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Molecule List for pathway Shared_Object_AMPAR_CaMKII_strong_coupling (Pathway Number 271)

	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	AMPAR_bulk	0.0093	5	Yes

5	Anchor	27.3333	0.01	No

6	basal_CaMKII_cyt	2	0.09	Yes

7	basal_CaMKII_PSD	2	0.01	No

8	basal_CaMKII_PSD_control	2	0.01	Yes

9	Ca	0.08	0.09	No

10	Ca-PSD	0.08	0.01	No

11	CaM-Ca3	0	0.09	No

12	CaM-Ca3-PSD	0.0025	0.01	No

13	CaM-Ca4	0	0.09	No

14	CaM-Ca4-PSD	0	0.01	No

15	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.
16	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.
17	CaMKII***-PSD	0	0.01	No

18	CaMKII-CaM-PSD	0	0.01	No

19	CaMKII-PSD	0	0.01	No

20	CaMKII-thr286-CaM-PSD	0	0.01	No

21	CaMKII-thr286-PSD	0	0.01	No

22	CaMKII-thr305-PSD	0	0.01	No

23	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.
24	CaM_Ca_n-CaNAB	0	0.09	No

25	CaNAB-Ca4	0	0.09	No

26	Ca_control_cyt	0.08	0.09	Yes

27	Ca_control_PSD	0.08	0.01	Yes

28	I_845	0	0.09	No

29	I_845-P	0	0.09	No

30	I_845_PP	0	0.09	No

31	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.
32	PKA-active	0	0.09	No

33	PKC-active	0.1	0.09	No

34	PKC-control	0.1	0.09	Yes

35	PP1-active	1.8	0.09	No
	Cohen et al Meth Enz 159 390-408 is main source of info conc = 1.8 uM
36	PP1-active_PSD	8	0.01	No
	Cohen et al Meth Enz 159 390-408 is main source of info conc = 1.8 uM
37	PP2A	0.1111	0.09	No

38	Ser831	0	0.01	No

39	Ser831-P	0	0.01	No

40	Ser831-PP	0	0.01	No

41	Ser845	0	0.01	No

42	Ser845-P	0	0.01	No

43	Ser845-PP	0	0.01	No

44	temp-PIP2	2.5	0.09	Yes
	This isn't explicitly present in the M&L model, but is obviously needed. I assume its conc is fixed at 1uM for now, which is a bit high. PLA2 is stim 7x by PIP2 @ 0.5 uM (Leslie and Channon BBA 1045:261(1990) Leslie and Channon say PIP2 is present at 0.1 - 0.2mol% range in membs, which comes to 50 nM. Ref is Majerus et al Cell 37 pp 701-703 1984 Lets use a lower level of 30 nM, same ref....
45	tot-auto-PSD	2	0.01	No

46	tot-CaM-CaMKII-PSD	0	0.01	No

47	total_Int	0	0.09	No

48	tot_CaMKII_cyt	22	0.09	No

49	tot_CaMKII_PSD	2	0.01	No

50	tot_I_GluR12	0	0.09	No

51	tot_mem_GluR12	0	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	I_845	A831_B831 A_B831* A831*_B A_B
5	I_845-P	A831845_B831* A845_B831 A831845_B A845_B A831_B831845 A_B831845 A831_B845 A_B845*
6	I_845_PP	A835845_ B835845 A845_B831845* A831845_B845* A845_B845
7	Ser831	A845_B845 A_B845* A845*_B A_B
8	Ser831-P	A831845_B845* A845_B831845* A831_B845 A_B831845 A831845_B A845_B831 A831_B A_B831
9	Ser831-PP	A835845_ B835845 A831_B831845* A831845_B831* A831_B831
10	Ser845	A_B A831_B A_B831 A831_B831
11	Ser845-P	A845_B A831845_B A845_B831* A831845_B831* A_B845* A831_B845 A_B831845 A831_B831845*
12	Ser845-PP	A845_B845 A831845_B845* A845_B831845* A835845_ B835845
13	tot-auto-PSD	CaMKII-thr286-PS D CaMKII***-PSD basal_CaMKII_ PSD
14	tot-CaM-CaMKII-PSD	CaMKII-thr286-Ca M-PSD CaMKII-CaM-PSD
15	total_Int	tot_I_GluR12 GluR23_I
16	tot_CaMKII_cyt	CaMKII-CaM CaMKII-thr286-C aM CaMKII-thr286 CaMKII** CaMK-thr305 CaMKII basal_CaMKII_ cyt
17	tot_CaMKII_PSD	actCaMKII-PSD CaMKII-PSD CaMKII-thr305-PS D
18	tot_I_GluR12	I_845 I_845-P I_845_PP
19	tot_mem_GluR12	Ser845 Ser845-P Ser845-PP

Pathway Detail

Molecule List

Enzyme List

Reaction List