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 Parameter List for APC

The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by

color.

Statistics

*APC* participated as	Molecule	Sum total of	Enzyme	Substrate of an enzyme	Product of an enzyme	Substrate in Reaction	Product in Reaction
No. of occurrences	1	0	0	5	0	0	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
3d_fold_model	8	Network	Shared_Object_3d_fold_model, PKC, MAPK, PLA2, Ras
This model is an annotated version of the synaptic signaling network. The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated Bhalla US, Ram PT, Iyengar R. Science. 2002 Aug 9;297(5583):1018-23.

APC acting as a Molecule in 3d_fold_model Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
APC	3d_fold_model Accession No. : 8	PLA2 Pathway No. : 57	30	1000	Yes
arachodonylphosphatidylcholine is the favoured substrate from Wijkander and Sundler, JBC 202 pp 873-880, 1991. Their assay used 30 uM substrate, which is what the kinetics in this model are based on. For the later model we should locate a more realistic value for APC.

APC acting as a Substrate for an Enzyme in 3d_fold_model Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	PLA2-Ca* / kenz	3d_fold_model Accession No. : 8	PLA2 Pathway No. : 57	20	5.4	4	explicit E-S complex	Substrate APC Product AA
	10 x raise oct22 12 x oct 24, set k2 = 4 k3*
2	PIP2-PLA2* / kenz	3d_fold_model Accession No. : 8	PLA2 Pathway No. : 57	20	11.04	4	explicit E-S complex	Substrate APC Product AA
	10 X raise oct 22 12 X further raise oct 24 to allow for correct conc of enzyme
3	PIP2-Ca-PLA2* / kenz	3d_fold_model Accession No. : 8	PLA2 Pathway No. : 57	20	36	4	explicit E-S complex	Substrate APC Product AA
	10 x raise oct 22 12 x and rescale for k2 = 4 * k3 convention oct 24 Increase further to get the match to expt, which was spoilt due to large accumulation of PLA2 in the enzyme complexed forms. Lets raise k3, leaving the others at k1 = 1.5e-5 and k2 = 144 since they are large already.
4	DAG-Ca-PLA2* / kenz	3d_fold_model Accession No. : 8	PLA2 Pathway No. : 57	20	60	4	explicit E-S complex	Substrate APC Product AA
	10 X raise oct 22 12 X raise oct 24 + conversion to k2 =4 k3*
5	PLA2*-Ca / kenz	3d_fold_model Accession No. : 8	PLA2 Pathway No. : 57	20	120	4	explicit E-S complex	Substrate APC Product AA
	This form should be 3 to 6 times as fast as the Ca-only form. I have scaled by 4x which seems to give a 5x rise. 10x raise Oct 22 12 x oct 24, changed k2 = 4 k3*

APC acting as a Product in a reaction in 3d_fold_model Network

Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated. Kd for higher order reaction are not consider.

Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
Degrade-AA	3d_fold_model Accession No. : 8	PLA2 Pathway No. : 57	0.4 (s^-1)	0 (s^-1)	-	-	Substrate AA Product APC
I need to check if the AA degradation pathway really leads back to APC. Anyway, it is a convenient buffered pool to dump it back into. For the purposes of the full model we use a rate of degradation of 0.2/sec Raised decay to 0.4 : see PLA35.g notes for Feb17

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.