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

A unique cysteine-rich zinc finger domain present in a majority of class II ribonucleotide reductases mediates catalytic turnover

Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides, used in DNA synthesis and repair. Two different mechanisms help deliver the required electrons to the RNR active site. Formate can be used as reductant directly in the active site, or glutaredoxins or thioredoxins reduce a C-terminal cysteine pair, which then delivers the electrons to the active site. Here, we characterized a novel cysteine-rich C-terminal domain (CRD), which is present in most class II RNRs found in microbes. The NrdJd-type RNR from the bacterium Stackebrandtia nassauensis was used as a model enzyme. We show that the CRD is involved in both higher oligomeric state formation and electron transfer to the active site. The CRD-dependent formation of high oligomers, such as tetramers and hexamers, was induced by addition of dATP or dGTP, but not of dTTP or dCTP. The electron transfer was mediated by an array of six cysteine residues at the very C-terminal end, which also coordinated a zinc atom. The electron transfer can also occur between subunits, depending on the enzyme's oligomeric state. An investigation of the native reductant of the system revealed no interaction with glutaredoxins or thioredoxins, indicating that this class II RNR uses a different electron source. Our results indicate that the CRD has a crucial role in catalytic turnover and a potentially new terminal reduction mechanism and suggest that the CRD is important for the activities of many class II RNRs.

The [4Fe4S] cluster of human DNA primase functions as a redox switch using DNA charge transport

DNA charge transport chemistry offers a means of long-range, rapid redox signaling. We demonstrate that the [4Fe4S] cluster in human DNA primase can make use of this chemistry to coordinate the first steps of DNA synthesis. Using DNA electrochemistry, we found that a change in oxidation state of the [4Fe4S] cluster acts as a switch for DNA binding. Single-atom mutations that inhibit this charge transfer hinder primase initiation without affecting primase structure or polymerization. Generating a single base mismatch in the growing primer duplex, which attenuates DNA charge transport, inhibits primer truncation. Thus, redox signaling by [4Fe4S] clusters using DNA charge transport regulates primase binding to DNA and illustrates chemistry that may efficiently drive substrate handoff between polymerases during DNA replication.

Photolyase: Dynamics and electron-transfer mechanisms of DNA repair

Photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) and pyrimidine-pyrimidone (6-4) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair. Here, we review our comprehensive characterization of the dynamics of flavin cofactor and its repair photocycles by different classes of photolyases on the most fundamental level. Using femtosecond spectroscopy and molecular biology, significant advances have recently been made to map out the entire dynamical evolution and determine actual timescales of all the catalytic processes in photolyases. The repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. The unified, bifurcated ET mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. For 6-4 photoproduct repair, a similar cyclic ET mechanism operates and a new cyclic proton transfer with a conserved histidine residue at the active site of (6-4) photolyases is revealed.

Spectroscopic Evidence for a H Bond Network at Y356 Located at the Subunit Interface of Active E. coli Ribonucleotide Reductase

The reaction catalyzed by E. coli ribonucleotide reductase (RNR) composed of α and β subunits that form an active α2β2 complex is a paradigm for proton-coupled electron transfer (PCET) processes in biological transformations. β2 contains the diferric tyrosyl radical (Y₁₂₂·) cofactor that initiates radical transfer (RT) over 35 Å via a specific pathway of amino acids (Y₁₂₂· ⇆ [W₄₈] ⇆ Y₃₅₆ in β2 to Y₇₃₁ ⇆ Y₇₃₀ ⇆ C₄₃₉ in α2). Experimental evidence exists for colinear and orthogonal PCET in α2 and β2, respectively. No mechanistic model yet exists for the PCET across the subunit (α/β) interface. Here, we report unique EPR spectroscopic features of Y₃₅₆·-β, the pathway intermediate generated by the reaction of 2,3,5-F₃Y₁₂₂·-β2/CDP/ATP with wt-α2, Y₇₃₁F-α2, or Y₇₃₀F-α2. High field EPR (94 and 263 GHz) reveals a dramatically perturbed g tensor. [¹H] and [²H]-ENDOR reveal two exchangeable H bonds to Y₃₅₆·: a moderate one almost in-plane with the π-system and a weak one. DFT calculation on small models of Y· indicates that two in-plane, moderate H bonds (r_O-H ∼1.8-1.9 Å) are required to reproduce the g_x value of Y₃₅₆· (wt-α2). The results are consistent with a model, in which a cluster of two, almost symmetrically oriented, water molecules provide the two moderate H bonds to Y₃₅₆· that likely form a hydrogen bond network of water molecules involved in either the reversible PCET across the subunit interface or in H⁺ release to the solvent during Y₃₅₆ oxidation.

