Table 1 Basal parameter values yielding circadian oscillations in conditions corresponding to continuous darkness.
From: MiR-206-mediated dynamic mechanism of the mammalian circadian clock
Parameter | Definition | Set1 | Set2 | Set3 | Set4 | Determination |
|---|---|---|---|---|---|---|
k1(h-1) | Rate constant for entry of the BMAL1 protein into the nucleus | 0.4 | 0.4 | 0.4 | 0.4 | 38 |
k2(h-1) | Rate constant for exit of the BMAL1 protein from the nucleus | 0.2 | 0.2 | 0.2 | 0.2 | 38 |
k3(nM-1·h-1) | Rate constant for the formation of the inactive IN complex | 0.55 | 0.55 | 0.55 | 0.55 | 38 |
k4(h-1) | Rate constant for the dissociation of the IN complex | 0.1 | 0.1 | 0.1 | 0.1 | 38 |
k5(h-1) | Rate constant for entry of the CLOCK protein into the nucleus | 2.0 | 2.0 | 2.0 | 2.0 | 24 |
k6(h-1) | Rate constant for exit of the CLOCK protein from the nucleus | 1.0 | 1.0 | 1.0 | 1.0 | 24 |
d1(nM·h-1) | Rate constant for the production of the Bmal1 | 3.6 | 3.6 | 3.6 | 3.6 | 38, 43 |
d2(h-1) | Maximum rate of Bmal1 degradation | 0.9 | 0.9 | 0.9 | 0.9 | 38, 43 |
d3(nM·h-1) | Rate constant for the production of the Myod1 | 4.0 | 4.0 | 4.0 | 4.0 | 38, 43 |
d4(h-1) | Maximum rate of Myod1 degradation | 0.9 | 0.9 | 0.9 | 0.9 | 38, 43 |
d5(nM·h-1) | Rate constant for the production of the Clock | 4.0 | 4.0 | 4.0 | 4.0 | 38, 43 |
d6(h-1) | Maximum rate of Clock degradation | 0.9 | 0.9 | 0.9 | 0.9 | 38, 43 |
K IB (nM) | Inhibition constant for repression of Bmal1 expression by nuclear BMAL1 | 0.8 | 0.8 | 0.8 | 0.8 | 38 |
K I (nM) | Inhibition constant for repression of Clock expression by nuclear CLOCK | 2.0 | 2.0 | 2.0 | 2.0 | 24 |
K AM (nM) | Activation constant for enhancement of miR-206 expression by MYOD1 | 2.0 | 2.0 | 2.0 | 2.0 | 24, 38 |
K AC (nM) | Activation constant for enhancement of Myod1 expression by the IN complex | 0.8 | 0.8 | 0.8 | 0.8 | 38 |
k dmb (h-1) | Nonspecific degradation rate constant for Bmal1 mRNA | 0.01 | 0.01 | 0.01 | 0.01 | 38 |
k dmc (h-1) | Nonspecific degradation rate constant for Myod1 mRNA | 0.12 | 0.12 | 0.12 | 0.12 | 38 |
k dnc (h-1) | Nonspecific degradation rate constant for cytosolic non-phosphorylated MYOD1 | 0.5 | 0.5 | 0.5 | 0.5 | 38 |
kdn 1(h-1) | Nonspecific degradation rate constant for cytosolic dephosphorylated BMAL1 | 0.01 | 0.01 | 0.01 | 0.01 | 38 |
kdn 2(h-1) | Nonspecific degradation rate constant for cytosolic phosphorylated BMAL1 | 0.01 | 0.01 | 0.01 | 0.01 | 38 |
kdn 3(h-1) | Nonspecific degradation rate constant for nuclear dephosphorylated BMAL1 | 0.01 | 0.01 | 0.01 | 0.01 | 38 |
kdn 4(h-1) | Nonspecific degradation rate constant for cytosolic phosphorylated MYOD1 | 0.01 | 0.01 | 0.01 | 0.01 | 38 |
