Separation of photo-induced radical pair in cryptochrome to a functionally critical distance

Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.

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

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.

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

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.

The Effect of Spin Relaxation on Magnetic Compass Sensitivity in ErCry4a

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 recombination 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 for spin relaxation effects on chemical reactions with realistically modelled protein motion, relevant for studying radical pair reactions at finite temperature.

Structural Rearrangements of Pigeon Cryptochrome 4 Undergoing a Complete Redox Cycle

Cryptochrome is currently the major contender of a protein to underpin magnetoreception, the ability to sense the Earth's magnetic field. Among various types of cryptochromes, cryptochrome 4 has been identified as the likely magnetoreceptor in migratory birds. All-atom molecular dynamics (MD) studies have offered first insights into the structural dynamics of cryptochrome but are limited to a short time scale due to large computational demands. Here, we employ coarse-grained MD simulations to investigate the emergence of long-lived states and conformational changes in pigeon cryptochrome 4. Our coarse-grained simulations complete the picture by permitting observation on a significantly longer time scale. We observe conformational transitions in the phosphate-binding loop of pigeon cryptochrome 4 upon activation and identify prominent motions in residues 440-460, suggesting a possible role as a signaling state of the protein or as a gated interaction site for forming protein complexes that might facilitate downstream processes. The findings highlight the importance of considering longer time scales in studying cryptochrome dynamics and magnetoreception. Coarse-grained MD simulations offer a valuable tool to unravel the complex behavior of cryptochrome proteins and shed new light on the mechanisms underlying their role in magnetoreception. Further exploration of these conformational changes and their functional implications may contribute to a deeper understanding of the molecular mechanisms of magnetoreception in birds.

Activation of Cryptochrome 4 from Atlantic Herring

Marine fish migrate long distances up to hundreds or even thousands of kilometers for various reasons that include seasonal dependencies, feeding, or reproduction. The ability to perceive the geomagnetic field, called magnetoreception, is one of the many mechanisms allowing some fish to navigate reliably in the aquatic realm. While it is believed that the photoreceptor protein cryptochrome 4 (Cry4) is the key component for the radical pair-based magnetoreception mechanism in night migratory songbirds, the Cry4 mechanism in fish is still largely unexplored. The present study aims to investigate properties of the fish Cry4 protein in order to understand the potential involvement in a radical pair-based magnetoreception. Specifically, a computationally reconstructed atomistic model of Cry4 from the Atlantic herring (Clupea harengus) was studied employing classical molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) methods to investigate internal electron transfers and the radical pair formation. The QM/MM simulations reveal that electron transfers occur similarly to those found experimentally and computationally in Cry4 from European robin (Erithacus rubecula). It is therefore plausible that the investigated Atlantic herring Cry4 has the physical and chemical properties to form radical pairs that in turn could provide fish with a radical pair-based magnetic field compass sensor.

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

The ability of migratory birds to sense magnetic fields has been known for decades, although the understanding of the underlying mechanism is still elusive. Currently, the strongest magnetoreceptor candidate in birds is a protein called cryptochrome 4a. The cryptochrome 4a protein has changed through evolution, apparently endowing some birds with a more pronounced magnetic sensitivity than others. Using phylogenetic tools, we show that a specific tryptophan tetrad and a tyrosine residue predicted to be essential for cryptochrome activation are highly conserved in the avian clade. Through state-of-the-art molecular dynamics simulations and associated analyses, we also studied the role of these specific residues and the associated mutants on the overall dynamics of the protein. The analyses of the single residue mutations were used to judge how far a local change in the protein structure can impact specific dynamics of European robin cryptochrome 4a. We conclude that the replacements of each of the tryptophans one by one with a phenylalanine do not compromise the overall stability of the protein.

Dimerization of European Robin Cryptochrome 4a

Homo-dimer formation is important for the function of many proteins. Although dimeric forms of cryptochromes (Cry) have been found by crystallography and were recently observed in vitro for European robin Cry4a, little is known about the dimerization of avian Crys and the role it could play in the mechanism of magnetic sensing in migratory birds. Here, we present a combined experimental and computational investigation of the dimerization of robin Cry4a resulting from covalent and non-covalent interactions. Experimental studies using native mass spectrometry, mass spectrometric analysis of disulfide bonds, chemical cross-linking, and photometric measurements show that disulfide-linked dimers are routinely formed, that their formation is promoted by exposure to blue light, and that the most likely cysteines are C317 and C412. Computational modeling and molecular dynamics simulations were used to generate and assess a number of possible dimer structures. The relevance of these findings to the proposed role of Cry4a in avian magnetoreception is discussed.

QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase

Oxygenase activity of the flavin-dependent enzyme RutA is commonly associated with the formation of flavin-oxygen adducts in the enzyme active site. We report the results of quantum mechanics/molecular mechanics (QM/MM) modeling of possible reaction pathways initiated by various triplet state complexes of the molecular oxygen with the reduced flavin mononucleotide (FMN) formed in the protein cavities. According to the calculation results, these triplet-state flavin-oxygen complexes can be located at both re-side and si-side of the isoalloxazine ring of flavin. In both cases, the dioxygen moiety is activated by electron transfer from FMN, stimulating the attack of the arising reactive oxygen species at the C4a, N5, C6, and C8 positions in the isoalloxazine ring after the switch to the singlet state potential energy surface. The reaction pathways lead to the C(4a)-peroxide, N(5)-oxide, or C(6)-hydroperoxide covalent adducts or directly to the oxidized flavin, depending on the initial position of the oxygen molecule in the protein cavities.

