Protein-cofactor interactions and EPR parameters for the Q(H) quinone binding site of quinol oxidase. A density functional study

Searching for the low affinity ubiquinone binding site in cytochrome bo3 from Escherichia coli

The cytochrome bo₃ ubiquinol oxidase is one of three respiratory oxygen reductases in the aerobic respiratory chain of Escherichia coli. The generally accepted model of catalysis assumes that cyt bo₃ contains two distinct ubiquinol binding sites: (i) a low affinity (Q_L) site which is the traditional substrate binding site; and (ii) a high affinity (Q_H) site where a "permanently" bound quinone acts as a cofactor, taking two electrons from the substrate quinol and passing them one-by-one to the heme b component of the enzyme which, in turn, transfers them to the heme o₃/Cu_B active site. Whereas the residues at the Q_H site are well defined, the location of the Q_L site remains unknown. The published X-ray structure does not contain quinone, and substantial amounts of the protein are missing as well. A recent bioinformatics study by Bossis et al. [Biochem J. (2014) 461, 305-314] identified a sequence motif G¹⁶³EFX₃GWX₂Y¹⁷³ as the likely Q_L site in the family of related quinol oxidases. In the current work, this was tested by site-directed mutagenesis. The results show that these residues are not important for catalytic function and do not define the Q_L substrate binding site.

Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli

The respiratory cytochrome bo₃ ubiquinol oxidase from Escherichia coli has a high-affinity ubiquinone binding site that stabilizes the one-electron reduced ubisemiquinone (SQ_H), which is a transient intermediate during the electron-mediated reduction of O₂ to water. It is known that SQ_H is stabilized by two strong hydrogen bonds from R71 and D75 to ubiquinone carbonyl oxygen O1 and weak hydrogen bonds from H98 and Q101 to O4. In this work, SQ_H was investigated with orientation-selective Q-band (∼34 GHz) pulsed ¹H electron-nuclear double resonance (ENDOR) spectroscopy on fully deuterated cytochrome (cyt) bo₃ in a H₂O solvent so that only exchangeable protons contribute to the observed ENDOR spectra. Simulations of the experimental ENDOR spectra provided the principal values and directions of the hyperfine (hfi) tensors for the two strongly coupled H-bond protons (H1 and H2). For H1, the largest principal component of the proton anisotropic hfi tensor T_z' = 11.8 MHz, whereas for H2, T_z' = 8.6 MHz. Remarkably, the data show that the direction of the H1 H-bond is nearly perpendicular to the quinone plane (∼70° out of plane). The orientation of the second strong hydrogen bond, H2, is out of plane by ∼25°. Equilibrium molecular dynamics simulations on a membrane-embedded model of the cyt bo₃ Q_H site show that these H-bond orientations are plausible but do not distinguish which H-bond, from R71 or D75, is nearly perpendicular to the quinone ring. Density functional theory calculations support the idea that the distances and geometries of the H-bonds to the ubiquinone carbonyl oxygens, along with the measured proton anisotropic hfi couplings, are most compatible with an anionic (deprotonated) ubisemiquinone.

Interactions of intermediate semiquinone with surrounding protein residues at the Q(H) site of wild-type and D75H mutant cytochrome bo3 from Escherichia coli

Selective (15)N isotope labeling of the cytochrome bo(3) ubiquinol oxidase from Escherichia coli with auxotrophs was used to characterize the hyperfine couplings with the side-chain nitrogens from residues R71, H98, and Q101 and peptide nitrogens from residues R71 and H98 around the semiquinone (SQ) at the high-affinity Q(H) site. The two-dimensional ESEEM (HYSCORE) data have directly identified N(ε) of R71 as an H-bond donor carrying the largest amount of unpaired spin density. In addition, weaker hyperfine couplings with the side-chain nitrogens from all residues around the SQ were determined. These hyperfine couplings reflect a distribution of the unpaired spin density over the protein in the SQ state of the Q(H) site and the strength of interaction with different residues. The approach was extended to the virtually inactive D75H mutant, where the intermediate SQ is also stabilized. We found that N(ε) of a histidine residue, presumably H75, carries most of the unpaired spin density instead of N(ε) of R71, as in wild-type bo(3). However, the detailed characterization of the weakly coupled (15)N atoms from selective labeling of R71 and Q101 in D75H was precluded by overlap of the (15)N lines with the much stronger ~1.6 MHz line from the quadrupole triplet of the strongly coupled (14)N(ε) atom of H75. Therefore, a reverse labeling approach, in which the enzyme was uniformly labeled except for selected amino acid types, was applied to probe the contribution of R71 and Q101 to the (15)N signals. Such labeling has shown only weak coupling with all nitrogens of R71 and Q101. We utilize density functional theory-based calculations to model the available information about (1)H, (15)N, and (13)C hyperfine couplings for the Q(H) site and to describe the protein-substrate interactions in both enzymes. In particular, we identify the factors responsible for the asymmetric distribution of the unpaired spin density and ponder the significance of this asymmetry to the quinone's electron transfer function.