kdn 5(h-1) | Nonspecific degradation rate constant for IN complex | 0.01 | 0.01 | 0.01 | 0.01 | 38 |
kdn 6(h-1) | Nonspecific degradation rate constant for nuclear phosphorylated BMAL1 | 0.01 | 0.01 | 0.01 | 0.01 | 38 |
Kd 1(nM) | Michaelis constant for cytosolic phosphorylated BMAL1 degradation | 0.3 | 0.3 | 0.3 | 0.3 | 38 |
Kd 2(nM) | Michaelis constant for nuclear phosphorylated BMAL1 degradation | 0.3 | 0.3 | 0.3 | 0.3 | 38 |
Kd 3(nM) | Michaelis constant for cytosolic phosphorylated MYOD1 degradation | 0.3 | 0.3 | 0.3 | 0.3 | 38 |
Kd 4(nM) | Michaelis constant for IN complex degradation | 0.3 | 0.3 | 0.3 | 0.3 | 38 |
Kdp 1(nM) | Michaelis constant for cytosolic BMAL1 dephosphorylation | 0.3 | 0.3 | 0.3 | 0.3 | 38 |
Kdp 2(nM) | Michaelis constant for nuclear BMAL1 dephosphorylation | 0.3 | 0.3 | 0.3 | 0.3 | 38 |
Kdp 3(nM) | Michaelis constant for cytosolic MYOD1 dephosphorylation | 0.3 | 0.3 | 0.3 | 0.3 | 38 |
Kp 1(nM) | Michaelis constant for cytosolic BMAL1 phosphorylation | 0.1 | 0.1 | 0.1 | 0.1 | 38 |
Kp 2(nM) | Michaelis constant for nuclear BMAL1 phosphorylation | 0.1 | 0.1 | 0.1 | 0.1 | 38 |
Kp 3(nM) | Michaelis constant for cytosolic MYOD1 phosphorylation | 0.1 | 0.1 | 0.1 | 0.1 | 38 |
K vd (nM) | Michaelis constant for P2 degradation | 0.1 | 0.1 | 0.1 | 0.1 | 24 |
K1(nM) | Michaelis constant for P0 phosphorylation | 1.5 | 1.5 | 1.5 | 1.5 | 24 |
K2(nM) | Michaelis constant for P1 dephosphorylation | 2.0 | 2.0 | 2.0 | 2.0 | 24 |
K3(nM) | Michaelis constant for P1 phosphorylation | 1.5 | 1.5 | 1.5 | 1.5 | 24 |
K4(nM) | Michaelis constant for P2 dephosphorylation | 2.0 | 2.0 | 2.0 | 2.0 | 24 |
K mB (nM) | Michaelis constant for degradation of Bmal1 mRNA | 0.4 | 0.4 | 0.4 | 0.4 | 38 |
K mC (nM) | Michaelis constant for degradation of Myod1 mRNA | 0.1 | 0.1 | 0.1 | 0.1 | 38 |
K m (nM) | Michaelis constant for degradation of Clock mRNA | 0.2 | 0.2 | 0.2 | 0.2 | 24 |
k stot (h-1) | Rate constant for protein synthesis | 1.0 | 1.0 | 1.0 | 1.0 | 38 |
k sB (h-1) | Rate constant for synthesis of BMAL1 | 1.0kstot | 1.0kstot | 1.0kstot | 1.0kstot | 38 |
k sC (h-1) | Rate constant for synthesis of MYOD1 | 0.3kstot | 0.3kstot | 0.3kstot | 0.3kstot | 38 |
k s (h-1) | Rate constant for synthesis of CLOCK | 2.0 | 2.0 | 2.0 | 2.0 | 24 |
m 1 | Degree of cooperativity of repression of Bmal1 expression by nuclear dephosphorylation BMAL1 | 4.0 | 4.0 | 4.0 | 4.0 | 38 |
m 2 | Degree of cooperativity of repression of Clock expression by nuclear CLOCK | 4.0 | 4.0 | 4.0 | 4.0 | 38 |
n 1 | Degree of cooperativity of activation of Myod1 expression by IN complex | 4.0 | 4.0 | 4.0 | 4.0 | 38 |
