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 List for Accession CaMKII_model3 (Accession Number63)

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

arrow indicates that ordering is done according to ascending or descending order.
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
21	CaM-TR2-Ca2	Shared_Object_ CaMKII_model3 Pathway No. 263	Network	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.
22	CaM-TR2-Ca2-PSD	Shared_Object_ CaMKII_model3 Pathway No. 263	Network	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.
23	CaM.PDE1	AC Pathway No. 269	Network	0	0.09	No	-
	Activity up 6x following Ca-CaM binding.
24	CaMK-thr305	CaMKII Pathway No. 264	Network	0	0.09	No	-
	This forms due to basal autophosphorylation, but I think it has to be considered as a pathway even if some CaM is floating around. In either case it will tend to block further binding of CaM, and will not display any enzyme activity. See Hanson and Schulman JBC 267:24 pp17216-17224 1992
25	CaMKII	CaMKII Pathway No. 264	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.
26	CaMKII***	CaMKII Pathway No. 264	Network	0	0.09	No	-
	From Hanson and Schulman, the CaMKII does a lot of autophosphorylation just after the CaM is released. This prevents further CaM binding and renders the enzyme quite independent of Ca.
27	CaMKII***-PSD	Shared_Object_ CaMKII_model3 Pathway No. 263	Network	0	0.01	No	-
28	CaMKII-CaM	CaMKII Pathway No. 264	Network	0	0.09	No	-
29	CaMKII-CaM-PSD	Shared_Object_ CaMKII_model3 Pathway No. 263	Network	0	0.01	No	-
30	CaMKII-PSD	Shared_Object_ CaMKII_model3 Pathway No. 263	Network	0	0.01	No	-
31	CaMKII-thr286	CaMKII Pathway No. 264	Network	0	0.09	No	-
	I am not sure if we need to endow this one with a lot of enzs. It is likely to be a short-lived intermediate, since it will be phosphorylated further as soon as the CAM falls off.
32	CaMKII-thr286*-C aM	CaMKII Pathway No. 264	Network	0	0.09	No	-
	From Hanson and Schulman, the thr286 is responsible for autonomous activation of CaMKII.
33	CaMKII-thr286-Ca M-PSD	Shared_Object_ CaMKII_model3 Pathway No. 263	Network	0	0.01	No	-
34	CaMKII-thr286-PS D	Shared_Object_ CaMKII_model3 Pathway No. 263	Network	0	0.01	No	-
35	CaMKII-thr305-PS D	Shared_Object_ CaMKII_model3 Pathway No. 263	Network	0	0.01	No	-
36	cAMP	Shared_Object_ CaMKII_model3 Pathway No. 263	Network	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.
37	cAMP-PDE	AC Pathway No. 269	Network	0.5556	0.09	No	-
	The levels of the PDE are not known at this time. However, enough kinetic info and info about steady-state levels of cAMP etc are around to make it possible to estimate this. 18 Feb 2005: After some playing with initial conc, it is now back at 0.5 uM.
38	cAMP-PDE*	AC Pathway No. 269	Network	0	0.09	No	-
	This form has about 2X activity as plain PDE. See Sette et al JBC 269:28 18271-18274 1994.
39	cAMP_in_dend	AC Pathway No. 269	Network	0	5	No	-
	Assume a 5 uM long segment of 1 uM^2 Xsection dendrite.
40	CaM_Ca_n-CaNAB	Shared_Object_ CaMKII_model3 Pathway No. 263	Network	0	0.09	No	-

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.