusion and protein binding. AIM: The aim of this study was to investigate whether it is possible to develop stochastic simulation strategies for interpretation of FRAP kinetics. METHODS: A simulation algorithm based on a stochastic simulation of the time evolution of coupled reaction-diffusion biochemical systems was developed for investigating and interpreting FRAP experiments in terms of diffusion and binding. The proposed algorithm was compared with standard deterministic methods that are currently being used for analysis of FRAP curves. RESULTS AND DISCUSSION: Predictions of recovery times of FRAP curves and sum of residuals revealed a good agreement (Table I), at the level of both timescale and intensity, between the proposed model and the standard deterministic methods. The stochastic simulation algorithm presents a firmer physical basis that its deterministic counterparts and might be used to successfully model probabilistic events in the cell, deciphering information in FRAP experiments that cannot be computed using deterministic models