Radical initiation in the class I ribonucleotide reductase: long-range proton-coupled electron transfer?

Kinetic Effects of Hydrogen Bonds on Proton-Coupled Electron Transfer from Phenols

The kinetics and mechanism of proton-coupled electron transfer (PCET) from a series of phenols to a laser flash generated [Ru(bpy)(3)](3+) oxidant in aqueous solution was investigated. The reaction followed a concerted electron-proton transfer mechanism (CEP), both for the substituted phenols with an intramolecular hydrogen bond to a carboxylate group and for those where the proton was directly transferred to water. Without internal hydrogen bonds the concerted mechanism gave a characteristic pH-dependent rate for the phenol form that followed a Marcus free energy dependence, first reported for an intramolecular PCET in Sjödin, M. et al. J. Am. Chem. Soc. 2000, 122, 3932-3962 and now demonstrated also for a bimolecular oxidation of unsubstituted phenol. With internal hydrogen bonds instead, the rate was no longer pH-dependent, because the proton was transferred to the carboxylate base. The results suggest that while a concerted reaction has a relatively high reorganization energy (lambda), this may be significantly reduced by the hydrogen bonds, allowing for a lower barrier reaction path. It is further suggested that this is a general mechanism by which proton-coupled electron transfer in radical enzymes and model complexes may be promoted by hydrogen bonding. This is different from, and possibly in addition to, the generally suggested effect of hydrogen bonds on PCET in enhancing the proton vibrational wave function overlap between the reactant and donor states. In addition we demonstrate how the mechanism for phenol oxidation changes from a stepwise electron transfer-proton transfer with a stronger oxidant to a CEP with a weaker oxidant, for the same series of phenols. The hydrogen bonded CEP reaction may thus allow for a low energy barrier path that can operate efficiently at low driving forces, which is ideal for PCET reactions in biological systems.

The Involvement of Arg265 of Mouse Ribonucleotide Reductase R2 Protein in Proton Transfer and Catalysis

Ribonucleotide reductase class I enzymes consist of two non-identical subunits, R1 and R2, the latter containing a diiron carboxylate center and a stable tyrosyl radical (Tyr*), both essential for catalysis. Catalysis is known to involve highly conserved amino acid residues covering a range of approximately 35 A and a concerted mechanism involving long range electron transfer, probably coupled to proton transfer. A number of residues involved in electron transfer in both the R1 and R2 proteins have been identified, but no direct model has been presented regarding the proton transfer side of the process. Arg265 is conserved in all known sequences of class Ia R2. In this study we have used site-directed mutagenesis to gain insight into the role of this residue, which lies close to the catalytically essential Asp266 and Trp103. Mutants to Arg265 included replacement by Ala, Glu, Gln, and Tyr. All mutants of Arg265 were found to have no or low catalytic activity with the exception of Arg265 to Glu, which shows approximately 40% of the activity of native R2. We also found that the Arg mutants were capable of stable tyrosyl radical generation, with similar kinetics of radical formation and R1 binding as native R2. Our results, supported by molecular modeling, strongly suggest that Arg265 is involved in the proton-coupled electron transfer pathway and may act as a proton mediator during catalysis.

Cation mediation of radical transfer between Trp48 and Tyr356 during O2 activation by protein R2 of Escherichia coli ribonucleotide reductase: relevance to R1-R2 radical transfer in nucleotide reduction?

A tryptophan 48 cation radical (W48(+)(*)) forms concomitantly with the Fe(2)(III/IV) cluster, X, during activation of oxygen for tyrosyl radical (Y122.) production in the R2 subunit of class I ribonucleotide reductase (RNR) from Escherichia coli. W48(+)(*) is also likely to be an intermediate in the long-range radical transfer between R2 and its partner subunit, R1, during nucleotide reduction by the RNR holoenzyme. The kinetics of decay of W48(+)(*) and formation of tyrosyl radicals during O(2) activation (in the absence of R1) in wild-type (wt) R2 and in variants with either Y122, Y356 (the residue thought to propagate the radical from W48(+)(*) into R1 during turnover), or both replaced by phenylalanine (F) have revealed that the presence of divalent cations at concentrations similar to the [Mg(2+)] employed in the standard RNR assay (15 mM) mediates a rapid radical-transfer equilibrium between W48 and Y356. Cation-mediated propagation of the radical from W48 to Y356 gives rise to a fast phase of Y. production that is essentially coincident with W48(+)(*) formation and creates an efficient pathway for decay of W48(+)(*). Possible mechanisms of this cation mediation and its potential relevance to intersubunit radical transfer during nucleotide reduction are considered.

High-field pulsed electron-electron double resonance spectroscopy to determine the orientation of the tyrosyl radicals in ribonucleotide reductase

Class I ribonucleotide reductases (RNRs) are composed of two subunits, R1 and R2. The R2 subunit contains the essential diferric cluster-tyrosyl radical (Y.) cofactor, and R1 is the site of the conversion of nucleoside diphosphates to 2'-deoxynucleoside diphosphates. It has been proposed that the function of the tyrosyl radical in R2 is to generate a transient thiyl radical (C439.) in R1 over a distance of 35 A, which in turn initiates the reduction process. EPR distance measurements provide a tool with which to study the mechanism of radical initiation in class I RNRs. These types of experiments at low magnetic fields and frequencies (0.3 T, 9 GHz) give insight into interradical distances and populations. We present a pulsed electron-electron double resonance (PELDOR) experiment at high EPR frequency (180-GHz electron Larmor frequency) that detects the dipolar interaction between the Y.s in each protomer of RNR R2 from Escherichia coli. We observe a correlation between the orientation-dependent dipolar interaction and their resolved g-tensors. This information has allowed us to define the relative orientation of two radicals embedded in the active homodimeric protein in solution. This experiment demonstrates that high-field PELDOR spectroscopy is a powerful tool with which to study the assembly of proteins that contain multiple paramagnetic centers.

Mechanistic Studies of Hangman Salophen-Mediated Activation of O−O Bonds

Stopped-flow kinetic studies of a HSX-Mn-SalophOMe (1) catalyst provide spectroscopic evidence for the direct generation of a manganese(V) oxo salophen from a manganese(III) perbenzoate. The O-O bond heterolysis reaction that produces the oxo is not facilitated by intramolecular proton transfer from the acid hanging group of the HSX platform. Instead, the hanging group stabilizes the catalyst against oxidative degradation and, consistent with recent predictions of theory, is geometrically matched to promote the end-on coordination of a H2O2 substrate prior to its oxidation at the manganese(V) oxo center.

