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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	6	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
mRNA synthesis	94	Network	kinetics,  compartment_1,  compartment_2
The model consists of three major pathways: Calcium-calmodulin dependent protein kinase IV (CaMKIV), Mitogen-activated protein kinase (MAPK) and Protein Phosphatase 1 (PP1). Each of these converged on CREB activation. We also modeled further interactions with Transducer of regulated CREB activity 1 (TORC1) and the protein kinase A (PKA) pathway.

Ca acting as a Molecule in  mRNA synthesis Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Ca	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	0.08	1000	Yes

Ca acting as a Substrate in a reaction in  mRNA synthesis 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_dash_Ca3_ dash_bind_dash_ Ca	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	0.465 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 21.5051(uM)	-	Substrate Ca CaM_dash_Ca3 Product CaM_dash_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
2	CaM_dash_bind_ dash_Ca	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	8.4846 (uM^-1 s^-1)	8.4853 (s^-1)	Kd(bf) = 1.0001(uM)	-	Substrate Ca CaM Product CaM_dash_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
3	CaM_dash_Ca2_ dash_bind_dash_ Ca	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	3.6001 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 2.7777(uM)	-	Substrate Ca CaM_dash_Ca2 Product CaM_dash_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_dash_Ca_ dash_bind_dash_ Ca	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	8.4846 (uM^-1 s^-1)	8.4853 (s^-1)	Kd(bf) = 1.0001(uM)	-	Substrate Ca CaM_dash_Ca Product CaM_dash_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
5	Ca_dash_bind_ dash_CaNAB_ dash_Ca2	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	3599.928 (uM^-2 s^-1)	1 (s^-1)	Kd(af) = 0.0167(uM)	-	Substrate Ca Ca CaNAB_dash_Ca2 Product CaNAB_dash_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
6	Ca_dash_bind_ dash_CaNAB	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	10008360 (uM^-2 s^-1)	1 (s^-1)	Kd(af) = 0.0003(uM)	-	Substrate Ca Ca CaNAB Product CaNAB_dash_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 

Ca acting as a Product in a reaction in  mRNA synthesis 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	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	100 (s^-1)	100 (s^-1)	Keq = 1(uM)	0.005sec	Substrate Ca_input Product Ca