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Molecule Parameter List for CaM-Ca4

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 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_noPKA_ model3	62	Network	Shared_Object_CaMKII_noPKA_model3,  CaMKII,  CaM,   PP1,  PP2B,  PP1_PSD
This is the 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 does not include the full PKA regulatory pathway, and instead has a predefined initial amount of active PKA.

CaM-Ca4 acting as a Molecule in  CaMKII_noPKA_model3 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CaM-Ca4	CaMKII_noPKA_ model3 Accession No. : 62	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. : 257	0	0.09	No

CaM-Ca4 acting as a Substrate in a reaction in  CaMKII_noPKA_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	CaMKII_noPKA_ model3 Accession No. : 62	CaMKII Pathway No. : 258	49.9997 (uM^-1 s^-1)	5 (s^-1)	Kd(bf) = 0.1(uM)	-	Substrate CaM-Ca4 CaMKII Product CaMKII-CaM
	This is tricky. There is some cooperativity here arising from interactions between the subunits of the CAMKII holoenzyme. However, the stoichiometry is 1. Kb/Kf = 6e4 #/cell. Rate is fast (see Hanson et al Neuron 12 943-956 1994) so lets say kb = 10. This gives kf = 1.6667e-4 H&S AnnRev Biochem 92 give tau for dissoc as 0.2 sec at low Ca, 0.4 at high. Low Ca = 100 nM = physiol.
2	CaMK-thr286-bind -CaM	CaMKII_noPKA_ model3 Accession No. : 62	CaMKII Pathway No. : 258	1000.19 (uM^-1 s^-1)	0.1 (s^-1)	Kd(bf) = 0.0001(uM)	-	Substrate CaM-Ca4 CaMKII-thr286 Product CaMKII-thr286*-C aM
	Affinity is up 1000X. Time to release is about 20 sec, so the kb is OK at 0.1 This makes Kf around 1.6666e-3
3	CaMCa4-bind-CaNA B	CaMKII_noPKA_ model3 Accession No. : 62	PP2B Pathway No. : 261	599.994 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.0017(uM)	-	Substrate CaM-Ca4 CaNAB-Ca4 Product CaM_Ca_n-CaNAB

CaM-Ca4 acting as a Product in a reaction in  CaMKII_noPKA_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	equilib	CaMKII_noPKA_ model3 Accession No. : 62	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. : 257	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.
2	CaM-Ca3-bind-Ca	CaMKII_noPKA_ model3 Accession No. : 62	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. : 257	0.465 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 21.5054(uM)	-	Substrate Ca CaM-Ca3 Product CaM-Ca4
	Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10