EPR and ENDOR study of radiation-induced radical formation in purines: sodium inosine crystals X-irradiated at 10 K

X-irradiated single crystals of sodium inosine (Na(+)*Inosine(-)*2.5H(2)O), in which the hypoxanthine base is present as the N1-deprotonated anion, were investigated using K-band (24 GHz) electron paramagnetic resonance (EPR), electron-nuclear double resonance (ENDOR), and ENDOR induced EPR (EIE) techniques at 10 K. At least five different radicals were present immediately after irradiation at 10 K. R1, which decayed upon warming the crystals to 50 K, was identified as the electron-loss product of the parent N1-deprotonated hypoxanthine base. Hyperfine couplings to HC8 and HC2 were fully characterized with ENDOR spectroscopy, and the identification was supported by DFT calculations. R2, which also decayed on warming to 50 K, exhibited nearly equal couplings to HC2 and HC8. Taken in combination with an extensive set of DFT calculations, the experimental results indicate that R2 is the (doubly negative) product of electron-gain by the initially anionic N1-deprotonated hypoxanthine parent. R3, which exhibited hyperfine coupling only to HC8 could not be identified. R4, which persisted on annealing to 260 K, exhibited one large alpha-proton hyperfine coupling which was fully characterized by ENDOR. Based on DFT calculations and the experimental data, R4 was identified as the product of net H-abstraction from C5'. The remaining HC5' was the source of the measured alpha-proton coupling. R5, present at low temperature and the only observable radical after warming the crystals to room temperature, was identified as the C8-H addition radical. The alpha-coupling to HC2 and beta-couplings to the pair of C8 methlyene protons were fully characterized by ENDOR.     

Sensitivity of tyrosyl radical g-values to changes in protein structure: a high-field EPR study of mutants of ribonucleotide reductase.

The local electrostatic environment plays a critical role in determining the physicochemical properties of reactive radicals in proteins. High-field electron paramagnetic resonance (HF-EPR) spectroscopy has been used to determine the sensitivity of the tyrosyl radical g-values to local electrostatic environment. Site-specific mutants of ribonucleotide reductase from Escherichia coli were used to study the effect of introducing a charge group on the HF-EPR spectrum of the stable tyrosyl (Y122) radical. The changes affected by the mutations were small, but measurable. Mutation of isoleucine-74 to an arginine (I74R) or lysine (I74K) induced disorder in the hyperfine interactions. Similar effects were observed for the mutation of valine-136 to an arginine (V136R) or asparagine (V136N). For five or six mutants studied, the g(x)() component of the g-tensor was distributed. For the isoleucine-74 to lysine (I74K) and leucine-77 to phenylalanine (L77F) mutants, a shift of 1 x 10(-)(4) in g(x)() value was also detected. For the I74K mutant, it is shown that the shift is consistent with the introduction of a charged residue, but cannot be distinguished from changes in the electrostatic effect of the nearby diiron center. For the L77F mutant, the shift is induced by the diiron center. Using existing tyrosyl radical g-tensor measurements, we have developed a simple effective charge model that allows us to rationalize the effect of the local electrostatic environments in a number of proteins.     

Electron-mediating Cu(A) centers in proteins: a comparative high field (1)H ENDOR study