Long-range proton-coupled electron transfer in the Escherichia coli class Ia ribonucleotide reductase

Escherichia coli class Ia ribonucleotide reductase (RNR) catalyzes the conversion of nucleotides to 2'-deoxynucleotides using a radical mechanism. Each turnover requires radical transfer from an assembled diferric tyrosyl radical (Y•) cofactor to the enzyme active site over 35 Å away. This unprecedented reaction occurs via an amino acid radical hopping pathway spanning two protein subunits. To study the mechanism of radical transport in RNR, a suite of biochemical approaches have been developed, such as site-directed incorporation of unnatural amino acids with altered electronic properties and photochemical generation of radical intermediates. The resulting variant RNRs have been investigated using a variety of time-resolved physical techniques, including transient absorption and stopped-flow UV-Vis spectroscopy, as well as rapid freeze-quench EPR, ENDOR, and PELDOR spectroscopic methods. The data suggest that radical transport occurs via proton-coupled electron transfer (PCET) and that the protein structure has evolved to manage the proton and electron transfer co-ordinates in order to prevent 'off-pathway' reactivity and build-up of oxidised intermediates. Thus, precise design and control over the factors that govern PCET is key to enabling reversible and long-range charge transport by amino acid radicals in RNR.

Ribonucleotide Reductase Requires Subunit Switching in Hypoxia to Maintain DNA Replication

Cells exposed to hypoxia experience replication stress but do not accumulate DNA damage, suggesting sustained DNA replication. Ribonucleotide reductase (RNR) is the only enzyme capable of de novo synthesis of deoxyribonucleotide triphosphates (dNTPs). However, oxygen is an essential cofactor for mammalian RNR (RRM1/RRM2 and RRM1/RRM2B), leading us to question the source of dNTPs in hypoxia. Here, we show that the RRM1/RRM2B enzyme is capable of retaining activity in hypoxia and therefore is favored over RRM1/RRM2 in order to preserve ongoing replication and avoid the accumulation of DNA damage. We found two distinct mechanisms by which RRM2B maintains hypoxic activity and identified responsible residues in RRM2B. The importance of RRM2B in the response to tumor hypoxia is further illustrated by correlation of its expression with a hypoxic signature in patient samples and its roles in tumor growth and radioresistance. Our data provide mechanistic insight into RNR biology, highlighting RRM2B as a hypoxic-specific, anti-cancer therapeutic target.

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RRM2B is induced in response to hypoxia in both cell models and patient datasets

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RRM2B retains activity in hypoxic conditions and is the favored RNR subunit in hypoxia

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Loss of RRM2B has detrimental consequences for cell fate, specifically in hypoxia

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RRM2B depletion enhanced hypoxic-specific apoptosis and increased radiosensitivity

Glutamate 52-β at the α/β subunit interface of Escherichia coli class Ia ribonucleotide reductase is essential for conformational gating of radical transfer

Ribonucleotide reductases (RNRs) catalyze the conversion of nucleoside diphosphate substrates (S) to deoxynucleotides with allosteric effectors (e) controlling their relative ratios and amounts, crucial for fidelity of DNA replication and repair. Escherichia coli class Ia RNR is composed of α and β subunits that form a transient, active α2β2 complex. The E. coli RNR is rate-limited by S/e-dependent conformational change(s) that trigger the radical initiation step through a pathway of 35 Å across the subunit (α/β) interface. The weak subunit affinity and complex nucleotide-dependent quaternary structures have precluded a molecular understanding of the kinetic gating mechanism(s) of the RNR machinery. Using a docking model of α2β2 created from X-ray structures of α and β and conserved residues from a new subclassification of the E. coli Ia RNR (Iag), we identified and investigated four residues at the α/β interface (Glu³⁵⁰ and Glu⁵² in β2 and Arg³²⁹ and Arg⁶³⁹ in α2) of potential interest in kinetic gating. Mutation of each residue resulted in loss of activity and with the exception of E52Q-β2, weakened subunit affinity. An RNR mutant with 2,3,5-trifluorotyrosine radical (F₃Y₁₂₂^•) replacing the stable Tyr₁₂₂^• in WT-β2, a mutation that partly overcomes conformational gating, was placed in the E52Q background. Incubation of this double mutant with His₆-α2/S/e resulted in an RNR capable of catalyzing pathway-radical formation (Tyr^356•-β2), 0.5 eq of dCDP/F₃Y₁₂₂^•, and formation of an α2β2 complex that is isolable in pulldown assays over 2 h. Negative stain EM images with S/e (GDP/TTP) revealed the uniformity of the α2β2 complex formed.

