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Molecule Parameter List for NMDAR

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

NMDAR 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	2	2

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
AMPAR_CaMKII_ weak_coupling	65	Network	Shared_Object_AMPAR_CaMKII_weak_coupling,  CaMKII,  CaM,   PP1,  PP2B,  PP1_PSD,   AMPAR,  PKA,  AC,   AMPAR_memb,  PP1_CaMKII_PSD,  CaMKII_PSD
This is a model of weak coupling between the AMPAR traffikcing bistability, and the CaMKII autophosphorylation bistability. In this model, there are three stable states: Both off, AMPAR on, or both on. The fourth possible state: CaMKII on but AMPAR off, is not truly stable, since over the course of hours the AMPAR also turns on.

NMDAR acting as a Molecule in  AMPAR_CaMKII_weak_coupling Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
NMDAR	AMPAR_CaMKII_ weak_coupling Accession No. : 65	CaMKII_PSD Pathway No. : 292	120	0.01	No
The stochiometry is a bit off here. Each NMDAR actually binds to a holoenzyme, about 12 CaMKII subunits. But our CaMKII calculations are in terms of individual subunits. So as a hack, we put in much more NMDAR than is actually there.

NMDAR acting as a Substrate in a reaction in  AMPAR_CaMKII_weak_coupling 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	transloc_1	AMPAR_CaMKII_ weak_coupling Accession No. : 65	CaMKII_PSD Pathway No. : 292	0 (#^-1 s^-1)	0 (s^-1)	Not applicable**	-	Substrate CaMKII-CaM NMDAR Product CaMKII-CaM-PSD
	Rates to match curve in fig2 from Shen and Meyer, Science 284:162-166(1999), calculated for 6:1 alpha:beta CaMKII heterodimers Note that this reaction also incorporates a translocation between compartments of different volumes.
2	transloc_2	AMPAR_CaMKII_ weak_coupling Accession No. : 65	CaMKII_PSD Pathway No. : 292	0 (#^-1 s^-1)	0 (s^-1)	Not applicable**	-	Substrate CaMKII-thr286*-C aM NMDAR Product CaMKII-thr286-Ca M-PSD
	Same as for transloc_1

** 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

NMDAR acting as a Product in a reaction in  AMPAR_CaMKII_weak_coupling 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	back_2	AMPAR_CaMKII_ weak_coupling Accession No. : 65	CaMKII_PSD Pathway No. : 292	0.3 (s^-1)	0 (#^-1 s^-1)	Not applicable**	-	Substrate CaMKII-thr305-PS D Product CaMK-thr305 NMDAR
	Same as for back_1
2	back_1	AMPAR_CaMKII_ weak_coupling Accession No. : 65	CaMKII_PSD Pathway No. : 292	0.3 (s^-1)	0 (#^-1 s^-1)	Not applicable**	-	Substrate CaMKII-PSD Product CaMKII NMDAR
	Rates set by the translocation experiments of Shen and Meyer, Science 1999. Note that this reaction also incorporates a translocation between compartments of different volumes.

** 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