Insights into the Structure and Function of Redox-Active Tyrosines from Model Compounds

Structure, dynamics, and ionization equilibria of the tyrosine residues in Bacillus circulans xylanase

We have developed NMR spectroscopic methods to investigate the tyrosines within Bacillus circulans xylanase (BcX). Four slowly exchanging buried tyrosine hydroxyl protons with chemical shifts between 7.5 and 12.5 ppm were found using a long-range (13)C-HSQC experiment that exploits the (3)J(CH) coupling between the ring (1)H(η) and (13)C(ε) nuclei. The NMR signals from these protons were assigned via (13)C-tyrosine selective labelling and a suite of scalar and (13)C,(15)N-filtered/edited NOE correlation spectra. Of the fifteen tyrosines in BcX, only the buried Tyr79 and Tyr105 showed four distinct, rather than two averaged, signals from ring (13)C-(1)H pairs, indicative of slow flipping on the chemical shift timescale. Ring flipping rate constants of ~10 and ~0.2 s(-1) were measured for the two residues, respectively, using a (13)C longitudinal exchange experiment. The hydrogen bonding properties of the Tyr79 and Tyr105 hydroxyls were also defined by complementary NOE and J-coupling measurements. The (1)H(η) hydrogen-deuterium exchange rate constants of the buried tyrosines were determined from (13)C/(15)N-filtered spectra recorded as a function of pH. These exchange rate constants correspond to estimated protection factors of ~10(4)-10(8) relative to a random coil tyrosine. The phenolic sidechain pK (a) values were also measured by monitoring their pH-dependent (13)C(ζ) chemical shifts via (1)H(ε/δ)((13)C(ε))(13)C(ζ) correlation spectra. Exposed tyrosines had unperturbed pK (a) values of ~10.2, whereas buried residues remained predominantly neutral at or even above pH 11. Combined with selective isotope labelling, these NMR experiments should prove useful for investigating the structural and electrostatic properties of tyrosines in many interesting proteins.

Redox-active tyrosine residue in the microcin J25 molecule

Microcin J25 (MccJ25) is a 21 amino acid lasso-peptide antibiotic produced by Escherichia coli and composed of an 8-residues ring and a terminal 'tail' passing through the ring. We have previously reported two cellular targets for this antibiotic, bacterial RNA polymerase and the membrane respiratory chain, and shown that Tyr9 is essential for the effect on the membrane respiratory chain which leads to superoxide overproduction. In the present paper we investigated the redox behavior of MccJ25 and the mutant MccJ25 (Y9F). Cyclic voltammetry measurements showed irreversible oxidation of both Tyr9 and Tyr20 in MccJ25, but infrared spectroscopy studies demonstrated that only Tyr9 could be deprotonated upon chemical oxidation in solution. Formation of a long-lived tyrosyl radical in the native MccJ25 oxidized by H₂O₂ was demonstrated by Electron Paramagnetic Resonance Spectroscopy; this radical was not detected when the reaction was carried out with the MccJ25 (Y9F) mutant. These results show that the essential Tyr9, but not Tyr20, can be easily oxidized and form a tyrosyl radical.

pH-Potentiometric Investigation towards Chelating Tendencies of p-Hydroquinone and Phenol Iminodiacetate Copper(II) Complexes

Copper ions in the active sites of several proteins/enzymes interact with phenols and quinones, and this interaction is associated to the reactivity of the enzymes. In this study the speciation of the Cu²⁺ with iminodiacetic phenolate/hydroquinonate ligands has been examined by pH-potentiometry. The results reveal that the iminodiacetic phenol ligand forms mononuclear complexes with Cu²⁺ at acidic and alkaline pHs, and a binuclear O_phenolate-bridged complex at pH range from 7 to 8.5. The binucleating hydroquinone ligand forms only 2 : 1 metal to ligand complexes in solution. The pK values of the protonation of the phenolate oxygen of the two ligands are reduced about 2 units after complexation with the metal ion and are close to the pK values for the copper-interacting tyrosine phenol oxygen in copper enzymes.

