Eight Drosophila Circadian Clock Models

Goldbeter, 1995

Reference :

Goldbeter, A. (1995). A model for circadian oscillations in the Drosophila period protein (PER). Proc R Soc Lond B Biol Sci 261, 319-324.

Description :

The expression of per gene is self-regulated by its protein product, after undergoing two-step phosphorylation and being transported to the nucleus. This model shows that a self-feedback system is able to generate oscillations.

Description :

[ E-Cell SE 3 ] [ SBML ]

Goldbeter, 1995

• Reference:
  Goldbeter, A. (1995). A model for circadian oscillations in the Drosophila period protein (PER). Proc R Soc Lond B Biol Sci 261, 319-324.

• Description:
  The expression of per gene is self-regulated by its protein product, after undergoing two-step phosphorylation and being transported to the nucleus. This model shows that a self-feedback system is able to generate oscillations.
• Description(.zip) [ E-Cell SE 3 ] [ SBML ]

Tyson et al., 1999

• Reference:
  Tyson, J. J., Hong, C. I., Thron, C. D., and Novak, B. (1999). A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM. Biophys J 77, 2411-2417.

• Description:
  The self-feedback regulation model containing only the per mRNA and protein. Although having almost the same trough position, rapid rise in the mRNA concentration level introduces a time lag between the mRNA and protein peaks.
• Description(.zip) [ E-Cell SE 3 ] [ SBML ]

Scheper et al., 1999

• Reference:
  Scheper, T. O., Klinkenberg, D., van Pelt, J., and Pennartz, C. (1999). A model of molecular circadian clocks: multiple mechanisms for phase shifting and a requirement for strong nonlinear interactions. J Biol Rhythms 14, 213-220.

• Description:
  The self-feedback regulation model containing only the per mRNA and protein. Inclusion of the time delay of transcription realizes the generation of oscillation even with very simplified equations for transcription and translation.
• Description(.zip) [ E-Cell SE 3 ] [ SBML ]

Leloup et al., 1999

• Reference:
  Leloup, J. C., and Goldbeter, A. (1999). Chaos and birhythmicity in a model for circadian oscillations of the PER and TIM proteins in drosophila. J Theor Biol 198, 445-459.

• Description:
  Based on the model by Goldbeter, this model is expanded to include per and tim genes, the expression of which is regulated by PER-TIM heterodimer transported to the nucleus.
• Description(.zip) [ E-Cell SE 3 ]

Petri et al., 2001

• Reference:
  Petri, B., and Stengl, M. (2001). Phase response curves of a molecular model oscillator: implications for mutual coupling of paired oscillators. J Biol Rhythms 16, 125-141.

• Description:
  This model modifies the parameter sets and the mRNA/Protein degradation processes of the model by Leloup et al. The expression levels correlate better with the experimental data and the oscillation phases remain almost the same as the original model.
• Description(.zip) [ E-Cell SE 3 ] [ SBML ]

Ueda et al., 2001

• Reference:
  Ueda, H. R., Hagiwara, M., and Kitano, H. (2001). Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm. J Theor Biol 210, 401-406.

• Description:
  The model is comprised of per, tim and Clk mRNA and proteins, assuming constant concentration of the CYC protein. The gene expression is regulated by PER-TIM and CLK-CYC heterodimers that are transported to the nucleus.
• Description(.zip) [ E-Cell SE 3 ]

Smolen et al., 2002

• Reference:
  Smolen, P., Baxter, D. A., and Byrne, J. H. (2002). A reduced model clarifies the role of feedback loops and time delays in the Drosophila circadian oscillator. Biophys J 83, 2349-2359.

• Description:
  This model simplifies the interlocked feedback loops and only contains the PER and CLK proteins. Free CLK proteins that do not form heterodimers with PER regulates the gene expression with a time delay.
• Description(.zip) [ E-Cell SE 3 ] [ SBML ]

Smolen et al., 2004

• Reference:
  Smolen, P., Hardin, P. E., Lo, B. S., Baxter, D. A., and Byrne, J. H. (2004). Simulation of Drosophila circadian oscillations, mutations, and light responses by a model with VRI, PDP-1, and CLK. Biophys J 86, 2786-2802.

• Description:
  The first model that reproduced CLK expression regulation by VRI and PDP-1. PER protein undergoes two-step phosphorylation in cytoplasm and nucleus, and only PDP-1 expression is modeled with time delay.
• Description(.zip) [ E-Cell SE 3 ] [ SBML ]