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Accession Type:
Network

CaMKII_model3

		Shared_Object_ CaMKII_model3
		Molecule
		Enzyme
		Reaction

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Molecule List for pathway Shared_Object_CaMKII_model3 (Pathway Number 263)

	Name	Initial Conc. (uM)	Volume (fL)	Buffered
1	286P-PSD	0	0.01	No

2	actCaMKII-PSD	2	0.01	No

3	act_CaMKII_cyt	2	0.09	No

4	basal_CaMKII_cyt	2	0.09	Yes

5	basal_CaMKII_PSD	2	0.01	No

6	basal_CaMKII_PSD_control	2	0.01	Yes

7	Ca	0.08	0.09	No

8	Ca-PSD	0.08	0.01	No

9	CaM-Ca3	0	0.09	No

10	CaM-Ca3-PSD	0.0025	0.01	No

11	CaM-Ca4	0	0.09	No

12	CaM-Ca4-PSD	0	0.01	No

13	CaM-TR2-Ca2	0	0.09	No
	This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not.
14	CaM-TR2-Ca2-PSD	0	0.01	No
	This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not.
15	CaMKII***-PSD	0	0.01	No

16	CaMKII-CaM-PSD	0	0.01	No

17	CaMKII-PSD	0	0.01	No

18	CaMKII-thr286-CaM-PSD	0	0.01	No

19	CaMKII-thr286-PSD	0	0.01	No

20	CaMKII-thr305-PSD	0	0.01	No

21	cAMP	0	0.09	No
	The conc of this has been a problem. Schaecter and Benowitz use 50 uM, but Shinomura et al have < 5. So I have altered the cAMP-dependent rates in the PKA model to reflect this.
22	CaM_Ca_n-CaNAB	0	0.09	No

23	CaNAB-Ca4	0	0.09	No

24	Ca_control_cyt	0.08	0.09	Yes

25	Ca_control_PSD	0.08	0.01	Yes

26	NMDAR	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.
27	PKA-active	0	0.09	No

28	PKC-active	0.1	0.09	No

29	PKC-control	0.1	0.09	Yes

30	PP1-active	1.8	0.09	No
	Cohen et al Meth Enz 159 390-408 is main source of info conc = 1.8 uM
31	PP1-active_PSD	4	0.01	No
	Cohen et al Meth Enz 159 390-408 is main source of info conc = 1.8 uM
32	PP2A	0.1111	0.09	No

33	tot-auto-PSD	2	0.01	No

34	tot-CaM-CaMKII-PSD	0	0.01	No

35	tot_CaMKII_cyt	22	0.09	No

36	tot_CaMKII_PSD	2	0.01	No

Summed Molecule List

	Target	Inputs
1	286P-PSD	CaMKII-thr286-Ca M-PSD CaMKII-thr286-PS D
2	actCaMKII-PSD	CaMKII-thr286-Ca M-PSD CaMKII-CaM-PSD tot-auto-PSD
3	act_CaMKII_cyt	tot_CaM_CaMKII tot_autonomous_ CaMKII
4	tot-auto-PSD	CaMKII-thr286-PS D CaMKII***-PSD basal_CaMKII_ PSD
5	tot-CaM-CaMKII-PSD	CaMKII-thr286-Ca M-PSD CaMKII-CaM-PSD
6	tot_CaMKII_cyt	CaMKII-CaM CaMKII-thr286-C aM CaMKII-thr286 CaMKII** CaMK-thr305 CaMKII basal_CaMKII_ cyt
7	tot_CaMKII_PSD	actCaMKII-PSD CaMKII-PSD CaMKII-thr305-PS D

Pathway Details Molecule List Enzyme List Reaction List

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