Molecular dynamics simulations disclose early stages of the photoactivation of cryptochrome 4

Daniel R. Kattnig, Claus Nielsen, Ilia A. Solov'yov
New Journal of Physics
20
083018
2018
abstract
Birds appear to be equipped with a light-dependent, radical-pair-based magnetic compass that relieson truly quantum processes. While the identity of the sensory protein has remained speculative cryptochrome 4 has recently been identified as the most auspicious candidate. Here, we report on allatom molecular dynamics (MD) simulations addressing the structural reorganisations that accompany the photoreduction of the flavin cofactor in the European robin cryptochrome 4 (ErCry4). Extensive MDsimulations reveal that the photo-activation of ErCry4 induces large-scale conformational changes on short (hundreds of nanoseconds) timescales. Specifically, the photo-reduction is accompanied with the release of the C-terminal tail, structural rearrangements in the vicinity of the FAD-binding site, and the noteworthy formation of an α-helical segment at the N-terminal part. Some of these rearrangements appear to expose potential phosphorylation sites.Wedescribe the conformational dynamics of the protein using a graph-based approach that is informed by the adjacency of residues and the correlation of their local motions. This approach reveals densely coupled reorganisation entities, i.e. graph communities, which could facilitate an efficient signal transduction due to a high density of hubs. These communities are interconnected by a small number of highly important residues. The network approach clearly identifies the sites restructuring upon photoactivation which appear as protrusions or delicate bridges in the reorganisation network.Wealso find that, unlike in the homologous cryptochrome from D. melanogaster, the release of the C-terminal domain does not appear to be correlated with the transposition of a histidine residue close to the FAD cofactor.