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Team:UNIK Copenhagen/Modelling
From 2014.igem.org
MODELLING
The dynamics in Quenchibodies leading to the emission of light upon antigen binding is due to structural changes within the FAB fragment. Abe et al. (2011) showed that tryptophan residues are responsible for the quenching the fluorescence from the fluorophore, this quenching is then abolished when the fluorophore is not in close proximity to the tryptophan residues.
A functional Quenchibody would therefore have to undergo a conformational change upon binding, which distances the fluorophore from the tryptophan residues.
Knowledge about the exact dynamics of the Quenchibody has not yet been determined but Abe et al. (2014) has produced several functional ones. To determine if our Quenchibodies would be functional we compared the dynamics of the fab-fragment from a functional Quenchibody upon binding with the binding dynamics of our chosen FAB fragments.
The cocaine detecting fab-fragment has tryptophan residue in the variable region that will change position upon binding of the fab-fragment to the antigen.
The change in tryptophan residues upon binding of the progesterone fab-fragment resembles that of the cocaine fab-fragment.
No change in the tryptophan residues of the estradiol binding fab fragment is seen.
References:
Abe, R. et al., 2011. “Quenchbodies”: quench-based antibody probes that show antigen-dependent fluorescence. Journal of the American Chemical Society, 133(43), pp.17386–94. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3983608&tool=pmcentrez&rendertype=abstract [Accessed April 18, 2014
Abe, R. et al., 2014. Ultra Q-bodies: quench-based antibody probes that utilize dye-dye interactions with enhanced antigen-dependent fluorescence. Scientific reports, 4, p.4640. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3983608&tool=pmcentrez&rendertype=abstract [Accessed April 18, 2014].