Quantum-mechanical insights into the anisotropic response of the cryptochrome radical pair to a weak magnetic field

Cryptochrome photoreceptors contain a photochemically generated radical pair, which is thought to mediate sensing of the geomagnetic field direction in many living organisms. To gain insight into the response of the cryptochrome to a weak magnetic field, we have studied the quantum-mechanical hyperfine spin states of the radical pair. We identify quantum states responsible for the precise detection of the magnetic field direction, taking into account the strongly axial hyperfine interactions of each radical in the radical pair. The contribution of these states to the formation of the cryptochrome signaling state sharply increases when the magnetic field becomes orthogonal to the hyperfine axis of either radical. Due to such a response, the radical pair may be able to detect the particular field direction normal to the plane containing the hyperfine axes of the radicals.

Diamond surface engineering for molecular sensing with nitrogen-vacancy centers

Quantum sensing using optically addressable atomic-scale defects, such as the nitrogen-vacancy (NV) center in diamond, provides new opportunities for sensitive and highly localized characterization of chemical functionality. Notably, near-surface defects facilitate detection of the minute magnetic fields generated by nuclear or electron spins outside of the diamond crystal, such as those in chemisorbed and physisorbed molecules. However, the promise of NV centers is hindered by a severe degradation of critical sensor properties, namely charge stability and spin coherence, near surfaces (< ca. 10 nm deep). Moreover, applications in the chemical sciences require methods for covalent bonding of target molecules to diamond with robust control over density, orientation, and binding configuration. This forward-looking Review provides a survey of the rapidly converging fields of diamond surface science and NV-center physics, highlighting their combined potential for quantum sensing of molecules. We outline the diamond surface properties that are advantageous for NV-sensing applications, and discuss strategies to mitigate deleterious effects while simultaneously providing avenues for chemical attachment. Finally, we present an outlook on emerging applications in which the unprecedented sensitivity and spatial resolution of NV-based sensing could provide unique insight into chemically functionalized surfaces at the single-molecule level.

Long-Time Oxygen Localization in Electron Transfer Flavoprotein

Reactive oxygen species (ROS) exert a wide range of biological effects from beneficial regulatory function to deleterious oxidative stress. The electron transfer flavoprotein (ETF) is ubiquitous to life and is associated with aerobic metabolism and ROS production due to its location in the mitochondria. Quantifying oxygen localization within the ETF complex is critical for understanding the potential for electron transfer and radical pair formation between flavin adenine dinucleotide (FAD) cofactor and superoxide during ROS formation. Our study employed all-atom molecular dynamics simulations and identified several novel, long-lived oxygen binding sites within the ETF complex that appear near the FAD cofactor. Site locations, the local electrostatic environment, and characteristic oxygen binding times for each site were evaluated to establish factors that may lead to possible charge transfer reactions and superoxide formation within the ETF complex. The study revealed that some oxygen binding sites are naturally linked to protein domain features, suggesting opportunities to engineer and control ROS production and subsequent dynamics.

Computational Reconstruction and Analysis of Structural Models of Avian Cryptochrome 4

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.

Orientations and water dynamics of photoinduced secondary charge-separated states for magnetoreception by cryptochrome

In the biological magnetic compass, blue-light photoreceptor protein of cryptochrome is thought to conduct the sensing of the Earth's magnetic field by photoinduced sequential long-range charge-separation (CS) through a cascade of tryptophan residues, W_A(H), W_B(H) and W_C(H). Mechanism of generating the weak-field sensitive radical pair (RP) is poorly understood because geometries, electronic couplings and their modulations by molecular motion have not been investigated in the secondary CS states generated prior to the terminal RP states. In this study, water dynamics control of the electronic coupling is revealed to be a key concept for sensing the direction of weak magnetic field. Geometry and exchange coupling (singlet-triplet energy gap: 2J) of photoinduced secondary CS states composed of flavin adenine dinucleotide radical anion (FAD^-•) and radical cation W_B(H)^+• in the cryptochrome DASH from Xenopus laevis were clarified by time-resolved electron paramagnetic resonance. We found a time-dependent energetic disorder in 2J and was interpreted by a trap CS state capturing one reorientated water molecule at 120 K. Enhanced electron-tunneling by water-libration was revealed for the terminal charge-separation event at elevated temperature. This highlights importance of optimizing the electronic coupling for regulation of the anisotropic RP yield on the possible magnetic compass senses.

Exploring Post-activation Conformational Changes in Pigeon Cryptochrome 4

A widespread hypothesis ascribes the ability of migratory birds to navigate over large distances to an inclination compass realized by the protein cryptochrome in the birds' retinae. Cryptochromes are activated by blue light, which induces a radical pair state, the spin dynamics of which may become sensitive to earth's weak magnetic fields. The magnetic information is encoded and passed on to downstream processes by structural rearrangements of the protein, the details of which remain vague. We utilize extensive all-atom molecular dynamics simulations to probe the conformational changes of pigeon cryptochrome 4 upon light activation. The structural dynamics are analyzed based on principal component analysis and with the help of distance matrices, which reveal significant changes in selected inter-residue distances. The results are evaluated and discussed with reference to the protein structure and its putative function as a magnetoreceptor. It is suggested that the phosphate-binding loop could act as a gate controlling the access to the flavin adenine dinucleotide cofactor depending on the redox state of the protein.

