Modelling

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Revision as of 15:11, 6 July 2009

To find

PDB files of LOV domain, TrpR repressor: PDB database

To do

OK - Set up day of starting modeling, do a planning for modeling so see with Matteo Dal Peraro will be setted up as soon as the exams are over

Ask Matteo to send all the required starting papers, files, and links to tutorials BEFORE the end of the exams (around midjune)

- 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 (Pubmed)

- Model the fusion of LOV domain with other transcription factors

To envisage

- Molecular mutationnal assay

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 :- 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.
 <span style="color:midnightblue">We will follow the following article protocol: </span>