Determination of the proton environment of high stability Menasemiquinone intermediate in Escherichia coli nitrate reductase A by pulsed EPR

Escherichia coli nitrate reductase A (NarGHI) is a membrane-bound enzyme that couples quinol oxidation at a periplasmically oriented Q-site (Q(D)) to proton release into the periplasm during anaerobic respiration. To elucidate the molecular mechanism underlying such a coupling, endogenous menasemiquinone-8 intermediates stabilized at the Q(D) site (MSQ(D)) of NarGHI have been studied by high-resolution pulsed EPR methods in combination with (1)H2O/2H2O exchange experiments. One of the two non-exchangeable proton hyperfine couplings resolved in hyperfine sublevel correlation (HYSCORE) spectra of the radical displays characteristics typical from quinone methyl protons. However, its unusually small isotropic value reflects a singularly low spin density on the quinone carbon α carrying the methyl group, which is ascribed to a strong asymmetry of the MSQ(D) binding mode and consistent with single-sided hydrogen bonding to the quinone oxygen O1. Furthermore, a single exchangeable proton hyperfine coupling is resolved, both by comparing the HYSCORE spectra of the radical in 1H2O and 2H2O samples and by selective detection of the exchanged deuterons using Q-band 2H Mims electron nuclear double resonance (ENDOR) spectroscopy. Spectral analysis reveals its peculiar characteristics, i.e. a large anisotropic hyperfine coupling together with an almost zero isotropic contribution. It is assigned to a proton involved in a short ∼1.6 Å in-plane hydrogen bond between the quinone O1 oxygen and the Nδ of the His-66 residue, an axial ligand of the distal heme b(D). Structural and mechanistic implications of these results for the electron-coupled proton translocation mechanism at the Q(D) site are discussed, in light of the unusually high thermodynamic stability of MSQ(D).

Structure of the biliverdin radical intermediate in phycocyanobilin:ferredoxin oxidoreductase identified by high-field EPR and DFT

The cyanobacterial enzyme phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the two-step four-electron reduction of biliverdin IXalpha to phycocyanobilin, the precursor of biliprotein chromophores found in phycobilisomes. It is known that catalysis proceeds via paramagnetic radical intermediates, but the structure of these intermediates and the transfer pathways for the four protons involved are not known. In this study, high-field electron paramagnetic resonance (EPR) spectroscopy of frozen solutions and single crystals of the one-electron reduced protein-substrate complex of two PcyA mutants D105N from the cyanobacteria Synechocystis sp. PCC6803 and Nostoc sp. PCC7120 are examined. Detailed analysis of Synechocystis D105N mutant spectra at 130 and 406 GHz reveals a biliverdin radical with a very narrow g tensor with principal values 2.00359(5), 2.00341(5), and 2.00218(5). Using density-functional theory (DFT) computations to explore the possible protonation states of the biliverdin radical, it is shown that this g tensor is consistent with a biliverdin radical where the carbonyl oxygen atoms on both the A and the D pyrrole rings are protonated. This experimentally confirms the reaction mechanism recently proposed (Tu, et al. Biochemistry 2007, 46, 1484).

The correlation of cathodic peak potentials of vitamin K(3) derivatives and their calculated electron affinities. The role of hydrogen bonding and conformational changes

2-methyl-1,4-naphtoquinone 1 (vitamin K(3), menadione) derivatives with different substituents at the 3-position were synthesized to tune their electrochemical properties. The thermodynamic midpoint potential (E(1/2)) of the naphthoquinone derivatives yielding a semi radical naphthoquinone anion were measured by cyclic voltammetry in the aprotic solvent dimethoxyethane (DME). Using quantum chemical methods, a clear correlation was found between the thermodynamic midpoint potentials and the calculated electron affinities (E(A)). Comparison of calculated and experimental values allowed delineation of additional factors such as the conformational dependence of quinone substituents and hydrogen bonding which can influence the electron affinities (E(A)) of the quinone. This information can be used as a model to gain insight into enzyme-cofactor interactions, particularly for enzyme quinone binding modes and the electrochemical adjustment of the quinone motif.

