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Molecule Parameter List for CaNAB_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

CaNAB_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	1	0	0	3	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.

CaNAB_dash_Ca4 acting as a Molecule in  mRNA synthesis Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CaNAB_dash_Ca4	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	0	1000	No

CaNAB_dash_Ca4 acting as an Enzyme in  mRNA synthesis Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
CaNAB_dash_Ca4 / dephosph_ inhib1_noCaM	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	4.9708	0.034	4	explicit E-S complex	Substrate I1_star Product I1
The rates here are so slow I do not know if we should even bother with this enz reacn. These numbers are from Liu and Storm. Other refs suggest that the Km stays the same but the Vmax goes to 10% of the CaM stim levels. Prev: k1=2.2e-9, k2 = 0.0052, k3 = 0.0013 New : k1=5.7e-8, k2=.136, k3=.034

CaNAB_dash_Ca4 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_Ca2_ dash_bind_dash_ CaNAB	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	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
2	CaMCa3_dash_ bind_dash_CaNAB	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	2.238 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.4468(uM)	-	Substrate CaM_dash_Ca3 CaNAB_dash_Ca4 Product CaMCa3_dash_ CaNAB
3	CaMCa4_dash_ bind_dash_CaNAB	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	600 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.0017(uM)	-	Substrate CaM_dash_Ca4 CaNAB_dash_Ca4 Product CaMCa4_dash_ CaNAB

CaNAB_dash_Ca4 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_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