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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
CaMKII_noPKA_ model3	62	Network	Shared_Object_CaMKII_noPKA_model3,  CaMKII,  CaM,   PP1,  PP2B,  PP1_PSD
This is the model of CaMKII bistability, model 3. It exhibits bistability in CaMKII activation due to autophosphorylation at the PSD and local saturation of PP1. This version of model 3 does not include the full PKA regulatory pathway, and instead has a predefined initial amount of active PKA.

Ca acting as a Molecule in  CaMKII_noPKA_model3 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Ca	CaMKII_noPKA_ model3 Accession No. : 62	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. : 257	0.08	0.09	No

Ca acting as a Substrate in a reaction in  CaMKII_noPKA_model3 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	CaM-TR2-bind-Ca	CaMKII_noPKA_ model3 Accession No. : 62	CaM Pathway No. : 259	71.999 (uM^-2 s^-1)	72 (s^-1)	Kd(af) = 1(uM)	-	Substrate Ca Ca CaM Product 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-Ca2-bind -Ca	CaMKII_noPKA_ model3 Accession No. : 62	CaM Pathway No. : 259	3.6 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 2.7778(uM)	-	Substrate Ca CaM-TR2-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
3	Ca-bind-CaNAB-Ca 2	CaMKII_noPKA_ model3 Accession No. : 62	PP2B Pathway No. : 261	3.6001 (uM^-2 s^-1)	1 (s^-1)	Kd(af) = 0.527(uM)	-	Substrate Ca Ca CaNAB-Ca2 Product CaNAB-Ca4
	This process is probably much more complicated and involves CaM. However, as I can't find detailed info I am bundling this into a single step. Based on Steemer and Klee pg 6863, the Kact is 0.5 uM. kf/kb = 1/(0.5 * 6e5)^2 = 1.11e-11
4	Ca-bind-CaNAB	CaMKII_noPKA_ model3 Accession No. : 62	PP2B Pathway No. : 261	10008 (uM^-2 s^-1)	1 (s^-1)	Kd(af) = 0.01(uM)	-	Substrate Ca Ca CaNAB Product CaNAB-Ca2
	going on the experience with CaM, we put the fast (high affinity) sites first. We only know (Stemmer and Klee) that the affinity is < 70 nM. Assuming 10 nM at first, we get kf = 2.78e-8, kb = 1. Try 20 nM. kf = 7e-9, kb = 1 
5	CaM-Ca3-bind-Ca	CaMKII_noPKA_ model3 Accession No. : 62	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. : 257	0.465 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 21.5054(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

Ca acting as a Product in a reaction in  CaMKII_noPKA_model3 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_stoch_cyt	CaMKII_noPKA_ model3 Accession No. : 62	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. : 257	100 (s^-1)	100 (s^-1)	Keq = 1(uM)	0.005sec	Substrate Ca_control_cyt Product Ca