A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation

Abstract

Subcellular compartmentation of the ubiquitous second messenger cAMP has been widely proposed as a mechanism to explain unique receptor-dependent functional responses. How exactly compartmentation is achieved, however, has remained a mystery for more than 40 years. In this study, we developed computational and mathematical models to represent a subcellular sarcomeric space in a cardiac myocyte with varying detail. We then used these models to predict the contributions of various mechanisms that establish subcellular cAMP microdomains. We used the models to test the hypothesis that phosphodiesterases act as functional barriers to diffusion, creating discrete cAMP signaling domains. We also used the models to predict the effect of a range of experimentally measured diffusion rates on cAMP compartmentation. Finally, we modeled the anatomical structures in a cardiac myocyte diad, to predict the effects of anatomical diffusion barriers on cAMP compartmentation. When we incorporated experimentally informed model parameters to reconstruct an in silico subcellular sarcomeric space with spatially distinct cAMP production sites linked to caveloar domains, the models predict that under realistic conditions phosphodiesterases alone were insufficient to generate significant cAMP gradients. This prediction persisted even when combined with slow cAMP diffusion. When we additionally considered the effects of anatomic barriers to diffusion that are expected in the cardiac myocyte dyadic space, cAMP compartmentation did occur, but only when diffusion was slow. Our model simulations suggest that additional mechanisms likely contribute to cAMP gradients occurring in submicroscopic domains. The difference between the physiological and pathological effects resulting from the production of cAMP may be a function of appropriate compartmentation of cAMP signaling. Therefore, understanding the contribution of factors that are responsible for coordinating the spatial and temporal distribution of cAMP at the subcellular level could be important for developing new strategies for the prevention or treatment of unfavorable responses associated with different disease states.

Geometric control of frequency modulation of cAMP oscillations due to Ca2+-bursts in dendritic spines

“…It is also well-known that calcium spikes are necessary for changes in cAMP concentrations, but only certain bursts of calcium spikes increase cAMP levels in neurons [11]. The dynamics of calcium-induced cAMP has been modeled by us and others [15,22,24,46] with a focus on identifying the mechanisms underlying interdependent oscillations. We showed that cAMP is primarily sensitive to the longer timescale effects of calcium rather than the shorter time scales [15].…”

“…The head shape, neck length, and neck diameter in spines can change during the synaptic plasticity [21]; changes in spine morphology and spine density are associated with learning and memory [21]. In other cell types, it is well-known that the spatial localization of cAMP regulating molecules and spatial aspects of signaling can govern its dynamics [22,23]. Two key types of enzymes that produce and degrade cAMP are believed to be responsible for cAMP subcellular compartmentalization.…”

Geometric principles of second messenger dynamics in dendritic spines

“…To decode how these two quantities affect the spatiotemporal dynamics of C, we conducted the following simulations -(i) spine apparatus size was varied by changing ρ; we used three different values of ρ (0.1, 0.5, and 0.9) to capture the extreme volume changes due to small, medium, and large spine apparatus. (ii) The diffusion constant of C was varied to capture the range of intracellular diffusion from a crowded regime to free diffusion (1, 10, 100 µm 2 /s) [70][71][72][73][74][75][76]. We found that with small spine apparatus (ρ = 0.1), a significant concentration gradient exists in the radial direction when the diffusion coefficient is small (D = 1µm 2 /s) at early time points but not for larger diffusion coefficients (Figure 4a).…”

Spatially compartmentalized phase regulation of a Ca2+-cAMP-PKA oscillatory circuit

“…Although our system does show the ability to oscillate in and out of phase in a well-behaved manner, this will not produce our desired form if a homogenous boundary is present. Previous studies have looked at spatial gradients in the context of cAMP and PKA and found out that a localization must occur for the system to form one (Yang et al 2016). Therefore, when moving to a 3D spatial map, we must consider how two solution regimes can be recovered.…”