Electrocatalytic Oxidation of Tyrosine by Parallel Rate-Limiting Proton Transfer and Multisite Electron−Proton Transfer

The oxidation of the amino acids tyrosine and tryptophan by complexes based on M(bpy)33+ (M = Ru, Os) was studied by monitoring the cyclic voltammetry of the metal complex in the presence of the oxidizable amino acids. Addition of both amino acids to aqueous solutions of the metal complexes in phosphate buffer produced electrocatalytic enhancement in the oxidative wave observed at indium tin oxide electrodes. The kinetics for the oxidation by the Ru(III) and Os(III) forms was determined by digital simulation. The oxidation kinetics for tryptophan were consistent with outer-sphere electron transfer, giving an expected dependence of the oxidation rate constant on the reduction potential of the metal complex. In contrast, oxidation of tyrosine at pH 7.5 did not give an appreciable dependence on the metal complex potential. These results were explained by a kinetic model where proton transfer from tyrosine to phosphate can be the rate-limiting step in competition with a concerted, multisite electron-proton-transfer pathway that is observed at lower base concentrations. These results suggest that tyrosine oxidation in enzymes can access both pathways depending on the solvent accessibility of the oxidized residue and the availability of a suitable proton acceptor.

Correlating structure with function in bacterial multicomponent monooxygenases and related diiron proteins

Bacterial multicomponent monooxygenases (BMMs) catalyze the O2-dependent hydroxylation of hydrocarbons at a carboxylate-bridged diiron center similar to those that occur in a variety of dimetallic oxygen-utilizing enzymes. BMMs have found numerous biodegradation and biocatalytic applications. Recent investigations have begun to reveal how BMMs perform their C-H bond activation chemistry and why these enzymes may be mechanistically different from other related diiron proteins. The structures of the BMM component proteins and of complexes between them provide insights into the tuning of the dinuclear iron center and the enzyme mechanism. Selected findings are compared and contrasted with the properties of other carboxylate-bridged diiron proteins, revealing common structural and functional themes.

Orientation of the tyrosyl radical in Salmonella typhimurium class Ib ribonucleotide reductase determined by high field EPR of R2F single crystals

The R2 protein of class I ribonucleotide reductase (RNR) generates and stores a tyrosyl radical, located next to a diferric iron center, which is essential for ribonucleotide reduction and thus DNA synthesis. X-ray structures of class Ia and Ib proteins from various organisms served as bases for detailed mechanistic suggestions. The active site tyrosine in R2F of class Ib RNR of Salmonella typhimurium is located at larger distance to the diiron site, and shows a different side chain orientation, as compared with the tyrosine in R2 of class Ia RNR from Escherichia coli. No structural information has been available for the active tyrosyl radical in R2F. Here we report on high field EPR experiments of single crystals of R2F from S. typhimurium, containing the radical Tyr-105*. Full rotational pattern of the spectra were recorded, and the orientation of the g-tensor axes were determined, which directly reflect the orientation of the radical Tyr-105* in the crystal frame. Comparison with the orientation of the reduced tyrosine Tyr-105-OH from the x-ray structure reveals a rotation of the tyrosyl side chain, which reduces the distance between the tyrosyl radical and the nearest iron ligands toward similar values as observed earlier for Tyr-122* in E. coli R2. Presence of the substrate binding subunit R1E did not change the EPR spectra of Tyr-105*, indicating that binding of R2E alone induces no structural change of the diiron site. The present study demonstrates that structural and functional information about active radical states can be obtained by combining x-ray and high-field-EPR crystallography.

Hydrogen Atom Abstraction by a Mononuclear Ferric Hydroxide Complex: Insights into the Reactivity of Lipoxygenase

The lipoxygenase mimic [Fe(III)(PY5)(OH)](CF3SO3)2 is synthesized from the reaction of [Fe(II)(PY5)(MeCN)](CF3SO3)2 with iodosobenzene, with low-temperature studies suggesting the possible intermediacy of an Fe(IV) oxo species. The Fe(III)-OH complex is isolated and identified by a combination of solution and solid-state methods, including EPR and IR spectroscopy. [Fe(III)(PY5)(OH)](2+) reacts with weak X-H bonds in a manner consistent with hydrogen-atom abstraction. The composition of this complex allows meaningful comparisons to be made with previously reported Mn(III)-OH and Fe(III)-OMe lipoxygenase mimics. The bond dissociation energy (BDE) of the O-H bond formed upon reduction to [Fe(II)(PY5)(H2O)]2+ is estimated to be 80 kcal mol(-1), 2 kcal mol(-1) lower than that in the structurally analogous [Mn(II)(PY5)(H2O)]2+ complex, supporting the generally accepted idea that Mn(III) is the thermodynamically superior oxidant at parity of coordination sphere. The identity of the metal has a large influence on the entropy of activation for the reaction with 9,10-dihydroanthracene; [Mn(III)(PY5)(OH)]2+ has a 10 eu more negative DeltaS++ value than either [Fe(III)(PY5)(OH)]2+ or [Fe(III)(PY5)(OMe)]2+, presumably because of the increased structural reorganization that occurs upon reduction to [Mn(II)(PY5)(H2O)]2+. The greater enthalpic driving force for the reduction of Mn(III) correlates with [Mn(III)(PY5)(OH)]2+ reacting more quickly than [Fe(III)(PY5)(OH)]2+. Curiously, [Fe(III)(PY5)(OMe)]2+ reacts with substrates only about twice as fast as [Fe(III)(PY5)(OH)]2+, despite a 4 kcal mol(-1) greater enthalpic driving force for the methoxide complex.

Carboxylates as Proton-Accepting Groups in Concerted Proton−Electron Transfers. Electrochemistry of the 2,5-Dicarboxylate 1,4-Hydrobenzoquinone/2,5-Dicarboxy 1,4-Benzoquinone Couple

Concerted proton and electron transfers (CPET) currently attract considerable theoretical and experimental attention, notably in view of their likely involvement in many enzymatic reactions. The role of carboxylate groups as proton-accepting sites in CPET reactions is explored by means of a cyclic voltammetric investigation of the 2,5-dicarboxy 1,4-benzoquinone/2,5-dicarboxylate 1,4-hydrobenzoquinone couple in a nonaqueous medium. The presence of carboxylate groups ortho to the phenol groups induces the removal of an electron to be coupled with the transfer of the phenolic proton to a carboxylate oxygen. The kinetics of the electrochemical reaction and the observation of a significant hydrogen/deuterium kinetic isotope effect unambiguously indicate that electron transfer and proton transfer are concerted, thus providing an additional demonstration of the role of carboxylate groups as proton-accepting sites in concerted proton-electron transfer reactions.

Ribonucleotide Reductases

Ribonucleotide reductases (RNRs) transform RNA building blocks to DNA building blocks by catalyzing the substitution of the 2'OH-group of a ribonucleotide with a hydrogen by a mechanism involving protein radicals. Three classes of RNRs employ different mechanisms for the generation of the protein radical. Recent structural studies of members from each class have led to a deeper understanding of their catalytic mechanism and allosteric regulation by nucleoside triphosphates. The main emphasis of this review is on regulation of RNR at the molecular and cellular level. Conformational transitions induced by nucleotide binding determine the regulation of substrate specificity. An intricate interplay between gene activation, enzyme inhibition, and protein degradation regulates, together with the allosteric effects, enzyme activity and provides the appropriate amount of deoxynucleotides for DNA replication and repair. In spite of large differences in the amino acid sequences, basic structural features are remarkably similar and suggest a common evolutionary origin for the three classes.

