Exploring Post-activation Conformational Changes in Pigeon Cryptochrome 4
Journal of Physical Chemistry B
A widespread hypothesis ascribes the ability of migratory birdsto navigate over large distances to an inclination compass realized by theprotein cryptochrome in the birdsâretinae. Cryptochromes are activated byblue light, which induces a radical pair state, the spin dynamics of which maybecome sensitive to earthâs weak magneticfields. The magnetic information isencoded and passed on to downstream processes by structural rearrangementsof the protein, the details of which remain vague. We utilize extensive all-atommolecular dynamics simulations to probe the conformational changes ofpigeon cryptochrome 4 upon light activation. The structural dynamics areanalyzed based on principal component analysis and with the help of distancematrices, which reveal significant changes in selected inter-residue distances.The results are evaluated and discussed with reference to the protein structureand its putative function as a magnetoreceptor. It is suggested that thephosphate-binding loop could act as a gate controlling the access to theflavinadenine dinucleotide cofactor depending on the redox state of the protein.