n 2 | Degree of cooperativity of activation of miR-206 synthesis by cytosolic dephosphorylation MYOD1 | 4.0 | 4.0 | 4.0 | 4.0 | 38 |
V1B(nM·h-1) | Maximum rate of cytosolic BMAL1 phosphorylation | 1.0 | 1.0 | 1.0 | 1.0 | 38 |
V2B(nM·h-1) | Maximum rate of cytosolic BMAL1 dephosphorylation | 0.1 | 0.1 | 0.1 | 0.1 | 38 |
V3B(nM·h-1) | Maximum rate of nuclear BMAL1 phosphorylation | 1.0 | 1.0 | 1.0 | 1.0 | 38 |
V4B(nM·h-1) | Maximum rate of nuclear BMAL1 dephosphorylation | 0.2 | 0.2 | 0.2 | 0.2 | 38 |
V1c(nM·h-1) | Maximum rate of cytosolic MYOD1 phosphorylation | 1.0 | 1.0 | 1.0 | 1.0 | 38 |
V2c(nM·h-1) | Maximum rate of cytosolic MYOD1 dephosphorylation | 0.5 | 0.5 | 0.5 | 0.5 | 38 |
V1(nM·h-1) | Maximum rate of cytosolic P0 phosphorylation | 6.0 | 6.0 | 6.0 | 6.0 | 24 |
V2(nM·h-1) | Maximum rate of cytosolic P1 dephosphorylation | 3.0 | 3.0 | 3.0 | 3.0 | 24 |
V3(nM·h-1) | Maximum rate of cytosolic P1 phosphorylation | 6.0 | 6.0 | 6.0 | 6.0 | 24 |
V4(nM·h-1) | Maximum rate of cytosolic P2 dephosphorylation | 3.0 | 3.0 | 3.0 | 3.0 | 24 |
V dBC (Nm·h-1) | Maximum rate of degradation of cytosolic phosphorylated BMAL1 | 1.0 | 1.0 | 1.0 | 1.0 | 38 |
V dBN (nM·h-1) | Maximum rate of degradation of nuclear phosphorylated BMAL1 | 1.0 | 1.0 | 1.0 | 1.0 | 38 |
V dcc (nM·h-1) | Maximum rate of degradation of cytosolic phosphorylated MYOD1 | 0.1 | 0.1 | 0.1 | 0.1 | 38 |
V dIN (nM·h-1) | Maximum rate of degradation of IN complex | 0.6 | 0.6 | 0.6 | 0.6 | 38 |
V mB (nM·h-1) | Maximum rate of Bmal1 mRNA degradation | 0.3 | 0.3 | 0.3 | 0.3 | 38 |
V mC (nM·h-1) | Maximum rate of Myod1 mRNA degradation | 0.12 | 0.12 | 0.12 | 0.12 | 38 |
V d (nM·h-1) | Maximum rate of P2 degradation | 1.5 | 1.5 | 1.5 | 1.5 | 24 |
v stot (nM·h-1) | Maximum transcription rate | 1.0 | 1.0 | 1.0 | 1.0 | 38 |
V sB (nM·h-1) | Maximum rate of Bmal1 mRNA synthesis | 0.28vstot | 0.28vstot | 0.28vstot | 0.28vstot | 38 |
V sC (nM·h-1) | Maximum rate of Myod1 mRNA synthesis | 0.95vstot | 0.95vstot | 0.95vstot | 0.95vstot | 38 |
V sM (nM·h-1) | Maximum rate of miR-206 synthesis | 1.0 | 1.0 | 1.0 | 1.0 | 24, 38 |
V s (nM·h-1) | Maximum rate of Clock mRNA synthesis | 0.5 | 0.5 | 0.5 | 0.5 | 24 |
V m (nM·h-1) | Maximum rate of Clock mRNA degradation | 0.3 | 0.3 | 0.3 | 0.3 | 24 |
C1(nM·h-1) | Rate constant for the production of the miR-206 | 0.01 | 0.01 | 0.01 | 0.01 | 43 |
C2(h-1) | Maximum rate of miR-206 degradation | 0.01 | 0.01 | 0.01 | 0.01 | 43 |
C3(nM-1·h-1) | Rate constant for the formation of the RISC complex | 0 | 0.5 | 1.0 | 1.5 | 43 |
C4(h-1) | Maximum rate of RISC complex degradation | 0.6 | 0.6 | 0.6 | 0.6 | 43 |