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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	1	1	1

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.

neurogranin_PSD acting as a Molecule in  AMPAR_traff_model0 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
neurogranin_PSD	AMPAR_traff_ model0 Accession No. : 59	CaM Pathway No. : 236	10	0.01	No
Also known as RC3 and p17 and BICKS. Conc in brain >> 2 uM from Martzen and Slemmon J neurosci 64 92-100 1995 but others say less without any #s. Conc in dend spines is much higher than overall, so it could be anywhere from 2 uM to 50. We will estimate 10 uM as a starting point. Gerendasy et al JBC 269:35 22420-22426 1994 have a skeleton model (no numbers) indicating CaM-Ca(n) binding.

neurogranin_PSD acting as a Substrate for an Enzyme in  AMPAR_traff_model0 Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PKC-active  / PKC-phosph-neuro granin_ PSD	AMPAR_traff_ model0 Accession No. : 59	Shared_Object_ AMPAR_traff_ model0 Pathway No. : 234	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

neurogranin_PSD acting as a Product of an Enzyme in  AMPAR_traff_model0 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_ model0 Accession No. : 59	PP2B Pathway No. : 238	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 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
neurogranin-bind -CaM_ PSD	AMPAR_traff_ model0 Accession No. : 59	CaM Pathway No. : 236	0.3 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 3.3333(uM)	-	Substrate CaM-PSD neurogranin_PSD Product neurogranin-CaM_ PSD
Surprisingly, no direct info on rates from neurogranin at this time. These rates are based on GAP-43 binding studies. As GAP-43 and neurogranin share near identity in the CaM/PKC binding regions, and also similarity in phosph and dephosph rates, I am borrowing GAP-43 kinetic info. See Alexander et al JBC 262:13 6108-6113 1987

neurogranin_PSD acting as a Product 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
dephosph-neurogr anin_ PSD	AMPAR_traff_ model0 Accession No. : 59	CaM Pathway No. : 236	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.