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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
PDE1 participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1010010

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
CaMKII_model363Network
Shared_Object_CaMKII_model3 CaMKII CaM 
PP1 PP2B PP1_PSD 
AC PKA 
This is the complete model of CaMKII bistability, model 3. It exhibits bistability in CaMKII activation due to autophosphorylation at the PSD and local saturation of PP1. This version of model 3 includes PKA regulatory input. This has little effect on the deterministic calculations, but the PKA pathway introduces a lot of noise which causes a difference in stochastic runs.

PDE1 acting as a Molecule in  
CaMKII_model3 Network
NameAccession NamePathway NameInitial Conc.
(uM)
Volume
(fL)
Buffered
PDE1CaMKII_model3
Accession No. : 63
AC
Pathway No. : 269
2.59260.09No
CaM-Dependent PDE. Amount calculated from total rate in brain vs. specific rate.

PDE1 acting as an Enzyme in  
CaMKII_model3 Network
Enzyme Molecule /
Enzyme Activity
Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
PDE1 /
PDE1
CaMKII_model3
Accession No. : 63
AC
Pathway No. : 269
39.69991.6674.0012explicit E-S complexSubstrate
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  
CaMKII_model3 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.
NameAccession NamePathway NameKfKbKdtauReagents
CaM_bind_PDE1CaMKII_model3
Accession No. : 63
AC
Pathway No. : 269
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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