| Concentrations, copy number per cell |
| [MTOR] = 2×104
|
Assumed amount of MTOR available to interact with ULK1 |
| [RPTOR] = 2×104
|
RPTOR abundance was set to equal the abundance of MTOR |
| [ULK1] = 1×104
|
Measured abundance of ULK1 |
| [rapamycin*] |
Adjustable input (an independent variable of the model) |
| [AMPK*] |
Adjustable input (an independent variable of the model) |
| [EIF4EBP1] = 1×104
|
EIF4EBP1 was introduced to measure MTORC1 activity |
| [AMBRA1] = 1×104
|
AMBRA1 was introduced to measure ULK1 activity |
| Rate constants for (bimolecular) association reactions, (molecules/cell)−1s−1
|
|
a
1 = 10−3
|
Rapamycin* binds MTOR, Equation (1)
|
|
a
2 = 10−3
|
RPTOR binds MTOR, Equation (2)
|
|
a
3 = 10−3
|
RPTOR binds ULK1, Equation (3A)
|
|
a
4 = 10−5
|
RPTOR binds EIF4EBP1, Equation (4A)
|
|
a
5 = 10−5
|
AMPK binds ULK1, Equation (5A)
|
| Rate constants for (unimolecular) dissociation reactions, s−1
|
|
d
1 = 10−2
|
Rapamycin* releases MTOR, Equation (1)
|
|
d
2 = 10−1
|
RPTOR releases MTOR, Equation (2)
|
|
d
3 = 10−1
|
RPTOR slowly releases ULK1, Equation (3B)
|
|
d
3,max = 10 |
RPTOR quickly releases ULK1, Equation (3C)
|
|
d
4 = 1 |
RPTOR releases EIF4EBP1, Equation (4B)
|
|
d
5 = 10 |
AMPK releases ULK1, Equation (5B)
|
| Rate constants for (pseudo first-order) phosphorylation reactions, s−1
|
|
p
1 = 10 |
MTORC1 phosphorylates ULK1, Equation (6)
|
|
p
2 = 10 |
MTORC1 phosphorylates EIF4EBP1, Equation (7)
|
|
p
3 = 10 |
ULK1 phosphorylates S792 in RPTOR, Equation (8A)
|
|
p
4 = 10 |
ULK1 phosphorylates S855/S859 in RPTOR, Equation (8B,C) |
|
p
7 = 10 |
AMPK phosphorylates S317 in ULK1, Equation (11A)
|
|
p
8 = 10 |
AMPK phosphorylates S778 in ULK1, Equation (11B)
|
| Rate constants for (pseudo second-order) phosphorylation reactions, (molecules/cell)−1s−1
|
|
p
5 = 10−4
|
ULK1 phosphorylates AMBRA1, Equation (9)
|
|
p
6 = 10−6
|
ULK1 phosphorylates AMPK, Equation (10)
|
|
p
9 = 0 or small enough |
AMPK phosphorylates RPTOR, Equation (12)
|
| Rate constants for (pseudo first-order) dephosphorylation reactions, s−1
|
|
u
1 = 10−3
|
Dephosphorylation of S792 in RPTOR, Equation (15A)
|
|
u
2 = 10−4
|
Dephosphorylation of inhibitory sites in AMPK, Equation (17)
|
|
u
0 = 10−2
|
All other sites, Equations (13), (14), (15B,C), (16), (18A,B), and (19) |
