Team:EPF-Lausanne/Modeling
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==Implementation of the simulation== | ==Implementation of the simulation== | ||
- | + | <br> We generated all the files needed to do the simulation, thanks to the tutorial of NAMD, which can be found on the following page: | |
+ | <br> http://www.ks.uiuc.edu/Training/Tutorials/ | ||
+ | Steps are explained in a little bit more detail on this page: [[Team:EPF-Lausanne/Modeling/Simulation|Simulation]] | ||
==To envisage == | ==To envisage == |
Revision as of 15:17, 21 July 2009
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 ([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
Implementation of the simulation
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/
Steps are explained in a little bit more detail on this page: Simulation
To envisage
- Molecular mutationnal assay
Already done
Here is our first movie from the modeling, showing the behavior of the protein in the dark state condition: Dark State
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: Light State with FMN without water