Concerted proton-electron transfer in the oxidation of hydrogen-bonded phenols

Three phenols with pendant, hydrogen-bonded bases (HOAr-B) have been oxidized in MeCN with various one-electron oxidants. The bases are a primary amine (-CPh(2)NH(2)), an imidazole, and a pyridine. The product of chemical and quasi-reversible electrochemical oxidations in each case is the phenoxyl radical in which the phenolic proton has transferred to the base, (*)OAr-BH(+), a proton-coupled electron transfer (PCET) process. The redox potentials for these oxidations are lower than for other phenols, predominately from the driving force for proton movement. One-electron oxidation of the phenols occurs by a concerted proton-electron transfer (CPET) mechanism, based on thermochemical arguments, isotope effects, and DeltaDeltaG(++)/DeltaDeltaG degrees . The data rule out stepwise paths involving initial electron transfer to form the phenol radical cations [(*)(+)HOAr-B] or initial proton transfer to give the zwitterions [(-)OAr-BH(+)]. The rate constant for heterogeneous electron transfer from HOAr-NH(2) to a platinum electrode has been derived from electrochemical measurements. For oxidations of HOAr-NH(2), the dependence of the solution rate constants on driving force, on temperature, and on the nature of the oxidant, and the correspondence between the homogeneous and heterogeneous rate constants, are all consistent with the application of adiabatic Marcus theory. The CPET reorganization energies, lambda = 23-56 kcal mol(-)(1), are large in comparison with those for electron transfer reactions of aromatic compounds. The reactions are not highly non-adiabatic, based on minimum values of H(rp) derived from the temperature dependence of the rate constants. These are among the first detailed analyses of CPET reactions where the proton and electron move to different sites.

Concerted proton-electron transfer in the oxidation of hydrogen-bonded phenols

Three phenols with pendant, hydrogen-bonded bases (HOAr-B) have been oxidized in MeCN with various one-electron oxidants. The bases are a primary amine (-CPh(2)NH(2)), an imidazole, and a pyridine. The product of chemical and quasi-reversible electrochemical oxidations in each case is the phenoxyl radical in which the phenolic proton has transferred to the base, (*)OAr-BH(+), a proton-coupled electron transfer (PCET) process. The redox potentials for these oxidations are lower than for other phenols, predominately from the driving force for proton movement. One-electron oxidation of the phenols occurs by a concerted proton-electron transfer (CPET) mechanism, based on thermochemical arguments, isotope effects, and DeltaDeltaG(++)/DeltaDeltaG degrees . The data rule out stepwise paths involving initial electron transfer to form the phenol radical cations [(*)(+)HOAr-B] or initial proton transfer to give the zwitterions [(-)OAr-BH(+)]. The rate constant for heterogeneous electron transfer from HOAr-NH(2) to a platinum electrode has been derived from electrochemical measurements. For oxidations of HOAr-NH(2), the dependence of the solution rate constants on driving force, on temperature, and on the nature of the oxidant, and the correspondence between the homogeneous and heterogeneous rate constants, are all consistent with the application of adiabatic Marcus theory. The CPET reorganization energies, lambda = 23-56 kcal mol(-)(1), are large in comparison with those for electron transfer reactions of aromatic compounds. The reactions are not highly non-adiabatic, based on minimum values of H(rp) derived from the temperature dependence of the rate constants. These are among the first detailed analyses of CPET reactions where the proton and electron move to different sites.

Site-specific replacement of Y356 with 3,4-dihydroxyphenylalanine in the beta2 subunit of E. coli ribonucleotide reductase

E. coli ribonucleotide reductase (RNR), composed of the homodimeric subunits alpha2 and beta2, catalyzes the conversion of nucleotides to deoxynucleotides via complex radical chemistry. The radical initiation process involves a putative proton-coupled electron transfer (PCET) pathway over 35 A between alpha2 and beta2. Y356 in beta2 has been proposed to lie on this pathway. To test this model, intein technology has been used to make beta2 semi-synthetically in which Y356 is replaced with a DOPA-amino acid. Analysis of this mutant with alpha2 and various combinations of substrate and effector by SF UV-vis spectroscopy and EPR methods demonstrates formation of a DOPA radical concomitant with disappearance of the tyrosyl radical, which initiates the reaction. The results reveal that Y356 lies on the PCET pathway and demonstrate the first kinetically competent conformational changes prior to ET. They further show that substrate binding brings about rapid conformational changes which place the complex into its active form(s) and suggest that the RNR complex is asymmetric.

pH Rate profiles of FnY356-R2s (n = 2, 3, 4) in Escherichia coli ribonucleotide reductase: evidence that Y356 is a redox-active amino acid along the radical propagation pathway

The Escherichia coli ribonucleotide reductase (RNR), composed of two subunits (R1 and R2), catalyzes the conversion of nucleotides to deoxynucleotides. Substrate reduction requires that a tyrosyl radical (Y(122)*) in R2 generate a transient cysteinyl radical (C(439)*) in R1 through a pathway thought to involve amino acid radical intermediates [Y(122)* --> W(48) --> Y(356) within R2 to Y(731) --> Y(730) --> C(439) within R1]. To study this radical propagation process, we have synthesized R2 semisynthetically using intein technology and replaced Y(356) with a variety of fluorinated tyrosine analogues (2,3-F(2)Y, 3,5-F(2)Y, 2,3,5-F(3)Y, 2,3,6-F(3)Y, and F(4)Y) that have been described and characterized in the accompanying paper. These fluorinated tyrosine derivatives have potentials that vary from -50 to +270 mV relative to tyrosine over the accessible pH range for RNR and pK(a)s that range from 5.6 to 7.8. The pH rate profiles of deoxynucleotide production by these F(n)()Y(356)-R2s are reported. The results suggest that the rate-determining step can be changed from a physical step to the radical propagation step by altering the reduction potential of Y(356)* using these analogues. As the difference in potential of the F(n)()Y* relative to Y* becomes >80 mV, the activity of RNR becomes inhibited, and by 200 mV, RNR activity is no longer detectable. These studies support the model that Y(356) is a redox-active amino acid on the radical-propagation pathway. On the basis of our previous studies with 3-NO(2)Y(356)-R2, we assume that 2,3,5-F(3)Y(356), 2,3,6-F(3)Y(356), and F(4)Y(356)-R2s are all deprotonated at pH > 7.5. We show that they all efficiently initiate nucleotide reduction. If this assumption is correct, then a hydrogen-bonding pathway between W(48) and Y(356) of R2 and Y(731) of R1 does not play a central role in triggering radical initiation nor is hydrogen-atom transfer between these residues obligatory for radical propagation.