Anion-regulated electronic communication in a cyclometalated diruthenium complex with a urea bridge

A combined study of electrochemical measurements, intervalence charge transfer analysis, and DFT calculations suggests that the degree of urea-mediated electronic coupling between two cyclometalated ruthenium sites is enhanced by the coordination of urea with Br^- or Cl^-via hydrogen bonding. In contrast, the redox waves of the diruthenium complex become highly irreversible in the presence of relatively strong basic anions such as H₂PO₄^-, F^-, or OAc^-. This work demonstrates that the anion-urea interaction can be employed to regulate the electronic coupling and electron transfer between redox-active sites, suggesting the potential applications of the urea-functionalized diruthenium complex in anion sensing and stimuli-responsive molecular electronics.

Formal Reduction Potentials of Difluorotyrosine and Trifluorotyrosine Protein Residues: Defining the Thermodynamics of Multistep Radical Transfer

Redox-active tyrosines (Ys) play essential roles in enzymes involved in primary metabolism including energy transduction and deoxynucleotide production catalyzed by ribonucleotide reductases (RNRs). Thermodynamic characterization of Ys in solution and in proteins remains a challenge due to the high reduction potentials involved and the reactive nature of the radical state. The structurally characterized α₃Y model protein has allowed the first determination of formal reduction potentials (E°') for a Y residing within a protein (Berry, B. W.; Martı́nez-Rivera, M. C.; Tommos, C. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 9739-9743). Using Schultz's technology, a series of fluorotyrosines (F_nY, n = 2 or 3) was site-specifically incorporated into α₃Y. The global protein properties of the resulting α₃(3,5)F₂Y, α₃(2,3,5)F₃Y, α₃(2,3)F₂Y and α₃(2,3,6)F₃Y variants are essentially identical to those of α₃Y. A protein film square-wave voltammetry approach was developed to successfully obtain reversible voltammograms and E°'s of the very high-potential α₃F_nY proteins. E°'(pH 5.5; α₃F_nY(O•/OH)) spans a range of 1040 ± 3 mV to 1200 ± 3 mV versus the normal hydrogen electrode. This is comparable to the potentials of the most oxidizing redox cofactors in nature. The F_nY analogues, and the ability to site-specifically incorporate them into any protein of interest, provide new tools for mechanistic studies on redox-active Ys in proteins and on functional and aberrant hole-transfer reactions in metallo-enzymes. The former application is illustrated here by using the determined α₃F_nY ΔE°'s to model the thermodynamics of radical-transfer reactions in F_nY-RNRs and to experimentally test and support the key prediction made.

Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ)

Coproheme decarboxylase catalyzes two sequential oxidative decarboxylations with H2O2 as the oxidant, coproheme III as substrate and cofactor, and heme b as the product. Each reaction breaks a C-C bond and results in net loss of hydride, via steps that are not clear. Solution and solid-state structural characterization of the protein in complex with a substrate analog revealed a highly unconventional H2O2-activating distal environment with the reactive propionic acids (2 and 4) on the opposite side of the porphyrin plane. This suggested that, in contrast to direct C-H bond cleavage catalyzed by a high-valent iron intermediate, the coproheme oxidations must occur through mediating amino acid residues. A tyrosine that hydrogen bonds to propionate 2 in a position analogous to the substrate in ascorbate peroxidase is essential for both decarboxylations, while a lysine that salt bridges to propionate 4 is required solely for the second. A mechanism is proposed in which propionate 2 relays an oxidizing equivalent from a coproheme compound I intermediate to the reactive deprotonated tyrosine, forming Tyr•. This residue then abstracts a net hydrogen atom (H•) from propionate 2, followed by migration of the unpaired propionyl electron to the coproheme iron to yield the ferric harderoheme and CO2 products. A similar pathway is proposed for decarboxylation of propionate 4, but with a lysine residue as an essential proton shuttle. The proposed reaction suggests an extended relay of heme-mediated e-/H+ transfers and a novel route for the conversion of carboxylic acids to alkenes.

