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Molecule Parameter List for CaM_dash_Ca4

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_Ca4 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	1	6	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_Ca4 acting as a Molecule in  Differential synthesis of mRNA Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CaM_dash_Ca4	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	0	1000	No

CaM_dash_Ca4 acting as a Product of an Enzyme in  Differential synthesis of mRNA Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PKA_dash_active  / CaMKKphosph	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	4.6999	0.6833	3.99997073156	explicit E-S complex	Substrate CaMKK_CaM_Ca_c Product CaMKKp CaM_dash_Ca4

CaM_dash_Ca4 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_bind_ dash_AC1	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	49.9998 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.02(uM)	-	Substrate AC1 CaM_dash_Ca4 Product AC1_dash_CaM
2	CaM_bind_PDE1	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	720 (uM^-1 s^-1)	5 (s^-1)	Kd(bf) = 0.0069(uM)	-	Substrate CaM_dash_Ca4 PDE1 Product CaM.PDE1
3	CaM_dash_bind_ dash_GEF	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	60 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.0167(uM)	-	Substrate CaM_dash_Ca4 inact_dash_GEF Product CaM_dash_GEF
	We have no numbers for this. It is probably between the two extremes represented by the CaMKII phosph states, and I have used guesses based on this. kf=1e-4 kb=1 The reaction is based on Farnsworth et al Nature 376 524-527 1995
4	CaMCa4_dash_ bind_dash_CaNAB	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	600 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.0017(uM)	-	Substrate CaM_dash_Ca4 CaNAB_dash_Ca4 Product CaMCa4_dash_ CaNAB
5	CaMKIVcomplx	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	0.0133 (uM^-1 s^-1)	0.01 (s^-1)	Kd(bf) = 0.7508(uM)	-	Substrate CaMKIVc CaM_dash_Ca4 Product CaMKIV_CaM_Ca_c
	Kd from PMID: 9705275
6	CaMKKcomplx	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	4.05 (uM^-1 s^-1)	0.02 (s^-1)	Kd(bf) = 0.0049(uM)	-	Substrate CaMKK_c CaM_dash_Ca4 Product CaMKK_CaM_Ca_c
	Kd from PMID: 9705275

CaM_dash_Ca4 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_Ca3_ dash_bind_dash_ Ca	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	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