Model of calcium sparks generation in a spatially realistic calcium release unit
We have created a detailed computational model of a CRU, and developed novel tools to generate the computational geometry from electron tomographic images. Ca(2+) diffusion was modelled within the SR and the cytosol to examine the effects of localization and density of the Na(+)/Ca(2+) exchanger, sarco/endoplasmic reticulum Ca(2+)-ATPase 2 (SERCA), and calsequestrin on spark dynamics.
We reconcile previous model predictions of approximately 90% local Ca(2+) depletion in junctional SR, with experimental reports of about 40%. This analysis supports the hypothesis that dye kinetics and optical averaging effects can have a significant impact on measures of spark dynamics. Our model also predicts that distributing calsequestrin within non-junctional Z-disc SR compartments, in addition to the junctional compartment, prolongs spark release time as reported by Fluo5. By pumping Ca(2+) back into the SR during a release, SERCA is able to prolong a Ca(2+) spark, and this may contribute to SERCA-dependent changes in Ca(2+) wave speed. Finally, we show that including the Na(+)/Ca(2+) exchanger inside the dyadic cleft does not alter local [Ca(2+)] during a spark.
NBCR researchers developed the underlying models and software to perform the simulations and to capture the mathematical mesh for the geometry that was used in the model (using NBCR developed Geometry-preserving Adaptive MeshER). BLAMer is Blender based GAMer, made possibly by NBCR developed uPY, a Python extension module to provide uniform abstractions of the AIP to several 3D graphics programs, such as Blender. The simulation we run using the NBCR software SubCell, written in python and using the FEniCS finite element library.
- Hake, J.; Edwards, A.G.; Yu, Z.; Kekenes-Huskey, P.M.; Michailova, A.P.; McCammon, J.A.; Holst, M.J.; Hoshijima, M.; McCulloch, A.D., Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit. J Physiol 2012, 590, (18), 4403-4422, PMC3477749 T0002,0003
Researchers: NBCR: Pete Kekenes-Huskey, Anushka Michailova, Andy McCammon, Michael Holst, Andrew McCulloch; Collaborator Zeyun Yu (U Wisconsin-Milwaukee)
Figure 1: A volumetric representation of the calcium concentration in the cytosol. The time is 5 ms after the trigger of a calcium spark.
Figure 2: The annotated surface mesh generated using BLAMer using a reconstructed and segmented stack of electron tomography images.