Electrochemical and Homogeneous Proton-Coupled Electron Transfers: Concerted Pathways in the One-Electron Oxidation of a Phenol Coupled with an Intramolecular Amine-Driven Proton Transfer

Proton-coupled electron transfers currently attract considerable attention in view of their likely involvement in many natural processes. Electrochemistry, through techniques such as cyclic voltammetry, is an efficient way of investigating the reaction mechanism of these reactions, and deciding whether proton and electron transfers are concerted or occur in a stepwise manner. The oxidation of an ortho-substituted 4,6-di (tert-butyl)-phenol in which the phenolic hydrogen atom is transferred during the reaction to the nitrogen atom of a nearby amine is taken as illustrative example. A careful analysis of the cyclic voltammetric responses obtained with this compound and its OD derivative allows, after estimation of the various thermodynamic parameters, ruling out the occurrence of the square scheme mechanism involving the proton-electron and electron-proton sequences. Simulation and comparison of the rate constant and H/D kinetic isotope effect with theoretical predictions show that the experimental value of the preexponential factor is ca. 1 order of magnitude larger than the theoretical value. Detailed calculations suggest that an electric field effect is responsible for this discrepancy.

Stalking intermediates in oxygen activation by iron enzymes: motivation and method

The study of high-valent-iron enzyme intermediates began in the mid-1900s with the discovery of compounds I (or ES) and II in the heme peroxidases, progressed to non-heme-diiron enzymes in the 1990s with the detection and characterization of the Fe(III)-Fe(IV) complex, X, and the Fe(IV)-Fe(IV) complex, Q, in O(2) activation by ribonucleotide reductase R2 (RNR-R2) and soluble methane monooxygenase (sMMO), respectively, and was most recently extended to mononuclear non-heme-iron oxygenases with the trapping and spectroscopic characterization of the Fe(IV)-oxo intermediate, J, in the reaction of taurine:alpha-ketoglutarate dioxygenase (TauD). Individually, each of these landmark studies helped reveal the chemical logic of that particular enzyme system. Collectively, they have significantly advanced our understanding of Nature's strategies for oxidative transformation of biomolecules (both natural and "xenobiotic"). With high-valent complexes now having been described in representatives of three major classes of iron enzymes, it is an appropriate time to ask whether and what additional insights might be gleaned from further stalking of related intermediates in other systems. In this review, we advocate that there is still much to be learned from this pursuit and summarize the insight provided by two of the landmark discoveries mentioned above (the latter two) and the subsequent studies that they spurred to support our contention. In addition, we attempt to provide, to the extent that it is possible to do so, a "how-to" guide for detection and characterization of such intermediates, focusing primarily on enzymes in which they form by activation of molecular oxygen. In this latter objective, we have drawn from an earlier review by Johnson (Enzymes, third ed. vol. 20, 1992, pp. 1-61) covering, more generally, dissection of enzyme reaction pathways by transient-state kinetic methods. That work elegantly illustrated that, although it may be impossible to develop a true algorithm for the process, a synthesis of guidelines and general principles can be of considerable value.

Avoiding high-valent iron intermediates: superoxide reductase and rubrerythrin

The Fenton or Fenton-type reaction between aqueous ferrous ion and hydrogen peroxide generates a highly oxidizing species, most often formulated as hydroxyl radical or ferryl ([Fe(IV)O](2+)). Intracellular Fenton-type chemistry can be lethal if not controlled. Nature has, therefore, evolved enzymes to scavenge superoxide and hydrogen peroxide, the reduced dioxygen species that initiate intracellular Fenton-type chemistry. Two such enzymes found predominantly in air-sensitive bacteria and archaea, superoxide reductase (SOR) and rubrerythrin (Rbr), functioning as a peroxidase (hydrogen peroxide reductase), contain non-heme iron. The iron coordination spheres in these enzymes contain five or six protein ligands from His and Glu residues, and, in the case of SOR, a Cys residue. SOR contains a mononuclear active site that is designed to protonate and rapidly expel peroxide generated as a product of the enzymatic reaction. The ferrous SOR reacts adventitiously but relatively slowly (several seconds to a few minutes) with exogenous hydrogen peroxide, presumably in a Fenton-type reaction. The diferrous active site of Rbr reacts more rapidly with hydrogen peroxide but can divert Fenton-type reactions towards the two-electron reduction of hydrogen peroxide to water. Proximal aromatic residues may function as radical sinks for Fenton-generated oxidants. Fenton-initiated damage to these iron active sites may become apparent only under extremely oxidizing intracellular conditions.

Spectroscopic and computational studies of the de novo designed protein DF2t: correlation to the biferrous active site of ribonucleotide reductase and factors that affect O2 reactivity

DF2t, a de novo designed protein that mimics the active-site structure of many non-heme biferrous enzymes, has been studied using a combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature variable-field (VTVH) MCD. The active site of DF2t is found to have one five-coordinate iron and one four-coordinate iron, which are weakly antiferromagnetically coupled through a mu-1,3 carboxylate bridge. These results bear a strong resemblance to the spectra of Escherichia coli ribonucleotide reductase (R2), and density functional theory calculations were conducted on the W48F/D84E R2 mutant in order to determine the energetics of formation of a monodentate end-on-bound O2 to one iron in the binuclear site. The mu-1,3 carboxylate bridges found in O2-activating enzymes lack efficient superexchange pathways for the second electron transfer (i.e., the OH/oxo bridge in hemerythrin), and simulations of the binding of O2 in a monodentate end-on manner revealed that the bridging carboxylate ligands do not appear capable of transferring an electron to O2 from the remote Fe. Comparison of the results from previous studies of the mu-1,2 biferric-peroxo structure, which bridges both irons, finds that the end-on superoxide mixed-valent species is considerably higher in energy than the bridging peroxo-diferric species. Thus, one of the differences between O2-activating and O2-binding proteins appears to be the ability of O2 to bridge both Fe centers to generate a peroxo intermediate capable of further reactivity.

Mono-, Di-, Tri-, and Tetra-Substituted Fluorotyrosines: New Probes for Enzymes That Use Tyrosyl Radicals in Catalysis†

A set of N-acylated, carboxyamide fluorotyrosine (F(n)()Y) analogues [Ac-3-FY-NH(2), Ac-3,5-F(2)Y-NH(2), Ac-2,3-F(2)Y-NH(2), Ac-2,3,5-F(3)Y-NH(2), Ac-2,3,6-F(3)Y-NH(2) and Ac-2,3,5,6-F(4)Y-NH(2)] have been synthesized from their corresponding amino acids to interrogate the detailed reaction mechanism(s) accessible to F(n)()Y*s in small molecules and in proteins. These Ac-F(n)()Y-NH(2) derivatives span a pK(a) range from 5.6 to 8.4 and a reduction potential range of 320 mV in the pH region accessible to most proteins (6-9). DFT electronic-structure calculations capture the observed trends for both the reduction potentials and pK(a)s. Dipeptides of the methyl ester of 4-benzoyl-l-phenylalanyl-F(n)()Ys at pH 4 were examined with a nanosecond laser pulse and transient absorption spectroscopy to provide absorption spectra of F(n)()Y*s. The EPR spectrum of each F(n)()Y* has also been determined by UV photolysis of solutions at pH 11 and 77 K. The ability to vary systematically both pK(a) and radical reduction potential, together with the facility to monitor radical formation with distinct absorption and EPR features, establishes that F(n)()Ys will be useful in the study of biological charge-transport mechanisms involving tyrosine. To demonstrate the efficacy of the fluorotyrosine method in unraveling charge transport in complex biological systems, we report the global substitution of tyrosine by 3-fluorotyrosine (3-FY) in the R2 subunit of ribonucleotide reductase (RNR) and present the EPR spectrum along with its simulation of 3-FY122*. In the companion paper, we demonstrate the utility of F(n)()Ys in providing insight into the mechanism of tyrosine oxidation in biological systems by incorporating them site-specifically at position 356 in the R2 subunit of Escherichia coli RNR.

