Influence of Protein Environment on the Electron Paramagnetic Resonance Properties of Flavoprotein Radicals: A QM/MM Study

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

The radicals derived from flavin adenine dinucleotide (FAD) are a corner stone of recent hypotheses about magnetoreception, including the compass of migratory songbirds. These models attribute a magnetic sense to coherent spin dynamics in radical pairs within the flavo-protein cryptochrome. The primary determinant of sensitivity and directionality of this process are the hyperfine interactions of the involved radicals. Here, we present a comprehensive computational study of the hyperfine couplings in the protonated and unprotonated FAD radicals in cryptochrome 4 from C. livia. We combine long (800 ns) molecular dynamics trajectories to accurate quantum chemistry calculations. Hyperfine parameters are derived using auxiliary density functional theory applied to cluster and hybrid QM/MM (Quantum Mechanics/Molecular Mechanics) models comprising the FAD and its significant surrounding environment, as determined by a detailed sensitivity analysis. Thanks to this protocol we elucidate the sensitivity of the hyperfine interaction parameters to structural fluctuations and the polarisation effect of the protein environment. We find that the ensemble-averaged hyperfine interactions are predominantly governed by thermally induced geometric distortions of the flavin. We discuss our results in view of the expected performance of these radicals as part of a magnetoreceptor. Our data could be used to parametrize spin Hamiltonians including not only average values but also standard deviations.

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.

Coupled Methyl Group Rotation in FMN Radicals Revealed by Selective Deuterium Labeling

Flavin semiquinones are common intermediate redox states in flavoproteins, and thus, knowledge of their electronic structure is essential for fully understanding their chemistry and chemical versatility. In this contribution, we use a combination of high-field electron nuclear double resonance spectroscopy and selective deuterium labeling of flavin mononucleotide (FMN) with subsequent incorporation as cofactor into a variant Avena sativa LOV domain to extract missing traits of the electronic structure of a protein-bound FMN radical. From these experiments, precise values of small proton hyperfine and deuterium nuclear quadrupole couplings could be extracted. Specifically, isotropic hyperfine couplings of -3.34, -0.11, and +0.91 MHz were obtained for the protons H(6), H(9), and H(7α), respectively. These values are discussed in the light of specific protein-cofactor interactions. Furthermore, the temperature behavior of the H(7α) methyl-group rotation elicited by its energy landscape was analyzed in greater detail. Pronounced interplay between the two methyl groups at C(7) and C(8) of FMN could be revealed. Most strikingly, this rotational behavior could be modulated by selective deuterium editing.

Selected-Nuclei Method for the Computation of Hyperfine Coupling Constants within Second-Order Møller-Plesset Perturbation Theory

We introduce a new ansatz to compute hyperfine coupling constants of selected nuclei at the level of second-order Møller-Plesset perturbation (MP2) and double-hybrid density functional theory with reduced computational effort, opening the route to the analyis of hyperfine coupling constants of large molecular structures. Our approach is based on a reformulation of the canonical MP2 term in atomic orbitals, thus exploiting the locality of electron correlation. We show that a perturbation-including integral screening reduces the scaling behavior of the number of significant two-electron integrals to sublinear. This selected-nuclei approach allows for an efficient computation within scaled-opposite spin (SOS) RI-MP2 on massively parallelized architectures such as graphical processor units (GPUs), thus enabling studies on the influence of the environment on hyperfine coupling constants.

Inhomogeneous ensembles of radical pairs in chemical compasses

The biophysical basis for the ability of animals to detect the geomagnetic field and to use it for finding directions remains a mystery of sensory biology. One much debated hypothesis suggests that an ensemble of specialized light-induced radical pair reactions can provide the primary signal for a magnetic compass sensor. The question arises what features of such a radical pair ensemble could be optimized by evolution so as to improve the detection of the direction of weak magnetic fields. Here, we focus on the overlooked aspect of the noise arising from inhomogeneity of copies of biomolecules in a realistic biological environment. Such inhomogeneity leads to variations of the radical pair parameters, thereby deteriorating the signal arising from an ensemble and providing a source of noise. We investigate the effect of variations in hyperfine interactions between different copies of simple radical pairs on the directional response of a compass system. We find that the choice of radical pair parameters greatly influences how strongly the directional response of an ensemble is affected by inhomogeneity.

The electronic structure of the neutral isoalloxazine semiquinone within Anabaena flavodoxin: new insights from HYSCORE experiments

A complete study of Anabaena flavodoxin in the neutral semiquinone state by means of the EPR pulse technique HYSCORE is here presented. The results provide new information about the hyperfine interactions of the unpaired electronic spin and the nuclei in the isoalloxazine ring. This allows a better knowledge of the electronic structure of the neutral flavin radical within the protein. Combination of these results with other previously obtained by using other EPR related techniques allowed producing a very precise mapping of the flavin spin distribution in the neutral semiquinone state. This information can be very useful for determining the relationship between the electronic structure and mechanisms in flavoproteins. An experimental protocol for measuring the electronic structure details available to date is suggested.

The Protonation States of the Active-Site Histidines in (6-4) Photolyase

The active sites of the (6-4) photolyases contain two conserved histidine residues, which, in the Drosophila melanogaster enzyme, correspond to His365 and His369. While there are nine combinations in which the three possible protonation states of the two histidines (with protons on Nδ (HID), Nε (HIE), or both Nδ and Nε (HIP)) can be paired, there is presently no consensus as to which of these states is present, let alone mechanistically relevant. EPR hyperfine couplings for selected protons of the FADH(•) radical have previously been used to address this issue. Our QM/MM calculations show, however, that the experimental couplings are equally well reproduced by each of the nine combinations. Since the EPR results seemingly cannot be used to unequivocally assign the protonation states, the pKa values of the two histidines were calculated using the popular PROPKA, H++, and APBS approaches, in various environments and for several lesions. These techniques consistently indicate that, at pH = 7, both His365 and His369 should be neutral, although His369 is found to be more prone to becoming protonated. In a comparative approach, a series of molecular dynamics simulations was performed with all nine combinations, employing various reference crystal structures and different oxidation states of the FAD cofactor. The overall result of this approach is in agreement with our pKa results. Consequently, although the introduction of the reduced cofactor results in an increased stability for selected protonated states, particularly the His365═HID and His369═HIP combination, the neutral combination His365═HID and His365═HIE stands out as the most relevant state for the activity of the enzyme.