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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_ model0	59	Network	Shared_Object_AMPAR_traff_model0,  CaMKII,  CaM,   PP1,  PP2B,  PP1_PSD,   PKA,  AC,  AMPAR,   AMPAR_memb
This is model 0 from Hayer and Bhalla, PLoS Comput Biol 2005. It has a bistable model of AMPAR traffick, plus a non-bistable model of CaMKII. This differs from the reference model (model 1) in that model0 lacks degradation and turno ver reactions for AMPAR.

PKA-active acting as a Molecule in  AMPAR_traff_model0 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
PKA-active	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	0	0.09	No

PKA-active acting as an Enzyme in  AMPAR_traff_model0 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_ model0 Accession No. : 59	PKA Pathway No. : 240	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_ model0 Accession No. : 59	PKA Pathway No. : 240	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_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50008	9	4	explicit E-S complex	Substrate I1 Product I1*
4	PKA-active / PKA[17]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A_B Product A845*_B
5	PKA-active / PKA[16]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*_B Product A831*845*_B
6	PKA-active / PKA[18]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A_B831* Product A845*_B831*
7	PKA-active / PKA[19]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*_B831* Product A831*845*_B831*
8	PKA-active / PKA[20]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A_B Product A_B845*
9	PKA-active / PKA[21]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*_B Product A831*_B845*
10	PKA-active / PKA[22]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A_B831* Product A_B831*845*
11	PKA-active / PKA[23]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*_B831* Product A831*_B831*845*
12	PKA-active / PKA[24]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A_B845* Product A845*_B845*
13	PKA-active / PKA[25]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*_B845* Product A831*845*_B845*
14	PKA-active / PKA[26]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A_B831*845* Product A845*_B831*845*
15	PKA-active / PKA[27]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*_B831*845* Product A835*845*_ B835*845*
16	PKA-active / PKA[28]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A845*_B Product A845*_B845*
17	PKA-active / PKA[29]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*845*_B Product A831*845*_B845*
18	PKA-active / PKA[30]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A845*_B831* Product A845*_B831*845*
19	PKA-active / PKA[31]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*845*_B831* Product A835*845*_ B835*845*
20	PKA-active / PKA	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A_B845* Product A845*_B845*
21	PKA-active / PKA[1]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A845*_B Product A845*_B845*
22	PKA-active / PKA[2]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A_B Product A845*_B
23	PKA-active / PKA[3]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A_B Product A_B845*
24	PKA-active / PKA[4]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*_B845* Product A831*845*_B845*
25	PKA-active / PKA[5]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*845*_B Product A831*845*_B845*
26	PKA-active / PKA[6]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*_B Product A831*_B845*
27	PKA-active / PKA[7]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*_B Product A831*845*_B
28	PKA-active / PKA[8]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A_B831*845* Product A845*_B831*845*
29	PKA-active / PKA[9]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A845*_B831* Product A845*_B831*845*
30	PKA-active / PKA[10]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A_B831* Product A_B831*845*
31	PKA-active / PKA[11]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A_B831* Product A845*_B831*
32	PKA-active / PKA[12]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*_B831*845* Product A835*845*_ B835*845*
33	PKA-active / PKA[13]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*845*_B831* Product A835*845*_ B835*845*
34	PKA-active / PKA[14]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*_B831* Product A831*_B831*845*
35	PKA-active / PKA[15]	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	7.50021	6	4	explicit E-S complex	Substrate A831*_B831* Product A831*845*_B831*

PKA-active acting as a Substrate in a reaction in  AMPAR_traff_model0 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_ model0 Accession No. : 59	PKA Pathway No. : 240	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_model0 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	Release-C1	AMPAR_traff_ model0 Accession No. : 59	PKA Pathway No. : 240	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_ model0 Accession No. : 59	PKA Pathway No. : 240	60 (s^-1)	17.9998 (uM^-1 s^-1)	Kd(cb) = 0.3(uM)	-	Substrate R2C-cAMP4 Product PKA-active R2-cAMP4