Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach

Calcium/calmodulin-dependent protein kinase II (CaMKII) holoenzymes play a critical role in decoding Ca(2+) signals in neurons. Understanding how this occurs has been the focus of numerous studies including many that use models. However, CaMKII is notoriously difficult to simulate in detail because of its multi-subunit nature, which causes a combinatorial explosion in the number of species that must be modeled. To study the Ca(2+)-calmodulin-CaMKII reaction network with detailed kinetics while including the effect of diffusion, we have customized an existing stochastic particle-based simulator, Smoldyn, to manage the problem of combinatorial explosion. With this new method, spatial and temporal aspects of the signaling network can be studied without compromising biochemical details. We used this new method to examine how calmodulin molecules, both partially loaded and fully loaded with Ca(2+), choose pathways to interact with and activate CaMKII under various Ca(2+) input conditions. We found that the dependence of CaMKII phosphorylation on Ca(2+) signal frequency is intrinsic to the network kinetics and the activation pattern can be modulated by the relative amount of Ca(2+) to calmodulin and by the rate of Ca(2+) diffusion. Depending on whether Ca(2+) influx is saturating or not, calmodulin molecules could choose different routes within the network to activate CaMKII subunits, resulting in different frequency dependence patterns. In addition, the size of the holoenzyme produces a subtle effect on CaMKII activation. The more extended the subunits are organized, the easier for calmodulin molecules to access and activate the subunits. The findings suggest that particular intracellular environmental factors such as crowding and calmodulin availability can play an important role in decoding Ca(2+) signals and can give rise to distinct CaMKII activation patterns in dendritic spines, Ca(2+) channel nanodomains and cytoplasm.