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Team:EPF-Lausanne/Modeling
From 2009.igem.org
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Both LOV domain crystallography files were obtained from [http://www.rcsb.org/pdb/home/home.do RCSB]: | Both LOV domain crystallography files were obtained from [http://www.rcsb.org/pdb/home/home.do RCSB]: | ||
| - | + | :[http://www.rcsb.org/pdb/explore/explore.do?structureId=2V0W Light activated LOV domain] | |
| - | + | :[http://www.rcsb.org/pdb/explore/explore.do?structureId=2V0U Dark LOV domain] | |
These crystallographies were done by [http://www.ncbi.nlm.nih.gov/pubmed/18001137 Halavaty et al.]. | These crystallographies were done by [http://www.ncbi.nlm.nih.gov/pubmed/18001137 Halavaty et al.]. | ||
Revision as of 07:43, 21 September 2009
Contents |
Protein domain of interest
Our protein of interest is LOVTAP. This protein was sythetically engineered by Sosnick group. It is a fusion protein between a LOV domain (Avena Sativa phototropin 1) and the E. Coli tryptophan repressor. This protein undergoes changes under light activation as shown by Sosnick et al, in fact when the protein is activated by light it binds DNA and inversely. For more information about LOVTAP protein please click here.
Goal
Starting material
Both LOV domain crystallography files were obtained from RCSB:
These crystallographies were done by Halavaty et al..
Molecular dynamics: a little theory
Steps
References
Analysis methodology
Results
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 structural 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.
- - Between Light state and Dark State
- - RMS between light state and dark state
- - length between the two arms N C
- - only cytochrome with interactions in light state and dark state
To envisage
- Molecular mutational assay
