Construction and analysis of a comprehensive model of calcium wave dynamics based on experimental image, biochemical, and electrophysiological data

Calcium waves are a much studied and important physiological phenomenon in many cell types (e.g. oocytes, astroctyes, neurons, fibroblasts), but how calcium waves propagate with a particular geometry and oscillatory behavior in a given cell type is still poorly understood. Bradykinin-induced calcium waves, mediated by InsP3 release from endoplasmic reticulum (ER) stores, have been imaged in N1E-115 neuroblastoma cells. A model of this process was built using the “Virtual Cell”, a general computational system, integrating new experimental data from competitive radioligand binding assays, quantitative flash photolysis of caged InsP3 and the 3D intracellular distributions of the bradykinin receptor, the InsP3 receptor, and the SERCA pump. The model geometry was based on a cell for which the calcium wave had been experimentally recorded. Biochemical and electrophysiological data on the rate of InsP3 production, InsP3R levels, single channel kinetics of the InsP3R, calcium flux through the InsP3R channel, binding to fixed and mobile buffers, and the rate of calcium-activated pumping by SERCA were all used to constrain the model. The simulation matched the spatial and temporal characteristics of the experimental calcium wave. To further test the model, different patterns of calcium signals following InsP3 uncaging, focal BK application, or for different cell geometries were examined. Simulations also suggest that initiation of the wave in the center of the neurite derives from an interplay of soma-biased ER distribution and InsP3 generation biased toward the neurite. Mobile buffers (like the indicator fura-2) are predicted to significantly delay initiation and lower the amplitude of the wave, whereas, the propagation of the wave is predicted to be largely independent of calcium diffusion. This work demonstrates how the use of physiological experiments with computer simulations can provide insight into the mechanisms of calcium wave dynamics that couldn\u27t be obtained by using either method alone.