Regulatory Impact of the C-Terminal Tail on Charge Transfer Pathways in Drosophila Cryptochrome

Interconnected transcriptional and translational feedback loops are at the core of the molecular mechanism of the circadian clock. Such feedback loops are synchronized to external light entrainment by the blue light photoreceptor cryptochrome (CRY) that undergoes conformational changes upon light absorption by an unknown photoexcitation mechanism. Light-induced charge transfer (CT) reactions in Drosophila CRY (dCRY) are investigated by state-of-the-art simulations that reveal a complex, multi-redox site nature of CT dynamics on the microscopic level. The simulations consider redox-active chromophores of the tryptophan triad (Trp triad) and further account for pathways mediated by W314 and W422 residues proximate to the C-terminal tail (CTT), thus avoiding a pre-bias to specific W-mediated CT pathways. The conducted dissipative quantum dynamics simulations employ microscopically derived model Hamiltonians and display complex and ultrafast CT dynamics on the picosecond timescale, subtly balanced by the electrostatic environment of dCRY. In silicio point mutations provide a microscopic basis for rationalizing particular CT directionality and demonstrate the degree of electrostatic control realized by a discrete set of charged amino acid residues. The predicted participation of CT states in proximity to the CTT relates the directionality of CT reactions to the spatial vicinity of a linear interaction motif. The results stress the importance of CTT directional charge transfer in addition to charge transfer via the Trp triad and call for the use of full-length CRY models including the interactions of photolyase homology region (PHR) and CTT domains.

Molecular Oxygen Binding in the Mitochondrial Electron Transfer Flavoprotein

Reactive oxygen species such as superoxide are potentially harmful byproducts of the aerobic metabolism in the inner mitochondrial membrane, and complexes I, II, III of the electron transport chain have been identified as primary sources. The mitochondrial fatty acid b-oxidation pathway may also play a yet uncharacterized role in reactive oxygen species generation, apparently at the level of the electron transfer flavoprotein:ubiquinone oxidoreductase (ETF:QO) and/or its redox partner electron-transfer flavoprotein (ETF). These enzymes comprise a key pathway through which electrons are sequentially shuttled from several dehydrogenases to the respiratory chain. The exact mechanisms of superoxide production have not been fully established, but a crucial starting point would be the binding of molecular oxygen within one of the protein complexes. The present investigation offers a comprehensive computational approach for the determination of binding modes and characteristic binding times of small molecules inside proteins, which is then used to reveal several O₂ binding sites near the flavin adenine dinucleotide cofactor of the ETF enzyme. The binding sites are further characterized to extract the necessary parameters for further studies of possible electron transfer between flavin and O₂ leading to radical pair formation and possible superoxide production.

Biological relevance of charge transfer branching pathways in photolyases

The repair of sun-induced DNA lesions by photolyases is driven by a photoinduced electron transfer from a fully reduced FAD to the damaged DNA. A chain of several aromatic residues connecting FAD to solvent ensures the prior photoreduction of the FAD cofactor. In PhrA, a class III CPD photolyase, two branching tryptophan charge transfer pathways have been characterized. According to previous experiments, both pathways play a role in the FAD photoreduction. To provide a molecular insight to the charge transfer abilities of both pathways, we perform multiscales simulations where the protein motion and the positive charge are simultaneously propagated. Our computational approach reveals that one pathway drives a very fast charge transfer whereas the other pathway provides a very good thermodynamic stabilization of the positive charge. During the simulations, the positive charge firstly moves on the fast triad, while a reorganization of the close FAD˙^- environment occurs. Then, backward transfers can lead to the propagation of the positive charge on the second pathway. After one nanosecond, we observe a nearly equal probability to find the charge at ending tryptophan of either pathway; eventually the charge distribution will likely evolve towards a charge stabilization on the last tryptophan of the slowest pathway. Our results highlight the role the protein environment, which manages the association of a kinetic and a thermodynamic pathways to trigger a fast and efficient FAD photoreduction.

What accounts for the different functions in photolyases and cryptochromes: a computational study of proton transfers to FAD

Photolyases (PL) and cryptochromes (CRY) are light-sensitive flavoproteins, respectively, involved in DNA repair and signal transduction. Their activation is triggered by an electron transfer process, which partially or fully reduces the photo-activated FAD cofactor. The full reduction additionally requires a proton transfer to the isoalloxazine ring. In plant CRY, an efficient proton transfer takes place within several μs, enabled by a conserved aspartate working as a proton donor, whereas in E. coli PL a proton transfer occurs in the 4 s timescale without any obvious proton donor, indicating the presence of a long-range proton transfer pathway. Unexpectedly, the insertion of an aspartate as a proton donor in a suitable position for proton transfer in E. coli PL does not initiate a transfer process similar to plant CRY, but even prevents the formation of a protonated FAD. In the present work, thanks to a combination of classical molecular dynamics and state-of-the-art DFTB3/MM simulations, we identify a proton transfer pathway from bulk to FAD in E. coli PL associated with a free energy profile in agreement with the experimental kinetics data. The free energy profiles of the proton transfer between aspartate and FAD show an inversion of the driving force between plant CRY and E. coli PL mutants. In the latter, the proton transfer from the aspartate is faster than in plant CRY but also thermodynamically disfavoured, in agreement with the experimental data. Our results further illustrate the fine tuning of the electrostatic FAD environment and the adaptability of the FAD pocket to ensure the divergent functions of the members of the PL-CRY family.

