Computational Reconstruction and Analysis of Structural Models of Avian Cryptochrome 4

Abstract

A recent study by Xu et al. (Nature, 2021, 594, 535–540) provided strong evidence that cryptochrome 4 (Cry4) is a key protein to endow migratory birds with the magnetic compass sense. The investigation compared the magnetic field response of Cry4 from migratory and nonmigratory bird species and suggested that a difference in magnetic sensitivity could exist. This finding prompted an in-depth investigation into Cry4 protein differences on the structural and dynamic levels. In the present study, the pigeon Cry4 (ClCry4) crystal structure was used to reconstruct the missing avian Cry4 protein structures via homology modeling for carefully selected bird species. The reconstructed Cry4 structure from European robin, Eurasian blackcap, zebra finch, chicken, and pigeon were subsequently simulated dynamically and analyzed. The studied avian Cry4 structures show flexibility in analogous regions pointing to similar activation mechanisms and/or signaling interaction partners. It can be concluded that the experimentally recorded difference in the magnetic field sensitivity of Cry4 from different birds is unlikely to be due to solely intrinsic dynamics of the proteins but requires additional factors that have not yet been identified.

On the energetic differences of avian cryptochromes 4 from selected species

“…It is not yet established how the differences in magnetic sensitivity occur, but the functioning of Cry4a depends on the non-covalently bound flavin adenine dinucleotide (FAD) cofactor [17,24] (see Fig. 1) and a cascade of electron transfers that involve a chain of conserved tryptophan residues [9,[25][26][27], connecting the FAD cofactor with the protein surface at a combined transfer length of approximately 15 Å in avian Cry4a [9].…”

“…The studied models were previously homology modeled, and simulated [9,27,31]. Specifically we focus on the structure of the pigeon cryptochrome 4 ClCry4a derived from a crystal structure [32], along with the reconstructed structures of European robin (Erithacus rubecula) cryptochrome 4, ErCry4a [9], Chicken (Gallus gallus) cryptochrome 4a, GgCry4a, Eurasian blackcap (Sylvia atricapilla) cryptochrome 4a, SaCry4a, and Zebra finch (Taeniopygia guttata) cryptochrome 4a, TgCry4a, displayed in Fig.…”

“…Specifically we focus on the structure of the pigeon cryptochrome 4 ClCry4a derived from a crystal structure [32], along with the reconstructed structures of European robin (Erithacus rubecula) cryptochrome 4, ErCry4a [9], Chicken (Gallus gallus) cryptochrome 4a, GgCry4a, Eurasian blackcap (Sylvia atricapilla) cryptochrome 4a, SaCry4a, and Zebra finch (Taeniopygia guttata) cryptochrome 4a, TgCry4a, displayed in Fig. 1 [27]. Furthermore, the global structural differences between avian Cry4a proteins are linked to the aforementioned energetical studies and sites where an energetical difference can be ascribed to be due to a difference in sequences have been highlighted.…”

“…The analysis of Cry4a energetics was performed for proteins that were simulated dynamically in earlier studies [9,23,27,31]. The simulations utilized NAMD [33][34][35] through the VIKING platform [36] to carry out the computations.…”

Across atoms to crossing continents: application of similarity measures to biological location data

“…Alternatively, a comparison of fluctuations within a protein structure may be performed through the root mean square fluctuation (RMSF) approach. 39 Both of these strategies are, however, inadequate when comparing two dynamic trajectories of a protein qualitatively as both approaches only involve a comparison of structures to a reference one and not a dynamic protein trajectory.…”