Mutational Study of the Tryptophan Tetrad Important for Electron Transfer in European Robin Cryptochrome 4a

Frederiksen, Anders; Langebrake, Corinna; Hanić, Maja; Manthey, Georg; Mouritsen, Henrik; Liedvogel, Miriam; Solov’yov, Ilia A.

doi:10.1021/acsomega.3c02963

Cited by 4 publications

(4 citation statements)

References 73 publications

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“…To investigate the stability of the constructed aquatic CRY4 models, the temporal evolution of the root mean square deviation (RMSD) was calculated for the simulated CRY4 models. Figure 5a shows the resulting RMSD plots for ChCRY4, DrCRY4 and ErCRY4a, and it also demonstrates that for the simulated proteins, the RMSD saturates around 3 Å, indicating a stable structure based on RMSD analysis from similar studies [42,61]. Following earlier analysis of CRYs, the calculated RMSD values are considered typical for stable structures [42].…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 72%

“…The results are given in figure 5b and show that the general profiles of the RMSF plots are overall similar for the investigated protein models, meaning the CRY4 models all exhibit regions with high mobility (high RMSF) or rigidity/stability (low RMSF). An example of the similarity is that all structures have a fluctuating area 220-240, which is a known flexible part of CRY4, usually noted as the phosphate binding loop [41,59,61]. Overall, the data suggest a highly comparable dynamic behaviour of the investigated proteins.…”

Section: Gene Expression Analysismentioning

confidence: 73%

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Magnetic orientation in juvenile Atlantic herring ( Clupea harengus ) could involve cryptochrome 4 as a potential magnetoreceptor

Laurien,

Mende,

Luhrmann

et al. 2024

J. R. Soc. Interface.

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The Earth’s magnetic field can provide reliable directional information, allowing migrating animals to orient themselves using a magnetic compass or estimate their position relative to a target using map-based orientation. Here we show for the first time that young, inexperienced herring ( Clupea harengus , Ch) have a magnetic compass when they migrate hundreds of kilometres to their feeding grounds. In birds, such as the European robin ( Erithacus rubecula ), radical pair-based magnetoreception involving cryptochrome 4 (ErCRY4) was demonstrated; the molecular basis of magnetoreception in fish is still elusive. We show that cry4 expression in the eye of herring is upregulated during the migratory season, but not before, indicating a possible use for migration. The amino acid structure of herring ChCRY4 shows four tryptophans and a flavin adenine dinucleotide-binding site, a prerequisite for a magnetic receptor. Using homology modelling, we successfully reconstructed ChCRY4 of herring, DrCRY4 of zebrafish ( Danio rerio ) and StCRY4 of brown trout ( Salmo trutta ) and showed that ChCRY4, DrCRY4 and ErCRY4a, but not StCRY4, exhibit very comparable dynamic behaviour. The electron transfer could take place in ChCRY4 in a similar way to ErCRY4a. The combined behavioural, transcriptomic and simulation experiments provide evidence that CRY4 could act as a magnetoreceptor in Atlantic herring.

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Section: Molecular Dynamics Simulationsmentioning

confidence: 72%

Section: Gene Expression Analysismentioning

confidence: 73%

Magnetic orientation in juvenile Atlantic herring ( Clupea harengus ) could involve cryptochrome 4 as a potential magnetoreceptor

Laurien,

Mende,

Luhrmann

et al. 2024

J. R. Soc. Interface.

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“…Their unpaired electron spins can be either antiparallel ↑↓ (singlet state) or parallel ↑↑ (triplet state). ,, In Cry4, one radical is formed from the flavin adenine dinucleotide (FAD) cofactor, which is a cofactor that can bind noncovalently inside the protein. The other radical is formed from the tryptophan (W) amino acid residue in Cry4, where one of the four tryptophans of the well-conserved Trp-tetrad is involved. − ,− …”