Post-translational modification of ribosomally synthesized peptides by a radical SAM epimerase in Bacillus subtilis

Ribosomally synthesized peptides are built out of L-amino acids, whereas D-amino acids are generally the hallmark of non-ribosomal synthetic processes. Here we show that the model bacterium Bacillus subtilis is able to produce a novel type of ribosomally synthesized and post-translationally modified peptide that contains D-amino acids, and which we propose to call epipeptides. We demonstrate that a two [4Fe-4S]-cluster radical S-adenosyl-L-methionine (SAM) enzyme converts L-amino acids into their D-counterparts by catalysing C_α-hydrogen-atom abstraction and using a critical cysteine residue as the hydrogen-atom donor. Unexpectedly, these D-amino acid residues proved to be essential for the activity of a peptide that induces the expression of LiaRS, a major component of the bacterial cell envelope stress-response system. Present in B. subtilis and in several members of the human microbiome, these epipeptides and radical SAM epimerases broaden the landscape of peptidyl structures accessible to living organisms.

Glutamate 350 Plays an Essential Role in Conformational Gating of Long-Range Radical Transport in Escherichia coli Class Ia Ribonucleotide Reductase

Escherichia coli class Ia ribonucleotide reductase (RNR) is composed of two subunits that form an active α2β2 complex. The nucleoside diphosphate substrates (NDP) are reduced in α2, 35 Å from the essential diferric-tyrosyl radical (Y₁₂₂^•) cofactor in β2. The Y₁₂₂^•-mediated oxidation of C₄₃₉ in α2 occurs by a pathway (Y₁₂₂ ⇆ [W₄₈] ⇆ Y₃₅₆ in β2 to Y₇₃₁ ⇆ Y₇₃₀ ⇆ C₄₃₉ in α2) across the α/β interface. The absence of an α2β2 structure precludes insight into the location of Y₃₅₆ and Y₇₃₁ at the subunit interface. The proximity in the primary sequence of the conserved E₃₅₀ to Y₃₅₆ in β2 suggested its importance in catalysis and/or conformational gating. To study its function, pH-rate profiles of wild-type β2/α2 and mutants in which 3,5-difluorotyrosine (F₂Y) replaces residue 356, 731, or both are reported in the presence of E₃₅₀ or E₃₅₀X (X = A, D, or Q) mutants. With E₃₅₀, activity is maintained at the pH extremes, suggesting that protonated and deprotonated states of F₂Y₃₅₆ and F₂Y₇₃₁ are active and that radical transport (RT) can occur across the interface by proton-coupled electron transfer at low pH or electron transfer at high pH. With E₃₅₀X mutants, all RNRs were inactive, suggesting that E₃₅₀ could be a proton acceptor during oxidation of the interface Ys. To determine if E₃₅₀ plays a role in conformational gating, the strong oxidants, NO₂Y₁₂₂^•-β2 and 2,3,5-F₃Y₁₂₂^•-β2, were reacted with α2, CDP, and ATP in E₃₅₀ and E₃₅₀X backgrounds and the reactions were monitored for pathway radicals by rapid freeze-quench electron paramagnetic resonance spectroscopy. Pathway radicals are generated only when E₃₅₀ is present, supporting its essential role in gating the conformational change(s) that initiates RT and masking its role as a proton acceptor.

Evidence for a Di-μ-oxo Diamond Core in the Mn(IV)/Fe(IV) Activation Intermediate of Ribonucleotide Reductase from Chlamydia trachomatis

High-valent iron and manganese complexes effect some of the most challenging biochemical reactions known, including hydrocarbon and water oxidations associated with the global carbon cycle and oxygenic photosynthesis, respectively. Their extreme reactivity presents an impediment to structural characterization, but their biological importance and potential chemical utility have, nevertheless, motivated extensive efforts toward that end. Several such intermediates accumulate during activation of class I ribonucleotide reductase (RNR) β subunits, which self-assemble dimetal cofactors with stable one-electron oxidants that serve to initiate the enzyme's free-radical mechanism. In the class I-c β subunit from Chlamydia trachomatis, a heterodinuclear Mn(II)/Fe(II) complex reacts with dioxygen to form a Mn(IV)/Fe(IV) intermediate, which undergoes reduction of the iron site to produce the active Mn(IV)/Fe(III) cofactor. Herein, we assess the structure of the Mn(IV)/Fe(IV) activation intermediate using Fe- and Mn-edge extended X-ray absorption fine structure (EXAFS) analysis and multifrequency pulse electron paramagnetic resonance (EPR) spectroscopy. The EXAFS results reveal a metal-metal vector of 2.74-2.75 Å and an intense light-atom (C/N/O) scattering interaction 1.8 Å from the Fe. Pulse EPR data reveal an exchangeable deuterium hyperfine coupling of strength |T| = 0.7 MHz, but no stronger couplings. The results suggest that the intermediate possesses a di-μ-oxo diamond core structure with a terminal hydroxide ligand to the Mn(IV).

