Team:EPF-Lausanne/Modeling

                               

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. Light activated LOV domain Dark LOV domain 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