Modelling

From 2009.igem.org

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==To find==
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PDB files of LOV domain, TrpR repressor: [http://www.rcsb.org/pdb/home/home.do PDB database]
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==To do==
 
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<br> <span style="color:red"> <font size=3>OK </font size></span>- Set up day of starting modeling, do a planning for modeling so see with Matteo Dal Peraro <span style="color:red">'''  will be setted up as soon as the exams are over'''</span>
 
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<br> <span style="color:green">''' Ask Matteo to send all the required starting papers, files, and links to tutorials BEFORE the end of the exams (around midjune) ''' </span>
 
;- Model allosteric interactions between LOVTAP & TrpR:
;- Model allosteric interactions between LOVTAP & TrpR:

Revision as of 15:08, 6 July 2009



Contents

To find

PDB files of LOV domain, TrpR repressor: [http://www.rcsb.org/pdb/home/home.do PDB database]


- 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
- Model sturctural changes that enhance the switch feature of LOVTAP e.g. in dark phase: really weak interaction between LOVTAP and the corresponding DNA sequence, in light phase: strong binding of LOVTAP on DNA.


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

To envisage


- Molecular mutationnal assay

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