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Molecule Parameter List for PKA-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-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	35	0	0	1	2

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
AMPAR_traff_ model1	60	Network	Shared_Object_AMPAR_traff_model1, CaMKII, CaM, PP1, PP2B, PP1_PSD, PKA, AC, AMPAR, AMPAR_memb
This is the basic model of AMPAR trafficking bistability. It is based on Hayer and Bhalla, PLoS Comput. Biol. 2005. It includes the degradation and turnover of AMPARs. The CaMKII portion of the model is not bistable.

PKA-active acting as a Molecule in AMPAR_traff_model1 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
PKA-active	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	0	0.09	No

PKA-active acting as an Enzyme in AMPAR_traff_model1 Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	PKA-active / phosph-PDE	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50008	9	4	explicit E-S complex	Substrate cAMP-PDE Product cAMP-PDE*
	Same rates as PKA-phosph-I1
2	PKA-active / PKA-phosph-I1	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50008	9	4	explicit E-S complex	Substrate I1 Product I1*
	#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.
3	PKA-active / PKA-phosph-I1_ PSD	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50008	9	4	explicit E-S complex	Substrate I1 Product I1*
4	PKA-active / PKA[17]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B Product A845*_B
5	PKA-active / PKA[16]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831_B Product* A831845_B
6	PKA-active / PKA[18]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B831* Product A845_B831
7	PKA-active / PKA[19]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831_B831 Product A831845_B831*
8	PKA-active / PKA[20]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B Product A_B845*
9	PKA-active / PKA[21]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831_B Product* A831_B845
10	PKA-active / PKA[22]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B831* Product A_B831845
11	PKA-active / PKA[23]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831_B831 Product A831_B831845*
12	PKA-active / PKA[24]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B845* Product A845_B845
13	PKA-active / PKA[25]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831_B845 Product A831845_B845*
14	PKA-active / PKA[26]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B831845 Product A845_B831845*
15	PKA-active / PKA[27]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831_B831845* Product A835845_ B835845
16	PKA-active / PKA[28]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A845_B Product* A845_B845
17	PKA-active / PKA[29]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831845_B Product A831845_B845*
18	PKA-active / PKA[30]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A845_B831 Product A845_B831845*
19	PKA-active / PKA[31]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831845_B831* Product A835845_ B835845
20	PKA-active / PKA	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B845* Product A845_B845
21	PKA-active / PKA[1]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A845_B Product* A845_B845
22	PKA-active / PKA[2]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B Product A845*_B
23	PKA-active / PKA[3]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B Product A_B845*
24	PKA-active / PKA[4]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831_B845 Product A831845_B845*
25	PKA-active / PKA[5]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831845_B Product A831845_B845*
26	PKA-active / PKA[6]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831_B Product* A831_B845
27	PKA-active / PKA[7]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831_B Product* A831845_B
28	PKA-active / PKA[8]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B831845 Product A845_B831845*
29	PKA-active / PKA[9]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A845_B831 Product A845_B831845*
30	PKA-active / PKA[10]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B831* Product A_B831845
31	PKA-active / PKA[11]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B831* Product A845_B831
32	PKA-active / PKA[12]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831_B831845* Product A835845_ B835845
33	PKA-active / PKA[13]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831845_B831* Product A835845_ B835845
34	PKA-active / PKA[14]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831_B831 Product A831_B831845*
35	PKA-active / PKA[15]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A831_B831 Product A831845_B831*

PKA-active acting as a Substrate in a reaction in AMPAR_traff_model1 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
inhib-PKA	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	59.9994 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.0167(uM)	-	Substrate PKA-active PKA-inhibitor Product inhibited-PKA
This has to be set to zero for matching the expts in vitro. In vivo we need to consider the inhibition though. kf = 1e-5 kb = 1

PKA-active acting as a Product in a reaction in AMPAR_traff_model1 Network

	Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
1	Release-C1	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	60 (s^-1)	17.9998 (uM^-1 s^-1)	Kd(cb) = 0.3(uM)	-	Substrate R2C2-cAMP4 Product PKA-active R2C-cAMP4
	This has to be fast, as the activation of PKA by cAMP is also fast. kf was 10
2	Release-C2	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	60 (s^-1)	17.9998 (uM^-1 s^-1)	Kd(cb) = 0.3(uM)	-	Substrate R2C-cAMP4 Product PKA-active R2-cAMP4

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