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Modelling
From 2009.igem.org
To find
PDB files of LOV domain, TrpR repressor => [http://www.rcsb.org/pdb/home/home.do PDB database]
To do
OK - Set up day of starting modeling, do a planning for modeling => see with Matteo Dal Peraro ----> will be setted up as soon as the exams are over
- Model allosteric interactions between LOVTAP & TrpR:
What will be done:
- -> model of LOVTAP in dark phase
- -> model of LOVTAP in light phase
- -> characterize how the J-alpha helix changes
We will follow the following article protocol:
Freddolino, P.L., Dittrich M., Schulten K., Dynamic Switching Mechanisms in LOV1 and LOV2 Domains of Plant Phototropins. Biophysical Journal, 91 , 3630-3639, 2006 ([http://www.ncbi.nlm.nih.gov/ Pubmed] => PMC1630464)
- Model the fusion of LOV domain with other transcription factors
- Maybe do a mutational assay to change specificity of LOVTAP:
- Direct mutational assay: Insert mutation in specific sites thanks to the known structure of LOVTAP (already modeled on computer)
- Indirect mutational assay: Random mutations, then selection of the "right" protein according to a set of selected conditions
To envisage
- Molecular mutationnal assay
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