Improving artificial metalloenzymes' activity by optimizing electron transfer

This feature article discusses the strategies to optimize electron transfer efficiency, towards enhancing the activity of artificial metalloenzymes.

OH cleavage from tyrosine: debunking a myth

During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C-O bond cleavage in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr -OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr -OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr -OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr -OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions, is also presented. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.

Autophagy induction causes a synthetic lethal sensitization to ribonucleotide reductase inhibition in breast cancer cells

Macroautophagy can promote cellular survival or death depending on the cellular context and its extent. We hypothesized that autophagy induction would synergize with a therapeutic agent targeting the autophagic cargo. To test this hypothesis, we treated breast cancer MDA-MB-231 cells with tamoxifen (TMX), which induces autophagy through an estrogen receptor-independent pathway. Induction of autophagy reduced cellular levels of RRM2, a subunit of ribonucleotide reductase (RR), the rate limiting enzyme in the production of deoxyribonucleotide triphosphates (dNTPs). This autophagy inducer was combined with COH29, an inhibitor developed in our laboratory that targets RR through a novel mechanism. The combination therapy showed synergistic effects on cytotoxicity in vitro and in an in vivo xenograft model. This cytotoxicity was blocked by knockdown of the autophagy protein ATG5 or addition of chloroquine, an autophagy inhibitor. The combined therapy also induced dNTP depletion and massive genomic instability, leading us to hypothesize that combining autophagy induction with RR inhibition can lead to mitotic catastrophe in rapidly dividing cells. We propose that this TMX + COH29 combined therapy may have clinical benefit. Furthermore, autophagy induction may be a general mechanism for augmenting the effects of chemotherapeutic agents.

A >200 meV Uphill Thermodynamic Landscape for Radical Transport in Escherichia coli Ribonucleotide Reductase Determined Using Fluorotyrosine-Substituted Enzymes

Escherichia coli class Ia ribonucleotide reductase (RNR) converts ribonucleotides to deoxynucleotides. A diferric-tyrosyl radical (Y₁₂₂•) in one subunit (β2) generates a transient thiyl radical in another subunit (α2) via long-range radical transport (RT) through aromatic amino acid residues (Y₁₂₂ ⇆ [W₄₈] ⇆ Y₃₅₆ in β2 to Y₇₃₁ ⇆ Y₇₃₀ ⇆ C₄₃₉ in α2). Equilibration of Y₃₅₆•, Y₇₃₁•, and Y₇₃₀• was recently observed using site specifically incorporated unnatural tyrosine analogs; however, equilibration between Y₁₂₂• and Y₃₅₆• has not been detected. Our recent report of Y₃₅₆• formation in a kinetically and chemically competent fashion in the reaction of β2 containing 2,3,5-trifluorotyrosine at Y₁₂₂ (F₃Y₁₂₂•-β2) with α2, CDP (substrate), and ATP (effector) has now afforded the opportunity to investigate equilibration of F₃Y₁₂₂• and Y₃₅₆•. Incubation of F₃Y₁₂₂•-β2, Y₇₃₁F-α2 (or Y₇₃₀F-α2), CDP, and ATP at different temperatures (2–37 °C) provides ΔE°′(F₃Y₁₂₂•–Y₃₅₆•) of 20 ± 10 mV at 25 °C. The pH dependence of the F₃Y₁₂₂• ⇆ Y₃₅₆• interconversion (pH 6.8–8.0) reveals that the proton from Y₃₅₆ is in rapid exchange with solvent, in contrast to the proton from Y₁₂₂. Insertion of 3,5-difluorotyrosine (F₂Y) at Y₃₅₆ and rapid freeze-quench EPR analysis of its reaction with Y₇₃₁F-α2, CDP, and ATP at pH 8.2 and 25 °C shows F₂Y₃₅₆• generation by the native Y₁₂₂•. F_nY-RNRs (n = 2 and 3) together provide a model for the thermodynamic landscape of the RT pathway in which the reaction between Y₁₂₂ and C₄₃₉ is ∼200 meV uphill.

