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Molecule Parameter List for neurogranin*

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* 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
Ajay_Bhalla_ 2004_PKM_Tuning	76	Network	PKC, Shared_Object_Ajay_Bhalla_2004_PKM_tuning, PLA2, PLCbeta, Gq, MAPK, Ras, EGFR, Sos, PLC_g, CaMKII, CaM, PP1, PP2B, PKA, AC, PKM
This model is taken from the Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the reference feedforward model from Figure 8a.

neurogranin* acting as a Molecule in Ajay_Bhalla_2004_PKM_Tuning Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
neurogranin*	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	CaM Pathway No. : 323	0	1.5	No
The phosph form does not bind CaM (Huang et al ABB 305:2 570-580 1993)

neurogranin* acting as a Substrate for an Enzyme in Ajay_Bhalla_2004_PKM_Tuning Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
CaM(Ca)n-CaNAB / dephosph_ neurogranin	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	Shared_Object_ Ajay_Bhalla_ 2004_PKM_tuning Pathway No. : 312	10.0119	0.67	3.98507	explicit E-S complex	Substrate neurogranin* Product neurogranin
From Seki et al ABB 316(2):673-679

neurogranin* acting as a Product of an Enzyme in Ajay_Bhalla_2004_PKM_Tuning 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	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	Shared_Object_ Ajay_Bhalla_ 2004_PKM_tuning Pathway No. : 312	28.6283	0.58	4.03448	explicit E-S complex	Substrate neurogranin Product neurogranin*
	Rates from Huang et al ABB 305:2 570-580 1993
2	PKC-active / PKC-phosph-ng-Ca M	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	Shared_Object_ Ajay_Bhalla_ 2004_PKM_tuning Pathway No. : 312	28.5948	0.35	4	explicit E-S complex	Substrate neurogranin-CaM Product CaM neurogranin*
	Rates are 60% those of PKC-phosph-neurogranin. See Huang et al ABB 305:2 570-580 1993

neurogranin* acting as a Substrate in a reaction in Ajay_Bhalla_2004_PKM_Tuning 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	Ajay_Bhalla_ 2004_PKM_Tuning Accession No. : 76	CaM Pathway No. : 323	0.005 (s^-1)	0 (s^-1)	-	-	Substrate neurogranin* Product neurogranin
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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