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Molecule Parameter List for Ca

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

Ca 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	0	0	5	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Ajay_Bhalla_ 2007_PKM	80	Network	Shared_Object_Ajay_Bhalla_2007_PKM,  PKC,  MAPK,   Ras,  CaM,  PKM
This is a non-bistable model of ERKII signaling that also incorporates PKM synthesis triggered by Ca influx. It is a simplified variant of the model of Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80.

Ca acting as a Molecule in  Ajay_Bhalla_2007_PKM Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Ca	Ajay_Bhalla_ 2007_PKM Accession No. : 80	Shared_Object_ Ajay_Bhalla_ 2007_PKM Pathway No. : 369	0.08	1.5	No

Ca acting as a Substrate in a reaction in  Ajay_Bhalla_2007_PKM 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
1	PKC-act-by-Ca	Ajay_Bhalla_ 2007_PKM Accession No. : 80	PKC Pathway No. : 370	0.6 (uM^-1 s^-1)	0.5 (s^-1)	Kd(bf) = 0.8333(uM)	-	Substrate Ca PKC-cytosolic Product PKC-Ca
	Need est of rate of assoc of Ca and PKC. Assume it is fast The original parameter-searched kf of 439.4 has been scaled by 1/6e8 to account for change of units to n. Kf now 8.16e-7, kb=.6085 Raised kf to 1e-6 to match Ca curve, kb to .5
2	CaM-Ca3-bind-Ca	Ajay_Bhalla_ 2007_PKM Accession No. : 80	CaM Pathway No. : 373	0.465 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 21.5053(uM)	-	Substrate Ca CaM-Ca3 Product CaM-Ca4
	Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10
3	CaM-bind-Ca	Ajay_Bhalla_ 2007_PKM Accession No. : 80	CaM Pathway No. : 373	8.4848 (uM^-1 s^-1)	8.4853 (s^-1)	Kd(bf) = 1.0001(uM)	-	Substrate Ca CaM Product CaM-Ca
	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 !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853
4	CaM-Ca2-bind-Ca	Ajay_Bhalla_ 2007_PKM Accession No. : 80	CaM Pathway No. : 373	3.6 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 2.7778(uM)	-	Substrate Ca CaM-Ca2 Product 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
5	CaM-Ca-bind-Ca	Ajay_Bhalla_ 2007_PKM Accession No. : 80	CaM Pathway No. : 373	8.4848 (uM^-1 s^-1)	8.4853 (s^-1)	Kd(bf) = 1.0001(uM)	-	Substrate Ca CaM-Ca Product CaM-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 !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853

Ca acting as a Product in a reaction in  Ajay_Bhalla_2007_PKM 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
Ca_diff	Ajay_Bhalla_ 2007_PKM Accession No. : 80	Shared_Object_ Ajay_Bhalla_ 2007_PKM Pathway No. : 369	5 (s^-1)	5 (s^-1)	Keq = 1(uM)	0.1sec	Substrate Ca_input Product Ca