Modelling

From 2009.igem.org

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{{EPF-Lausanne09}}
 
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<div CLASS="epfltrick">__TOC__
 
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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>- 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'''
 
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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>
 
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;- Model allosteric interactions between LOVTAP & TrpR:
 
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:What will be done:
 
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:- Model of LOVTAP in dark phase
 
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:- Model of LOVTAP in light phase
 
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:- Characterize how the J-alpha helix changes
 
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:- 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.
 
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<span style="color:midnightblue">We will follow the following article protocol:</span>
 
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<br> 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])
 
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;- Model the fusion of LOV domain with other transcription factors
 
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==To envisage ==
 
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<br>- Molecular mutationnal assay
 
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
 
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!align="center"|[[Team:EPF-Lausanne|Home]]
 
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!align="center"|[[Team:EPF-Lausanne/Team|The Team]]
 
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!align="center"|[[Team:EPF-Lausanne/Project|The Project]]
 
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!align="center"|[[Team:EPF-Lausanne/Parts|Parts Submitted to the Registry]]
 
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!align="center"|[[Team:EPF-Lausanne/Modeling|Modeling]]
 
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!align="center"|[[Team:EPF-Lausanne/Notebook|Notebook]]
 
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!align="center"|[[Team:EPF-Lausanne/Lectures|Lectures]]
 
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!align="center"|[[Team:EPF-Lausanne/Team Management|Team Management]]
 
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!align="center"|[[Team:EPF-Lausanne/References|References]]
 
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|}
 
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</div><div CLASS="epfl09bouchon"></div>
 

Latest revision as of 20:10, 10 July 2009