Modeling of Particle Number Fluctuations in Entire Cells

Abstract

In a recent study we developed a method to model protein diffusion in cells [1], where special attention was given to generating from image data of the measured cell a realistic digital model cell in which protein dynamics were simulated. The method was shown to be well suited for modeling non-equilibrium situations that arise, e.g., in photobleaching experiments, and to be capable of producing more detailed information about protein motion than traditional modeling.Another experimental way to assess protein dynamics is to study fluctuations in the local protein number, as it is done, e.g., in fluorescence correlation spectroscopy (FCS), or in similar measurements that apply single-plane illumination spectroscopy (SPIM).Here we introduce a new, efficient method for modeling FCS-type measurements, based on the digital model cell mentioned above, that can reproduce the local particle number fluctuations at the level of imaging resolution. This method allows local variations in, e.g., the diffusion coefficients, average particle numbers, and binding/dissociation coefficients. In combination with FCS-type experiments, and with SPIM in particular, this method can be used to map the parameters important to protein dynamics in an entire cell. Furthermore, in contrast with traditional analytical models currently applied, it can also be used to model non-equilibrium situations.[1] Kuhn T, Ihalainen T O, Hyvaluoma J, Dross N, Willman S F, Langowski J, Vihinen-Ranta M and Timonen J. 2011 Protein Diffusion in Mammalian Cell Cytoplasm. PLoS ONE 6(8): e22962