Team:EPF-Lausanne/Modeling

From 2009.igem.org

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(→Modeling)
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:- 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.
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==Already done==
 
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Here is our first movie from the modeling, showing the behavior of the protein in the dark state condition:
 
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[[Media:2v0u_dark_state.mov | Dark State]]
 
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After having modified some parameters in the parameter files, here is our second movie, concerning the light state of the protein this time, with the FMN:
 
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[[Media:Light_FMN_without_water.mov‎  | Light State with FMN without water]]
 
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Revision as of 10:09, 27 July 2009



Contents

Modeling

To do

- 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.


To envisage


- Molecular mutationnal assay



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