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Molecule List for Accession AMPAR_CaMKII_strong_coupling (Accession Number64)

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

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color.

	Name	Pathway Name / Pathway No.	Accession Type	Initial Conc. (uM)	Volume (fL)	Buffered	Sum Total Of
1	ATP	AC Pathway No. 278	Network	2000	0.09	Yes	-
	ATP is present in all cells between 2 and 10 mM. See Lehninger
2	NMDAR	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271	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.
3	Anchor	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271	Network	27.3333	0.01	No	-
4	CaM	CaM Pathway No. 273	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.
5	CaM-PSD	CaM Pathway No. 273	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.
6	tot_CaMKII_cyt	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271	Network	22	0.09	No	CaMKII-CaM CaMKII-thr286-C aM CaMKII-thr286 CaMKII** CaMK-thr305 CaMKII basal_CaMKII_ cyt
7	CaMKII	CaMKII Pathway No. 272	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. This comes to about 70 uM.
8	neurogranin	CaM Pathway No. 273	Network	10	0.09	No	-
	Also known as RC3 and p17 and BICKS. Conc in brain >> 2 uM from Martzen and Slemmon J neurosci 64 92-100 1995 but others say less without any #s. Conc in dend spines is much higher than overall, so it could be anywhere from 2 uM to 50. We will estimate 10 uM as a starting point. Gerendasy et al JBC 269:35 22420-22426 1994 have a skeleton model (no numbers) indicating CaM-Ca(n) binding ....
9	neurogranin_PSD	CaM Pathway No. 273	Network	10	0.01	No	-
	Also known as RC3 and p17 and BICKS. Conc in brain >> 2 uM from Martzen and Slemmon J neurosci 64 92-100 1995 but others say less without any #s. Conc in dend spines is much higher than overall, so it could be anywhere from 2 uM to 50. We will estimate 10 uM as a starting point. Gerendasy et al JBC 269:35 22420-22426 1994 have a skeleton model (no numbers) indicating CaM-Ca(n) binding ....
10	I1	PP1_PSD Pathway No. 279	Network	8	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.
11	PP1-active_PSD	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271	Network	8	0.01	No	-
	Cohen et al Meth Enz 159 390-408 is main source of info conc = 1.8 uM
12	GluR23_M	AMPAR Pathway No. 280	Network	3.5	0.01	No	-
13	PDE1	AC Pathway No. 278	Network	2.5926	0.09	No	-
	CaM-Dependent PDE. Amount calculated from total rate in brain vs. specific rate.
14	temp-PIP2	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271	Network	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....
15	basal_CaMKII_ PSD	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271	Network	2	0.01	No	-
16	basal_CaMKII_ cyt	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271	Network	2	0.09	Yes	-
17	basal_CaMKII_ PSD_control	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271	Network	2	0.01	Yes	-
18	tot_autonomous_ CaMKII	CaMKII Pathway No. 272	Network	2	0.09	No	CaMKII-thr286 CaMKII*** basal_CaMKII_ cyt
19	tot-auto-PSD	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271	Network	2	0.01	No	CaMKII-thr286-PS D CaMKII***-PSD basal_CaMKII_ PSD
20	actCaMKII-PSD	Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271	Network	2	0.01	No	CaMKII-thr286-Ca M-PSD CaMKII-CaM-PSD tot-auto-PSD

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