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Molecule Parameter List for CaM-Ca3-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-Ca3-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	1	1

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-Ca3-PSD acting as a Molecule in  AMPAR_traff_model1 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CaM-Ca3-PSD	AMPAR_traff_ model1 Accession No. : 60	CaM Pathway No. : 246	0	0.01	No

CaM-Ca3-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
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

CaM-Ca3-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
CaM-TR2-Ca2-bind -Ca-PSD	AMPAR_traff_ model1 Accession No. : 60	CaM Pathway No. : 246	3.6 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 2.7778(uM)	-	Substrate Ca-PSD CaM-TR2-Ca2-PSD Product CaM-Ca3-PSD
K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10