Role of conserved tyrosine residues in NiSOD catalysis: a case of convergent evolution

Superoxide dismutases rely on protein structural elements to adjust the redox potential of the metallocenter to an optimum value near 300 mV (vs NHE), to provide a source of protons for catalysis, and to control the access of anions to the active site. These aspects of the catalytic mechanism are examined herein for recombinant preparations of the nickel-dependent SOD (NiSOD) from Streptomyces coelicolor and for a series of mutants that affect a key tyrosine residue, Tyr9 (Y9F-, Y62F-, Y9F/Y62F-, and D3A-NiSOD). Structural aspects of the nickel sites are examined by a combination of EPR and X-ray absorption spectroscopies, and by single-crystal X-ray diffraction at approximately 1.9 A resolution in the case of Y9F- and D3A-NiSODs. The functional effects of the mutations are examined by kinetic studies employing pulse radiolytic generation of O2- and by redox titrations. These studies reveal that although the structure of the nickel center in NiSOD is unique, the ligand environment is designed to optimize the redox potential at 290 mV and results in the oxidation of 50% of the nickel centers in the oxidized hexamer. Kinetic investigations show that all of the mutant proteins have considerable activity. In the case of Y9F-NiSOD, the enzyme exhibits saturation behavior that is not observed in wild-type (WT) NiSOD and suggests that release of peroxide is inhibited. The crystal structure of Y9F-NiSOD reveals an anion binding site that is occupied by either Cl- or Br- and is located close to but not within bonding distance of the nickel center. The structure of D3A-NiSOD reveals that in addition to affecting the interaction between subunits, this mutation repositions Tyr9 and leads to altered chemistry with peroxide. Comparisons with Mn(SOD) and Fe(SOD) reveal that although different strategies for adjusting the redox potential and supply of protons are employed, NiSOD has evolved a similar strategy for controlling the access of anions to the active site.

Functional biomimetic models for the active site in the respiratory enzyme cytochrome c oxidase

A functional analog of the active site in the respiratory enzyme, cytochrome c oxidase (CcO) reproduces every feature in CcO's active site: a myoglobin-like heme (heme a3), a distal tridentate imidazole copper complex (Cu(B)), a phenol (Tyr244), and a proximal imidazole. When covalently attached to a liquid-crystalline SAM film on an Au electrode, this functional model continuously catalyzes the selective four-electron reduction of dioxygen at physiological potential and pH, under rate-limiting electron flux (as occurs in CcO).

Three different tyrosyl radicals identified in L-tyrosine HCl crystals upon gamma-irradiation: magnetic characterization and temporal evolution

High-frequency electron paramagnetic resonance (EPR) and X-band electron-nuclear double resonance (ENDOR) spectroscopies were used to investigate the effect of gamma-irradiation on single crystals of L-tyrosine hydrochloride at room temperature. The oxidation product is the tyrosyl radical formed by hydrogen abstraction from the phenolic group; interestingly, on freshly irradiated crystals, two tyrosyl radicals were identified, characterized by slightly different magnetic parameters. In particular, one of the two radicals, with a gxx value of 2.00621, has its phenoxyl oxygen strongly hydrogen-bonded to one or more donors; to our knowledge, this is the lower gxx value reported for tyrosyl radicals. These two oxidation radicals are found to evolve very slowly to a third, single more stable radical conformation. To interpret the experimental data, a possible molecular scenario is presented, where the process of radical formation can be seen as a hydrogen atom transfer or a proton-coupled electron transfer. These processes seem to be controlled by the specific network of hydrogen-bond interactions present in the crystal. The results are discussed in relation to their relevance for the interpretation of EPR spectra of tyrosyl radicals in biological systems.

Characterization of the phenoxyl radical in model complexes for the Cu(B) site of cytochrome c oxidase: steady-state and transient absorption measurements, UV resonance raman spectroscopy, EPR spectroscopy, and DFT calculations for M-BIAIP

Physicochemical properties of the covalently cross-linked tyrosine-histidine-Cu(B) (Tyr-His-Cu(B)) unit, which is a minimal model complex [M(II)-BIAIPBr]Br (M = Cu(II), Zn(II)) for the Cu(B) site of cytochrome c oxidase, were investigated with steady-state and transient absorption measurements, UV resonance Raman (UVRR) spectroscopy, X-band continuous-wave electron paramagnetic resonance (EPR) spectroscopy, and DFT calculations. The pH dependency of the absorption spectra reveals that the pK(a) of the phenolic hydroxyl is ca. 10 for the Cu(II) model complex (Cu(II)-BIAIP) in the ground state, which is similar to that of p-cresol (tyrosine), contrary to expectations. The bond between Cu(II) and nitrogen of cross-linked imidazole cleaves at pH 4.9. We have successfully obtained UVRR spectra of the phenoxyl radical form of BIAIPs and have assigned bands based on the previously reported isotope shifts of Im-Ph (2-(1-imidazoyl)-4-methylphenol) (Aki, M.; Ogura, T.; Naruta, Y.; Le, T. H.; Sato, T.; Kitagawa, T. J. Phys. Chem. A 2002, 106, 3436-3444) in combination with DFT calculations. The upshifts of the phenoxyl vibrational frequencies for 8a (C-C stretching), 7a' (C-O stretching), and 19a, and the Raman-intensity enhancements of 19b, 8b, and 14 modes indicate that UVRR spectra are highly sensitive to imidazole-phenol covalent linkage. Both transient absorption measurements and EPR spectra suggest that the Tyr-His-Cu(B) unit has only a minor effect on the electronic structure of the phenoxyl radical form, although our experimental results appear to indicate that the cross-linked Tyr radical exhibits no EPR. The role of the Tyr-His-Cu(B) unit in the enzyme is discussed in terms of the obtained spectroscopic parameters of the model complex.

Probing the Environment of CuB in Heme−Copper Oxidases

Time-resolved step-scan FTIR (TRS2-FTIR) and density functional theory have been applied to probe the structural dynamics of CuB in heme-copper oxidases at room temperature. The TRS2-FTIR data of cbb3 from Pseudomonas stutzeri indicate a small variation in the frequency of the transient CO bound to CuB in the pH/pD 7-9 range. This observation in conjunction with density functional theory calculations, in which significant frequency shifts of the nu(CO) are observed upon deprotonation and/or detachment of the CuB ligands, demonstrates that the properties of the CuB ligands including the cross-linked tyrosine, in contrast to previous reports, remain unchanged in the pH 7-9 range. We attribute the small variations in the nu(CO) of CuB to protein conformational changes in the vicinity of CuB. Consequently, the split of the heme Fe-CO vibrations (alpha-, beta-, and gamma-forms) is not due to changes in the ligation and/or protonation states of the CuB ligands or to the presence of one or more ionizable groups, as previously suggested, but the result of global protein conformational changes in the vicinity of CuB which, in turn, affect the position of CuB with respect to the heme Fe.

Synthetic Models of the Active Site of Cytochromec Oxidase: Influence of Tridentate or Tetradentate Copper Chelates Bearing a HisTyr Linkage Mimic on Dioxygen Adduct Formation by Heme/Cu Complexes

Two synthetic models of the active site of cytochrome c oxidase--[(LN4-OH)CuI-FeII(TMP)]+ (1 a) and [(LN3-OH)CuI-FeII(TMP)]+ (2 a)-have been designed and synthesized. These models each contain a heme and a covalently attached copper moiety supported either by a tetradentate N4-copper chelate or by a tridentate N3-copper chelate including a moiety that acts as a mimic of the crosslinked His-Tyr component of cytochrome c oxidase. Low-temperature oxygenation reactions of these models have been investigated by spectroscopic methods including UV/Vis, resonance Raman, ESI-MS, and EPR spectroscopy. Oxygenation of the tetradentate model 1 a in MeCN and in other solvents produces a low-temperature-stable dioxygen-bridged peroxide [(LN4-OH)CuII-O2-FeIII(TMP)]+ {nuO--O=799 (16O2)/752 cm(-1) (18O2)}, while a heme superoxide species [(TMP)FeIII(O2-)CuIILN3-OH] {nuFe--O2: 576 (16O2)/551 cm(-1) (18O2)} is generated when the tridentate model 2 a is oxygenated in EtCN solution under similar experimental conditions. The coexistence of a heme superoxide species [(TMP)FeIII(O2-)CuIILN3-OH] and a bridged peroxide [(LN3-OH)CuII-O2-FeIII(TMP)]+ species in equal amounts is observed when the oxygenation reaction of 2 a is performed in CH2Cl(2)/7 % EtCN, while the percentage of the peroxide (approximately 70 %) in relation to superoxide (approximately 30 %) increases further when the crosslinked phenol moiety in 2 a is deprotonated to produce the bridged peroxide [(LN3-OH)CuII-O2-FeIII(TMP)]+ {nuO--O: 812 (16O2)/765 cm(-1) (18O2)} as the main dioxygen intermediate. The weak reducibility and decreased O2 reactivity of the tricoordinated CuI site in 2 a are responsible for the solvent-dependent formation of dioxygen adducts. The initial binding of dioxygen to the copper site en route to the formation of a bridged heme-O2-Cu intermediate by model 2 a is suggested and the deprotonated crosslinked His-Tyr moiety might contribute to enhancement of the O2 affinity of the CuI site at an early stage of the dioxygen-binding process.

Normal modes of redox-active tyrosine: conformation dependence and comparison to experiment

Redox-active tyrosine residues play important roles in long-distance electron reactions in enzymes such as prostaglandin H synthase, ribonucleotide reductase, and photosystem II (PSII). Spectroscopic characterization of tyrosyl radicals in these systems provides a powerful experimental probe into the role of the enzyme in mediation of long-range electron transfer processes. Interpretation of such data, however, relies critically on first establishing a spectroscopic fingerprint of isotopically labeled tyrosinate and tyrosyl radicals in nonenzymatic environments. In this report, FT-IR results obtained from tyrosinate, tyrosyl radical (produced by ultraviolet photolysis of polycrystalline tyrosinate), and their isotopologues at 77 K are presented. Assignment of peaks and isotope shifts is aided by density-functional B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) calculations of tyrosine and tyrosyl radical in several different charge and protonation states. In addition, characterization of the potential energy surfaces of tyrosinate and tyrosyl radical as a function of the backbone and ring torsion angles provides detailed insight into the sensitivity of the vibrational frequencies to conformational changes. These results provide a detailed spectroscopic interpretation, which will elucidate the structures of redox-active tyrosine residues in complex protein environments. Specific application of these data is made to enzymatic systems.

Further Insights into the Spectroscopic Properties, Electronic Structure, and Kinetics of Formation of the Heme−Peroxo−Copper Complex [(F8TPP)FeIII−(O22-)−CuII(TMPA)]+

In the further development and understanding of heme-copper O2-reduction chemistry inspired by the active-site chemistry in cytochrome c oxidase, we describe a dioxygen adduct, [(F8TPP)FeIII-(O22-)-CuII(TMPA)](ClO4) (3), formed by addition of O2 to a 1:1 mixture of the porphyrinate-iron(II) complex (F8TPP)FeII (1a) {F8TPP = tetrakis(2,6-difluorophenyl)porphyrinate dianion} and the copper(I) complex [(TMPA)CuI(MeCN)](ClO4) (1b) {TMPA = tris(2-pyridylmethyl)amine}. Complex 3 forms in preference to heme-only or copper-only binuclear products, is remarkably stable {t1/2 (RT; MeCN) approximately 20 min; lambda max = 412 (Soret), 558 nm; EPR silent}, and is formulated as a peroxo complex on the basis of manometry {1a/1b/O2 = 1:1:1}, MALDI-TOF mass spectrometry {16O2, m/z 1239 [(3 + MeCN)+]; 18O2, m/z 1243}, and resonance Raman spectroscopy {nu(O-O) = 808 cm-1; Delta16O2/18O2 = 46 cm-1; Delta16O2/16/18O2 = 23 cm-1}. Consistent with a mu-eta2:eta1 bridging peroxide ligand, two metal-O stretching frequencies are observed {nu(Fe-O) = 533 cm-1, nu(Fe-O-Cu) = 511 cm-1}, and supporting normal coordinate analysis is presented. 2H and 19F NMR spectroscopies reveal that 3 is high-spin {also muB = 5.1 +/- 0.2, Evans method} with downfield-shifted pyrrole and upfield-shifted TMPA resonances, similar to the pattern observed for the structurally characterized mu-oxo complex [(F8TPP)FeIII-O-CuII(TMPA)]+ (4) (known S = 2 system, antiferromagnetically coupled high-spin FeIII and CuII). Mössbauer spectroscopy exhibits a sharp quadrupole doublet (zero field; delta = 0.57 mm/s, |DeltaEQ| = 1.14 mm/s) for 3, with isomer shift and magnetic field dependence data indicative of a peroxide ligand and S = 2 formulation. Both UV-visible-monitored stopped-flow kinetics and Mössbauer spectroscopic studies reveal the formation of heme-only superoxide complex (S)(F8TPP)FeIII-(O2-) (2a) (S = solvent molecule) prior to 3. Thermal decomposition of mu-peroxo complex 3 yields mu-oxo complex 4 with concomitant release of approximately 0.5 mol O2 per mol 3. Characterization of the reaction 1a/1b + O2 --> 2 --> 3 --> 4, presented here, advances our understanding and provides new insights to heme/Cu dioxygen-binding and reduction.

Proton-coupled electron transfer in a biomimetic peptide as a model of enzyme regulatory mechanisms

Proton-coupled electron-transfer reactions are central to enzymatic mechanism in many proteins. In several enzymes, essential electron-transfer reactions involve oxidation and reduction of tyrosine side chains. For these redox-active tyrosines, proton transfer couples with electron transfer, because the phenolic pKA of the tyrosine is altered by changes in the tyrosine redox state. To develop an experimentally tractable peptide system in which the effect of proton and electron coupling can be investigated, we have designed a novel amino acid sequence that contains one tyrosine residue. The tyrosine can be oxidized by ultraviolet photolysis or electrochemical methods and has a potential cross-strand interaction with a histidine residue. NMR spectroscopy shows that the peptide forms a beta-hairpin with several interstrand dipolar contacts between the histidine and tyrosine side chains. The effect of the cross-strand interaction was probed by electron paramagnetic resonance and electrochemistry. The data are consistent with an increase in histidine pKA when the tyrosine is oxidized; the effect of this thermodynamic coupling is to increase tyrosyl radical yield at low pH. The coupling mechanism is attributed to an interstrand pi-cation interaction, which stabilizes the tyrosyl radical. A similar interaction between histidine and tyrosine in enzymes provides a regulatory mechanism for enzymatic electron-transfer reactions.

Synthesis and structural characterization of cross-linked histidine–phenol Cu(ii) complexes as cytochrome c oxidase active site models

Tridentate cross-linked histidine-phenol Cu(ii) ether and ester complexes, chemical analogs of the active site of several heme-copper oxidases, have been synthesized and crystallized.

Model studies of the CuBsite of cytochrome c oxidase utilizing a Zn(ii) complex containing an imidazole–phenol cross-linked ligand

Cytochrome c oxidase, the enzyme complex responsible for the four-electron reduction of O2 to H2O, contains an unusual histidine-tyrosine cross-link in its bimetallic heme a3-CuB active site. We have synthesised an unhindered, tripodal chelating ligand, BPAIP, containing the unusual ortho-imidazole-phenol linkage, which mimics the coordination environment of the CuB center. The ligand was used to investigate the physicochemical (pKa, oxidation potential) and coordination properties of the imidazole-phenol linkage when bound to a dication. Zn(II) coordination lowers the pKa of the phenol by 0.6 log units, and increases the potential of the phenolate/phenoxyl radical couple by approximately 50 mV. These results are consistent with inductive withdrawal of electron density from the phenolic ring. Spectroscopic data and theoretical calculations (DFT) were used to establish that the cationic complex [Zn(BPAIP)Br]+ has an axially distorted trigonal bipyramidal structure, with three coordinating nitrogen ligands (two pyridine and one imidazole) occupying the equatorial plane and the bromide and the tertiary amine nitrogen of the tripod in the axial positions. Interestingly, the Zn-Namine bonding interaction is weak or absent in [Zn(BPAIP)Br]+ and the complex gains stability in basic solutions, as indicated by 1H NMR spectroscopy. These observations are supported by theoretical calculations (DFT), which suggest that the electron-donating capacity of the equatorial imidazole ligand can be varied by modulation of the protonation and/or redox state of the cross-linked phenol. Deprotonation of the phenol makes the equatorial imidazole a stronger sigma-donor, resulting in an increased Zn-Nimd interaction and thereby leading to distortion of the axial ligand axis toward a more tetrahedral geometry.

Redox-Active Tyrosine Residues in Pentapeptides

Tyrosyl radicals are important in long-range electron transfer in several enzymes, but the protein environmental factors that control midpoint potential and electron-transfer rate are not well understood. To develop a more detailed understanding of the effect of protein sequence on their photophysical properties, we have studied the spectroscopic properties of tyrosyl radicals at 85 K. Tyrosyl radical was generated by UV-photolysis of pentapeptides in polycrystalline samples. The sequence of the pentapeptides was chosen to mimic peptide sequences found in redox-active tyrosine containing enzymes, ribonucleotide reductase and photosystem II. From EPR studies, we report that the EPR line shape of the tyrosyl radical depends on peptide sequence. We also present the first evidence for a component of the tyrosyl radical EPR signal, which decays on the seconds time scale at 85 K. We suggest that this transient results from a spontaneous, small conformational rearrangement in the radical. From FT-IR studies, we show that amide I vibrational bands (1680-1620 cm(-1)) and peptide bond skeletal vibrations (1230-1090 cm(-1)) are observed in the photolysis spectra of tyrosine-containing pentapeptides. From these data, we conclude that oxidation of the tyrosine aromatic ring perturbs the electronic structure of the peptide bond in tyrosine-containing oligopeptides. We also report sequence-dependent alterations in these bands. These results support the previous suggestion (J. Am. Chem. Soc. 2002, 124, 5496) that spin delocalization can occur from the tyrosine aromatic ring into the peptide bond. We hypothesize that these sequence-dependent effects are mediated either by electrostatics or by changes in conformer preference in the peptides. Our findings suggest that primary structure influences the functional properties of redox-active tyrosines in enzymes.