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Molecule List for Accession CaMKII_noPKA_model3 (Accession Number62)

Default ordering is done according to Pathway Number. Table headers can be used for changing the default ordering.

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The entries are grouped according to Pathway Number and are alternately color coded using

and

color.

	Name	Pathway Name / Pathway No.	Accession Type	Initial Conc. (uM)	Volume (fL)	Buffered	Sum Total Of
1	NMDAR	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. 257	Network	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.
2	CaM	CaM Pathway No. 259	Network	26.3333	0.09	No	-
	There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al) Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying it is comparable to CaMK levels.
3	CaM-PSD	CaM Pathway No. 259	Network	26.3333	0.01	No	-
	There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al) Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying it is comparable to CaMK levels.
4	tot_CaMKII_cyt	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. 257	Network	22	0.09	No	CaMKII-CaM CaMKII-thr286-C aM CaMKII-thr286 CaMKII** CaMK-thr305 CaMKII basal_CaMKII_ cyt
5	CaMKII	CaMKII Pathway No. 258	Network	20	0.09	No	-
	Huge conc of CaMKII. In PSD it is 20-40% of protein, so we assume it is around 2.5% of protein in spine as a whole. This level is so high it is unlikely to matter much if we are off a bit.
6	I1	PP1_PSD Pathway No. 262	Network	4	0.01	No	-
	I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet inhibitor (Foulkes et al Eur J Biochem 132 309-313 9183). We treat it as non-compet, so it just turns the enz off without interacting with the binding site. Cohen et al ann rev bioch refer to results where conc is 1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM, we need >= 1.8 uM.
7	PP1-active_PSD	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. 257	Network	4	0.01	No	-
	Cohen et al Meth Enz 159 390-408 is main source of info conc = 1.8 uM
8	basal_CaMKII_ PSD	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. 257	Network	2	0.01	No	-
9	basal_CaMKII_ cyt	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. 257	Network	2	0.09	Yes	-
10	basal_CaMKII_ PSD_control	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. 257	Network	2	0.01	Yes	-
11	tot_autonomous_ CaMKII	CaMKII Pathway No. 258	Network	2	0.09	No	CaMKII-thr286 CaMKII*** basal_CaMKII_ cyt
12	tot-auto-PSD	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. 257	Network	2	0.01	No	CaMKII-thr286-PS D CaMKII***-PSD basal_CaMKII_ PSD
13	actCaMKII-PSD	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. 257	Network	2	0.01	No	CaMKII-thr286-Ca M-PSD CaMKII-CaM-PSD tot-auto-PSD
14	tot_CaMKII_PSD	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. 257	Network	2	0.01	No	actCaMKII-PSD CaMKII-PSD CaMKII-thr305-PS D
15	act_CaMKII_cyt	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. 257	Network	2	0.09	No	tot_CaM_CaMKII tot_autonomous_ CaMKII
16	PP1-active	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. 257	Network	1.8	0.09	No	-
	Cohen et al Meth Enz 159 390-408 is main source of info conc = 1.8 uM
17	I1	PP1 Pathway No. 260	Network	1.8	0.09	No	-
	I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet inhibitor (Foulkes et al Eur J Biochem 132 309-313 9183). We treat it as non-compet, so it just turns the enz off without interacting with the binding site. Cohen et al ann rev bioch refer to results where conc is 1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM, we need >= 1.8 uM.
18	CaNAB	PP2B Pathway No. 261	Network	1	0.09	No	-
	We assume that the A and B subunits of PP2B are always bound under physiol conditions. Up to 1% of brain protein = 25 uM. I need to work out how it is distributed between cytosolic and particulate fractions. Tallant and Cheung '83 Biochem 22 3630-3635 have conc in many species, average for mammalian brain is around 1 uM.
19	PP2A	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. 257	Network	0.1111	0.09	No	-
20	Ca	Shared_Object_ CaMKII_noPKA_ model3 Pathway No. 257	Network	0.08	0.09	No	-

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