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Molecule Parameter List for R2C2-cAMP

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

R2C2-cAMP 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	0	0	1	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
AMPAR_CaMKII_ strong_coupling	64	Network	Shared_Object_AMPAR_CaMKII_strong_coupling,  CaMKII,  CaM,   PP1,  AMPAR_memb,  PP2B,   PKA,  AC,  PP1_PSD,   AMPAR
This is a model of tight coupling between the AMPAR trafficking bistability, and the CaMKII autophosphorylation bistability. In this model, the CaMKII activity is self sustaining only when AMPAR is turned on. Further, CaMKII turns on when AMPAR is turned on.

R2C2-cAMP acting as a Molecule in  AMPAR_CaMKII_strong_coupling Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
R2C2-cAMP	AMPAR_CaMKII_ strong_coupling Accession No. : 64	PKA Pathway No. : 277	0	0.09	No
CoInit was .0624

R2C2-cAMP acting as a Substrate in a reaction in  AMPAR_CaMKII_strong_coupling 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
cAMP-bind-site-B 2	AMPAR_CaMKII_ strong_coupling Accession No. : 64	PKA Pathway No. : 277	54 (uM^-1 s^-1)	33 (s^-1)	Kd(bf) = 0.6111(uM)	-	Substrate R2C2-cAMP cAMP Product R2C2-cAMP2
For now let us set this to the same Km (1e-7M) as site B. This gives kf/kb = .7e-7M * 1e6 / (6e5^2) : 1/(6e5^2) = 2e-13:2.77e-12 Smith et al have better values. They say that this is cooperative, so the consts are now kf/kb =8.3e-4

R2C2-cAMP acting as a Product in a reaction in  AMPAR_CaMKII_strong_coupling 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
cAMP-bind-site-B 1	AMPAR_CaMKII_ strong_coupling Accession No. : 64	PKA Pathway No. : 277	54 (uM^-1 s^-1)	33 (s^-1)	Kd(bf) = 0.6111(uM)	-	Substrate R2C2 cAMP Product R2C2-cAMP
Hasler et al FASEB J 6:2734-2741 1992 say Kd =1e-7M for type II, 5.6e-8 M for type I. Take mean which comes to 2e-13 #/cell Smith et al PNAS USA 78:3 1591-1595 1981 have better data. First kf/kb=2.1e7/M = 3.5e-5 (#/cell). Ogreid and Doskeland Febs Lett 129:2 287-292 1981 have figs suggesting time course of complete assoc is < 1 min.