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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> <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">''' ----> will be setted up as soon as the exams are over'''
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| - |
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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) '''
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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:red">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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| - |
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| - | ;- Model the fusion of LOV domain with other transcription factors
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| - |
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| - |
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| - | ==To envisage ==
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| - | <br>- Molecular mutationnal assay
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| - | ----
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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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| - | |}
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