Analyzing optical imaging of Ca signals via TIRF microscopy: The limits on resolution due to chemical rates and depth of the channels.

High resolution total internal reflection (TIRF) microscopy (TIRFM) together with detailed computational modeling provides a powerful approach towards the understanding of a wide range of Ca signals mediated by the ubiquitous inositol 1,4,5-trisphosphate (IP) receptor (IPR) channel. Exploiting this fruitful collaboration further requires close agreement between the models and observations. However, elementary Ca release events, puffs, imaged through TIRFM do not show the rapid single-channel openings and closings during and between puffs as are present in simulated puffs using data-driven single channel models. TIRFM also shows a rapid equilibration of 10ms after a channel opens or closes which is not achievable in simulation using standard Ca diffusion coefficients and reaction rates between indicator dye and Ca. Furthermore, TIRFM imaging cannot decipher the depth of the channel with respect to the microscope, which will affect the change in fluorescence that the microscope detects, thereby affecting its sensitivity to fast single-channel activity. Using the widely used Ca diffusion coefficients and reaction rates, our simulations show equilibration rates that are eight times slower than TIRFM imaging. We show that to get equilibrium rates consistent with observed values, the diffusion coefficients and reaction rates have to be significantly higher than the values reported in the literature, and predict the channel depth to be 200-250nm. Finally, we show that with the addition of noise, short events due to 1-2ms opening and closing of channels that are observed in computational models can be missed in TIRFM.