High field (W-band, 95 GHz) pulsed electron-nuclear double resonance (ENDOR) measurements were carried out on a number of proteins that contain the mixed-valence, binuclear electron-mediating Cu(A) center. These include nitrous oxide reductase (N(2)OR), the recombinant water-soluble fragment of subunit II of Thermus thermophilus cytochrome c oxidase (COX) ba(3) (M160T9), its M160QT0 mutant, where the weak axial methionine ligand has been replaced by a glutamine, and the engineered "purple" azurin (purpAz). The three-dimensional (3-D) structures of these proteins, apart from the mutant, are known. The EPR spectra of all samples showed the presence of a mononuclear Cu(II) impurity with EPR characteristics of a type II copper. At W-band, the g( perpendicular) features of this center and of Cu(A) are well resolved, thus allowing us to obtain a clean Cu(A) ENDOR spectrum. The latter consists of two types of ENDOR signals. The first includes the signals of the four strongly coupled cysteine beta-protons, with isotropic hyperfine couplings, A(iso), in the 7-15 MHz range. The second group consists of weakly coupled protons with a primarily anisotropic character with A(zz) < 3 MHz. Orientation selective ENDOR spectra were collected for N(2)OR, M160QT0, and purpAz, and simulations of the cysteine beta-protons signals provided their isotropic and anisotropic hyperfine interactions. A linear correlation with a negative slope was found between the maximum A(iso) value of the beta-protons and the copper hyperfine interaction. Comparison of the best-fit anisotropic hyperfine parameters with those calculated from dipolar interactions extracted from the available 3-D structures sets limit to the sulfur spin densities. Similarly, the small coupling spectral region was simulated on the basis of the 3-D structures and compared with the experimental spectra. It was found that the width of the powder patterns of the weakly coupled protons recorded at g(perpendicular) is mainly determined by the histidine H(epsilon)(1) protons. Furthermore, the splitting in the outer wings of these powder patterns indicates differences in the positions of the imidazole rings relative to the Cu(2)S(2) core. Comparison of the spectral features of the weakly coupled protons of M160QT0 with those of the other investigated proteins shows that they are very similar to those of purpAz, where the Cu(A) center is the most symmetric, but the copper spin density and the H(epsilon)(1)-Cu distances are somewhat smaller. All proteins show the presence of a proton with a significantly negative A(iso) value which is assigned to an amide proton of one of the cysteines. The simulations of both strongly and weakly coupled protons, along with the known copper hyperfine couplings, were used to estimate and compare the spin density distribution in the various Cu(A) centers. The largest sulfur spin density was found in M160T9, and the lowest was found in purpAz. In addition, using the relation between the A(iso) values of the four cysteine beta-protons and the H-C-S-S dihedral angles, the relative contribution of the hyperconjugation mechanism to A(iso) was determined. The largest contribution was found for M160T9, and the lowest was found for purpAz. Possible correlations between the spin density distribution, structural features, and electron-transfer functionality are finally suggested.     

EPR and ENDOR study of radiation-induced radical formation in purines: hypoxanthine hydrochloride monohydrate crystals X-irradiated at 10 K

Electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR) study of hypoxanthine.HCl.H(2)O crystals irradiated at low temperatures (10 K) identified three radical species. In these crystals, the parent molecules exist in a cationic form with a proton at N7. R1 was the product of net hydrogen addition to N3 and exhibited alpha-proton hyperfine couplings to HC2, HN1, HC8, and HN3. The coupling to HC2 has an isotropic component smaller than usual, evidently an indication that the bonds to C2 are nonplanar. R2 was the product of net hydrogen loss from N7, equivalent to the one-electron oxidation product of neutral hypoxanthine, and exhibited alpha-proton hyperfine couplings to HC2 and HC8. Both couplings are characteristic of planar bonding arrangements at the centers of spin. R3 was provisionally identified as the product of net hydrogen addition to O6 and exhibited hyperfine alpha-proton couplings to HC8 and NH1. To identify the set of radicals, the experiments employed four crystal types: normal, deuterated only at NH positions, deuterated at HC8 and NH positions, and deuterated at HC8 only. The low-temperature data also showed clear evidence for H/D isotope effects in formation and/or stabilization of all radicals. To aid and support the identifications, the experimental results were compared to DFT calculations performed on a variety of radical structures plausible for the parent molecule and molecular packing within the crystal.     

High-frequency (140-GHz) time domain EPR and ENDOR spectroscopy: the tyrosyl radical-diiron cofactor in ribonucleotide reductase from yeast