A tryptophan neutral radical in the oxidized state of versatile peroxidase from Pleurotus eryngii: a combined multifrequency EPR and density functional theory study

Versatile peroxidases are heme enzymes that combine catalytic properties of lignin peroxidases and manganese peroxidases, being able to oxidize Mn(2+) as well as phenolic and non-phenolic aromatic compounds in the absence of mediators. The catalytic process (initiated by hydrogen peroxide) is the same as in classical peroxidases, with the involvement of 2 oxidizing equivalents and the formation of the so-called Compound I. This latter state contains an oxoferryl center and an organic cation radical that can be located on either the porphyrin ring or a protein residue. In this study, a radical intermediate in the reaction of versatile peroxidase from the ligninolytic fungus Pleurotus eryngii with H(2)O(2) has been characterized by multifrequency (9.4 and 94 GHz) EPR and assigned to a tryptophan residue. Comparison of experimental data and density functional theory theoretical results strongly suggests the assignment to a tryptophan neutral radical, excluding the assignment to a tryptophan cation radical or a histidine radical. Based on the experimentally determined side chain orientation and comparison with a high resolution crystal structure, the tryptophan neutral radical can be assigned to Trp(164) as the site involved in long-range electron transfer for aromatic substrate oxidation.

Electron-Transfer Oxidation Properties of Unsaturated Fatty Acids and Mechanistic Insight into Lipoxygenases

Rate constants of photoinduced electron-transfer oxidation of unsaturated fatty acids with a series of singlet excited states of oxidants in acetonitrile at 298 K were examined and the resulting electron-transfer rate constants (k(et)) were evaluated in light of the free energy relationship of electron transfer to determine the one-electron oxidation potentials (E(ox)) of unsaturated fatty acids and the intrinsic barrier of electron transfer. The k(et) values of linoleic acid with a series of oxidants are the same as the corresponding k(et) values of methyl linoleate, linolenic acid, and arachidonic acid, leading to the same E(ox) value of linoleic acid, methyl linoleate, linolenic acid, and arachidonic acid (1.76 V vs SCE), which is significantly lower than that of oleic acid (2.03 V vs SCE) as indicated by the smaller k(et) values of oleic acid than those of other unsaturated fatty acids. The radical cation of linoleic acid produced in photoinduced electron transfer from linoleic acid to the singlet excited state of 10-methylacridinium ion as well as that of 9,10-dicyanoanthracene was detected by laser flash photolysis experiments. The apparent rate constant of deprotonation of the radical cation of linoleic acid was determined as 8.1 x 10(3) s(-1). In the presence of oxygen, the addition of oxygen to the deprotonated radical produces the peroxyl radical, which has successfully been detected by ESR. No thermal electron transfer or proton-coupled electron transfer has occurred from linoleic acid to a strong one-electron oxidant, Ru(bpy)3(3+) (bpy = 2,2'-bipyridine) or Fe(bpy)3(3+). The present results on the electron-transfer and proton-transfer properties of unsaturated fatty acids provide valuable mechanistic insight into lipoxygenases to clarify the proton-coupled electron-transfer process in the catalytic function.

Mimicking the electron donor side of Photosystem II in artificial photosynthesis

This review focuses on our recent efforts in synthetic ruthenium-tyrosine-manganese chemistry mimicking the donor side reactions of Photosystem II. Tyrosine and tryptophan residues were linked to ruthenium photosensitizers, which resulted in model complexes for proton-coupled electron transfer from amino acids. A new mechanistic model was proposed and used to design complexes in which the mechanism could be switched between concerted and step-wise proton-coupled electron transfer. Moreover, a manganese dimer linked to a ruthenium complex could be oxidized in three successive steps, from Mn (2) (II,II) to Mn (2) (III,IV) by the photo-oxidized ruthenium sensitizer. This was possible thanks to a charge compensating ligand exchange in the manganese complex. Detailed studies of the ligand exchange suggested that at high water concentrations, each oxidation step is coupled to a proton-release of water-derived ligands, analogous to the oxidation steps of the manganese cluster of Photosystem II.

Phenoxyl radicals: H-bonded and coordinated to Cu(ii) and Zn(ii)

Two pro-ligands ((R)LH) comprised of an o,p-di-tert-butyl-substituted phenol covalently bonded to a benzimidazole ((Bz)LH) or a 4,5-di-p-methoxyphenyl substituted imidazole ((PhOMe)LH), have been structurally characterised. Each possesses an intramolecular O-H[dot dot dot]N hydrogen bond between the phenolic O-H group and an imidazole nitrogen atom and (1)H NMR studies show that this bond is retained in solution. Each (R)LH undergoes an electrochemically reversible, one-electron, oxidation to form the [(R)LH] (+) radical cation that is considered to be stabilised by an intramolecular O...H-N hydrogen bond. The (R)LH pro-ligands react with M(BF(4))(2).H(2)O (M = Cu or Zn) in the presence of Et(3)N to form the corresponding [M((R)L)(2)] compound. [Cu((Bz)L)(2)] (), [Cu((PhOMe)L)(2)] (), [Zn((Bz)L)(2)] and [Zn((PhOMe)L)(2)] have been isolated and the structures of .4MeCN, .2MeOH, .2MeCN and .2MeCN determined by X-ray crystallography. In each compound the metal possesses an N(2)O(2)-coordination sphere: in .4MeCN and .2MeOH the {CuN(2)O(2)} centre has a distorted square planar geometry; in .2MeCN and .2MeCN the {ZnN(2)O(2)} centre has a distorted tetrahedral geometry. The X-band EPR spectra of both and , in CH(2)Cl(2)-DMF (9 : 1) solution at 77 K, are consistent with the presence of a Cu(ii) complex having the structure identified by X-ray crystallography. Electrochemical studies have shown that each undergo two, one-electron, oxidations; the potentials of these processes and the UV/vis and EPR properties of the products indicate that each oxidation is ligand-based. The first oxidation produces [M(II)((R)L)((R)L )](+), comprising a M(ii) centre bound to a phenoxide ((R)L) and a phenoxyl radical ((R)L ) ligand; these cations have been generated electrochemically and, for R = PhOMe, chemically by oxidation with Ag[BF(4)]. The second oxidation produces [M(II)((R)L )(2)](2+). The information obtained from these investigations shows that a suitable pro-ligand design allows a relatively inert phenoxyl radical to be generated, stabilised by either a hydrogen bond, as in [(R)LH] (+) (R = Bz or PhOMe), or by coordination to a metal, as in [M(II)((R)L)((R)L )](+) (M = Cu or Zn; R = Bz or PhOMe). Coordination to a metal is more effective than hydrogen bonding in stabilising a phenoxyl radical and Cu(ii) is slightly more effective than Zn(II) in this respect.