Section: Introductionmentioning

confidence: 99%

“…The other radical is formed from the tryptophan (W) amino acid residue in Cry4, where one of the four tryptophans of the well-conserved Trp-tetrad is involved. 8 − 10 , 14 − 16 …”

Section: Introductionmentioning

confidence: 99%

Understanding the Red Shift in the Absorption Spectrum of the FAD Cofactor in ClCry4 Protein

Kretschmer,

Frederiksen,

Reinholdt

et al. 2024

J. Phys. Chem. B

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It is still a puzzle that has not been entirely solved how migratory birds utilize the Earth's magnetic field for biannual migration. The most consistent explanation thus far is rooted in the modulation of the biological function of the cryptochrome 4 (Cry4) protein by an external magnetic field. This phenomenon is closely linked with the flavin adenine dinucleotide (FAD) cofactor that is noncovalently bound in the protein. Cry4 is activated by blue light, which is absorbed by the FAD cofactor. Subsequent electron and proton transfers trigger radical pair formation in the protein, which is sensitive to the external magnetic field. An important long-lasting redox state of the FAD cofactor is the signaling (FADH • ) state, which is present after the transient electron transfer steps have been completed. Recent experimental efforts succeeded in crystallizing the Cry4 protein from Columbia livia (ClCry4) with all of the important residues needed for protein photoreduction. This specific crystallization of Cry4 protein so far is the only avian cryptochrome crystal structure available, which, however, has great similarity to the Cry4 proteins of night migratory birds. The previous experimental studies of the ClCry4 protein included the absorption properties of the protein in its different redox states. The absorption spectrum of the FADH • state demonstrated a peculiar red shift compared to the photoabsorption properties of the FAD cofactor in its FADH • state in other Cry proteins from other species. The aim of this study is to understand this red shift by employing the tools of computational microscopy and, in particular, a QM/MM approach that relies on the polarizable embedding approximation.

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The Effect of Spin Relaxation on Magnetic Compass Sensitivity in ErCry4a

Grüning,

Gerhards,

Wong

et al. 2024

ChemPhysChem

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This study explores the impact of thermal motion on the magnetic compass mechanism in migratory birds, focusing on the radical pair mechanism within cryptochrome photoreceptors. The coherence of radical pairs, crucial for magnetic field inference, is curbed by spin relaxation induced by intra‐protein motion. Molecular dynamics simulations, density‐functional‐theory‐based calculations, and spin dynamics calculations were employed, utilizing Bloch‐Redfield‐Wangsness (BRW) relaxation theory, to investigate compass sensitivity. Previous research hypothesized that European robin’s cryptochrome 4a (ErCry4a) optimized intra‐protein motion to minimize spin relaxation, enhancing magnetic sensing compared to the plant Arabidopsis thaliana’s cryptochrome 1 (AtCry1). Different correlation times of the nuclear hyperfine coupling constants in AtCry1 and ErCry4a were indeed found, leading to distinct radical pair yields in the two species, with ErCry4a showing optimized sensitivity. However, this optimization is likely negligible in realistic spin systems with numerous nuclear spins. Beyond insights in magnetic sensing, the study presents a detailed method employing molecular dynamics simulations to assess spin relaxation effects on chemical reactions with realistically modelled protein motion, relevant for studying radical pair reactions at finite temperature.

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Mutational Study of the Tryptophan Tetrad Important for Electron Transfer in European Robin Cryptochrome 4a

Cited by 4 publications

References 73 publications

Magnetic orientation in juvenile Atlantic herring ( Clupea harengus ) could involve cryptochrome 4 as a potential magnetoreceptor

Magnetic orientation in juvenile Atlantic herring ( Clupea harengus ) could involve cryptochrome 4 as a potential magnetoreceptor

Understanding the Red Shift in the Absorption Spectrum of the FAD Cofactor in ClCry4 Protein

The Effect of Spin Relaxation on Magnetic Compass Sensitivity in ErCry4a

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