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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 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	1	0	0	1	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
AMPAR_traff_ model0	59	Network	Shared_Object_AMPAR_traff_model0,  CaMKII,  CaM,   PP1,  PP2B,  PP1_PSD,   PKA,  AC,  AMPAR,   AMPAR_memb
This is model 0 from Hayer and Bhalla, PLoS Comput Biol 2005. It has a bistable model of AMPAR traffick, plus a non-bistable model of CaMKII. This differs from the reference model (model 1) in that model0 lacks degradation and turno ver reactions for AMPAR.

PDE1 acting as a Molecule in  AMPAR_traff_model0 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
PDE1	AMPAR_traff_ model0 Accession No. : 59	AC Pathway No. : 241	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_model0 Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PDE1 / PDE1	AMPAR_traff_ model0 Accession No. : 59	AC Pathway No. : 241	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_model0 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_ model0 Accession No. : 59	AC Pathway No. : 241	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