Multiscale description of avian migration: from chemical compass to behaviour modeling

Pedersen, J. Boiden; Nielsen, Claus; Solov’yov, Ilia A.

doi:10.1038/srep36709

Cited by 29 publications

(59 citation statements)

References 60 publications

(93 reference statements)

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“…Here, we focus on a radical pair state that is formed in a photo-induced electron transfer reaction from the darkstate protein containing the FAD cofactor in the fully oxidised form. It is currently unknown and intensely debated whether this state could form the basis of a magnetic compass [14,16,29,31,32,35,36,86]. Some evidence in favour of the alternative radical pair resulting from the re-oxidation of the fully reduced cryptochrome by e.g.…”

Section: Discussionmentioning

confidence: 99%

Molecular dynamics simulations disclose early stages of the photo-activation of cryptochrome 4

2018

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Birds appear to be equipped with a light-dependent, radical-pair-based magnetic compass that relies on 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 MD simulations 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. We describe 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. We also 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.

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Section: Discussionmentioning

confidence: 99%

Molecular dynamics simulations disclose early stages of the photo-activation of cryptochrome 4

2018

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“…Furthermore, here we focus on a radical pair state that is formed in a photo-induced electron transfer reaction from the dark-state protein containing the FAD cofactor in the fully oxidized form. It is currently unknown and intensely debated whether this state could form the basis of a magnetic compass [10,12,25,35,43,[76][77][78]. Some evidence in favour of the alternative radical pair resulting from the re-oxidation of the fully reduced cryptochrome by e.g.…”

Section: Discussionmentioning

confidence: 99%

Molecular dynamics simulations disclose early stages of the photo-activation of cryptochrome 4

Kattnig¹,

Nielsen²,

Solov’yov³

2018

Preprint

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Birds appear to be equipped with a light-dependent, radical-pair-based magnetic compass that relies on 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 a model of the European robin cryptochrome 4 (ErCry4). Extensive MD simulations 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 -helical segment at the N-terminal part. Some of these rearrangements appear to expose potential phosphorylation sites. We describe 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 communities, which facilitate an efficient signal transduction due to a high density of hubs. These communities are interconnected by a small number of highly important residues characterized by high betweenness centrality. The network approach clearly identifies the sites restructuring upon photoactivation, which appear as protrusions or delicate bridges in the reorganisation network. We also 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.

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“…In general, when considering unequal reaction rate constants, it is deemed adequate, except when the triplet and singlet channels are characterized by vastly (by an order of magnitude or more) different rates. While such scenarios have been considered, they appear to be rather exotic [41]. The effects of inter-radical interactions could be small in the actual sensor [65].…”

Section: The Model and Its Limitationsmentioning

confidence: 99%

“…As far as the relative orientation is concerned, ΔS and ΓS provide essentially conforming conclusions and this distinction does not appear to be relevant. However, two recent works argue that the spikiness of the anisotropy pattern might be more relevant than the absolute size of the effect, as it could provide a pathway to, and rationale for, the remarkable acuity of the avian compass [38,41]. Solov'yov and co-workers have suggested an alternative measure, referred to as optimality, which quantifies spikiness [41].…”

Section: Orientational Magnetosensitivity In [F •− W •+ ]mentioning

confidence: 99%

“…Motivated by the complexity involved with experimental studies, several theoretical approaches have aimed to further clarify the anisotropic MFEs on cryptochromes, in turn, providing predictions for reaction anisotropies in various scenarios [35][36][37][38][39][40][41][42][43]. Many investigations have addressed the fundamental principles and feasibility of highly simplified models for radical pair states within cryptochrome.…”

Section: Introductionmentioning

confidence: 99%

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On the optimal relative orientation of radicals in the cryptochrome magnetic compass

Atkins

Bajpai

Rumball

et al. 2019

The Journal of Chemical Physics

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Birds appear to be equipped with an innate magnetic compass. One biophysical model of this sense relies on spin dynamics in photo-generated radical pairs in the protein cryptochrome. This study employs a systematic approach to predict the dependence of the compass sensitivity on the relative orientation of the constituent radicals for spin systems comprising up to 21 hyperfine interactions. Evaluating measures of compass sensitivity (anisotropy) and precision (optimality) derived from the singlet yield, we find the ideal relative orientations for the radical pairs consisting of the flavin anion (F •-) coupled with a tryptophan cation (W •+) or tyrosine radical (Y •). For the geomagnetic field, the two measures are found to be anti-correlated in [F •-W •+ ]. The angle spanned by the normals to the aromatic planes of the radicals is the decisive parameter determining the compass sensitivity. The third tryptophan of the tryptophan triad/tetrad, which has been implicated with magnetosensitive responses, exhibits a comparably large anisotropy, but unfavorable optimality. Its anisotropy could be boosted by an additional ~50 % by optimizing the relative orientation of the radicals. For a coherent lifetime of 1 μs, the maximal relative anisotropy of [F •-W •+ ] is 0.27 %. [F •-Y • ] radical pairs outperform [F •-W •+ ] for most relative orientations. Furthermore, anisotropy and optimality can be simultaneously maximized. The entanglement decays rapidly, implicating it as a situational byproduct rather than a fundamental driver within the avian compass. In magnetic fields of higher intensity, the relative orientation of radicals in [F •-W •+ ] is less important than for the geomagnetic field.

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Multiscale description of avian migration: from chemical compass to behaviour modeling

Cited by 29 publications

References 60 publications

Molecular dynamics simulations disclose early stages of the photo-activation of cryptochrome 4

Molecular dynamics simulations disclose early stages of the photo-activation of cryptochrome 4

Molecular dynamics simulations disclose early stages of the photo-activation of cryptochrome 4

On the optimal relative orientation of radicals in the cryptochrome magnetic compass

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