Design of Ru(II) Complexes Based on Anthraimidazoledione-Functionalized Terpyridine Ligand for Improvement of Room-Temperature Luminescence Characteristics and Recognition of Selective Anions: Experimental and DFT/TD-DFT Study

In this work we report synthesis and characterization of three rigid and linear rodlike monometallic Ru(II) complexes based on a terpyridine ligand tightly connected to 9,10-anthraquinone electron-acceptor unit through phenyl-imidazole spacer. The motivation of designing these complexes is to enhance their excited-state lifetimes at room temperature. Interestingly it is found that all three complexes exhibit luminescence at room temperature with excited-state lifetimes in the range of 1.6-52.8 ns, depending upon the coligand as well as the solvent. Temperature-dependent luminescence investigations indicate that the energy gap between the emitting ³MLCT state and nonemitting metal-centered state ³MC in the complexes increased enormously compared with parent [Ru(tpy)₂]²⁺. In addition, by taking advantage of the imidazole NH proton(s), which became appreciably acidic upon combined effect of electron accepting anthraquinone moiety as well as metal ion coordination, we also examined anion recognition and sensing behaviors of the complexes in organic, mixed aqueous-organic as well as in solid medium through different optical channels such as absorption, steady-state and time-resolved emission, and ¹H NMR spectroscopic techniques. In conjunction with the experiment, computational investigation was also employed to examine the electronic structures of the complexes and accurate assignment of experimentally observed spectral and redox behaviors.

Electron flow through biological molecules: does hole hopping protect proteins from oxidative damage?

Biological electron transfers often occur between metal-containing cofactors that are separated by very large molecular distances. Employing photosensitizer-modified iron and copper proteins, we have shown that single-step electron tunneling can occur on nanosecond to microsecond timescales at distances between 15 and 20 Å. We also have shown that charge transport can occur over even longer distances by hole hopping (multistep tunneling) through intervening tyrosines and tryptophans. In this perspective, we advance the hypothesis that such hole hopping through Tyr/Trp chains could protect oxygenase, dioxygenase, and peroxidase enzymes from oxidative damage. In support of this view, by examining the structures of P450 (CYP102A) and 2OG-Fe (TauD) enzymes, we have identified candidate Tyr/Trp chains that could transfer holes from uncoupled high-potential intermediates to reductants in contact with protein surface sites.

Mechanistic stratification in electroactive biofilms of Geobacter sulfurreducens mediated by pilus nanowires

Electricity generation by Geobacter sulfurreducens biofilms grown on electrodes involves matrix-associated electron carriers, such as c-type cytochromes. Yet, the contribution of the biofilm's conductive pili remains uncertain, largely because pili-defective mutants also have cytochrome defects. Here we report that a pili-deficient mutant carrying an inactivating mutation in the pilus assembly motor PilB has no measurable defects in cytochrome expression, yet forms anode biofilms with reduced electroactivity and is unable to grow beyond a threshold distance (∼10 μm) from the underlying electrode. The defects are similar to those of a Tyr3 mutant, which produces poorly conductive pili. The results support a model in which the conductive pili permeate the biofilms to wire the cells to the conductive biofilm matrix and the underlying electrode, operating coordinately with cytochromes until the biofilm reaches a threshold thickness that limits the efficiency of the cytochrome pathway but not the functioning of the conductive pili network.

The roles played by cytochromes and conductive filamentous appendages (pili) in the electrical conductivity of Geobacter bacterial biofilms are controversial. Here, Steidl et al. present evidence that both mechanisms cooperate in thin biofilms, while pili are important for conductivity across thicker biofilms.

Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes: E. coli Ribonucleotide Reductase As an Example

Fluorinated tyrosines (F_nY’s, n = 2 and 3) have been site-specifically incorporated into E. coli class Ia ribonucleotide reductase (RNR) using the recently evolved M. jannaschii Y-tRNA synthetase/tRNA pair. Class Ia RNRs require four redox active Y’s, a stable Y radical (Y·) in the β subunit (position 122 in E. coli), and three transiently oxidized Y’s (356 in β and 731 and 730 in α) to initiate the radical-dependent nucleotide reduction process. F_nY (3,5; 2,3; 2,3,5; and 2,3,6) incorporation in place of Y₁₂₂-β and the X-ray structures of each resulting β with a diferric cluster are reported and compared with wt-β2 crystallized under the same conditions. The essential diferric-F_nY· cofactor is self-assembled from apo F_nY-β2, Fe²⁺, and O₂ to produce ∼1 Y·/β2 and ∼3 Fe³⁺/β2. The F_nY· are stable and active in nucleotide reduction with activities that vary from 5% to 85% that of wt-β2. Each F_nY·-β2 has been characterized by 9 and 130 GHz electron paramagnetic resonance and high-field electron nuclear double resonance spectroscopies. The hyperfine interactions associated with the ¹⁹F nucleus provide unique signatures of each F_nY· that are readily distinguishable from unlabeled Y·’s. The variability of the abiotic F_nY pK_a’s (6.4 to 7.8) and reduction potentials (−30 to +130 mV relative to Y at pH 7.5) provide probes of enzymatic reactions proposed to involve Y·’s in catalysis and to investigate the importance and identity of hopping Y·’s within redox active proteins proposed to protect them from uncoupled radical chemistry.

Photochemical Generation of a Tryptophan Radical within the Subunit Interface of Ribonucleotide Reductase

The Escherichia coli class Ia ribonucleotide reductase (RNR) achieves forward and reverse proton-coupled electron transfer (PCET) over a pathway of redox active amino acids (β-Y122 ⇌ β-Y356 ⇌ α-Y731 ⇌ α-Y730 ⇌ α-C439) spanning ∼35 Å and two subunits every time it turns over. We have developed photoRNRs that allow radical transport to be phototriggered at tyrosine (Y) or fluorotyrosine (FnY) residues along the PCET pathway. We now report a new photoRNR in which photooxidation of a tryptophan (W) residue replacing Y356 within the α/β subunit interface proceeds by a stepwise ET/PT (electron transfer then proton transfer) mechanism and provides an orthogonal spectroscopic handle with respect to radical pathway residues Y731 and Y730 in α. This construct displays an ∼3-fold enhancement in photochemical yield of W(•) relative to F3Y(•) and a ∼7-fold enhancement relative to Y(•). Photogeneration of the W(•) radical occurs with a rate constant of (4.4 ± 0.2) × 10(5) s(-1), which obeys a Marcus correlation for radical generation at the RNR subunit interface. Despite the fact that the Y → W variant displays no enzymatic activity in the absence of light, photogeneration of W(•) within the subunit interface results in 20% activity for turnover relative to wild-type RNR under the same conditions.

Modulation of Proton-Coupled Electron Transfer through Molybdenum-Quinonoid Interactions

An expanded series of π-bound molybdenum-quinonoid complexes supported by pendant phosphines has been synthesized. These compounds formally span three protonation-oxidation states of the quinonoid fragment (catechol, semiquinone, quinone) and two different oxidation states of the metal (Mo(0), Mo(II)), notably demonstrating a total of two protons and four electrons accessible in the system. Previously, the reduced Mo(0)-catechol complex 1 and its reaction with dioxygen to yield the two-proton/two-electron oxidized Mo(0)-quinone compound 4 was explored, while, herein, the expansion of the series to include the two-electron oxidized Mo(II)-catechol complex 2, the one-proton/two-electron oxidized Mo-semiquinone complex 3, and the two-proton/four-electron oxidized Mo(II)-quinone complexes 5 and 6 is reported. Transfer of multiple equivalents of protons and electrons from the Mo(0) and Mo(II) catechol complexes, 1 and 2, to H atom acceptor TEMPO suggests the presence of weak O-H bonds. Although thermochemical analyses are hindered by the irreversibility of the electrochemistry of the present compounds, the reactivity observed suggests weaker O-H bonds compared to the free catechol, indicating that proton-coupled electron transfer can be facilitated significantly by the π-bound metal center.