Molecular Insights into Variable Electron Transfer in Amphibian Cryptochrome

Cryptochrome proteins are activated by the absorption of blue light, leading to the formation of radical pairs through electron transfer in the active site. Recent experimental studies have shown that once some of the amino acid residues in the active site of Xenopus laevis cryptochrome DASH are mutated, radical-pair formation is still observed. In this study, we computationally investigate electron-transfer pathways in the X. laevis cryptochrome DASH by extensively equilibrating a previously established homology model using molecular dynamics simulations and then mutating key amino acids involved in the electron transfer. The electron-transfer pathways are then probed by using tight-binding density-functional theory. We report the alternative electron-transfer pathways resolved at the molecular level and, through comparison of amino acid sequences for cryptochromes from different species, we demonstrate that one of these alternative electron-transfer pathways could be general for all cryptochrome DASH proteins.

Modeling MesoBioNano systems with MBN Studio made easy

This paper introduces MesoBioNano (MBN) Studio - a graphical user interface for a popular multiscale simulation package MBN Explorer. MBN Studio has been developed to facilitate setting up and starting MBN Explorer calculations, monitoring their progress and examining the calculation results. It is tailored for any calculations that are supported by MBN Explorer, such as for example the single-point energy calculations, structure optimization, molecular dynamics, and kinetic Monte Carlo simulations. Apart from that MBN Studio has built-in tools allowing the calculation and analysis of specific characteristics that are determined by the output of the simulations, such as the diffusion coefficients of molecular species, melting temperatures and associated heat capacities, radial distribution function; a dedicated modeling plug-in allows constructing molecular systems in a quick and efficient manner. Employing this plug-in, one can easily construct molecular systems of different geometries (e.g., spherical or ellipsoidal nanoparticles, cubic crystalline samples) with various atomic composition. The paper presents the first public release of MBN Studio and provides an overview of its significant capabilities, as well as the reference point for further extensions.

An open quantum system approach to the radical pair mechanism

The development of the radical pair mechanism has allowed for theoretical explanation of the fact that magnetic fields are observed to have an effect on chemical reactions. The mechanism describes how an external magnetic field can alter chemical yields by interacting with the spin state of a pair of radicals. In the field of quantum biology, there has been some interest in the application of the mechanism to biological systems. This paper takes an open quantum systems approach to a model of the radical pair mechanism in order to derive a master equation in the Born-Markov approximation for the case of two electrons, each interacting with an environment of nuclear spins as well as the external magnetic field, then placed in a dissipative bosonic bath. This model is used to investigate two different cases relating to radical pair dynamics. The first uses a collective coupling approach to simplify calculations for larger numbers of nuclei interacting with the radical pair. The second looks at the effects of different hyperfine configurations of the radical pair model, for instance the case in which one of the electrons interact with two nuclei with different hyperfine coupling constants. The results of these investigations are analysed to see if they offer any insights into the biological application of the radical pair mechanism in avian magnetoreception.

Ascorbic acid may not be involved in cryptochrome-based magnetoreception

Seventeen years after it was originally suggested, the photoreceptor protein cryptochrome remains the most probable host for the radical pair intermediates that are thought to be the sensors in the avian magnetic compass. Although evidence in favour of this hypothesis is accumulating, the intracellular interaction partners of the sensory protein are still unknown. It has been suggested that ascorbate ions could interact with surface-exposed tryptophan radicals in photoactivated cryptochromes, and so lead to the formation of a radical pair comprised of the reduced form of the flavin adenine dinucleotide cofactor, FAD^•-, and the ascorbate radical, Asc^•- This species could provide a more sensitive compass than a FAD-tryptophan radical pair. In this study of Drosophila melanogaster cryptochrome and Erithacus rubecula (European robin) cryptochrome 1a, we use molecular dynamics simulations to characterize the transient encounters of ascorbate ions with tryptophan radicals in cryptochrome in order to assess the likelihood of the [FAD^•- Asc^•-]-pathway. It is shown that ascorbate ions are expected to bind near the tryptophan radicals for periods of a few nanoseconds. The rate at which these encounters happen is low, and it is therefore concluded that ascorbate ions are unlikely to be involved in magnetoreception if the ascorbate concentration is only of the order of 1 mM or less.

