<i>Ab initio</i> derivation of flavin hyperfine interactions for the protein magnetosensor cryptochrome

Deviers, Jean; Cailliez, Fabien; Gutiérrez, Bernardo Zúñiga; Kattnig, Daniel R.; Lande, Aurélien de la

doi:10.1039/d1cp05804e

Cited by 8 publications

(2 citation statements)

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“…The RPC and RPD states (ClC and ClD) of pigeon (Columba livia) cryptochrome 4a (ClCry4a), from which a structure of ErCry4a was constructed via homology modeling, , were also studied and compared with the results for AtCry1 and ErCry4a. It was found in an earlier study that the dynamical behavior of ErCry4a and ClCry4a differs even though ErCry4a was constructed using ClCry4a as a homology template. , Molecular dynamics (MD) simulations provide a valuable tool to investigate the dynamics of biomolecules, , including local dynamical fluctuations of small molecules bound to proteins. − Here, MD simulations were performed to determine the relevant structural and dynamic properties of Trp •+ and FAD •– in the five RP states from which the most important hyperfine interactions were calculated using density functional theory (DFT). Finally, the magnetic sensitivity of AtCry1 and ErCry4a was compared using the time-averaged hyperfine interactions to simulate the quantum yields of the reaction products by means of the spin dynamics software package MolSpin …”

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confidence: 99%

Effects of Dynamical Degrees of Freedom on Magnetic Compass Sensitivity: A Comparison of Plant and Avian Cryptochromes

et al. 2022

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The magnetic compass of migratory birds is thought to rely on a radical pair reaction inside the blue-light photoreceptor protein cryptochrome. The sensitivity of such a sensor to weak external magnetic fields is determined by a variety of magnetic interactions, including electron-nuclear hyperfine interactions. Here, we investigate the implications of thermal motion, focusing on fluctuations in the dihedral and librational angles of flavin adenine dinucleotide (FAD) and tryptophan (Trp) radicals in cryptochrome 4a from European robin (Erithacus rubecula, ErCry4a) and pigeon (Columba livia, ClCry4a) and cryptochrome 1 from the plant Arabidopsis thaliana (AtCry1). Molecular dynamics simulations and density functional theory-derived hyperfine interactions are used to calculate the quantum yield of radical pair recombination dependent on the direction of the geomagnetic field. This quantity and various dynamical parameters are compared for [FAD •− Trp •+ ] in ErCry4a, ClCry4a, and AtCry1, with TrpC or TrpD being the third and fourth components of the tryptophan triad/tetrad in the respective proteins. We find that (i) differences in the average dihedral angles in the radical pairs are small, (ii) the librational motions of TrpC •+ in the avian cryptochromes are appreciably smaller than in AtCry1, (iii) the rapid vibrational motions of the radicals leading to strong fluctuations in the hyperfine couplings affect the spin dynamics depending on the usage of instantaneous or time-averaged interactions. Future investigations of radical pair compass sensitivity should therefore not be based on single snapshots of the protein structure but should include the ensemble properties of the hyperfine interactions.

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Section: Introductionmentioning

confidence: 99%

Effects of Dynamical Degrees of Freedom on Magnetic Compass Sensitivity: A Comparison of Plant and Avian Cryptochromes

et al. 2022

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“…We have undertaken extensive all-atom molecular dynamics simulation of cryptochrome 4 from Columba livia , Cl Cry4, binding the FAD cofactor in its semiquinone form, FADH • . The starting configuration corresponded to the most frequently occurring conformation as observed in our previous study, based on a clustering analysis of the trajectory of a 800-ns MD simulation [59] . The starting point of this earlier study was the crystal structure of Cl Cry4, as deposited in the PDB (identifier: 6PU0), with the phosphate binding loop reconstructed as described in [60] .…”

Section: Resultsmentioning

confidence: 99%

Avian cryptochrome 4 binds superoxide

Deviers,

Cailliez,

de la Lande

et al. 2024

Computational and Structural Biotechnology Journal

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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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Ab initio derivation of flavin hyperfine interactions for the protein magnetosensor cryptochrome

Abstract: The radicals derived from the flavin adenine dinucleotide cofactor (FAD) are a corner stone of recent hypotheses of magnetoreception, including the compass of migratory songbirds. These models attribute the magnetic...

Cited by 8 publications

References 80 publications

Effects of Dynamical Degrees of Freedom on Magnetic Compass Sensitivity: A Comparison of Plant and Avian Cryptochromes

Effects of Dynamical Degrees of Freedom on Magnetic Compass Sensitivity: A Comparison of Plant and Avian Cryptochromes

Avian cryptochrome 4 binds superoxide

The Effect of Spin Relaxation on Magnetic Compass Sensitivity in ErCry4a

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