MPW1K Performs Much Better than B3LYP in DFT Calculations on Reactions that Proceed by Proton-Coupled Electron Transfer (PCET)

DFT calculations have been performed with the B3LYP and MPW1K functional on the hydrogen atom abstraction reactions of ethenoxyl with ethenol and of phenoxyl with both phenol and alpha-naphthol. Comparison with the results of G3 calculations shows that B3LYP seriously underestimates the barrier heights for the reaction of ethenoxyl with ethenol by both proton-coupled electron transfer (PCET) and hydrogen atom transfer (HAT) mechanisms. The MPW1K functional also underestimates the barrier heights, but by much less than B3LYP. Similarly, comparison with the results of experiments on the reaction of phenoxyl radical with alpha-naphthol indicates that the barrier height for the preferred PCET mechanism is calculated more accurately by MPW1K than by B3LYP. These findings indicate that the MPW1K functional is much better suited than B3LYP for calculations on hydrogen abstraction reactions by both HAT and PCET mechanisms.

Models for proton-coupled electron transfer in photosystem II

The coupling of proton and electron transfers is a key part of the chemistry of photosynthesis. The oxidative side of photosystem II (PS II) in particular seems to involve a number of proton-coupled electron transfer (PCET) steps in the S-state transitions. This mini-review presents an overview of recent studies of PCET model systems in the authors' laboratory. PCET is defined as a chemical reaction involving concerted transfer of one electron and one proton. These are thus distinguished from stepwise pathways involving initial electron transfer (ET) or initial proton transfer (PT). Hydrogen atom transfer (HAT) reactions are one class of PCET, in which H(+) and e (-) are transferred from one reagent to another: AH + B --> A + BH, roughly along the same path. Rate constants for many HAT reactions are found to be well predicted by the thermochemistry of hydrogen transfer and by Marcus Theory. This includes organic HAT reactions and reactions of iron-tris(alpha-diimine) and manganese-(mu-oxo) complexes. In PS II, HAT has been proposed as the mechanism by which the tyrosine Z radical (Y(Z)*) oxidizes the manganese cluster (the oxygen evolving complex, OEC). Another class of PCET reactions involves transfer of H(+) and e (-) in different directions, for instance when the proton and electron acceptors are different reagents, as in AH-B + C(+) --> A-HB(+) + C. The oxidation of Y(Z) by the chlorophyll P680 + has been suggested to occur by this mechanism. Models for this process - the oxidation of phenols with a pendent base - are described. The oxidation of the OEC by Y(Z)* could also occur by this second class of PCET reactions, involving an Mn-O-H fragment of the OEC. Initial attempts to model such a process using ruthenium-aquo complexes are described.

Vitamin B12: chemistry and biochemistry

Vitamin B12, the 'antipernicious anaemia factor', is required for human and animal metabolism. It was discovered in the late 1940s and its unique corrin ligand was revealed approx. 10 years later by X-ray crystallography. The B12-coenzymes are cofactors in various important enzymatic reactions and are particularly relevant in the metabolism of anaerobic microorganisms. Microorganisms are the only natural sources of the B12-derivatives, whereas most spheres of life (except for the higher plants) depend on these cobalt corrinoids.

Spectroscopic and theoretical approaches for studying radical reactions in class I ribonucleotide reductase

Ribonucleotide reductases (RNRs) catalyze the production of deoxyribonucleotides, which are essential for DNA synthesis and repair in all organisms. The three currently known classes of RNRs are postulated to utilize a similar mechanism for ribonucleotide reduction via a transient thiyl radical, but they differ in the way this radical is generated. Class I RNR, found in all eukaryotic organisms and in some eubacteria and viruses, employs a diferric iron center and a stable tyrosyl radical in a second protein subunit, R2, to drive thiyl radical generation near the substrate binding site in subunit R1. From extensive experimental and theoretical research during the last decades, a general mechanistic model for class I RNR has emerged, showing three major mechanistic steps: generation of the tyrosyl radical by the diiron center in subunit R2, radical transfer to generate the proposed thiyl radical near the substrate bound in subunit R1, and finally catalytic reduction of the bound ribonucleotide. Amino acid- or substrate-derived radicals are involved in all three major reactions. This article summarizes the present mechanistic picture of class I RNR and highlights experimental and theoretical approaches that have contributed to our current understanding of this important class of radical enzymes.

Electron Flow in Multicenter Enzymes: Theory, Applications, and Consequences on the Natural Design of Redox Chains

In protein film voltammetry, a redox enzyme is directly connected to an electrode; in the presence of substrate and when the driving force provided by the electrode is appropriate, a current flow reveals the steady-state turnover. We show that, in the case of a multicenter enzyme, this signal reports on the energetics and kinetics of electron transfer (ET) along the redox chain that wires the active site to the electrode, and this provides a new strategy for studying intramolecular ET. We propose a model which takes into account all the enzyme's redox microstates, and we prove it useful to interpret data for various enzymes. Several general ideas emerge from this analysis. Considering the reversibility of ET is a requirement: the usual picture, where ET is depicted as a series of irreversible steps, is oversimplified and lacks the important features that we emphasize. We give justification to the concept of apparent reduction potential on the time scale of turnover and we explain how the value of this potential relates to the thermodynamic and kinetic properties of the system. When intramolecular ET does not limit turnover, the redox chain merely mediates the driving force provided by the electrode or the soluble redox partner, whereas when intramolecular ET is slow, the enzyme behaves as if its active active site had apparent redox properties which depend on the reduction potentials of the relays. This suggests an alternative to the idea that redox chains are optimized in terms of speed: evolutionary pressure may have resulted in slowing down intramolecular ET in order to tune the enzyme's "operating potential".

Photoelectron Spectra and Ion Chemistry of Imidazolide†

The 351.1 nm photoelectron spectrum of imidazolide anion has been measured. The electron affinity (EA) of the imidazolyl radical is determined to be 2.613 +/- 0.006 eV. Vibrational frequencies of 955 +/- 15 and 1365 +/- 20 cm(-1) are observed in the spectrum of the (2)B1 ground state of the imidazolyl radical. The main features in the spectrum are well-reproduced by Franck-Condon simulation based on the optimized geometries and the normal modes obtained at the B3LYP/6-311++G(d,p) level of density functional theory. The two vibrational frequencies are assigned to totally symmetric modes with C-C and N-C stretching motions. Overtone peaks of an in-plane nontotally symmetric mode are observed in the spectrum and attributed to Fermi resonance. Also observed is the photoelectron spectrum of the anion formed by deprotonation of imidazole at the C5 position. The EA of the corresponding radical, 5-imidazolyl, is 1.992 +/- 0.010 eV. The gas phase acidity of imidazole has been determined using a flowing afterglow-selected ion tube; delta(acid)G298 = 342.6 +/- 0.4 and delta(acid)H298 = 349.7 +/- 0.5 kcal mol(-1). From the EA of imidazolyl radical and gas phase acidity of imidazole, the bond dissociation energy for the N-H bond in imidazole is determined to be 95.1 +/- 0.5 kcal mol(-1). These thermodynamic parameters for imidazole and imidazolyl radical are compared with those for pyrrole and pyrrolyl radical, and the effects of the additional N atom in the five-membered ring are discussed.