Atomistic Insights into Cryptochrome Interprotein Interactions

It is striking that the mechanism by which birds sense geomagnetic fields during the biannual migration seasons is not entirely understood. A protein believed to be responsible for avian magnetoreception is the flavoprotein cryptochrome (CRY), which fulfills many of the criteria for a magnetic field sensor. Some experiments, however, indicate that magnetoreception in birds may be disturbed by extremely weak radio frequency fields, an effect that likely cannot be described by an isolated CRY protein. An explanation can possibly be delivered if CRY binds to another protein inside a cell that would possess certain biochemical properties, and it is, therefore, important to identify possible intracellular CRY interaction partners. The goal of this study is to investigate a possible interaction between CRY4 and the iron-sulfur-containing assembly protein (ISCA1) from Erithacus rubecula (European robin), which has recently been proposed to be relevant for magnetic field sensing. The interaction between the proteins is established through classical molecular dynamics simulations for several possible protein-docking modes. The analysis of these simulations concludes that the ISCA1 complex and CRY4 are capable of binding; however, the peculiarities of this binding argue strongly against ISCA1 as relevant for magnetoreception.

Absorption Spectra of FAD Embedded in Cryptochromes

The magnetic compass sense utilized by migratory birds for long-distance navigation functions only once light of a certain wavelength is present. This piece of evidence fits partially with the popular hypothesis of chemical magnetoreception in cryptochrome proteins, located in the bird retina. According to this hypothesis a magnetosensitive radical pair is produced after photoexcitation of an FAD cofactor inside cryptochrome, and as such the absorption properties of FAD are of crucial importance for cryptochrome activation. However, we reveal that absorption spectra of FAD show very little variation between six different cryptochromes, suggesting that the electronic transitions are barely affected by the chemical differences in the proteins. This conclusion hints on the presence of a secondary photoreceptor or cofactor that could be necessary to explain green-light-activated magnetoreception in birds.

Photoreceptors Take Charge: Emerging Principles for Light Sensing

The first stage in biological signaling is based on changes in the functional state of a receptor protein triggered by interaction of the receptor with its ligand(s). The light-triggered nature of photoreceptors allows studies on the mechanism of such changes in receptor proteins using a wide range of biophysical methods and with superb time resolution. Here, we critically evaluate current understanding of proton and electron transfer in photosensory proteins and their involvement both in primary photochemistry and subsequent processes that lead to the formation of the signaling state. An insight emerging from multiple families of photoreceptors is that ultrafast primary photochemistry is followed by slower proton transfer steps that contribute to triggering large protein conformational changes during signaling state formation. We discuss themes and principles for light sensing shared by the six photoreceptor families: rhodopsins, phytochromes, photoactive yellow proteins, light-oxygen-voltage proteins, blue-light sensors using flavin, and cryptochromes.

Autoantibody Profiling in Lupus Patients using Synthetic Nucleic Acids

Autoantibodies to nuclear components of cells (antinuclear antibodies, ANA), including DNA (a-DNA), are widely used in the diagnosis and subtyping of certain autoimmune diseases, including systemic lupus erythematosus (SLE). Despite clinical use over decades, precise, reproducible measurement of a-DNA titers remains difficult, likely due to the substantial sequence and length heterogeneity of DNA purified from natural sources. We designed and tested a panel of synthetic nucleic acid molecules composed of native deoxyribonucleotide units to measure a-DNA. ELISA assays using these antigens show specificity and reproducibility. Applying the ELISA tests to serological studies of pediatric and adult SLE, we identified novel clinical correlations. We also observed preferential recognition of a specific synthetic antigen by antibodies in SLE sera. We determined the probable basis for this finding using computational analyses, providing valuable structural information for future development of DNA antigens. Synthetic nucleic acid molecules offer the opportunity to standardize assays and to dissect antibody-antigen interactions.

Switching from adduct formation to electron transfer in a light-oxygen-voltage domain containing the reactive cysteine

LOV (light-, oxygen- or voltage-sensitive) domains act as photosensory units of many prokaryotic and eukaryotic proteins. Upon blue light excitation they undergo a photocycle via the excited triplet state of their flavin chromophore yielding the flavin-cysteinyl adduct. Adduct formation is highly conserved among all LOV domains and constitutes the primary step of LOV domain signaling. But recently, it has been shown that signal propagation can also be triggered by flavin photoreduction to the neutral semiquinone offering new prospects for protein engineering. This, however, requires mutation of the photo-active Cys. Here, we report on LOV1 mutants of C. reinhardtii phototropin in which adduct formation is suppressed although the photo-active Cys is present. Introduction of a Tyr into the LOV core induces a proton coupled electron transfer towards the flavin chromophore. Flavin radical species are formed via either the excited flavin singlet or triplet state depending on the geometry of donor and acceptor. This photoreductive pathway resembles the photoreaction observed in other blue light photoreceptors, e.g. blue-light sensors using flavin adenine dinucleotide (BLUF) domains or cryptochromes. The ability to tune the photoreactivity of the flavin chromophore inside the LOV core has implications for the mechanism of adduct formation in the wild type and may be of use for protein engineering.

