Limits...
The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations.

Oliveira RF, Terrin A, Di Benedetto G, Cannon RC, Koh W, Kim M, Zaccolo M, Blackwell KT - PLoS ONE (2010)

Bottom Line: Cyclic AMP (cAMP) and its main effector Protein Kinase A (PKA) are critical for several aspects of neuronal function including synaptic plasticity.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.

View Article: PubMed Central - PubMed

Affiliation: The Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia, United States of America.

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.

Show MeSH
Validation of NeuroRD.Simulations show good agreement between NeuroRD, Smoldyn [25] and deterministic solutions (XPPAUT [38] or Chemesis [39]). (A) Validation of diffusion alone. Deterministic trace generated using Chemesis; (B) Validation of reactions alone. The deterministic trace is generated using XPPAUT; (C and D) Validation of reaction-diffusion. The deterministic trace is generated using Chemesis. In all panels Distance refers to the Euclidean distance in microns between center of source subvolume and center of other subvolumes. Panel C shows molecule “A” which has a relatively high concentration and fast dynamics, whereas Panel D shows molecule “C”, which has a low concentration and slower dynamics.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2908681&req=5

pone-0011725-g003: Validation of NeuroRD.Simulations show good agreement between NeuroRD, Smoldyn [25] and deterministic solutions (XPPAUT [38] or Chemesis [39]). (A) Validation of diffusion alone. Deterministic trace generated using Chemesis; (B) Validation of reactions alone. The deterministic trace is generated using XPPAUT; (C and D) Validation of reaction-diffusion. The deterministic trace is generated using Chemesis. In all panels Distance refers to the Euclidean distance in microns between center of source subvolume and center of other subvolumes. Panel C shows molecule “A” which has a relatively high concentration and fast dynamics, whereas Panel D shows molecule “C”, which has a low concentration and slower dynamics.

Mentions: NeuroRD is validated by comparison with an existing stochastic simulator (Smoldyn 2.05 [25] and deterministic solutions (XPPAUT 5.6.9 [38], Chemesis 2.1 [39]). The first validation evaluates NeuroRD simulations of diffusion of a single molecule species in a 10×11×1 µm rectangular cuboid subdivided into 110 subvolumes of size 1×1×1 µm. 2000 diffusing molecules (D = 300 µm2/s) are placed in the center of one edge of the slab (the source subvolume). The number of molecules in a given subvolume (or defined region in Smoldyn) reveals good agreement between Smoldyn and NeuroRD, both of which agree with the deterministic solution, illustrated in Fig. 3A for subvolumes at several distances from the source subvolume. The second validation set evaluates NeuroRD simulations of reactions alone in the same morphology as the first validation using two reversible bimolecular reactions (A+B↔C and A+C↔D). Although all four molecular species diffuse (required for reactions to proceed in Smoldyn), the molecules are distributed homogeneously in space so that there are no diffusional gradients. Fig. 3B shows that the time course and steady state values for Smoldyn and NeuroRD agree with each other and the deterministic solution. Note that the results for NeuroRD do not change if the molecules are made non-diffusible.


The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations.

Oliveira RF, Terrin A, Di Benedetto G, Cannon RC, Koh W, Kim M, Zaccolo M, Blackwell KT - PLoS ONE (2010)

Validation of NeuroRD.Simulations show good agreement between NeuroRD, Smoldyn [25] and deterministic solutions (XPPAUT [38] or Chemesis [39]). (A) Validation of diffusion alone. Deterministic trace generated using Chemesis; (B) Validation of reactions alone. The deterministic trace is generated using XPPAUT; (C and D) Validation of reaction-diffusion. The deterministic trace is generated using Chemesis. In all panels Distance refers to the Euclidean distance in microns between center of source subvolume and center of other subvolumes. Panel C shows molecule “A” which has a relatively high concentration and fast dynamics, whereas Panel D shows molecule “C”, which has a low concentration and slower dynamics.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2908681&req=5

pone-0011725-g003: Validation of NeuroRD.Simulations show good agreement between NeuroRD, Smoldyn [25] and deterministic solutions (XPPAUT [38] or Chemesis [39]). (A) Validation of diffusion alone. Deterministic trace generated using Chemesis; (B) Validation of reactions alone. The deterministic trace is generated using XPPAUT; (C and D) Validation of reaction-diffusion. The deterministic trace is generated using Chemesis. In all panels Distance refers to the Euclidean distance in microns between center of source subvolume and center of other subvolumes. Panel C shows molecule “A” which has a relatively high concentration and fast dynamics, whereas Panel D shows molecule “C”, which has a low concentration and slower dynamics.
Mentions: NeuroRD is validated by comparison with an existing stochastic simulator (Smoldyn 2.05 [25] and deterministic solutions (XPPAUT 5.6.9 [38], Chemesis 2.1 [39]). The first validation evaluates NeuroRD simulations of diffusion of a single molecule species in a 10×11×1 µm rectangular cuboid subdivided into 110 subvolumes of size 1×1×1 µm. 2000 diffusing molecules (D = 300 µm2/s) are placed in the center of one edge of the slab (the source subvolume). The number of molecules in a given subvolume (or defined region in Smoldyn) reveals good agreement between Smoldyn and NeuroRD, both of which agree with the deterministic solution, illustrated in Fig. 3A for subvolumes at several distances from the source subvolume. The second validation set evaluates NeuroRD simulations of reactions alone in the same morphology as the first validation using two reversible bimolecular reactions (A+B↔C and A+C↔D). Although all four molecular species diffuse (required for reactions to proceed in Smoldyn), the molecules are distributed homogeneously in space so that there are no diffusional gradients. Fig. 3B shows that the time course and steady state values for Smoldyn and NeuroRD agree with each other and the deterministic solution. Note that the results for NeuroRD do not change if the molecules are made non-diffusible.

Bottom Line: Cyclic AMP (cAMP) and its main effector Protein Kinase A (PKA) are critical for several aspects of neuronal function including synaptic plasticity.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.

View Article: PubMed Central - PubMed

Affiliation: The Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia, United States of America.

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.

Show MeSH