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Molecule Parameter List for A_B

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

*A_B* participated as	Molecule	Sum total of	Enzyme	Substrate of an enzyme	Product of an enzyme	Substrate in Reaction	Product in Reaction
No. of occurrences	2	3	0	6	8	1	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.

A_B acting as a Molecule in AMPAR_traff_model1 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
A_B	AMPAR_traff_ model1 Accession No. : 60	AMPAR Pathway No. : 252	0	0.09	No

A_B	AMPAR_traff_ model1 Accession No. : 60	AMPAR_memb Pathway No. : 253	0	0.01	No

A_B acting as a Summed Molecule in AMPAR_traff_model1 Network

	Accession Nane	Pathway Name	Target	Input
1	AMPAR_traff_ model1 Accession No. : 60	AMPAR Pathway No. : 252	I_845	A831_B831 A_B831* A831_B A_B*
2	AMPAR_traff_ model1 Accession No. : 60	AMPAR_memb Pathway No. : 253	Ser845	A_B A831_B A_B831 A831_B831
3	AMPAR_traff_ model1 Accession No. : 60	AMPAR_memb Pathway No. : 253	Ser831	A845_B845 A_B845* A845_B A_B*

A_B acting as a Substrate for an Enzyme in AMPAR_traff_model1 Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	actCaMKII-PSD / CaMKII[3]	AMPAR_traff_ model1 Accession No. : 60	CaMKII Pathway No. : 245	90.0006	0.5	4	explicit E-S complex	Substrate A_B Product A831*_B
2	actCaMKII-PSD / CaMKII[7]	AMPAR_traff_ model1 Accession No. : 60	CaMKII Pathway No. : 245	90.0006	0.5	4	explicit E-S complex	Substrate A_B Product A_B831*
3	PKA-active / PKA[17]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B Product A845*_B
4	PKA-active / PKA[20]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B Product A_B845*
5	PKA-active / PKA[2]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B Product A845*_B
6	PKA-active / PKA[3]	AMPAR_traff_ model1 Accession No. : 60	PKA Pathway No. : 250	7.50021	6	4	explicit E-S complex	Substrate A_B Product A_B845*

A_B acting as a Product of an Enzyme in AMPAR_traff_model1 Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	CaM_Ca_n-CaNAB / PP2B[17]	AMPAR_traff_ model1 Accession No. : 60	PP2B Pathway No. : 248	4.97061	2	4	explicit E-S complex	Substrate A845_B Product* A_B
2	CaM_Ca_n-CaNAB / PP2B[21]	AMPAR_traff_ model1 Accession No. : 60	PP2B Pathway No. : 248	4.97061	2	4	explicit E-S complex	Substrate A_B845* Product A_B
3	CaM_Ca_n-CaNAB / PP2B[2]	AMPAR_traff_ model1 Accession No. : 60	PP2B Pathway No. : 248	4.97061	2	4	explicit E-S complex	Substrate A_B845* Product A_B
4	CaM_Ca_n-CaNAB / PP2B[3]	AMPAR_traff_ model1 Accession No. : 60	PP2B Pathway No. : 248	4.97061	2	4	explicit E-S complex	Substrate A845_B Product* A_B
5	PP1-active_PSD / PP1[2]	AMPAR_traff_ model1 Accession No. : 60	PP1_PSD Pathway No. : 249	0.971451	0.17	4	explicit E-S complex	Substrate A845_B Product* A_B
6	PP1-active_PSD / PP1[3]	AMPAR_traff_ model1 Accession No. : 60	PP1_PSD Pathway No. : 249	0.971451	0.17	4	explicit E-S complex	Substrate A_B845* Product A_B
7	PP1-active_PSD / PP1[11]	AMPAR_traff_ model1 Accession No. : 60	PP1_PSD Pathway No. : 249	2.00005	0.35	4	explicit E-S complex	Substrate A831_B Product* A_B
8	PP1-active_PSD / PP1[23]	AMPAR_traff_ model1 Accession No. : 60	PP1_PSD Pathway No. : 249	2.00005	0.35	4	explicit E-S complex	Substrate A_B831* Product A_B

A_B 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
recycle__	AMPAR_traff_ model1 Accession No. : 60	AMPAR Pathway No. : 252	0.0008 (s^-1)	0 (#^-1 s^-1)	Not applicable**	-	Substrate A_B Product A_B Anchor

** 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

A_B acting as a Product in a reaction in AMPAR_traff_model1 Network

	Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
1	recycle__	AMPAR_traff_ model1 Accession No. : 60	AMPAR Pathway No. : 252	0.0008 (s^-1)	0 (#^-1 s^-1)	Not applicable**	-	Substrate A_B Product A_B Anchor
2	turnover	AMPAR_traff_ model1 Accession No. : 60	AMPAR Pathway No. : 252	0.018 (s^-1)	1 (s^-1)	Not applicable**	-	Substrate AMPAR_bulk Product A_B
	Represents both synthesis and degradation of the receptor. The rate is set to be rather fast for now. The forward rate also includes scaling terms because the AMPAR_bulk is in the dendritic volume of 5e-18. This means that we need to lower Kf to account for the difference in volumes. Effectively Kf is 1/sec, but the scaled version becomes 9e-20/5e-18 = 0.018

** 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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