Functional role of an unusual tyrosine residue in the electron transfer chain of a prokaryotic (6-4) photolyase

Cryptochromes and photolyases form a flavoprotein family in which the FAD chromophore undergoes light induced changes of its redox state. During this process, termed photoreduction, electrons flow from the surface via conserved amino acid residues to FAD. The bacterial (6-4) photolyase PhrB belongs to a phylogenetically ancient group. Photoreduction of PhrB differs from the typical pattern because the amino acid of the electron cascade next to FAD is a tyrosine (Tyr391), whereas photolyases and cryptochromes of other groups have a tryptophan as direct electron donor of FAD. Mutagenesis studies have identified Trp342 and Trp390 as essential for charge transfer. Trp342 is located at the periphery of PhrB while Trp390 connects Trp342 and Tyr391. The role of Tyr391, which lies between Trp390 and FAD, is however unclear as its replacement by phenylalanine did not block photoreduction. Experiments reported here, which replace Tyr391 by Ala, show that photoreduction is blocked, underlining the relevance of Tyr/Phe at position 391 and indicating that charge transfer occurs via the triad 391-390-342. This raises the question, why PhrB positions a tyrosine at this location, having a less favourable ionisation potential than tryptophan, which occurs at this position in many proteins of the photolyase/cryptochrome family. Tunnelling matrix calculations show that tyrosine or phenylalanine can be involved in a productive bridged electron transfer between FAD and Trp390, in line with experimental findings. Since replacement of Tyr391 by Trp resulted in loss of FAD and DMRL chromophores, electron transfer cannot be studied experimentally in this mutant, but calculations on a mutant model suggest that Trp might participate in the electron transfer cascade. Charge transfer simulations reveal an unusual stabilization of the positive charge on site 391 compared to other photolyases or cryptochromes. Water molecules near Tyr391 offer a polar environment which stabilizes the positive charge on this site, thereby lowering the energetic barrier intrinsic to tyrosine. This opens a second charge transfer channel in addition to tunnelling through the tyrosine barrier, based on hopping and therefore transient oxidation of Tyr391, which enables a fast charge transfer similar to proteins utilizing a tryptophan-triad. Our results suggest that evolution of the first site of the redox chain has just been possible by tuning the protein structure and environment to manage a downhill hole transfer process from FAD to solvent.

Computational reconstruction reveals a candidate magnetic biocompass to be likely irrelevant for magnetoreception

Birds use the magnetic field of the Earth to navigate during their annual migratory travel. The possible mechanism to explain the biophysics of this compass sense involves electron transfers within the photoreceptive protein cryptochrome. The magnetoreceptive functioning of cryptochromes is supposedly facilitated through an iron rich polymer complex which couples to multiple cryptochromes. The present investigation aims to independently reconstruct this complex and describe its interaction with Drosophila melanogaster cryptochromes. The polymer complex consists of ISCA1 protein monomers with internally bound iron sulphur clusters and simultaneously binds ten cryptochromes. Through molecular dynamics we have analysed the stability of the ISCA1-cryptochrome complex and characterized the interaction at the binding sites between individual cryptochrome and ISCA1. It is found that the cryptochrome binding to the ISCA1 polymer is not uniform and that the binding affinity depends on its placement along the ISCA1 polymer. This finding supports the claim that the individual ISCA1 monomer acts as possible intracellular interaction partner of cryptochrome, but the proposed existence of an elongated ISCA1 polymer with multiple attached cryptochromes appears to be questionable.

Biological cell as a soft magnetoelectric material: Elucidating the physical mechanisms underpinning the detection of magnetic fields by animals

Sharks, birds, bats, turtles, and many other animals can detect magnetic fields. Aside from using this remarkable ability to exploit the terrestrial magnetic field map to sense direction, a subset is also able to implement a version of the so-called geophysical positioning system. How do these animals detect magnetic fields? The answer to this rather deceptively simple question has proven to be quite elusive. The currently prevalent theories, while providing interesting insights, fall short of explaining several aspects of magnetoreception. For example, minute magnetic particles have been detected in magnetically sensitive animals. However, how is the detected magnetic field converted into electrical signals given any lack of experimental evidence for relevant electroreceptors? In principle, a magnetoelectric material is capable of converting magnetic signals into electricity (and vice versa). This property, however, is rare and restricted to a rather small set of exotic hard crystalline materials. Indeed, such elements have never been detected in the animals studied so far. In this work we quantitatively outline the conditions under which a biological cell may detect a magnetic field and convert it into electrical signals detectable by biological cells. Specifically, we prove the existence of an overlooked strain-mediated mechanism and show that most biological cells can act as nontrivial magnetoelectric materials provided that the magnetic permeability constant is only slightly more than that of a vacuum. The enhanced magnetic permeability is easily achieved by small amounts of magnetic particles that have been experimentally detected in magnetosensitive animals. Our proposed mechanism appears to explain most of the experimental observations related to the physical basis of magnetoreception.

Magnetic field effect in natural cryptochrome explored with model compound

Many animals sense the Earth's magnetic-field and use it for navigation. It is proposed that a light-dependent quantum effect in cryptochrome proteins, residing in the retina, allows for such an iron-free spin-chemical compass. The photochemical processes, spin-dynamics and its magnetic field dependence in natural cryptochrome are not fully understood by the in vivo and in vitro studies. For a deeper insight into these biophysical mechanisms in cryptochrome, we had introduced a flavin-tryptophan dyad (F10T). Here we present the magnetic field dependence of 1H photo-CIDNP NMR on F10T and a theoretical model for low-field photo-CIDNP of F10T. This model provides mixing mechanism of energy-levels and spin-dynamics at low magnetic fields. Photo-CIDNP has been observed even at Earth's magnetic field (~0.05 mT). These experiments prove F10T to be an excellent model compound establishing the key mechanism of avian-magnetoreception and provide insight into the optimal behaviour of cryptochrome at Earth's magnetic field.