EPR distance measurements support a model for long-range radical initiation in E. coli ribonucleotide reductase

The class I E. coli ribonucleotide reductase, composed of homodimers of R1 and R2, catalyzes the conversion of nucleoside diphosphates to deoxynucleoside diphosphates. The reduction process involves the tyrosyl radical on R2 that generates a transient thiyl radical on R1 over a proposed distance of 35 A. A mechanism-based inhibitor, 2'-azido-2'-deoxyuridine-5'-diphosphate, that reduces the tyrosyl radical on R2 and forms a nitrogen-centered radical on R1 has provided a method to measure the diagonal distance between the two subunits. PELDOR and DQC paramagnetic resonance methods give rise to a distance of 48 A, similar to that calculated from a docking model of the R1 and R2 structures.

Molecular Chemistry of Consequence to Renewable Energy

Energy conversion cycles are aimed at driving unfavorable, small-molecule activation reactions with a photon harnessed directly by a transition-metal catalyst or indirectly by a transition-metal catalyst at the surface of a photovoltaic cell. The construction of such cycles confronts daunting challenges because they rely on chemical transformations not understood at the most basic levels. These transformations include multielectron transfer, proton-coupled electron transfer, and bond-breaking and -making reactions of energy-poor substrates. We have begun to explore these poorly understood areas of molecular science with transition-metal complexes that promote hydrogen production and oxygen bond-breaking and -making chemistry of consequence to water splitting.

Moving a Phenol Hydroxyl Group from the Surface to the Interior of a Protein: Effects on the Phenol Potential and pKA

De novo protein design and electrochemistry were used to measure changes in the potential and pK(A) of a phenol when its OH group is moved from a solvent-exposed to a sequestered protein position. A "phenol rotation strategy" was adopted in which phenols, containing a SH in position 4, 3, or 2 relative to the OH group, were bound to a buried protein site. The alpha(3)C protein used here is a tryptophan to cysteine variant of the structurally defined alpha(3)W protein (Dai et al. (2002) J. Am. Chem. Soc. 124, 10952-10953). The protein characteristics of alpha(3)C and the three mercaptophenol-alpha(3)C (MP-alpha(3)C) proteins are shown to be close to those of alpha(3)W. Moreover, the phenol OH group is fully solvent exposed in 4MP-alpha(3)C and more sequestered in 3MP-alpha(3)C and 2MP-alpha(3)C. Here we compare the redox properties of the three mercaptophenols when bound to alpha(3)C and to cysteine free in water. The pK(A) and E(peak) values are essential identical when 4MP is ligated to alpha(3)C relative to when it is free in solution. In contrast, these values are increased in 3MP-alpha(3)C and 2MP-alpha(3)C relative to the solvated compounds. The E(peak) vs pH plots all display a approximately 59 mV/pH unit dependence. We conclude that interactions with the OH group dominate the phenol redox characteristics. In 3MP-alpha(3)C and 2MP-alpha(3)C, hydrogen bonds between the protein and the bound phenols appear to either stabilize the reduced phenol or destabilize the radical, relative to the aqueous buffer, raising the potential by 0.11 and 0.12 V, respectively.

A stable FeIII-FeIV replacement of tyrosyl radical in a class I ribonucleotide reductase

Ribonucleotide reductase (RNR) of Chlamydia trachomatis is a class I RNR enzyme composed of two homodimeric components, proteins R1 and R2. In class I RNR, R1 has the substrate binding site, whereas R2 has a diferric site and normally in its active form a stable tyrosyl free radical. C. trachomatis RNR is unusual, because its R2 component has a phenylalanine in the place of the radical carrier tyrosine. Replacing the tyrosyl radical, a paramagnetic Fe(III)-Fe(IV) species (species X, normally a transient intermediate in the process leading to radical formation) may provide the oxidation equivalent needed to start the catalytic process via long range electron transfer from the active site in R1. Here EPR spectroscopy shows that in C. trachomatis RNR, species X can become essentially stable when formed in a complete RNR (R1/R2/substrate) complex, adding further weight to the possible role of this species X in the catalytic reaction.

Direct Tyrosine Oxidation Using the MLCT Excited States of Rhenium Polypyridyl Complexes

Rhenium(I) polypyridyl complexes have been designed for the intramolecular photogeneration of tyrosyl radical. Tyrosine (Y) and phenylalanine (F) have each been separately appended to a conventional Re(I)(bpy)(CO)(3)CN framework via an amide linkage to the bipyridine (bpy) ligand. Comparative time-resolved emission quenching and transient absorption spectra of Re(bpy-Y)(CO)(3)CN and Re(bpy-F)(CO)(3)CN show that Y is oxidized only upon its deprotonation at pH 12. In an effort to redirect electron transport so that it is more compatible with intramolecular Y oxidation, polypyridyl Re(I) complexes have been prepared with the amide bond functionality located on a pendant phosphine ligand. A [Re(phen)(PP-Bn)(CO)(2)](PF(6)) (PP = bis(diphenylphosphino)ethylene) complex has been synthesized and crystallographically characterized. Electrochemistry and phosphorescence measurements of this complex indicate a modest excited-state potential for tyrosine oxidation, similar to that for the (bpy)Re(I)(CO)(3)CN framework. The excited-state oxidation potential can be increased by introducing a monodentate phosphine to the Re(I)(NN)(CO)(3)(+) framework (NN = polypyridyl). In this case, Y is oxidized at all pHs when appended to the triphenylphosphine (P) of [Re(phen)(P-Y)(CO(3))](PF(6)). Analysis of the pH dependence of the rate constant for tyrosyl radical generation is consistent with a proton-coupled electron transfer (PCET) quenching mechanism.

Artificial diiron proteins: from structure to function

De novo protein design provides an attractive approach for the construction of models to probe the features required for the function of complex metalloproteins. These minimal models contain the essential elements believed necessary for activity of the protein. In this article, we summarize the design, structure determination, and functional properties of a family of artificial diiron proteins.

