The Role of Type 4 Phosphodiesterases in Generating Microdomains of cAMP: Large Scale Stochastic Simulations

Abstract

Cyclic AMP (cAMP) and its main effector Protein Kinase A (PKA) are critical for several aspects of neuronal function including synaptic plasticity. Specificity of synaptic plasticity requires that cAMP activates PKA in a highly localized manner despite the speed with which cAMP diffuses. Two mechanisms have been proposed to produce localized elevations in cAMP, known as microdomains: impeded diffusion, and high phosphodiesterase (PDE) activity. This paper investigates the mechanism of localized cAMP signaling using a computational model of the biochemical network in the HEK293 cell, which is a subset of pathways involved in PKA-dependent synaptic plasticity. This biochemical network includes cAMP production, PKA activation, and cAMP degradation by PDE activity. The model is implemented in NeuroRD: novel, computationally efficient, stochastic reaction-diffusion software, and is constrained by intracellular cAMP dynamics that were determined experimentally by real-time imaging using an Epac-based FRET sensor (H30). The model reproduces the high concentration cAMP microdomain in the submembrane region, distinct from the lower concentration of cAMP in the cytosol. Simulations further demonstrate that generation of the cAMP microdomain requires a pool of PDE4D anchored in the cytosol and also requires PKA-mediated phosphorylation of PDE4D which increases its activity. The microdomain does not require impeded diffusion of cAMP, confirming that barriers are not required for microdomains. The simulations reported here further demonstrate the utility of the new stochastic reaction-diffusion algorithm for exploring signaling pathways in spatially complex structures such as neurons.

Systems analysis of GLP-1 receptor signaling in pancreatic β-cells

“…Interestingly, our diffusion model also generated a similar [cAMP] gradient of ϳ4 M (Fig. 7C) when simulated using the V PDE equivalent to that used in the Oliveira et al (47). However, their V PDE was much higher (ϳ100 hold) than that determined by the model fitting to the published experimental data in the present study.…”

CFTR regulation in human airway epithelial cells requires integrity of the actin cytoskeleton and compartmentalized cAMP and PKA activity

“…Although PDE activity has been shown to be sufficient to restrict cAMP diffusion to defined subcellular compartments in certain cell types (Oliveira et al, 2010;Terrin et al, 2006), it has been argued that the densely packed subcortical cytoskeleton might constitute an efficient barrier to cAMP diffusion and promote compartmentalized cAMP and PKA signals by allowing cAMP to accumulate locally to a level sufficient to activate PKA, while preventing activation of PKA in the bulk cytosol (Rich et al, 2000). Here we show that the actin cytoskeleton can indeed act as a diffusional barrier for cAMP and that PDEs, although involved in the control of local cAMP levels, do not seem to play a major role in the generation of the membrane-to-cytosol cAMP gradient in the cells used in this study.…”

Asynchronous τ-leaping

“…49 In the following examples, we compare our new, asynchronous τ-leaping with the next reaction method, 10 and with previous version of NeuroRD implementing fixed step τ-leaping. 33,50 Our new method is implemented in the latest version of the NeuroRD simulator, 51 which allows for easy comparisons of speed and accuracy with an existing, verified implementation, as well as with the next reaction method implementation of the SSA, available in NeuroRD by disabling leaping.…”

“…21,[31][32][33] In the spatial variant of exact stochastic simulation, reactions within a single subvolume are described in the same way as previously, but molecules are allowed to diffuse between subvolumes. 11 Diffusion events are described in a manner identical to reaction events, and become another reaction channel, which "transforms" a molecule of a certain species in one subvolume into a molecule of the same species in a neighbouring subvolume.…”