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Molecule Parameter List for CaM_dash_Ca2

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

CaM_dash_Ca2 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	2	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Differential syn thesis of mRNA	95	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.

CaM_dash_Ca2 acting as a Molecule in  Differential synthesis of mRNA Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CaM_dash_Ca2	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	0	1000	No
This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not.

CaM_dash_Ca2 acting as a Substrate in a reaction in  Differential synthesis of mRNA 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_Ca2_ dash_bind_dash_ Ca	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	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
2	CaM_dash_Ca2_ dash_bind_dash_ CaNAB	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	0.24 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 4.1667(uM)	-	Substrate CaM_dash_Ca2 CaNAB_dash_Ca4 Product CaMCa2_dash_ CANAB
	Disabled. See notes for PP2B7.g

CaM_dash_Ca2 acting as a Product in a reaction in  Differential synthesis of mRNA 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
CaM_dash_Ca_ dash_bind_dash_ Ca	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	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