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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_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.

NMDAR acting as a Molecule in AMPAR_traff_model1 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
NMDAR	AMPAR_traff_ model1 Accession No. : 60	CaMKII Pathway No. : 245	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_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	transloc_1	AMPAR_traff_ model1 Accession No. : 60	CaMKII Pathway No. : 245	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
2	transloc_2	AMPAR_traff_ model1 Accession No. : 60	CaMKII Pathway No. : 245	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_traff_model1 Network

	Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
1	back_2	AMPAR_traff_ model1 Accession No. : 60	CaMKII Pathway No. : 245	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_traff_ model1 Accession No. : 60	CaMKII Pathway No. : 245	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.

** 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

Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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