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Reaction List for pathway CaM (Pathway Number 283) in Accession AMPAR_CaMKII_weak_coupling (Accession Number 65)

Entries are grouped according to Pathway Number and they are alternately color coded using

and

color.
Further ordering can be done to the table header.

indicates that ordering is done according to ascending or descending order.
Keq is calculated only for first order reactions.
Kd is calculated only for second order reactions. [nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules]

	Reaction Name	Pathway Name / Pathway No.	Kf	Kb	Kd	tau	Reagents
1	CaM-TR2-bind-Ca	CaM Pathway No. 283	71.999 (uM^-2 s^-1)	72 (s^-1)	Kd(af) = 1(uM)	-	Substrate: CaM Ca Ca Products: CaM-TR2-Ca2
	Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !)....
2	CaM-TR2-bind-Ca- PSD	CaM Pathway No. 283	72 (uM^-2 s^-1)	72 (s^-1)	Kd(af) = 1(uM)	-	Substrate: CaM-PSD Ca-PSD Ca-PSD Products: CaM-TR2-Ca2-PSD
	Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !)....
3	CaM-TR2-Ca2-bind -Ca	CaM Pathway No. 283	3.6 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 2.7778(uM)	-	Substrate: CaM-TR2-Ca2 Ca Products: CaM-Ca3
	K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10
4	CaM-TR2-Ca2-bind -Ca-PSD	CaM Pathway No. 283	3.6 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 2.7778(uM)	-	Substrate: CaM-TR2-Ca2-PSD Ca-PSD Products: CaM-Ca3-PSD
	K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10
5	CaM-Ca3-bind-Ca- PSD	CaM Pathway No. 283	0.465 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 21.5048(uM)	-	Substrate: CaM-Ca3-PSD Ca-PSD Products: CaM-Ca4-PSD
	Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10
6	neurogranin-bind -CaM	CaM Pathway No. 283	0.3 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 3.3333(uM)	-	Substrate: neurogranin CaM Products: neurogranin-CaM
	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
7	neurogranin-bind -CaM_ PSD	CaM Pathway No. 283	0.3 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 3.3333(uM)	-	Substrate: neurogranin_PSD CaM-PSD Products: 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
8	dephosph-neurogr anin	CaM Pathway No. 283	0.005 (s^-1)	0 (s^-1)	-	-	Substrate: neurogranin* Products: 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.
9	dephosph-neurogr anin_ PSD	CaM Pathway No. 283	0.005 (s^-1)	0 (s^-1)	-	-	Substrate: neurogranin_ PSD Products:* 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.