High-frequency pulsed EPR and ENDOR have been employed to characterize the tyrosyl radical (Y*)-diiron cofactor in the Y2-containing R2 subunit of ribonucleotide reductase (RNR) from yeast. The present work represents the first use of 140-GHz time domain EPR and ENDOR to examine this system and demonstrates the capabilities of the method to elucidate the electronic structure and the chemical environment of protein radicals. Low-temperature spin-echo-detected EPR spectra of yeast Y* reveal an EPR line shape typical of a tyrosyl radical; however, when compared with the EPR spectra of Y* from E. coli RNR, a substantial upfield shift of the g(1)-value is observed. The origin of the shift in g(1) was investigated by 140-GHz (1)H and (2)H pulsed ENDOR experiments of the Y2-containing subunit in protonated and D(2)O-exchanged buffer. (2)H ENDOR spectra and simulations provide unambiguous evidence for one strongly coupled (2)H arising from a bond between the radical and an exchangeable proton of an adjacent residue or a water molecule. Orientation-selective 140-GHz ENDOR spectra indicate the direction of the hydrogen bond with respect to the molecular symmetry axes and the bond length (1.81 A). Finally, we have performed saturation recovery experiments and observed enhanced spin lattice relaxation rates of the Y* above 10 K. At temperatures higher than 20 K, the relaxation rates are isotropic across the EPR line, a phenomenon that we attribute to isotropic exchange interaction between Y* and the first excited paramagnetic state of the diiron cluster adjacent to it. From the activation energy of the rates, we determine the exchange interaction between the two irons of the cluster, J(exc) = -85 cm(-)(1). The relaxation mechanism and the presence of the hydrogen bond are discussed in terms of the differences in the structure of the Y*-diiron cofactor in yeast Y2 and other class I R2s.     

EPR/ENDOR study of an X-irradiated single crystal of: 1-triphenylphosphoranylidene-2-propanone: The role of hydrogen bonds in the trapping of radiogenic radicals

As shown from the crystal structure, the oxygen atom of Ph₃P=CH---C(O)CH₃ forms both intra and intermolecular hydrogen bonds. X-irradiation of this compounds produces a room-temperature-stable radical which was studied by single crystal EPR/ENDOR spectroscopy. Comparison of the experimental hyperfine couplings with those obtained from ab initio calculations shows that the radical cation Ph₃P⁺---CH=C(OH)CH₂ is formed under radiolysis. The principal directions of the hyperfine tensors indicate that, in this process, some of the hydrogen bonds are broken and that the radical undergoes a drastic reorientation around the Ph₃P---C bond.     

Homo-timeric structural model of human microsomal prostaglandin E synthase-1 and characterization of its substrate/inhibitor binding interactions

Inducible, microsomal prostaglandin E synthase 1 (mPGES-1), the terminal enzyme in the prostaglandin (PG) biosynthetic pathway, constitutes a promising therapeutic target for the development of new anti-inflammatory drugs. To elucidate structure–function relationships and to enable structure-based design, an mPGES-1 homology model was developed using the three-dimensional structure of the closest homologue of the MAPEG family (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism), mGST-1. The ensuing model of mPGES-1 is a homo-trimer, with each monomer consisting of four membrane-spanning segments. Extensive structure refinement revealed an inter-monomer salt bridge (K26-E77) as well as inter-helical interactions within each monomer, including polar hydrogen bonds (e.g. T78-R110-T129) and hydrophobic π-stacking (F82-F103-F106), all contributing to the overall stability of the homo-trimer of mPGES-1. Catalytic co-factor glutathione (GSH) was docked into the mPGES-1 model by flexible optimization of both the ligand and the protein conformations, starting from the initial location ascertained from the mGST-1 structure. Possible binding site for the substrate, prostaglandin H₂ (PGH₂), was identified by systematically probing the refined molecular structure of mPGES-1. A binding model was generated by induced fit docking of PGH₂ in the presence of GSH. The homology model prescribes three potential inhibitor binding sites per mPGES-1 trimer. This was further confirmed experimentally by equilibrium dialysis study which generated a binding stoichiometric ratio of approximately three inhibitor molecules to three mPGES-1 monomers. The structural model that we have derived could serve as a useful tool for structure-guided design of inhibitors for this emergently important therapeutic target.     

