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Molecule Parameter List for PDE | The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by  color. | | Statistics |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | | cGMP_regulation | 34 | Network |
Shared_Object_cGMP_regulation, GC, PDE | Though Corbin JD. et al. Eur J Biochem. (2000) 267(9):2760-7 has been mentioned in the citation, this model has been made with inputs from different literature sources, each of which has been mentioned in the notes sections. This model features hydrolysis of cGMP by bovine PDE, phosphorylation of PDE by bovine lung PKG, and activation of bovine lung PKG by cGMP binding. These mechanisms are known to be involved in cGMP level regulation. Rates have been used from different sources and the model has been tested based on Corbin JD. et al., since their work involved measuring the PDE phosphorylation and PDE activity.
On replicating Figures 2, 3 and 4 from their paper, there is approx 30% difference in results but the qualitative shape of the curves is very similar. This might be due to the fact that the Vmax values were used from different literature sources. This might lead to the discrepancy in the numbers in this model. The values shown in this model are near estimated physiological levels.In order to replicate the Figures more closely, we have run additional simulations with concentration terms changed so as to replicate the experimental conditions exactly. |
PDE acting as a Molecule in cGMP_regulation Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | PDE | cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 0.28 | 0.0016667 | No | | Phophosdiesterase. Degrades cGMP to 5primeGMP. Concentration used by Kuroda et al.,(J Neurosci, 2001,21(15): 5693-5702) and initially from Kotera et al., (1997, Eur J Biochem, 249:434-442). PDE 5 is highly specific for cGMP and is considered to be the main enzyme responsible for terminating the action of cGMP generated following the release of NO from nitrergic nerves, or from vascular endothelial cells. (Gibson,Eur J Pharmacol, 2001, 411:1-10). Occupation of the allosteric binding sites by cGMP is neessary for phosphorylation by PKG. In Corbinet al., EJBiochem, 2000, 267:2760-2767, Phosphorylation of PDE and PDE activity are measured, but as mentioned, due to the different sources of Vmax values the numbers could not be matched exactly with respect to the plots in the paper, and they were either more or less by a factor of two. To match the numbers exactly we have to replicate the experimental conditions exactly. |
PDE acting as an Enzyme in cGMP_regulation Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | PDE /
PDE_basal
| cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 0.979992 | 2.4 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
cGMP
Product
5primeGMP
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PDE acting as a Substrate in a reaction in cGMP_regulation Network
| Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated.
Kd for higher order reaction are not consider. |
| Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | PDEbind_cGMP | cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 10
(uM^-1 s^-1) | 13
(s^-1) | Kd(bf) = 1.3(uM) | - | Substrate
PDE
cGMP
Product
cGMP.PDE
| | Kd ~1.3 uM. (Turko et al., JBC, 1996, 271(36):22240-22244, and Corbin et al., Eur J Biochem, 2000,267:2760-2767) |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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