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Molecule Parameter List for neurogranin_PSD*

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

**neurogranin_PSD*** 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	1	2	1	0

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.

neurogranin*_PSD acting as a Molecule in AMPAR_traff_model1 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
neurogranin_PSD*	AMPAR_traff_ model1 Accession No. : 60	CaM Pathway No. : 246	0	0.01	No
The phosph form does not bind CaM (Huang et al ABB 305:2 570-580 1993)

neurogranin*_PSD acting as a Substrate for an Enzyme in AMPAR_traff_model1 Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
CaM_Ca_n-CaNAB / dephosph_ neurogranin_PSD	AMPAR_traff_ model1 Accession No. : 60	PP2B Pathway No. : 248	10.012	0.67	3.98507	explicit E-S complex	Substrate neurogranin_ PSD Product* neurogranin_PSD
From Seki et al ABB 316(2):673-679

neurogranin*_PSD acting as a Product of an Enzyme in AMPAR_traff_model1 Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	PKC-active / PKC-phosph-neuro granin_ PSD	AMPAR_traff_ model1 Accession No. : 60	Shared_Object_ AMPAR_traff_ model1 Pathway No. : 244	28.6273	0.58	4.03448	explicit E-S complex	Substrate neurogranin_PSD Product neurogranin*_ PSD
	Rates from Huang et al ABB 305:2 570-580 1993
2	PKC-active / PKC-phosph-ng-Ca M_ PSD	AMPAR_traff_ model1 Accession No. : 60	Shared_Object_ AMPAR_traff_ model1 Pathway No. : 244	28.5956	0.35	4	explicit E-S complex	Substrate neurogranin-CaM_ PSD Product CaM-PSD neurogranin*_ PSD
	Rates are 60% those of PKC-phosph-neurogranin. See Huang et al ABB 305:2 570-580 1993

neurogranin*_PSD 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
dephosph-neurogr anin_ PSD	AMPAR_traff_ model1 Accession No. : 60	CaM Pathway No. : 246	0.005 (s^-1)	0 (s^-1)	-	-	Substrate neurogranin_ PSD Product* neurogranin_PSD
This is put in to keep the basal levels of neurogranin* experimentally reasonable. From various papers, specially Ramakers et al JBC 270:23 1995 13892-13898, it looks like the basal level of phosph is between 20 and 40%. I est around 25 % The kf of 0.005 gives around this level at basal PKC activity levels of 0.1 uM active PKC.

Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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Molecule Parameter List for neurogranin*_PSD

Molecule Parameter List for neurogranin_PSD*