Structure-based QSAR study on differential inhibition of human prostaglandin endoperoxide H synthase-2 (COX-2) by nonsteroidal anti-inflammatory drugs

The prostaglandin-endoperoxide H synthase-1 (PGHS-1) and prostaglandin-endoperoxide H synthase-2 (PGHS-2) are the targets of nonsteroidal anti-inflammatory drugs (NSAIDs).It appears that the high degree of selectivity for inhibition of PGHS-2 shown by certain compounds is the result of two mechanisms (time-dependent, time-independent inhibition), by which they interact with each isoform. Molecular models of the complexes formed by indomethacin, sulindac, fenamates, 2-phenylpropionic acids and selective cyclooxygenase-2 (COX-2) inhibitors with the cyclooxygenase active site of human PGHS-2 have been built, paying particular attention to water molecules that participate in the hydrogen-bonding network at the polar active site entrance. The stability of the complexes has been assessed by molecular dynamics simulations and interaction energy decomposition analysis, and their biological significance has been discussed in light of available X-ray crystallographic and kinetic results. The selective PGHS-2 inhibitors exploit the extra space of a side-pocket in the active site of PGHS-2 that is not found in PGHS-1. The results suggest that active site hydration together with residues Tyr³⁵⁵, Glu⁵²⁴, Arg¹²⁰ and Arg⁵¹³ are crucial to understand the time-dependent inhibition mechanism. A marked relationship between the isoform selectivity and tightly interactions with residues into the side pocket bordered by Val⁵²³ is also found.     

The use of high field/frequency EPR in studies of radical and metal sites in proteins and small inorganic models

Low temperature electron paramagnetic resonance (EPR) spectroscopy with frequencies between 95 and 345 GHz and magnetic fields up to 12 T have been used to study radicals and metal sites in proteins and small inorganic model complexes. We have studied radicals, Fe, Cu and Mn containing proteins. For S = 1/2 systems, the high frequency method can resolve the g-value anisotropy. It was used in mouse ribonucleotide reductase (RNR) to show the presence of a hydrogen bond to the tyrosyl radical oxygen. At 285 GHz the type 2 Cu(II) signal in the complex enzyme laccase is clearly resolved from the Hg(II) containing laccase peroxide adduct. For simple metal sites, the systems over S = 1/2 can be described by the spin Hamiltonian: H(S) = BgS + D[Sz2 - S(S + 1)/3 + E/D (Sx2 - Sy2)]. From the high frequency EPR the D-value can be determined directly by, (I) shifts of g(eff) for half-integer spin systems with large D-values as observed at 345 GHz on an Fe(II)-NO-EDTA complex, which is best described as S = 3/2 system with D = 11.5 cm(-1), E = 0.1 cm(-1) and gx = gy = gz = 2.0; (II) measuring the outermost signal, for systems with small D values, distant of (2S - 1) x absolute value(D) from the center of the spectrum as observed in S= 5/2 Fe(III)-EDTA. In Mn(II) substituted mouse RNR R2 protein the weakly interacting Mn(II) at X-band could be observed as decoupled Mn(II) at 285 GHz.     

Interactions of an asymmetric amine with a non-C2 symmetric Cu-salen complex: an EPR/ENDOR and HYSCORE investigation

Single enantiomers of R-/S-methylbenzylamine (MBA) were found to selectively form adducts with the chiral non-C(2) symmetric Cu-salen complex N-(3,5-di-tert-butylsalicylidene)-N'-(salicylidene)-cyclohexane-1,2-diamine copper(II), hereafter labelled [Cu(3)]. The g/A spin Hamiltonian parameters of this Cu(II) complex showed a decrease in symmetry from axial to rhombic upon formation of the [Cu(3)] + MBA adducts. The selectivity in enantiomeric discrimination was found to be only 59 ± 5% in favour of the heterochiral R,R'-[Cu(3)] + S-MBA and S,S'-[Cu(3)] + R-MBA adducts. This was directly evidenced by W-band EPR spectroscopy. The observed low selectivity for enantiomer discrimination is primarily attributed to the loss of the bulky tert-butyl groups from the 3,5 positions of [Cu(3)] compared to the parent N,N'-bis(3,5-di-tert-butylsalicylidene)-cyclohexane-1,2-diamine copper(II) ligand (labelled [Cu(1)]). The structure of the [Cu(3)] complex in the presence and absence of coordinating amine was further investigated by analysis of the ligand hyperfine interactions, as revealed through Q-band CW-ENDOR, X-band Davies ENDOR and HYSCORE. (1)H couplings from the -NH(2) group of the amine, observed by ENDOR and HYSCORE, provided direct evidence of amine coordination.     

