Molecular dynamics simulations disclose early stages of the photo-Activation of cryptochrome 4 (article)
dc.contributor.author | Kattnig, DR | |
dc.contributor.author | Nielsen, C | |
dc.contributor.author | Solov'Yov, IA | |
dc.date.accessioned | 2018-12-10T16:20:59Z | |
dc.date.issued | 2018-08-10 | |
dc.description.abstract | 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 all-Atom 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 photo-Activation, 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. | en_GB |
dc.description.sponsorship | Engineering and Physical Sciences Research Council (EPSRC) | en_GB |
dc.description.sponsorship | Royal Society | en_GB |
dc.description.sponsorship | Lundbeck Foundation | en_GB |
dc.description.sponsorship | Danish Councils for Independent Research | en_GB |
dc.description.sponsorship | Russian Science Foundation | en_GB |
dc.identifier.citation | Vol. 20, article ) 083018 | en_GB |
dc.identifier.doi | 10.1088/1367-2630/aad70f | |
dc.identifier.grantnumber | EP/L000253/1 | en_GB |
dc.identifier.grantnumber | RG170378 | en_GB |
dc.identifier.grantnumber | EP/R021058/1 | en_GB |
dc.identifier.grantnumber | 17-72-2021 | en_GB |
dc.identifier.uri | http://hdl.handle.net/10871/35086 | |
dc.language.iso | en | en_GB |
dc.publisher | IOP Publishing for Deutsche Physikalische Gesellschaft | en_GB |
dc.relation.url | https://doi.org/10.24378/exe.363 | en_GB |
dc.rights | © 2018 The Author(s). Published by IOP Publishing Ltd on behalf of Deutsche Physikalische Gesellschaft. Open access. Original content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. | en_GB |
dc.title | Molecular dynamics simulations disclose early stages of the photo-Activation of cryptochrome 4 (article) | en_GB |
dc.type | Article | en_GB |
dc.date.available | 2018-12-10T16:20:59Z | |
dc.identifier.issn | 1367-2630 | |
dc.description | This is the final version. Available from IOP Publishing via the DOI in this record. | en_GB |
dc.description | The dataset associated with this article is in ORE: https://doi.org/10.24378/exe.363 | en_GB |
dc.identifier.journal | New Journal of Physics | en_GB |
dc.rights.uri | https://creativecommons.org/licenses/by/3.0/ | en_GB |
dcterms.dateAccepted | 2018-07-31 | |
rioxxterms.version | VoR | en_GB |
rioxxterms.licenseref.startdate | 2018-08-10 | |
rioxxterms.type | Journal Article/Review | en_GB |
refterms.dateFCD | 2018-12-10T16:16:09Z | |
refterms.versionFCD | VoR | |
refterms.dateFOA | 2018-12-10T16:21:01Z | |
refterms.panel | B | en_GB |
refterms.depositException | publishedGoldOA |
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