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Molecule Parameter List for PKA_dash_active

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

*PKA_dash_active* 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	6	0	0	4	3

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.

PKA_dash_active acting as a Molecule in mRNA synthesis Network

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

PKA_dash_active 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
1	PKA_dash_active / phosph_dash_PDE	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	7.5	9	4	explicit E-S complex	Substrate cAMP_dash_PDE Product cAMP_dash_PDE_ star

2	PKA_dash_active / Src_phospho	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	0.05	20	4	explicit E-S complex	Substrate Src Product Src_star

3	PKA_dash_active / PKA_dash_ phosph_dash_GEF	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	7.5	9	4	explicit E-S complex	Substrate inact_dash_GEF Product inact_dash_GEF_ star
	This pathway inhibits Ras when cAMP is elevated. See: Hordijk et al JBC 269:5 3534-3538 1994 Burgering et al EMBO J 12:11 4211-4220 1993 The rates are the same as used in PKA-phosph-I1
4	PKA_dash_active / PKA_dash_ phosph_dash_I1	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	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.
5	PKA_dash_active / CaMKKphosph	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	4.6999	0.6833	3.99997073156	explicit E-S complex	Substrate CaMKK_CaM_Ca_c Product CaMKKp CaM_dash_Ca4

6	PKA_dash_active / SIK2_phosp	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	4.5997	0.1	4	explicit E-S complex	Substrate SIK2 Product SIK2_star

PKA_dash_active 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	C1_dash_binding	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	799.02 (uM^-1 s^-1)	0.186 (s^-1)	Kd(bf) = 0.0002(uM)	-	Substrate PKA_dash_active R2 Product R2C1
	PMID: 11110787
2	C2_dash_binding	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	799.02 (uM^-1 s^-1)	0.186 (s^-1)	Kd(bf) = 0.0002(uM)	-	Substrate PKA_dash_active R2C1 Product R2C2

3	inhib_dash_PKA	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	60 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.0167(uM)	-	Substrate PKA_dash_active PKA_dash_ inhibitor Product inhibited_dash_ PKA

4	PKAimport	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	0.0003 (s^-1)	0.0005 (s^-1)	Keq = 1.5164(uM)	1250sec	Substrate PKA_dash_active Product PKA_dash_active

PKA_dash_active acting as a Product in a reaction in mRNA synthesis Network

	Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
1	Release_dash_C1	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	60 (s^-1)	18 (uM^-1 s^-1)	Kd(cb) = 0.3(uM)	-	Substrate R2C2_dash_cAMP4 Product PKA_dash_active R2C_dash_cAMP4

2	Release_dash_C2	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	60 (s^-1)	18 (uM^-1 s^-1)	Kd(cb) = 0.3(uM)	-	Substrate R2C_dash_cAMP4 Product PKA_dash_active R2_dash_cAMP4

3	PKAimport	mRNA synthesis Accession No. : 94	kinetics Pathway No. : 1112	0.0003 (s^-1)	0.0005 (s^-1)	Keq = 1.5164(uM)	1250sec	Substrate PKA_dash_active Product PKA_dash_active

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