Team:EPF-Lausanne/Modeling
From 2009.igem.org
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==Protein domain of interest== | ==Protein domain of interest== | ||
- | [https://2009.igem.org/Team:EPF-Lausanne/LOVTAP LOVTAP] | + | Our protein of interest is [https://2009.igem.org/Team:EPF-Lausanne/LOVTAP LOVTAP]. This protein was sythetically engineered by [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=18667691 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 [https://2009.igem.org/Team:EPF-Lausanne/LOVTAP click here]. | ||
==Goal== | ==Goal== |
Revision as of 07:31, 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
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