leloup6

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000171) Biomodels notes: The model has been simulated using copasi 4.3(build 25) For fig 4A one parameter, v_dT_fac, has been changed to 1 and the starting point of the simulation had to be changed to +32 hours to better fit the figure in the publication. JWS Online curation: This model was curated by reproducing Figure 4D.

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Abstract
The authors present a model for circadian oscillations of the Period (PER) and Timeless (TIM) proteins in Drosophila. The model for the circadian clock is based on multiple phosphorylation of PER and TIM and on the negative feedback exerted by a nuclear PER-TIM complex on the transcription of the per and tim genes. Periodic behavior occurs in a large domain of parameter space in the form of limit cycle oscillations. These sustained oscillations occur in conditions corresponding to continuous darkness or to entrainment by light-dark cycles and are in good agreement with experimental observations on the temporal variations of PER and TIM and of per and tim mRNAs. Birhythmicity (coexistence of two periodic regimes) and aperiodic oscillations (chaos) occur in a restricted range of parameter values. The results are compared to the predictions of a model based on the sole regulation by PER. Both the formation of a complex between PER and TIM and protein phosphorylation are found to favor oscillatory behavior. Determining how the period depends on several key parameters allows us to test possible molecular explanations proposed for the altered period in the per(l) and per(s) mutants. The extended model further allows the construction of phase-response curves based on the light-induced triggering of TIM degradation. These curves, established as a function of both the duration and magnitude of the effect of a light pulse, match the phase-response curves obtained experimentally in the wild type and per(s) mutant of Drosophila.

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
1e-09 mole
1e-09 mole litre^(-1.0)
3600.0 second
2.777777777777778e-13 second^(-1.0) mole litre^(-1.0)
0.0002777777777777778 second^(-1.0)
277777.7777777778 second^(-1.0) mole^(-1.0) litre
2.777777777777778e-13 mole second^(-1.0)
1.0 dimensionless
1.0 litre
Id Name Spatial dimensions Size
cytoplasm cytoplasm 3.0 1.0 litre
nucleus 3.0 1.0 litre
Id Name Initial quantity Compartment Fixed
C PER_TIM complex cytoplasm 0.18 <substance_units>/litre cytoplasm (cytoplasm)
CN PER_TIM complex nuclear 1.2 <substance_units>/litre nucleus
M_P per mRNA 0.09 <substance_units>/litre cytoplasm (cytoplasm)
M_T tim mRNA 1.41 <substance_units>/litre cytoplasm (cytoplasm)
P0 PER 0.02 <substance_units>/litre cytoplasm (cytoplasm)
P1 PER-p 0.02 <substance_units>/litre cytoplasm (cytoplasm)
P2 PER-pp 0.01 <substance_units>/litre cytoplasm (cytoplasm)
Pt total PER <assignment rule> <substance_units>/litre cytoplasm (cytoplasm)
T0 TIM 0.54 <substance_units>/litre cytoplasm (cytoplasm)
T1 TIM-p 0.79 <substance_units>/litre cytoplasm (cytoplasm)
T2 TIM-pp 4.65 <substance_units>/litre cytoplasm (cytoplasm)
Tt total TIM <assignment rule> <substance_units>/litre cytoplasm (cytoplasm)

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
CN_decay nuclear PER_TIM compl. decay CN > ∅

kd_CN * CN * nucleus
C_decay cytopl. PER_TIM compl. decay C > ∅

kd_C * C * cytoplasm
C_form Per_TIM complex formation P2 + T2 > C

(k3 * T2 * P2 - k4 * C) * cytoplasm
C_transp PER_TIM complex shuttling C = CN

k1 * C * cytoplasm - k2 * CN * nucleus
M_P_decay per mRNA decay M_P > ∅

(v_mP / (K_mP + M_P) + kd) * M_P * cytoplasm
M_T_decay tim mRNA decay M_T > ∅

(v_mT / (K_mT + M_T) + kd) * M_T * cytoplasm
P1_decay PER-p decay P1 > ∅

kd * P1 * cytoplasm
P1_depho PER-p dephosphorylation P1 > P0

V_2P * P1 / (K_2P + P1) * cytoplasm
P1_pho PER-p phosphorylation P1 > P2

V_3P * P1 / (K_3P + P1) * cytoplasm
P2_decay PER-pp decay P2 > ∅

kd * P2 * cytoplasm
P2_depho PER-pp dephosphorylation P2 > P1

V_4P * P2 / (K_4P + P2) * cytoplasm
P2_light_deact PER-pp light deactivation P2 > ∅

