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Molecule Parameter List for CaM-Ca4-PSD

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

CaM-Ca4-PSD 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	3	2

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
CaMKII_model3	63	Network	Shared_Object_CaMKII_model3,  CaMKII,  CaM,   PP1,  PP2B,  PP1_PSD,   AC,  PKA
This is the complete model of CaMKII bistability, model 3. It exhibits bistability in CaMKII activation due to autophosphorylation at the PSD and local saturation of PP1. This version of model 3 includes PKA regulatory input. This has little effect on the deterministic calculations, but the PKA pathway introduces a lot of noise which causes a difference in stochastic runs.

CaM-Ca4-PSD acting as a Molecule in  CaMKII_model3 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CaM-Ca4-PSD	CaMKII_model3 Accession No. : 63	Shared_Object_ CaMKII_model3 Pathway No. : 263	0	0.01	No

CaM-Ca4-PSD acting as a Substrate in a reaction in  CaMKII_model3 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	CaMKII-bind-CaM- PSD	CaMKII_model3 Accession No. : 63	Shared_Object_ CaMKII_model3 Pathway No. : 263	49.9998 (uM^-1 s^-1)	0 (s^-1)	-	-	Substrate CaM-Ca4-PSD CaMKII-PSD Product CaMKII-CaM-PSD
2	CaMKII-thr286-bi nd-CaM-PSD	CaMKII_model3 Accession No. : 63	Shared_Object_ CaMKII_model3 Pathway No. : 263	1000.02 (uM^-1 s^-1)	0.1 (s^-1)	Kd(bf) = 0.0001(uM)	-	Substrate CaM-Ca4-PSD CaMKII-thr286-PS D Product CaMKII-thr286-Ca M-PSD
	Same values as for the main compartment Can the main compartment pool of Ca/CaM be used?
3	equilib	CaMKII_model3 Accession No. : 63	Shared_Object_ CaMKII_model3 Pathway No. : 263	540 (s^-1)	60 (s^-1)	Not applicable**	-	Substrate CaM-Ca4-PSD Product CaM-Ca4
	Diffusional equilibrium between PSD- and cytosolic compartment. According to D. Bary in Cell Movements 2nd ed 2001 D for proteins is 5e-7 cm^2/s giving 10 ms for a translocation of 1 um.

** This is a trasport reation between compartments of different volumes. Therefore Kd is not applicable. Please Note Kf, Kb units are in number of molecules instead of concentration

CaM-Ca4-PSD acting as a Product in a reaction in  CaMKII_model3 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	CaM-Ca3-bind-Ca- PSD	CaMKII_model3 Accession No. : 63	CaM Pathway No. : 265	0.465 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 21.5048(uM)	-	Substrate Ca-PSD CaM-Ca3-PSD Product CaM-Ca4-PSD
	Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10
2	CaMKII-diss-CaM	CaMKII_model3 Accession No. : 63	Shared_Object_ CaMKII_model3 Pathway No. : 263	5 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate CaMKII-CaM-PSD Product CaM-Ca4-PSD CaMKII-PSD