Rapid freeze-quench ENDOR study of chloroperoxidase compound I: the site of the radical

The classical heme-monooxygenase active intermediate, compound I (Cpd-I), incorporates a heme which is oxidized by two equivalents above the resting ferric state, one equivalent associated with a ferryl center, [Fe=O]2+ (FeS = 1), and the other with an active-site radical (RS = 1/2). Theoretical calculations on models of a Cpd-I with a thiolato axial ligand have presented divergent views about its electronic structure. In one picture, the radical is on the porphyrin; in the other, it is on the sulfur. In this report, ENDOR spectroscopy answers the question, does Cpd-I of the enzyme chloroperoxidase contain a porphyrin pi-cation radical or an iron-bound cysteinyl radical: the radical is predominantly on the porphyrin, with spin density on sulfur having an upper bound, rhoS 相似文献   

EPR and ESEEM study of the plastoquinone anion radical QA in photosystem II treated at high pH

The effect of treatment at pH = 11 on the photosystem II was studied by EPR and electron spin echo envelope modulation (ESEEM). The magnetic interaction between the semiquinone Q_A^−. and the non-heme Fe²⁺ (S = 2) was absent. ESEEM showed that the Q_A^−. interacts magnetically with two ¹⁴N nuclei. The first interaction has a hyperfine coupling tensor (A_XX, A_YY, A_ZZ)=(2.0, 1.7, 2.3 MHz) and nuclear quadrupole interaction parameters e²qQ/h=3.24 MHz and η = 0.45 while those of the second are (A_XX, A_YY, A_ZZ)=(1.2, 1.5, 2.3 MHz), e²qQ/h = 1.56 MHz and η = 0.71. These are assigned to an amide nitrogen of the peptide backbone and the amino nitrogen of an imidazole respectively. By analogy to the bacterial reaction centre, these nitrogens are attributed to the Ala 261 and His 215 of the D2 protein. It was shown earlier that the imidazole coupling is absent in cyanide-treated PSII, its presence here is attributed to a difference in the position of the imidazole group itself.     

EPR, ENDOR and HYSCORE study of X-ray induced centres in K2YF5 thermoluminescent phosphors

X-Ray irradiation at room temperature produces several paramagnetic centres in rare-earth activated K2YF5 crystals, whose thermal annealing behaviour can be linked with the occurrence of thermoluminescence (TL) glow peaks. In this paper, continuous wave (CW) and pulsed paramagnetic resonance techniques are used to study the structure of a very stable radiation-induced centre, which may be involved in the TL peak at approximately 390 degrees C reported for Ce- and Tb-activated crystals. From the spectra the centre's g tensor and hyperfine (nuclear quadrupole) tensors for several 19F and 39K neighbouring nuclei are extracted, but no self-hyperfine interaction could be detected. Based on the analysis of the interaction tensors, a model is constructed consisting of an oxygen-related radical (e.g. O(-) or O2(-)) on a substitutional F(-) position in the mirror plane of the YF7 polyhedra. Such a centre most probably corresponds to a trapped-hole state.     

Multifrequency high-field EPR study of the tryptophanyl and tyrosyl radical intermediates in wild-type and the W191G mutant of cytochrome c peroxidase.

