Team:CIDEB-UANL Mexico/math union

Binding module

The binding module is based in the use of a fusion protein composed by L2 and AIDA. L2+AIDA is a protein which is not affected by external factors during its transcription as well as its translation, so we need to use the stablished parameters but with the data we obtained from it:

We used the parameters for translation and transcription rate from Singapore 2008 iGEM team as well as the speeds at which E. coli carry out transcription and translation assuming a transcription speed of 70nt/s and a translation speed of 40aa/s. So we used them in the equations below with the L2+AIDA gene length (2620nt) and protein length (856aa) respectively:

Then, we use the parameters for degradation rates for proteins and mRNAs from Beijing PKU 2009 iGEM team:

As the protein was the fusion of two we need to search for each half-life. The half-life of membrane proteins range between 2 to 20 hours in E. coli (Hare, 1991), and as AIDA-I is a membrane protein its half-life must be between that range since it is not determined the specific half-life of AIDA. To find the half-life of L2 we assumed it was 7.8 hours (Bergant, 2010). Bergant’s team made test with a homologous protein but found in the minor capsid of the Human Papillomavirus (HPV). Although the function of the L2 strand in HPV is viral, and in E. coli is ribosomal, both share similar structures and sequences. Once we have decided to use the half-life from the homologous L2 we determined to use it as the half-life for the fusion protein because it was between the range of AIDA-I, and also because it was the lower half-life assuming as E. coli start the L2 degradation, it would degrade the whole protein.