Local and global effects of metal binding within the small subunit of ribonucleotide reductase

Each beta-protomer of the small betabeta subunit of Escherichia coli ribonucleotide reductase (R2) contains a binuclear iron cluster with inequivalent binding sites: Fe(A) and Fe(B). In anaerobic Fe(II) titrations of apoprotein under standard buffer conditions, we show that the majority of the protein binds only one Fe(II) atom per betabeta subunit. Additional iron occupation can be achieved upon exposure to O2 or in high glycerol buffers. The differential binding affinity of the A- and B-sites allows us to produce heterobinuclear Mn(II)Fe(II) and novel Mn(III)Fe(III) clusters within a single beta-protomer of R2. The oxidized species are produced with H2O2 addition. We demonstrate that no significant exchange of metal occurs between the A- and B-sites, and thus the binding of the first metal is under kinetic control, as has been suggested previously. The binding of first Fe(II) atom to the active site in a beta-protomer (betaI) induces a global protein conformational change that inhibits access of metal to the active site in the other beta-protomer (betaII). The binding of the same Fe(II) atom also induces a local effect at the active site in betaI-protomer, which lowers the affinity for metal in the A-site. The mixed metal FeMn species are quantitatively characterized with electron paramagnetic resonance spectroscopy. The previously reported catalase activity of Mn2(II)R2 is shown not to be associated with Mn.

Exploring amino-acid radical chemistry: protein engineering and de novo design

Amino-acid radical enzymes are often highly complex structures containing multiple protein subunits and cofactors. These properties have in many cases hampered the detailed characterization of their amino-acid redox cofactors. To address this problem, a range of approaches has recently been developed in which a common strategy is to reduce the complexity of the radical-containing system. This work will be reviewed and it includes the light-induced generation of aromatic radicals in small-molecule and peptide systems. Natural redox proteins, including the blue copper protein azurin and a bacterial photosynthetic reaction center, have been engineered to introduce amino-acid radical chemistry. The redesign strategies to achieve this remarkable change in the properties of these proteins will be described. An additional approach to gain insights into the properties of amino-acid radicals is to synthesize de novo designed model proteins in which the redox chemistry of these species can be studied. Here we describe the design, synthesis and characteristics of monomeric three-helix bundle and four-helix bundle proteins designed to study the redox chemistry of tryptophan and tyrosine. This work demonstrates that de novo protein design combined with structural, electrochemical and quantum chemical analyses can provide detailed information on how the protein matrix tunes the thermodynamic properties of tryptophan.

Structure and interactions of amino acid radicals in class I ribonucleotide reductase studied by ENDOR and high-field EPR spectroscopy

This short review compiles high-field electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) studies on different intermediate amino acid radicals, which emerge in wild-type and mutant class I ribonucleotide reductase (RNR) both in the reaction of protein subunit R2 with molecular oxygen, which generates the essential tyrosyl radical, and in the catalytic reaction, which involves a radical transfer between subunits R2 and R1. Recent examples are presented, how different amino acid radicals (tyrosyl, tryptophan, and different cysteine-based radicals) were identified, assigned to a specific residue, and their interactions, in particular hydrogen bonding, were investigated using high-field EPR and ENDOR spectroscopy. Thereby, unexpected diiron-radical centers, which emerge in mutants of R2 with changed iron coordination, and an important catalytic cysteine-based intermediate in the substrate turnover reaction in R1 were identified and characterized. Experiments on the essential tyrosyl radical in R2 single crystals revealed the so far unknown conformational changes induced by formation of the radical. Interesting structural differences between the tyrosyl radicals of class Ia and Ib enzymes were revealed. Recently accurate distances between the tyrosyl radicals in the protein dimer R2 could be determined using pulsed electron-electron double resonance (PELDOR), providing a new tool for docking studies of protein subunits. These studies show that high-field EPR and ENDOR are important tools for the identification and investigation of radical intermediates, which contributed significantly to the current understanding of the reaction mechanism of class I RNR.

Light-driven enzymatic catalysis of DNA repair: a review of recent biophysical studies on photolyase

More than 50 years ago, initial experiments on enzymatic photorepair of ultraviolet (UV)-damaged DNA were reported [Proc. Natl. Acad. Sci. U. S. A. 35 (1949) 73]. Soon after this discovery, it was recognized that one enzyme, photolyase, is able to repair UV-induced DNA lesions by effectively reversing their formation using blue light. The enzymatic process named DNA photoreactivation depends on a non-covalently bound cofactor, flavin adenine dinucleotide (FAD). Flavins are ubiquitous redox-active catalysts in one- and two-electron transfer reactions of numerous biological processes. However, in the case of photolyase, not only the ground-state redox properties of the FAD cofactor are exploited but also, and perhaps more importantly, its excited-state properties. In the catalytically active, fully reduced redox form, the FAD absorbs in the blue and near-UV ranges of visible light. Although there is no direct experimental evidence, it appears generally accepted that starting from the excited singlet state, the chromophore initiates a reductive cleavage of the two major DNA photodamages, cyclobutane pyrimidine dimers and (6-4) photoproducts, by short-distance electron transfer to the DNA lesion. Back electron transfer from the repaired DNA segment is believed to eventually restore the initial redox states of the cofactor and the DNA nucleobases, resulting in an overall reaction with net-zero exchanged electrons. Thus, the entire process represents a true catalytic cycle. Many biochemical and biophysical studies have been carried out to unravel the fundamentals of this unique mode of action. The work has culminated in the elucidation of the three-dimensional structure of the enzyme in 1995 that revealed remarkable details, such as the FAD-cofactor arrangement in an unusual U-shaped configuration. With the crystal structure of the enzyme at hand, research on photolyases did not come to an end but, for good reason, intensified: the geometrical structure of the enzyme alone is not sufficient to fully understand the enzyme's action on UV-damaged DNA. Much effort has therefore been invested to learn more about, for example, the geometry of the enzyme-substrate complex, and the mechanism and pathways of intra-enzyme and enzyme <-->DNA electron transfer. Many of the key results from biochemical and molecular biology characterizations of the enzyme or the enzyme-substrate complex have been summarized in a number of reviews. Complementary to these articles, this review focuses on recent biophysical studies of photoreactivation comprising work performed from the early 1990s until the present.

pH Dependence of charge transfer between tryptophan and tyrosine in dipeptides

Time-resolved absorption spectroscopy has been employed to study the directionality and rate of charge transfer in W-Y and Ac-W-Y dipeptides as a function of pH. Excitation with 266-nm nanosecond laser pulses produces both W (or [WH](+), depending on pH) and Y. Between pH 6 and 10, W to was found to oxidize Y with k(X)=9.0x10(4) s(-1) and 1.8x10(4) s(-1) for the W-Y and Ac-W-Y dipeptide systems, respectively. The intramolecular charge transfer rate increases as the pH is lowered over the range 6>pH>2. For 10<pH<12, the rate of radical transport for the W-Y dipeptide decreases and becomes convoluted with other radical decay processes, the timescales of which have been identified in studies of control dipeptides Ac-F-Y and W-F. Further increases in pH prompt the reverse reaction to occur, W-Y-->W-Y(-) (Y(-), tyrosinate anion), with a rate constant of k(X)=1.2x10(5) s(-1). The dependence of charge transfer directionality between W and Y on pH is important to the enzymatic function of several model and natural biological systems as discussed here for ribonucleotide reductase.