Team:LCG-UNAM-Mexico/Notebook/2008-October
From 2008.igem.org
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+ | <p> <strong>Estimating the amount of AiiA per cell</strong> </p> | ||
+ | <p> AiiA is under the control of the lac promoter. The transcription and mRNA degradation rates help us estimate the amount of mRNA present on the cell. </p> | ||
+ | <p> “The half-life of protein A is assumed to be around 10 minutes which is similar to what is used in Elowitz’s repressilator model [1]. Furthermore, we assume that a more aggressive degradation tail can enable half-times on the order of two minutes for protein B.” </p> | ||
+ | <p> Modeling the Lux/AiiA Relaxation Oscillator </p> | ||
+ | <p> Christopher Batten </p> | ||
+ | <p> In the paper AiiA is called protein B. Therefore the degradation rate for AiiA with an aggressive degradation tail is 0.0058 <em>s</em>-1. This would give us a lower limit. </p> | ||
+ | <p> “Transcription initiation rate, km </p> | ||
+ | <p> Malan et al. (1984) measured the transcription initiation rate at P1 and report the following value: km ≈ 0.18min-1 </p> | ||
+ | <p> mRNA degradation rate, jM </p> | ||
+ | <p> Kennell and Riezman (1977), measured a lacZ mRNA half-life of 1.5 min: ξM = 0.46min-1 </p> | ||
+ | <p> lacZ mRNA translation initiation rate, кB </p> | ||
+ | <p> From Kennell and Riezman (1977), translation starts every 3.2 s at the lacZ mRNA. This leads to the following translation initiation rate: кB ≈ 18.8min-1” </p> | ||
+ | <p> Santillán M. and Mackey M. C. (2004). Influence of Catabolite Repression and Inducer Exclusion on the Bistable Behavior of the lac Operon. Biophys J 86:1282–1292 </p> | ||
+ | <p> We modified both transcription initiation and translation rates by multiplying both rates by 4. This due to the fact that LuxR is a four times smaller than LacZ: </p> | ||
+ | <p> LacZ has a length of 1024 aa </p> | ||
+ | <p> LuxR has a length of 250 aa </p> | ||
+ | <p> Simulating with simbiology, AiiA reaches stationary state at almost 3500 molecules per cell. </p> | ||
+ | <p> </p> | ||
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