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Molecule List for pathway EGFR (Pathway Number 223)

	Name	Initial Conc. (uM)	Volume (fL)	Buffered
1	EGF	0.666	1.6667E-6	No
	Taken from Kholodenko et al 1999 Simulations were done at EGF concentration set to 20nM and 2nM concentration. This concentration was multiplied by a constant factor Vm/Vcw = 33.3 to formally rescale it to the cytoplasmic water volume. So actual concentration to which EGF was set was 666nM and 66.6nM. Plots 1&3 of figure-5 and plot 1 of figure 4 are obtained by setting the EGF conc to 666nM. Plots 2&4 of figure-5 and plot 3 of figure 4 are obtained by setting the EGF conc to 66.6nM.
2	enz16	0.001	1.6667E-6	No
	Taken from Kholodenko et al 1999.
3	enz4	0.001	1.6667E-6	No
	The initial concentration was set to 1nM. Citation: Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
4	enz8	0.001	1.6667E-6	No
	The initial concentration was set to 1nM. Citation: Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
5	G-S	0.033	1.6667E-6	No
	Personal communication: Dr.Boris N. Kholodenko Citation: Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
6	Grb	0.052	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. To obtain plots as per figure-4 and 5 [Grb] is set to 51.954nM. instead of 85nM. Thanks to Dr. Boris N. Kholodenko for clarifying the ambiguity and furnishing us the above value. To obtain plots as per figure-7A [Grb] is set to 340nM (4-fold increase).
7	Grb2_Shc	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Total concentration of Grb2 bound to Shc isoforms= [Sh-G-S] [R-Sh-G] +[R-Sh-G-S] + [Sh-G]
8	Grb_EGFR	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Total concentration of Grb2 bound to EGFR forms = [R-G] + [R-G-S] + [R-Sh-G] + [R-Sh-G-S]
9	pEGFRtot	0	8.3335E-7	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Total phosphorylated EGFR = 2.([RP] + [R-PL] + [R-PLP] + [R-G] + [R-G-S] + [R-Sh] + [R-ShP] + [R-Sh-G] + [R-Sh-G-S] )
10	PLCr	0.105	1.6667E-6	No
	PLC gamma. Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
11	PLCr-I	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
12	PLCrP	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
13	pPLCr	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Total Phosphorylated PLCr = [R-PLP] + [PLCrP].
14	pShctot	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Total phosphorylated Shc = [ShP] + [Sh-G] + [ Sh-G-S] + [R-ShP] [R-Sh-G] + [R-Sh-G-S]
15	R	0.1	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. [EGFR] = 100nM. To obtain the plots as per figure-7B [EGFR] was increased 4-fold (400nM) to obtain plot-1 and decreased 4-fold (25nM) to obtain plot-2.
16	R-G	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
17	R-G-S	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
18	R-PL	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
19	R-PLP	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
20	R-Sh	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
21	R-Sh-G	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
22	R-Sh-G-S	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
23	R-ShP	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
24	R2	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
25	Ra	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
26	RP	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
27	Sh-G	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
28	Sh-G-S	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
29	Shc	0.15	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. To get plots in figure-4 and figure-5 [Shc] is set to 150nM To get plots in figure-7A [Shc] is set to 37.5nM (4-fold decrease).
30	Shc_EGFR	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Shc bound to EGFR = [R-ShP] + [ R-Sh-G] + [R-Sh-G-S]
31	ShP	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81.
32	SOS	0.001	1.6667E-6	No
	The initial concentration is set to 0.95421nM instead of 37nM which. Thanks to Dr. Boris N. Kholodenko for clarifying the ambiguity and furnishing the initial concentration.
33	SOS_EGFR	0	1.6667E-6	No
	Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Total Sos bound to EGFR = [R-G-S] + [R-Sh-G-S]

Summed Molecule List

	Target	Inputs
1	Grb2_Shc	R-Sh-G Sh-G R-Sh-G-S Sh-G-S
Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Total concentration of Grb2 bound to Shc isoforms= [Sh-G-S] [R-Sh-G] +[R-Sh-G-S] + [Sh-G]
2	Grb_EGFR	R-G R-G-S R-Sh-G R-Sh-G-S
Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Total concentration of Grb2 bound to EGFR forms = [R-G] + [R-G-S] + [R-Sh-G] + [R-Sh-G-S]
3	pEGFRtot	RP R-PL R-PLP R-G R-G-S R-Sh R-ShP R-Sh-G R-Sh-G-S
Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Total phosphorylated EGFR = 2.([RP] + [R-PL] + [R-PLP] + [R-G] + [R-G-S] + [R-Sh] + [R-ShP] + [R-Sh-G] + [R-Sh-G-S] )
4	pPLCr	R-PLP PLCrP
Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Total Phosphorylated PLCr = [R-PLP] + [PLCrP].
5	pShctot	R-ShP R-Sh-G R-Sh-G-S ShP Sh-G Sh-G-S
Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Total phosphorylated Shc = [ShP] + [Sh-G] + [ Sh-G-S] + [R-ShP] [R-Sh-G] + [R-Sh-G-S]
6	Shc_EGFR	R-ShP R-Sh-G R-Sh-G-S
Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Shc bound to EGFR = [R-ShP] + [ R-Sh-G] + [R-Sh-G-S]
7	SOS_EGFR	R-G-S R-Sh-G-S
Taken from Kholodenko BN et al J Biol Chem. (1999) 274(42):30169-81. Total Sos bound to EGFR = [R-G-S] + [R-Sh-G-S]

Pathway Detail

Molecule List

Enzyme List

Reaction List