Multifrequency (95, 190, and 285 GHz) high-field electron paramagnetic resonance (EPR) spectroscopy has been used to characterize radical intermediates in wild-type and Trp191Gly mutant cytochrome c peroxidase (CcP). The high-field EPR spectra of the exchange-coupled oxoferryl--trytophanyl radical pair that constitutes the CcP compound I intermediate [(Fe(IV)=O) Trp*(+)] were analyzed using a spin Hamiltonian that incorporated a general anisotropic spin-spin interaction term. Perturbation expressions of this Hamiltonian were derived, and their limitations under high-field conditions are discussed. Using numerical solutions of the completely anisotropic Hamiltonian, its was possible to simulate accurately the experimental data from 9 to 285 GHz using a single set of spin parameters. The results are also consistent with previous 9 GHz single-crystal studies. The inherent superior resolution of high-field EPR spectroscopy permitted the unequivocal detection of a transient tyrosyl radical that was formed 60 s after the addition of 1 equiv of hydrogen peroxide to the wild-type CcP at 0 degrees C and disappeared after 1 h. High-field EPR was also used to characterize the radical intermediate that was generated by hydrogen peroxide addition to the W191G CcP mutant. The g- values of this radical (g(x)= 2.00660, g(y) = 2.00425, and g(z)= 2.00208), as well as the wild-type transient tyrosyl radical, are essentially identical to those obtained from the high-field EPR spectra of the tyrosyl radical generated by gamma-irradiation of crystals of tyrosine hydrochloride (g(x)= 2.00658, g(y) = 2.00404, and g(z) = 2.00208). The low g(x)-value indicated that all three of the tyrosyl radicals were in electropositive environments. The broadening of the g(x) portion of the HF-EPR spectrum further indicated that the electrostatic environment was distributed. On the basis of these observations, possible sites for the tyrosyl radical(s) are discussed.     

Determination of the relevant magnetic interactions in low-dimensional molecular materials: the fundamental role of single crystal high frequency EPR

A new one-dimensional copper(II) complex with formula [Cu(hfac)(2)(N(3)TEMPO)](n) (hfac = hexafluoroacetylacetonate and N(3)TEMPO = 4-azido-2,2,6,6-tetramethylpiperidine-1-oxyl) has been synthesized and investigated by X-ray crystallography, magnetometry and multifrequency single crystal EPR. The system crystallizes in the P1 space group with two non equivalent copper(II) ions in the unit cell, the two nitroxide radicals being coordinated to Cu(1) in axial positions. The copper(II) ions are bridged by N(3)TEMPO radicals resulting in a zig-zag chain structure. The magnetic susceptibility data were at first satisfactorily modeled assuming an alternating spin chain along the monodimensional covalent skeleton, with a ferromagnetic interaction between Cu(1) and the nitroxide moieties and a weaker antiferromagnetic interaction between these and Cu(2) (J(1) = -13.8 cm(-1), J(2) = +2.4 cm(-1)). However, single crystal EPR studies performed at the X- and W-band clearly demonstrate that the observed magnetic monodimensional character of the complex is actually due to the intermolecular contacts involving N(3)TEMPO ligands. This prompted us to fit the magnetic data using a consistent model, pointing out the fundamental role of single crystal EPR data in defining a correct model to describe the magnetic properties of molecular low dimensional systems.     

1H NMR: a tool to study the fate of pollutants in the environment

In situ ¹H NMR, directly performed on biological fluids is a very powerful tool to study the fate of pollutants in the environment. The biodegradation of 2-aminobenzothiazole by Rhodococcus rhodochrous was monitored by reverse phase HPLC and by in situ ¹H NMR, methods performed directly on culture media without purification. The xenobiotic was biotransformed into a hydroxylated derivative. The chemical structure of this metabolite was determined by a long-range ¹H–¹⁵N heteronuclear shift correlation without any previous ¹⁵N enrichment of the compound. This approach allowed the assignment of the metabolite structure to 2-amino-6-hydroxybenzothiazole.     

ENDOR of spin-correlated radical pairs in photosynthesis at high magnetic field: a tool for mapping electron transfer pathways

A new phenomenon has been detected in the time-resolved electron-nuclear double resonance (ENDOR) spectra of the spin-correlated radical pairs in photosynthetic reaction center proteins. The observed effects result from both increased resolution and orientational selectivity provided by high magnetic field EPR and are manifest as specific, derivative-type lines in the ENDOR spectrum. Importantly, the positions and amplitudes of these lines contain information on the interaction of a particular nucleus with both correlated electron spins. Thus, spin density delocalization in the protein environment between the donor and acceptor in the SCRP can be revealed via SCRP ENDOR, providing a unique opportunity to probe the electron-transfer pathways in natural and artificial photosynthetic assemblies.