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Molecule Parameter List for I1_star

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

I1_star 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	3	1	1	0

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.

I1_star acting as a Molecule in  Differential synthesis of mRNA Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
I1_star	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	0.001	1000	No
Dephosph is mainly by PP2B

I1_star acting as a Substrate for 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
1	PP2A  / PP2A_dash_ dephosph_dash_ I1	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	7.8283	6	4.16666666667	explicit E-S complex	Substrate I1_star Product I1
	PP2A does most of the dephosph of I1 at basal Ca levels. See the review by Cohen in Ann Rev Biochem 1989. For now, lets halve Km. k1 was 3.3e-6, now 6.6e-6
2	CaNAB_dash_Ca4  / dephosph_ inhib1_noCaM	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	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
3	CaM_Ca_n_dash_ CaNAB  / dephosph_inhib1	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	4.9708	0.34	4	explicit E-S complex	Substrate I1_star Product I1

I1_star 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  / PKA_dash_ phosph_dash_I1	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	7.5	9	4	explicit E-S complex	Substrate I1 Product I1_star
#s from Bramson et al CRC crit rev Biochem 15:2 93-124. They have a huge list of peptide substrates and I have chosen high-ish rates. These consts give too much PKA activity, so lower Vmax 1/3. Now, k1 = 3e-5, k2 = 36, k3 = 9 (still pretty fast). Also lower Km 1/3 so k1 = 1e-5 Cohen et al FEBS Lett 76:182-86 1977 say rate =30% PKA act on phosphokinase beta.

I1_star 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
Inact_dash_PP1	Differential syn thesis of mRNA Accession No. : 95	kinetics Pathway No. : 1115	499.974 (uM^-1 s^-1)	0.1 (s^-1)	Kd(bf) = 0.0002(uM)	-	Substrate I1_star PP1_dash_ active_c Product PP1_dash_I1_ star
K inhib = 1nM from Cohen Ann Rev Bioch 1989, 4 nM from Foukes et al Assume 2 nM. kf /kb = 8.333e-4