v_dP * P2 / (K_dP + P2) * cytoplasm
PER_transl PER tranlation ∅ > P0

k_sP * M_P * cytoplasm
PO_decay PER decay P0 > ∅

kd * P0 * cytoplasm
P_pho PER phosphorylation P0 > P1

V_1P * P0 / (K_1P + P0) * cytoplasm
T0_decay TIM decay T0 > ∅

kd * T0 * cytoplasm
T1_decay TIM-p decay T1 > ∅

kd * T1 * cytoplasm
T1_depho TIM-p dephosphorylation T1 > T0

V_2T * T1 / (K_2T + T1) * cytoplasm
T1_pho TIM-p phosphorylation T1 > T2

V_3T * T1 / (K_3T + T1) * cytoplasm
T2_decay TIM-pp decay T2 > ∅

kd * T2 * cytoplasm
T2_depho TIM-pp dephosphorylation T2 > T1

V_4T * T2 / (K_4T + T2) * cytoplasm
T2_light_deact TIM-pp light deactivation T2 > ∅

v_dT * T2 / (K_dT + T2) * cytoplasm
TIM_transl TIM translation ∅ > T0

k_sT * M_T * cytoplasm
T_pho TIM phosphorylation T0 > T1

V_1T * T0 / (K_1T + T0) * cytoplasm
per_trans per transkription ∅ > M_P

v_sP * pow(Ki_P, n) / (pow(Ki_P, n) + pow(CN, n))
tim_trans tim transkription ∅ > M_T

v_sT * pow(Ki_T, n) / (pow(Ki_T, n) + pow(CN, n))

Global parameters

Id Value
kd 0.01
l_d 12.0
n 4.0 dimensionless
v_dT 2.0
v_dT_dark 2.0
v_dT_fac 2.0 dimensionless

Local parameters

Id Value Reaction
v_sP 0.8 per_trans (per transkription)
Ki_P 1.0 per_trans (per transkription)
v_sT 1.0 tim_trans (tim transkription)
Ki_T 1.0 tim_trans (tim transkription)
v_mT 0.7 M_T_decay (tim mRNA decay)
K_mT 0.2 M_T_decay (tim mRNA decay)
v_mP 0.8 M_P_decay (per mRNA decay)
K_mP 0.2 M_P_decay (per mRNA decay)
k_sP 0.9 PER_transl (PER tranlation)
k_sT 0.9 TIM_transl (TIM translation)
k3 1.2 C_form (Per_TIM complex formation)
k4 0.6 C_form (Per_TIM complex formation)
kd_C 0.01 C_decay (cytopl. PER_TIM compl. decay)
kd_CN 0.01 CN_decay (nuclear PER_TIM compl. decay)
k1 1.2 C_transp (PER_TIM complex shuttling)
k2 0.2 C_transp (PER_TIM complex shuttling)
V_1P 8.0 P_pho (PER phosphorylation)
K_1P 2.0 P_pho (PER phosphorylation)
V_3P 8.0 P1_pho (PER-p phosphorylation)
K_3P 2.0 P1_pho (PER-p phosphorylation)
K_2P 2.0 P1_depho (PER-p dephosphorylation)
V_2P 1.0 P1_depho (PER-p dephosphorylation)
V_4P 1.0 P2_depho (PER-pp dephosphorylation)
K_4P 2.0 P2_depho (PER-pp dephosphorylation)
V_1T 8.0 T_pho (TIM phosphorylation)
K_1T 2.0 T_pho (TIM phosphorylation)
V_3T 8.0 T1_pho (TIM-p phosphorylation)
K_3T 2.0 T1_pho (TIM-p phosphorylation)
K_2T 2.0 T1_depho (TIM-p dephosphorylation)
V_2T 1.0 T1_depho (TIM-p dephosphorylation)
V_4T 1.0 T2_depho (TIM-pp dephosphorylation)
K_4T 2.0 T2_depho (TIM-pp dephosphorylation)
K_dT 0.2 T2_light_deact (TIM-pp light deactivation)
v_dP 2.0 P2_light_deact (PER-pp light deactivation)
K_dP 0.2 P2_light_deact (PER-pp light deactivation)

Assignment rules

Definition
v_dT = (1.0 + (v_dT_fac - 1.0) * ceil(sin(time / l_d * pi) * 0.9)) * v_dT_dark
Pt = P0 + P1 + P2 + C + CN * nucleus / cytoplasm
Tt = T0 + T1 + T2 + C + CN * nucleus / cytoplasm

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments