Redox-Active Tyrosine Residues in Pentapeptides

Control of Tyrosyl Radical Stabilization by {SiO2@Oligopeptide} Hybrid Biomimetic Materials

Tyrosine radicals are notoriously short-lived/unstable in solution, while they present an impressive degree of stability and versatility in bioenzymes. Herein, we have developed a library of hybrid biomimetic materials (HBMs), which consists of tyrosine-containing oligopeptides covalently grafted on SiO₂ nanoparticles, and studied the formation, lifetime, and redox properties of tyrosyl radicals. Using electron paramagnetic resonance spectroscopy, we have studied the radical-spin distribution as a probe of the local microenvironment of the tyrosyl radicals in the HBMs. We find that the lifetime of the tyrosyl radical can be enhanced by up to 6 times, by adjusting three factors, namely, a proximal histidine, the length of the oligopeptide, and the interface with the SiO₂ nanomatrix. This is shown to be correlated to a significant lowering of E_1/2 from +736 mV, in free tyrosine, to +548 mV in the {12-peptide}@SiO₂ material. Moreover, we show that grafting on SiO₂ lowers the E_1/2 of tyrosine radicals by ∼50 mV in all oligopeptides. Analysis of the spin-distribution by EPR reveals that the positioning of a histidine at a H-bonding distance from the tyrosine further favors tyrosine radical stabilization.

Detection of Catalytically Linked Conformational Changes in Wild-Type Class Ia Ribonucleotide Reductase Using Reaction-Induced FTIR Spectroscopy

The enzyme, ribonucleotide reductase (RNR), is essential for DNA synthesis in all cells. The class Ia Escherichia coli RNR consists of two dimeric subunits, α₂ and β₂, which form an active but unstable heterodimer of dimers, α₂β₂. The structure of the wild-type form of the enzyme has been challenging to study due to the instability of the catalytic complex. A long-range proton-coupled electron-transfer (PCET) pathway facilitates radical migration from the Y122 radical-diiron cofactor in the β subunit to an active site cysteine, C439, in the α subunit to initiate the RNR chemistry. The PCET reactions and active site chemistry are spectroscopically masked by a rate-limiting, conformational gate. Here, we present a reaction-induced Fourier transform infrared (RIFTIR) spectroscopic method to monitor the mechanism of the active, wild-type RNR α₂β₂ complex. This method is employed to obtain new information about conformational changes accompanying RNR catalysis, including the role of carboxylate interactions, deprotonation, and oxidation of active site cysteines, and a detailed description of reversible secondary structural changes. Labeling of tyrosine revealed a conformationally active tyrosine in the β subunit, assigned to Y356β, which is part of the intersubunit PCET pathway. New insights into the roles of the inhibitors, azidoUDP and dATP, and the sensitivity of RIFTIR spectroscopy to detect subtle conformational motions arising from protein allostery are also presented.

A Proton Wire Mediates Proton Coupled Electron Transfer from Hydroxyurea and Other Hydroxamic Acids to Tyrosyl Radical in Class Ia Ribonucleotide Reductase

Proton-coupled electron transfer (PCET) is fundamental to many important biological reactions, including solar energy conversion and DNA synthesis. For example, class Ia ribonucleotide reductases (RNRs) contain a tyrosyl radical-diiron cofactor with one aspartate ligand, D84. The tyrosyl radical, Y122^•, in the β2 subunit acts as a radical initiator and oxidizes an active site cysteine in the α2 subunit. A transient quaternary α2/β2 complex is induced by substrate and effector binding. The hydroxamic acid, hydroxyurea (HU), reduces Y122^• in a PCET reaction involving an electron and proton. This reaction is associated with the loss of activity, a conformational change at Y122, and a change in hydrogen bonding to the Fe1 ligand, D84. Here, we use isotopic labeling, solvent isotope exchange, proton inventories, and reaction-induced Fourier transform infrared (RIFT-IR) spectroscopy to show that the PCET reactions of hydroxamic acids are associated with a characteristic spectrum, which is assignable to electrostatic changes at nonligating aspartate residues. Notably, RIFT-IR spectroscopy reveals this characteristic spectrum when the effects of HU, hydroxylamine, and N-methylhydroxylamine are compared. A large solvent isotope effect is observed for each of the hydroxamic acid reactions, and proton inventories predict that the reactions are associated with the transfer of multiple protons in the transition state. The reduction of Y122^• with 4-methoxyphenol does not lead to these characteristic carboxylate shifts and is associated with only a small solvent isotope effect. In addition to studies of the effects of hydroxamic acids on β2 alone, the reactions involving the quaternary α2β2 complex were also investigated. HU treatment of the quaternary complex, α2/β2/ATP/CDP, leads to a similar carboxylate shift spectrum, as observed with β2 alone. The use of globally labeled ¹³C chimeras (¹³C α2, ¹³C β2) confirms the assignment. Because the spectrum is sensitive to ¹³C β2 labeling, but not ¹³C α2 labeling, the quaternary complex spectrum is assigned to electrostatic changes in β2 carboxylate groups. Examination of the β2 X-ray structure reveals a hydrogen-bonded network leading from the protein surface to Y122. This predicted network includes nonligating aspartates, glutamate ligands to the iron cluster, and predicted crystallographically resolved water molecules. The network is similar when class Ia RNR structures from Escherichia coli, human, and mouse are compared. We propose that the PCET reactions of hydroxamic acids are mediated by a hydrogen-bonded proton wire in the β2 subunit.

Calcium, conformational selection, and redox-active tyrosine YZ in the photosynthetic oxygen-evolving cluster

In Photosystem II (PSII), YZ (Tyr161D1) participates in radical transfer between the chlorophyll donor and the Mn₄CaO₅ cluster. Under flashing illumination, the metal cluster cycles among five S_n states, and oxygen is evolved from water. The essential YZ is transiently oxidized and reduced on each flash in a proton-coupled electron transfer (PCET) reaction. Calcium is required for function. Of reconstituted divalent ions, only strontium restores oxygen evolution. YZ is predicted to hydrogen bond to calcium-bound water and to His190D1 in PSII structures. Here, we report a vibrational spectroscopic study of YZ radical and singlet in the presence of the metal cluster. The S₂ state is trapped by illumination at 190 K; flash illumination then generates the S₂YZ radical. Using reaction-induced FTIR spectroscopy and divalent ion depletion/substitution, we identify calcium-sensitive tyrosyl radical and tyrosine singlet bands in the S₂ state. In calcium-containing PSII, two CO stretching bands are detected at 1,503 and 1,478 cm^-1 These bands are assigned to two different radical conformers in calcium-containing PSII. At pH 6.0, the 1,503-cm^-1 band shifts to 1,507 cm^-1 in strontium-containing PSII, and the band is reduced in intensity in calcium-depleted PSII. These effects are consistent with a hydrogen-bonding interaction between the calcium site and one conformer of radical YZ. Analysis of the amide I region indicates that calcium selects for a PCET reaction in a subset of the YZ conformers, which are trapped in the S₂ state. These results support the interpretation that YZ undergoes a redox-coupled conformational change, which is calcium dependent.

Redox-linked conformational control of proton-coupled electron transfer: Y122 in the ribonucleotide reductase β2 subunit

Tyrosyl radicals play essential roles in biological proton-coupled electron transfer (PCET) reactions. Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides and is vital in DNA replication in all organisms. Class Ia RNRs consist of α2 and β2 homodimeric subunits. In class Ia RNR, such as the E. coli enzyme, an essential tyrosyl radical (Y122O(•))-diferric cofactor is located in β2. Although Y122O(•) is extremely stable in free β2, Y122O(•) is highly reactive in the quaternary substrate-α2β2 complex and serves as a radical initiator in catalytic PCET between β2 and α2. In this report, we investigate the structural interactions that control the reactivity of Y122O(•) in a model system, isolated E. coli β2. Y122O(•) was reduced with hydroxyurea (HU), a radical scavenger that quenches the radical in a clinically relevant reaction. In the difference FT-IR spectrum, associated with this PCET reaction, amide I (CO) and amide II (CN/NH) bands were observed. Specific (13)C-labeling of the tyrosine C1 carbon assigned a component of these bands to the Y122-T123 amide bond. Comparison to density functional calculations on a model dipeptide, tyrosine-threonine, and structural modeling demonstrated that PCET is associated with a Y122 rotation and a 7.2 Å translation of the Y122 phenolic oxygen. To test for the functional consequences of this structural change, a proton inventory defined the origin of the large solvent isotope effect (SIE = 16.7 ± 1.0 at 25 °C) on this reaction. These data suggest that the one-electron, HU-mediated reduction of Y122O(•) is associated with two, rate-limiting (full or partial) proton transfer reactions. One is attributable to HU oxidation (SIE = 11.9, net H atom transfer), and the other is attributable to coupled, hydrogen-bonding changes in the Y122O(•)-diferric cofactor (SIE = 1.4). These results illustrate the importance of redox-linked changes to backbone and ring dihedral angles in high potential PCET and provide evidence for rate-limiting, redox-linked hydrogen-bonding interactions between Y122O(•) and the iron cluster.

Free-radical polymer science structural cancer model: a review

Polymer free-radical lipid alkene chain-growth biological models particularly for hypoxic cellular mitochondrial metabolic waste can be used to better understand abnormal cancer cell morphology and invasive metastasis. Without oxygen as the final electron acceptor for mitochondrial energy synthesis, protons cannot combine to form water and instead mitochondria produce free radicals and acid during hypoxia. Nonuniform bond-length shrinkage of membranes related to erratic free-radical covalent crosslinking can explain cancer-cell pleomorphism with epithelial-mesenchymal transition for irregular membrane borders that "ruffle" and warp over stiff underlying actin fibers. Further, mitochondrial hypoxic conditions produce acid that can cause molecular degradation. Subsequent low pH-activated enzymes then provide paths for invasive cell movement through tissue and eventually blood-born metastasis. Although free-radical crosslinking creates irregularly shaped membranes with structural actin-polymerized fiber extensions as filopodia and lamellipodia, due to rapid cell division the overall cell modulus (approximately stiffness) is lower than normal cells. When combined with low pH-activated enzymes and lower modulus cells, smaller cancer stem cells subsequently have a large advantage to follow molecular destructive pathways and leave the central tumor. In addition, forward structural spike-like lamellipodia protrusions can leverage to force lower-modulus cancer cells through narrow openings. By squeezing and deforming even smaller to allow for easier movement through difficult passageways, cancer cells can travel into adjacent tissues or possibly metastasize through the blood to new tissue.

Proton Coupled Electron Transfer and Redox Active Tyrosines: Structure and Function of the Tyrosyl Radicals in Ribonucleotide Reductase and Photosystem II

Proton coupled electron transfer (PCET) reactions are important in many biological processes. Tyrosine oxidation/reduction can play a critical role in facilitating these reactions. Two examples are photosystem II (PSII) and ribonucleotide reductase (RNR). RNR is essential in DNA synthesis in all organisms. In E. coli RNR, a tyrosyl radical, Y122(•), is required as a radical initiator. Photosystem II (PSII) generates molecular oxygen from water. In PSII, an essential tyrosyl radical, YZ(•), oxidizes the oxygen evolving center. However, the mechanisms, by which the extraordinary oxidizing power of the tyrosyl radical is controlled, are not well understood. This is due to the difficulty in acquiring high-resolution structural information about the radical state. Spectroscopic approaches, such as EPR and UV resonance Raman (UVRR), can give new information. Here, we discuss EPR studies of PCET and the PSII YZ radical. We also present UVRR results, which support the conclusion that Y122 undergoes an alteration in ring and backbone dihedral angle when it is oxidized. This conformational change results in a loss of hydrogen bonding to the phenolic oxygen. Our analysis suggests that access of water is an important factor in determining tyrosyl radical lifetime and function. TOC graphic.

Proton coupled electron transfer and redox active tyrosines in Photosystem II

In this article, progress in understanding proton coupled electron transfer (PCET) in Photosystem II is reviewed. Changes in acidity/basicity may accompany oxidation/reduction reactions in biological catalysis. Alterations in the proton transfer pathway can then be used to alter the rates of the electron transfer reactions. Studies of the bioenergetic complexes have played a central role in advancing our understanding of PCET. Because oxidation of the tyrosine results in deprotonation of the phenolic oxygen, redox active tyrosines are involved in PCET reactions in several enzymes. This review focuses on PCET involving the redox active tyrosines in Photosystem II. Photosystem II catalyzes the light-driven oxidation of water and reduction of plastoquinone. Photosystem II provides a paradigm for the study of redox active tyrosines, because this photosynthetic reaction center contains two tyrosines with different roles in catalysis. The tyrosines, YZ and YD, exhibit differences in kinetics and midpoint potentials, and these differences may be due to noncovalent interactions with the protein environment. Here, studies of YD and YZ and relevant model compounds are described.

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.

Control of proton and electron transfer in de novo designed, biomimetic β hairpins

Tyrosine side chains are involved in proton coupled electron transfer reactions (PCET) in many complex proteins, including photosystem II (PSII) and ribonucleotide reductase. For example, PSII contains two redox-active tyrosines, TyrD (Y160D2) and TyrZ (Y161D1), which have different protein environments, midpoint potentials, and roles in catalysis. TyrD has a midpoint potential lower than that of TyrZ, and its protein environment is distinguished by potential π-cation interactions with arginine residues. Designed biomimetic peptides provide a system that can be used to investigate how the protein matrix controls PCET reactions. As a model for the redox-active tyrosines in PSII, we are employing a designed, 18 amino acid β hairpin peptide in which PCET reactions occur between a tyrosine (Tyr5) and a cross-strand histidine (His14). In this peptide, the single tyrosine is hydrogen-bonded to an arginine residue, Arg16, and a second arginine, Arg12, has a π-cation interaction with Tyr5. In this report, the effect of these hydrogen bonding and electrostatic interactions on the PCET reactions is investigated. Electrochemical titrations show that histidine substitutions change the nature of PCET reactions, and optical titrations show that Arg16 substitution changes the pK of Tyr5. Removal of Arg16 or Arg12 increases the midpoint potential for tyrosine oxidation. The effects of Arg12 substitution are consistent with the midpoint potential difference, which is observed for the PSII redox-active tyrosine residues. Our results demonstrate that a π-cation interaction, hydrogen bonding, and PCET reactions alter redox-active tyrosine function. These interactions can contribute equally to the control of midpoint potential and reaction rate.

Redox-linked structural changes in ribonucleotide reductase

Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides. Class I RNRs are composed of two homodimeric proteins, alpha2 and beta2. The class Ia E. coli beta2 contains dinuclear, antiferromagnetically coupled iron centers and one tyrosyl free radical, Y122*/beta2. Y122* acts as a radical initiator in catalysis. Redox-linked conformational changes may accompany Y122 oxidation and provide local control of proton-coupled electron transfer reactions. To test for such redox-linked structural changes, FT-IR spectroscopy was employed in this work. Reaction-induced difference spectra, associated with the reduction of Y122* by hydroxyurea, were acquired from natural abundance, (2)H(4) tyrosine, and (15)N tyrosine labeled beta2 samples. Isotopic labeling led to the assignment of a 1514 cm(-1) band to the upsilon19a ring stretching vibration of Y122 and of a 1498 cm(-1) band to the upsilon7a CO stretching vibration of Y122*. The reaction-induced spectra also exhibited amide I bands, at 1661 and 1652 cm(-1). A similar set of amide I bands, with frequencies of 1675 and 1651 cm(-1), was observed when Y* was generated by photolysis in a pentapeptide, which matched the primary sequence surrounding Y122. This result suggests that reduction of Y122* is linked with structural changes at nearby amide bonds and that this perturbation is mediated by the primary sequence. To explain these data, we propose that a structural perturbation of the amide bond is driven by redox-linked electrostatic changes in the tyrosyl radical aromatic ring.

A spectroscopic investigation of a tridentate Cu-complex mimicking the tyrosine-histidine cross-link of cytochrome C oxidase

Heme-copper oxidases have a crucial role in the energy transduction mechanism, catalyzing the reduction of dioxygen to water. The reduction of dioxygen takes place at the binuclear center, which contains heme a3 and CuB. The X-ray crystal structures have revealed that the C6' of tyrosine 244 (bovine heart numbering) is cross-linked to a nitrogen of histidine 240, a ligand to CuB. The role of the cross-linked tyrosine at the active site still remains unclear. In order to provide insight into the function of the cross-linked tyrosine, we have investigated the spectroscopic and electrochemical properties of chemical analogues of the CuB-His-Tyr site. The analogues, a tridentate histidine-phenol cross-linked ether ligand and the corresponding Cu-containing complex, were previously synthesized in our laboratory (White, K.; et al. Chem. Commun. 2007, 3252-3254). Spectrophotometric titrations of the ligand and the Cu-complex indicate a pKa of the phenolic proton of 8.8 and 7.7, respectively. These results are consistent with the cross-linked tyrosine playing a proton delivery role at the cytochrome c oxidase active site. The presence of the phenoxyl radical was investigated at low temperature using electron paramagnetic resonance (EPR) and Fourier transform infrared (FT-IR) difference spectroscopy. UV photolysis of the ligand, without bound copper, generated a narrow g=2.0047 signal, attributed to the phenoxyl radial. EPR spectra recorded before and after UV photolysis of the Cu-complex showed a g=2 signal characteristic of oxidized copper, suggesting that the copper is not spin-coupled to the phenoxyl radical. An EPR signal from the phenoxyl radical was not observed in the Cu-complex, either due to spin relaxation of the two unpaired electrons or to masking of the narrow phenoxyl radical signal by the strong copper contribution. Stable isotope (13C) labeling of the phenol ring (C1') Cu-complex, combined with photoinduced difference FT-IR spectroscopy, revealed bands at 1485 and 1483 cm(-1) in the 12C-minus-13C-isotope-edited spectra of the ligand and Cu-complex, respectively. These bands are attributed to the radical v7a stretching frequency and are shifted to 1468 and 1472 cm(-1), respectively, with 13C1' labeling. These results show that a radical is generated in both the ligand and the Cu-complex and support the unambiguous assignment of a vibrational band to the phenoxyl radical v7a stretching mode. These data are discussed with respect to a possible role of the cross-linked tyrosine radical in cytochrome c oxidase.

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.

ESEEM studies of peptide nitrogen hyperfine coupling in tyrosyl radicals and model peptides

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, we have performed 14N and 15N electron spin echo envelope modulation (ESEEM) measurements on tyrosyl radical, generated either in polycrystalline tyrosinate or in its 15N-labeled isotopomer, by UV photolysis. 14N-ESEEM was also performed on tyrosyl radical generated in tyrosine-containing pentapeptide samples. Simulation of the 14N- and 15N-tyrosyl radical ESEEM measurements yielded no significant isotropic hyperfine splitting to the amine or amide nitrogen; the amplitude of the anisotropic, nitrogen hyperfine coupling (0.21 MHz) was consistent with a dipole-dipole distance of 3.0 A. Density functional theory was used to calculate the isotropic and anisotropic hyperfine couplings to the amino nitrogen in four different tyrosyl radical conformers. Comparison with the simulated data suggested that the lowest energy radical conformer, generated in tyrosine at pH 11, has a 76 degrees Calpha-Cbeta-C1'-C2' ring and a -73 degrees C-Calpha-Cbeta-C1' backbone dihedral angle. In addition, the magnitude, orientation, and asymmetry of the nuclear quadrupole coupling tensor were derived from analysis of the tyrosyl radical 14N-ESEEM. The simulations showed differences in the coupling and orientation of the nuclear quadrupole tensor, when the tyrosinate and pentapeptide samples were compared. These results suggest sequence- or conformation-induced changes in the ionic character of the NH bond in different tyrosine-containing peptides.

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.