Modelling

From 2009.igem.org

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Revision as of 14:38, 2 June 2009

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/sites/entrez?db=pmc&cmd=search&term=PMC1630464 Pubmed])

- 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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 We will follow the following article protocol:
-<br> Freddolino, P.L., Dittrich M., Schulten K., Dynamic Switching Mechanisms in LOV1 and LOV2 Domains of Plant Phototropins. Biophysical Journal, <b> 91 </b>, 3630-3639, 2006 ([http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=PMC1630464 PMC1630464])
+<br> Freddolino, P.L., Dittrich M., Schulten K., Dynamic Switching Mechanisms in LOV1 and LOV2 Domains of Plant Phototropins. Biophysical Journal, <b> 91 </b>, 3630-3639, 2006 ([http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=PMC1630464 Pubmed])
 <br>- Model the fusion of LOV domain with other transcription factors