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Molecule Parameter List for sGCfast | 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 |
| sGCfast participated as | Molecule | Sum total of | Enzyme | Substrate of an enzyme | Product of an enzyme | Substrate in Reaction | Product in Reaction | | No. of occurrences | 1 | 0 | 0 | 0 | 0 | 1 | 0 |
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. |
sGCfast acting as a Molecule in cGMP_regulation Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | sGCfast | cGMP_regulation
Accession No. : 34 | GC
Pathway No. : 177 | 3 | 0.0016667 | Yes | | Stone and Marletta, Biochemistry,35(4), 1996, They have reported that the binding of sGC with NO occurs through two phases;a slow process and a fast process. 30% of the sGC binds quickly to NO; but the rest 70% goes through a slow process which involves the binding of another NO to an unidentified non-heme site on the protein, which seems to be not necessarily the same site used in the initial two step binding to the heme. Stone and Marletta,1995,34;14668-14674;-- report that the native heme stoichiometry is 2 per heterodimer. spectrally only one type of heme is observed, indicating that both hemes are in similar environment. they conclude that each subunit of the heterodimer binds 1 equiv of heme at a site conserved between the two subunits. Concentration 3 uM assumed on the basis of reported data (Kuroda et al., J.Neurosci., 2001, 21(15): 5693-5702 ; Ariano et al., PNAS, 1982, 79:1316-1320) |
sGCfast 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 | | NO_bind_sGCfast | cGMP_regulation
Accession No. : 34 | GC
Pathway No. : 177 | 700
(uM^-1 s^-1) | 800
(s^-1) | Kd(bf) = 1.1429(uM) | - | Substrate
NO
sGCfast
Product
NO.sGCfast
| | This is the fast binding of NO to sGC, subsequently activating it, as proposed by Stone and Marletta. Rates of these binding reactions used directly from Stone and Marletta,1996, Biochemistry, 35(4):1093-1099, based on whose paper this model is made. Rates obtained from stopped flow kinetics detailed in their paper. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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