Modelling

From 2009.igem.org

(Difference between revisions)

Revision as of 15:03, 6 July 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 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 ([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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@@ Line 4: / Line 4: @@
 ==To find==
-PDB files of LOV domain, TrpR repressor => [http://www.rcsb.org/pdb/home/home.do PDB database]
+PDB files of LOV domain, TrpR repressor: [http://www.rcsb.org/pdb/home/home.do PDB database]
 ==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">''' ----> will be setted up as soon as the exams are over'''
+<br> <font size=3><span style="color:red"> OK </span></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'''
 <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) '''
@@ Line 13: / Line 13: @@
 ;- Model allosteric interactions between LOVTAP & TrpR:
 :What will be done:
-:-> Model of LOVTAP in dark phase
+:- Model of LOVTAP in dark phase
-:-> Model of LOVTAP in light phase
+:- Model of LOVTAP in light phase
-:-> Characterize how the J-alpha helix changes
+:- 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.
+:- 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.