Structure of the nucleotide radical formed during reaction of CDP/TTP with the E441Q-alpha2beta2 of E. coli ribonucleotide reductase

The Escherichia coli ribonucleotide reductase (RNR) catalyzes the conversion of nucleoside diphosphates to deoxynucleotides and requires a diferric-tyrosyl radical cofactor for catalysis. RNR is composed of a 1:1 complex of two homodimeric subunits: alpha and beta. Incubation of the E441Q-alpha mutant RNR with substrate CDP and allosteric effector TTP results in loss of the tyrosyl radical and formation of two new radicals on the 200 ms to min time scale. The first radical was previously established by stopped flow UV/vis spectroscopy and pulsed high field EPR spectroscopy to be a disulfide radical anion. The second radical was proposed to be a 4'-radical of a 3'-keto-2'-deoxycytidine 5'-diphosphate. To identify the structure of the nucleotide radical [1'-(2)H], [2'-(2)H], [4'-(2)H], [5'-(2)H], [U-(13)C, (15)N], [U-(15)N], and [5,6 -(2)H] CDP and [beta-(2)H] cysteine-alpha were synthesized and incubated with E441Q-alpha2beta2 and TTP. The nucleotide radical was examined by 9 GHz and 140 GHz pulsed EPR spectroscopy and 35 GHz ENDOR spectroscopy. Substitution of (2)H at C4' and C1' altered the observed hyperfine interactions of the nucleotide radical and established that the observed structure was not that predicted. DFT calculations (B3LYP/IGLO-III/B3LYP/TZVP) were carried out in an effort to recapitulate the spectroscopic observations and lead to a new structure consistent with all of the experimental data. The results indicate, unexpectedly, that the radical is a semidione nucleotide radical of cytidine 5'-diphosphate. The relationship of this radical to the disulfide radical anion is discussed.

Understanding the electon paramagnetic resonance parameters of protein-bound glycyl radicals

The number of enzymes that require a glycyl-based radical for their function is growing. Here, we provide systematic quantum-chemical studies of spin-density distributions, electronic g-tensors, and hyperfine couplings of various models of protein-bound glycyl radicals. Similarly to what is found in a companion paper on N-acetylglycyl, the small g-anisotropy for this delocalized, unsymmetrical system presents appreciable challenges to state-of-the-art computational methodology. This pertains to the quality of structure optimization, as well as to the choice of the spin-orbit Hamiltonian and the gauge origin of the magnetic vector potential. Environmental effects due to hydrogen bonding are complicated and depend in a subtle fashion on the different intramolecular hydrogen bonding for different conformations of the radical. Indeed, the conformation has the largest overall effect on the computed g-tensors (less so on the hyperfine tensors). This is discussed in the context of different g-tensors obtained by recent high-field electron paramagnetic resonance (EPR) measurements for three different enzymes. On the basis of results of a parallel calibration study for N-acetylglycyl, it is suggested that the glycyl radical observed for E. coli anaerobic RNR may have a fully extended conformation, which differs from those of the corresponding radicals in pyruvate formate-lyase or benzylsuccinate synthase.

Remote Position Substituents as Modulators of Conformational and Reactive Properties of Quinones. Relevance of the π/π Intramolecular Interaction

Several studies have described that quinoid rings with electron-rich olefins at remote position experience changes in their redox potential. Since the original description of these changes, different approaches have been developed to describe the properties of the binding sites of ubiquinones. The origin of this phenomenon has been attributed to lateral chain flexibility and its effect on the recognition between proteins and substrates associated with their important biological activity. The use of electrochemical-electron spin resonance (EC-ESR) assays and theoretical calculations at MP2/6-31G(d,p) and MP2/6-31++G(d,p)//MP2/6-31G(d,p) levels of several conformers of perezone [(2-(1,5-dimethyl-4-hexenyl)-3-hydroxy-5-methyl-1,4-benzoquinone] established that a weak pi-pi interaction controls not only the molecular conformation but also its diffusion coefficient and electrochemical properties. An analogous interaction can be suggested as the origin of similar properties of ubiquinone Q10. The use of nuclear magnetic resonance rendered, for the first time, direct evidence of the participation of different perezone conformers in solution and explained the cycloaddition process observed when the aforementioned quinone is heated to form pipitzols, sesquiterpenes with a cedrene skeleton. The fact that biological systems can modulate the redox potential of this type of quinones depending on the conformer recognized by an enzyme during a biological transformation is of great relevance.

Hyperfine Coupling Tensors of the Benzosemiquinone Radical Anion from Car–Parrinello Molecular Dynamics

Based on Car-Parrinello ab initio molecular dynamics simulations of the benzosemiquinone radical anion in both aqueous solution and the gas phase, density functional calculations provide the currently most refined EPR hyperfine coupling (HFC) tensors of semiquinone nuclei and solvent protons. For snapshots taken at regular intervals from the molecular dynamics trajectories, cluster models with different criteria for inclusion of water molecules and an additional continuum solvent model are used to analyse the HFCs. These models provide a detailed picture of the effects of dynamics and of different intermolecular interactions on the spin-density distribution and HFC tensors. Comparison with static calculations allows an assessment of the importance of dynamical effects, and of error compensation in static DFT calculations. Solvent proton HFCs depend characteristically on the position relative to the semiquinone radical anion. A point-dipolar model works well for in-plane hydrogen-bonded protons but deviates from the quantum chemical values for out-of-plane hydrogen bonding.

