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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
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-PSD acting as a Molecule in  AMPAR_traff_model1 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CaM-Ca4-PSD	AMPAR_traff_ model1 Accession No. : 60	CaM Pathway No. : 246	0	0.01	No

CaM-Ca4-PSD 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- PSD	AMPAR_traff_ model1 Accession No. : 60	CaMKII Pathway No. : 245	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	AMPAR_traff_ model1 Accession No. : 60	CaMKII Pathway No. : 245	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	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

CaM-Ca4-PSD 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	CaMKII-diss-CaM	AMPAR_traff_ model1 Accession No. : 60	CaMKII Pathway No. : 245	5 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate CaMKII-CaM-PSD Product CaM-Ca4-PSD CaMKII-PSD
2	CaM-Ca3-bind-Ca- PSD	AMPAR_traff_ model1 Accession No. : 60	CaM Pathway No. : 246	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