Team:EPF-Lausanne/Modeling
From 2009.igem.org
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.
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
Already done
We generated all the files needed to do the simulation, thanks to the tutorial of NAMD, which can be found on the following page:
http://www.ks.uiuc.edu/Training/Tutorials/
Here is our first movie from the modeling, showing the behavoir of the protein in the dark state condition: 2v0u_dark_state.mov