Theoretical investigation of the EPR hyperfine coupling constants in amino derivatives

The HFCCs of the radical cations of a series of amines have been determined at different levels of approximation including the CISD, QCISD, and CCSD ab initio correlated methods and density functional theory approaches employing the B3LYP, PBE0, BHandHLYP, TPSS, and BLYP exchange-correlation functionals. Although quantitative differences with respect to experimental data have been noticed, these are mostly systematic within a given class of N and H atoms. As a consequence, these different levels of theory are reliable in most cases to account for the substituent and structure effects on the HFCCs of amines. Linear regression fits have then been performed to reach quantitative agreement between the theoretical and experimental values. This has finally been substantiated by considering the EPR signal of the recently synthesized radical cations of two derivatives of [10-(4-aminophenyl)-9-anthryl]aniline as well as in confirming a recent assignment of the EPR signal of n-propylamine.

Understanding the EPR Parameters of Glycine-Derived Radicals: The Case of N-Acetylglycyl in the N-Acetylglycine Single-Crystal Environment

As a step toward an in-depth understanding of the electron paramagnetic resonance parameters of glycyl radicals in proteins, the hyperfine tensors and, particularly, the g-tensor of N-acetylglcyl in the environment of a single crystal of N-acetylglycine have been studied by systematic state-of-the-art quantum chemical calculations on various suitable model systems. The quantitative computation of the g-tensors for such glycyl-derived radicals is a veritable challenge, mainly because of the very small g-anisotropy combined with a nonsymmetrical, delocalized spin-density distribution and several atoms with comparable spin-orbit contributions to the g-tensors. The choice of gauge origin of the magnetic vector potential, and of approximate spin-orbit operators, both turn out to be more critical than found in previous studies of g-tensors for organic radicals. Environmental effects, included by supermolecular hydrogen-bonded models, were found to be moderate, because of a partial compensation between the influences from intramolecular and intermolecular hydrogen bonds. The largest effects on the g-tensor are caused by the conformation of the radical. The density functional theory methods employed systematically overestimate both the Delta gx and Delta gy components of the g-tensor. This is important for parallel investigations on the protein-glycyl radicals. The 1H alpha and 13C alpha hyperfine couplings depend only slightly on the supermolecular model chosen and appear less sensitive probes of detailed structure and environment.

Protein–cofactor interactions in bacterial reaction centers from Rhodobacter sphaeroides R-26: Effect of hydrogen bonding on the electronic and geometric structure of the primary quinone. A density functional theory study

The effect of hydrogen bonding to the primary quinone (Q(A) and Q(*)(-)(A)) in bacterial reaction centers was studied using density functional theory (DFT) calculations. The charge neutral state Q(A) was investigated by optimizing the hydrogen atom positions of model systems extracted from 15 different X-ray structures. From this analysis, mean values of the H-bond lengths and directions were derived. It was found that the N(delta)-H of His M219 forms a shorter H-bond to Q(A) than the N-H of Ala M260. The H-bond of His M219 is linear and more twisted out of the quinone plane. The radical anion Q(*)(-)(A) in the protein environment was investigated by using a mixed quantum mechanics/molecular mechanics (QM/MM) approach. Two geometry optimizations with a different number of flexible atoms were performed. H-bond lengths were obtained and spectroscopic parameters calculated, i.e. the hyperfine and nuclear quadrupole couplings of magnetic nuclei coupled to the radical. Good agreement was found with the results provided by EPR/ENDOR spectroscopy. This implies that the calculated lengths and directions of the H-bonds to Q(*)(-)(A) are reliable values. From a comparison of the neutral and reduced state of Q(A) it was concluded that the H-bond distances are shortened by approximately 0.17 Angstroms (His M219) and approximately 0.13 Angstroms (Ala M260) upon single reduction of the quinone. It is shown that the point-dipole approximation can not be used for an estimation of H-bond lengths from measured hyperfine couplings in a system with out-of-plane H-bonding. In contrast, the evaluation of the nuclear quadrupole couplings of (2)H nuclei substituted in the hydrogen bonds yields H-bond lengths close to the values that were deduced from DFT geometry optimizations. The significance of hydrogen bonding to the quinone cofactors in biological systems is discussed.