DOQCS database

NCBS Home page

Accession List

Pathway List

Authorized Users

Help

News archives

Enter a Search String

Special character and space not allowed in the query term. Search string should be at least 2 characters long.

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_CaMKII_ strong_coupling	64	Network	Shared_Object_AMPAR_CaMKII_strong_coupling, CaMKII, CaM, PP1, AMPAR_memb, PP2B, PKA, AC, PP1_PSD, AMPAR
This is a model of tight coupling between the AMPAR trafficking bistability, and the CaMKII autophosphorylation bistability. In this model, the CaMKII activity is self sustaining only when AMPAR is turned on. Further, CaMKII turns on when AMPAR is turned on.

A_B acting as a Molecule in AMPAR_CaMKII_strong_coupling Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
A_B	AMPAR_CaMKII_ strong_coupling Accession No. : 64	AMPAR Pathway No. : 280	0	0.09	No

A_B	AMPAR_CaMKII_ strong_coupling Accession No. : 64	AMPAR_memb Pathway No. : 275	0	0.01	No

A_B acting as a Summed Molecule in AMPAR_CaMKII_strong_coupling Network

	Accession Nane	Pathway Name	Target	Input
1	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	Ser845	A_B A831_B A_B831 A831_B831
2	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	Ser831	A845_B845 A_B845* A845_B A_B*
3	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	I_845	A831_B831 A_B831* A831_B A_B*

A_B acting as a Substrate for an Enzyme in AMPAR_CaMKII_strong_coupling Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	PKA-active / PKA[17]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	7.50021	6	4	explicit E-S complex	Substrate A_B Product A845*_B
2	PKA-active / PKA[20]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	7.50021	6	4	explicit E-S complex	Substrate A_B Product A_B845*
3	PKA-active / PKA[2]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	7.50021	6	4	explicit E-S complex	Substrate A_B Product A845*_B
4	PKA-active / PKA[3]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	7.50021	6	4	explicit E-S complex	Substrate A_B Product A_B845*
5	actCaMKII-PSD / CaMKII[3]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	90.0006	0.5	4	explicit E-S complex	Substrate A_B Product A831*_B
6	actCaMKII-PSD / CaMKII[7]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	90.0006	0.5	4	explicit E-S complex	Substrate A_B Product A_B831*

A_B acting as a Product of an Enzyme in AMPAR_CaMKII_strong_coupling Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	PP1-active_PSD / PP1[2]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	0.971451	0.17	4	explicit E-S complex	Substrate A845_B Product* A_B
2	PP1-active_PSD / PP1[3]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	0.971451	0.17	4	explicit E-S complex	Substrate A_B845* Product A_B
3	PP1-active_PSD / PP1[11]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	2.00005	0.35	4	explicit E-S complex	Substrate A831_B Product* A_B
4	PP1-active_PSD / PP1[23]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	2.00005	0.35	4	explicit E-S complex	Substrate A_B831* Product A_B
5	CaM_Ca_n-CaNAB / PP2B[17]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	4.97061	2	4	explicit E-S complex	Substrate A845_B Product* A_B
6	CaM_Ca_n-CaNAB / PP2B[21]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	4.97061	2	4	explicit E-S complex	Substrate A_B845* Product A_B
7	CaM_Ca_n-CaNAB / PP2B[2]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	4.97061	2	4	explicit E-S complex	Substrate A_B845* Product A_B
8	CaM_Ca_n-CaNAB / PP2B[3]	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	4.97061	2	4	explicit E-S complex	Substrate A845_B Product* A_B

A_B acting as a Substrate in a reaction in AMPAR_CaMKII_strong_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
recycle__	AMPAR_CaMKII_ strong_coupling Accession No. : 64	AMPAR Pathway No. : 280	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_CaMKII_strong_coupling Network

	Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
1	recycle__	AMPAR_CaMKII_ strong_coupling Accession No. : 64	AMPAR Pathway No. : 280	0.0008 (s^-1)	0 (#^-1 s^-1)	Not applicable**	-	Substrate A_B Product A_B Anchor
2	turnover	AMPAR_CaMKII_ strong_coupling Accession No. : 64	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. : 271	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
This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details.