The Grateful Infrared: Sequential Protein Structural Changes Resolved by Infrared Difference Spectroscopy

The catalytic activity of proteins is a function of structural changes. Very often these are as minute as protonation changes, hydrogen bonding changes, and amino acid side chain reorientations. To resolve these, a methodology is afforded that not only provides the molecular sensitivity but allows for tracing the sequence of these hierarchical reactions at the same time. This feature article showcases results from time-resolved IR spectroscopy on channelrhodopsin (ChR), light-oxygen-voltage (LOV) domain protein, and cryptochrome (CRY). All three proteins are activated by blue light, but their biological role is drastically different. Channelrhodopsin is a transmembrane retinylidene protein which represents the first light-activated ion channel of its kind and which is involved in primitive vision (phototaxis) of algae. LOV and CRY are flavin-binding proteins acting as photoreceptors in a variety of signal transduction mechanisms in all kingdoms of life. Beyond their biological relevance, these proteins are employed in exciting optogenetic applications. We show here how IR difference absorption resolves crucial structural changes of the protein after photonic activation of the chromophore. Time-resolved techniques are introduced that cover the time range from nanoseconds to minutes along with some technical considerations. Finally, we provide an outlook toward novel experimental approaches that are currently developed in our laboratories or are just in our minds ("Gedankenexperimente"). We believe that some of them have the potential to provide new science.

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

Despite decades of research the puzzle of the magnetic sense of migratory songbirds has still not been unveiled. Although the problem really needs a multiscale description, most of the individual research efforts were focused on single scale investigations. Here we seek to establish a multiscale link between some of the scales involved, and in particular construct a bridge between electron spin dynamics and migratory bird behaviour. In order to do that, we first consider a model cyclic reaction scheme that could form the basis of the avian magnetic compass. This reaction features a fast spin-dependent process which leads to an unusually precise compass. We then propose how the reaction could be realized in a realistic molecular environment, and argue that it is consistent with the known facts about avian magnetoreception. Finally we show how the microscopic dynamics of spins could possibly be interpreted by a migrating bird and used for the navigational purpose.

Role of the Molecular Environment in Flavoprotein Color and Redox Tuning: QM Cluster versus QM/MM Modeling

We investigate the origin of the excitation energy shifts induced by the apoprotein in the active site of the bacterial photoreceptor BLUF (Blue Light sensor Using Flavin adenine dinucleotide). In order to compute the vertical excitation energies of three low-lying electronic states, including two π-π* states of flavin (S1 and S2) and a π-π* tyrosine-flavin electron-transfer state (ET), with respect to the energy of the closed-shell ground state (S0), we prepared alternative quantum mechanical (QM) cluster and quantum mechanics/molecular mechanics (QM/MM) models. We found that the excitation energies computed with both types of models correlate with the magnitude of the charge transfer character of the excitation. Accordingly, we conclude that the small charge transfer character of the light absorbing S0-S1 transition and the substantial charge transfer character of the nonabsorbing but redox active S0-ET transition explain the small color changes but substantial redox tuning in BLUF and also in other flavoproteins. Further analysis showed that redox tuning is governed by the electrostatic interaction in the QM/MM model and transfer of charge between the active site and its environment in the QM cluster. Moreover, the wave function polarization of the QM subsystem by the MM subsystem influences the magnitude of the charge transfer, resulting in the QM/MM and QM excitation energies that are not entirely consistent.

Electron spin relaxation in cryptochrome-based magnetoreception

The magnetic compass sense of migratory birds is thought to rely on magnetically sensitive radical pairs formed photochemically in cryptochrome proteins in the retina. An important requirement of this hypothesis is that electron spin relaxation is slow enough for the Earth's magnetic field to have a significant effect on the coherent spin dynamics of the radicals. It is generally assumed that evolutionary pressure has led to protection of the electron spins from irreversible loss of coherence in order that the underlying quantum dynamics can survive in a noisy biological environment. Here, we address this question for a structurally characterized model cryptochrome expected to share many properties with the putative avian receptor protein. To this end we combine all-atom molecular dynamics simulations, Bloch-Redfield relaxation theory and spin dynamics calculations to assess the effects of spin relaxation on the performance of the protein as a compass sensor. Both flavin-tryptophan and flavin-Z˙ radical pairs are studied (Z˙ is a radical with no hyperfine interactions). Relaxation is considered to arise from modulation of hyperfine interactions by librational motions of the radicals and fluctuations in certain dihedral angles. For Arabidopsis thaliana cryptochrome 1 (AtCry1) we find that spin relaxation implies optimal radical pair lifetimes of the order of microseconds, and that flavin-Z˙ pairs are less affected by relaxation than flavin-tryptophan pairs. Our results also demonstrate that spin relaxation in isolated AtCry1 is incompatible with the long coherence times that have been postulated to explain the disruption of the avian magnetic compass sense by weak radiofrequency magnetic fields. We conclude that a cryptochrome sensor in vivo would have to differ dynamically, if not structurally, from isolated AtCry1. Our results clearly mark the limits of the current hypothesis and lead to a better understanding of the operation of radical pair magnetic sensors in noisy biological environments.

