The first step in our computational study of the LOV domain was to fuse the 2 domains of interest in VMD. We were then able to visualize the different proteins tried by Sosnick.
The working protein, that we call LovTAP is the result of the fusion at PHE22 of trpR and can be seen on the next video. The general LOV domain is in yellow. Please note the chromophore called Flavin (FMN) in red in the center of LOV2. The trpR dna binding domain is in orange and DNA in gray.
The fusion was made in VMD by aligning the alpha helix of both domains on the backbone of 3 residues. The secondary structure is quite strong and conserved, what makes this fusion realistic.
* @MET11: we clearly see the the j-alpha helix is not aligned with the helix of the trpR. It is also much longer than in the LovTAP. As we know that the change in the chromophore induced a change in the the j-alpha helix relatively to the beta-sheet of the LOV, we can imagine the j-alpha helix is not well positioned.
* @ALA12: same remarks as for the previous. Furthermore, it is clear that LOV is in interaction with bound DNA.
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