Modelling

From 2009.igem.org

(Difference between revisions)

Revision as of 14:41, 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 </span>
- 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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@@ Line 4: / Line 4: @@
 ==To do==
 <br> <font size=3><span style="color:red"> OK </span></font size>- Set up day of starting modeling, do a planning for modeling => see with Matteo Dal Peraro <span style="color:red"><b> ----> will be setted up as soon as the exams are over </span>
-:- Model allosteric interactions between LOVTAP & TrpR:
+<br>- Model allosteric interactions between LOVTAP & TrpR:
-What will be done:
+:What will be done:
 :-> model of LOVTAP in dark phase
 :-> model of LOVTAP in light phase