How Far Does a Receptor Influence Vibrational Properties of an Odorant?

The biophysical mechanism of the sense of smell, or olfaction, is still highly debated. The mainstream explanation argues for a shape-based recognition of odorant molecules by olfactory receptors, while recent investigations suggest the primary olfactory event to be triggered by a vibrationally-assisted electron transfer reaction. We consider this controversy by studying the influence of a receptor on the vibrational properties of an odorant in atomistic details as the coupling between electronic degrees of freedom of the receptor and the vibrations of the odorant is the key parameter of the vibrationally-assisted electron transfer. Through molecular dynamics simulations we elucidate the binding specificity of a receptor towards acetophenone odorant. The vibrational properties of acetophenone inside the receptor are then studied by the polarizable embedding density functional theory approach, allowing to quantify protein-odorant interactions. Finally, we judge whether the effects of the protein provide any indications towards the existing theories of olfaction.

Weak Broadband Electromagnetic Fields are More Disruptive to Magnetic Compass Orientation in a Night-Migratory Songbird (Erithacus rubecula) than Strong Narrow-Band Fields

Magnetic compass orientation in night-migratory songbirds is embedded in the visual system and seems to be based on a light-dependent radical pair mechanism. Recent findings suggest that both broadband electromagnetic fields ranging from ~2 kHz to ~9 MHz and narrow-band fields at the so-called Larmor frequency for a free electron in the Earth's magnetic field can disrupt this mechanism. However, due to local magnetic fields generated by nuclear spins, effects specific to the Larmor frequency are difficult to understand considering that the primary sensory molecule should be organic and probably a protein. We therefore constructed a purpose-built laboratory and tested the orientation capabilities of European robins in an electromagnetically silent environment, under the specific influence of four different oscillating narrow-band electromagnetic fields, at the Larmor frequency, double the Larmor frequency, 1.315 MHz or 50 Hz, and in the presence of broadband electromagnetic noise covering the range from ~2 kHz to ~9 MHz. Our results indicated that the magnetic compass orientation of European robins could not be disrupted by any of the relatively strong narrow-band electromagnetic fields employed here, but that the weak broadband field very efficiently disrupted their orientation.

Coherent chemical kinetics as quantum walks. II. Radical-pair reactions in Arabidopsis thaliana

We apply the quantum-walk approach proposed in the preceding paper [A. Chia et al., preceding paper, Phys. Rev. E 93, 032407 (2016)] to a radical-pair reaction where realistic estimates for the intermediate transition rates are available. The well-known average hitting time from quantum walks can be adopted as a measure of how quickly the reaction occurs and we calculate this for varying degrees of dephasing in the radical pair. The time for the radical pair to react to a product is found to be independent of the amount of dephasing introduced, even in the limit of no dephasing where the transient population dynamics exhibits strong coherent oscillations. This can be seen to arise from the existence of a rate-limiting step in the reaction and we argue that in such examples, a purely classical model based on rate equations can be used for estimating the time scale of the reaction but not necessarily its population dynamics.

Localisation of the Putative Magnetoreceptive Protein Cryptochrome 1b in the Retinae of Migratory Birds and Homing Pigeons

Cryptochromes are ubiquitously expressed in various animal tissues including the retina. Some cryptochromes are involved in regulating circadian activity. Cryptochrome proteins have also been suggested to mediate the primary mechanism in light-dependent magnetic compass orientation in birds. Cryptochrome 1b (Cry1b) exhibits a unique carboxy terminus exclusively found in birds so far, which might be indicative for a specialised function. Cryptochrome 1a (Cry1a) is so far the only cryptochrome protein that has been localised to specific cell types within the retina of migratory birds. Here we show that Cry1b, an alternative splice variant of Cry1a, is also expressed in the retina of migratory birds, but it is primarily located in other cell types than Cry1a. This could suggest different functions for the two splice products. Using diagnostic bird-specific antibodies (that allow for a precise discrimination between both proteins), we show that Cry1b protein is found in the retinae of migratory European robins (Erithacus rubecula), migratory Northern Wheatears (Oenanthe oenanthe) and pigeons (Columba livia). In all three species, retinal Cry1b is localised in cell types which have been discussed as potentially well suited locations for magnetoreception: Cry1b is observed in the cytosol of ganglion cells, displaced ganglion cells, and in photoreceptor inner segments. The cytosolic rather than nucleic location of Cry1b in the retina reported here speaks against a circadian clock regulatory function of Cry1b and it allows for the possible involvement of Cry1b in a radical-pair-based magnetoreception mechanism.

Quantifying electron transfer reactions in biological systems: what interactions play the major role?

Various biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve light absorption, excited electronic states formation, excitation energy transfer, electrons and protons tunnelling which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between quantum physics and biology. In this paper we consider electron transfer in biological processes, from a theoretical view-point; namely in terms of quantum mechanical and semi-classical models. We systematically characterize the interactions between the moving electron and its biological environment to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe specifically the electron transfer reactions in Arabidopsis thaliana cryptochrome-a signaling photoreceptor protein that became attractive recently due to its possible function as a biological magnetoreceptor.