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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	5	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.

CaM-Ca4 acting as a Molecule in  AMPAR_traff_model1 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CaM-Ca4	AMPAR_traff_ model1 Accession No. : 60	CaM Pathway No. : 246	0	0.09	No

CaM-Ca4 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
1	CaMKII-bind-CaM	AMPAR_traff_ model1 Accession No. : 60	CaMKII Pathway No. : 245	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	AMPAR_traff_ model1 Accession No. : 60	CaMKII Pathway No. : 245	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	AMPAR_traff_ model1 Accession No. : 60	PP2B Pathway No. : 248	599.994 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.0017(uM)	-	Substrate CaM-Ca4 CaNAB-Ca4 Product CaM_Ca_n-CaNAB
4	CaM-bind-AC1	AMPAR_traff_ model1 Accession No. : 60	AC Pathway No. : 251	49.9997 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.02(uM)	-	Substrate AC1 CaM-Ca4 Product AC1-CaM
	Half-max at 20 nM CaM (Tang et al JBC 266:13 8595-8603 1991 kb/kf = 20 nM = 12000 #/cell so kf = kb/12000 = kb * 8.333e-5
5	CaM_bind_PDE1	AMPAR_traff_ model1 Accession No. : 60	AC Pathway No. : 251	719.982 (uM^-1 s^-1)	5 (s^-1)	Kd(bf) = 0.0069(uM)	-	Substrate CaM-Ca4 PDE1 Product CaM.PDE1
	For olf epi PDE1, affinity is 7 nM. Assume same for brain. Reaction should be pretty fast. Assume kb = 5/sec. Then kf = 5 / (0.007 * 6e5) = 1.2e-3

CaM-Ca4 acting as a Product 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
1	CaM-Ca3-bind-Ca	AMPAR_traff_ model1 Accession No. : 60	CaM Pathway No. : 246	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
2	equilib	AMPAR_traff_ model1 Accession No. : 60	CaM Pathway No. : 246	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