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Molecule Parameter List for PDE1 | 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 | AMPAR_traff_
model1 | 60 | Network |
Shared_Object_AMPAR_traff_model1, CaMKII, CaM,
PP1, PP2B, PP1_PSD,
PKA, AC, AMPAR,
AMPAR_memb | | This is the basic model of AMPAR trafficking bistability. It is based on Hayer and Bhalla, PLoS Comput. Biol. 2005. It includes the degradation and turnover of AMPARs. The CaMKII portion of the model is not bistable. |
PDE1 acting as a Molecule in AMPAR_traff_model1 Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | PDE1 | AMPAR_traff_
model1
Accession No. : 60 | AC
Pathway No. : 251 | 2.5926 | 0.09 | No | | CaM-Dependent PDE. Amount calculated from total rate in brain vs. specific rate. |
PDE1 acting as an Enzyme in AMPAR_traff_model1 Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | PDE1 /
PDE1
| AMPAR_traff_
model1
Accession No. : 60 | AC
Pathway No. : 251 | 39.6999 | 1.667 | 4.0012 | explicit E-S complex | Substrate
cAMP
Product
AMP
| | Rate is 1/6 of the CaM stim form. We'll just reduce all lf k1, k2, k3 so that the Vmax goes down 1/6. |
PDE1 acting as a Substrate in a reaction in AMPAR_traff_model1 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 | | CaM_bind_PDE1 | AMPAR_traff_
model1
Accession No. : 60 | AC
Pathway No. : 251 | 719.982
(uM^-1 s^-1) | 5
(s^-1) | Kd(bf) = 0.0069(uM) | - | Substrate
CaM-Ca4
PDE1
Product
CaM.PDE1
| | For olf epi PDE1, affinity is 7 nM. Assume same for brain. Reaction should be pretty fast. Assume kb = 5/sec. Then kf = 5 / (0.007 * 6e5) = 1.2e-3 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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