Proton-Coupled Electron Transfer in Organic Synthesis: Fundamentals, Applications, and Opportunities

Proton-coupled electron transfers (PCETs) are unconventional redox processes in which both protons and electrons are exchanged, often in a concerted elementary step. While PCET is now recognized to play a central a role in biological redox catalysis and inorganic energy conversion technologies, its applications in organic synthesis are only beginning to be explored. In this chapter, we aim to highlight the origins, development, and evolution of the PCET processes most relevant to applications in organic synthesis. Particular emphasis is given to the ability of PCET to serve as a non-classical mechanism for homolytic bond activation that is complimentary to more traditional hydrogen atom transfer processes, enabling the direct generation of valuable organic radical intermediates directly from their native functional group precursors under comparatively mild catalytic conditions. The synthetically advantageous features of PCET reactivity are described in detail, along with examples from the literature describing the PCET activation of common organic functional groups.

Four-Electron Oxidation of Phenols to p-Benzoquinone Imines by a (Salen)ruthenium(VI) Nitrido Complex

Proton-coupled electron-transfer reactions of phenols have received considerable attention because of their fundamental interest and their relevance to many biological processes. Here we describe a remarkable four-electron oxidation of phenols by a (salen)ruthenium(VI) complex in the presence of pyridine in CH3OH to afford (salen)ruthenium(II) p-benzoquinone imine complexes. Mechanistic studies indicate that this reaction occurs in two phases. The first phase is proposed to be a two-electron transfer process that involves electrophilic attack by Ru≡N at the phenol aromatic ring, followed by proton shift to generate a Ru(IV) p-hydroxyanilido intermediate. In the second phase the intermediate undergoes intramolecular two-electron transfer, followed by rapid deprotonation to give the Ru(II) p-benzoquinone imine product.

Intramolecular electron transfer in the dihaem cytochrome c peroxidase of Pseudomonas aeruginosa

Mutant forms of the enzyme cytochrome c peroxidase from Pseudomonas aeruginosa, in which the peroxidatic haem ligand (H71) and putative haem-bridging amino acid (W94) have been mutated, were produced in an E. coli expression system as a means of investigating possible mechanisms of intramolecular electron transfer within the enzyme. EPR spectroscopy indicated the presence of a high-spin, presumably five-coordinate, peroxidatic haem site in the H71G and H71G/W94A mutants, whilst the W94A mutant apparently retained the normal six-coordinate haem structures. In turnover experiments, these mutants show 55, 4, and <1% activity, respectively, as compared to the wild-type enzyme. The W94A mutant shows essentially no activity in turnover experiments. Circular dichroism spectroscopy indicates no measurable difference in the secondary structure of the H71G mutant from that of the native enzyme, whilst some small differences are observed for the double mutant. Treatment of the oxidised mutant proteins with hydrogen peroxide, in the absence of preactivation or exogenous reductants, yields products that suggest the formation of a tryptophan radical species in the case of the H71 mutant and the production of a porphyrin radical in the case of the double mutant. These results are discussed in terms of the intramolecular electron transfer in this enzyme.

Marcus-type driving force correlations reveal the mechanism of proton-coupled electron transfer for phenols and [Ru(bpy)3]3+ in water at low pH

We examined PCET between a series of phenol derivatives and photogenerated [Ru(bpy)₃]³⁺ in low pH (≤4) water using the laser flash-quench technique.

Proton-coupled electron transfer (PCET) from tyrosine and other phenol derivatives in water is an important elementary reaction in chemistry and biology. We examined PCET between a series of phenol derivatives and photogenerated [Ru(bpy)₃]³⁺ in low pH (≤4) water using the laser flash-quench technique. From an analysis of the kinetic data using a Marcus-type free energy relationship, we propose that our model system follows a stepwise electron transfer-proton transfer (ETPT) pathway with a pH independent rate constant at low pH in water. This is in contrast to the concerted or proton-first (PTET) mechanisms that often dominate at higher pH and/or with buffers as primary proton acceptors. The stepwise mechanism remains competitive despite a significant change in the pK_a and redox potential of the phenols which leads to a span of rate constants from 1 × 10⁵ to 2 × 10⁹ M^–1 s^–1. These results support our previous studies which revealed separate mechanistic regions for PCET reactions and also assigned phenol oxidation by [Ru(bpy)₃]³⁺ at low pH to a stepwise PCET mechanism.

Radical transfer in E. coli ribonucleotide reductase: a NH2Y731/R411A-α mutant unmasks a new conformation of the pathway residue 731

Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides in all living organisms. The catalytic cycle of E. coli RNR involves a long-range proton-coupled electron transfer (PCET) from a tyrosyl radical (Y122˙) in subunit β2 to a cysteine (C439) in the active site of subunit α2, which subsequently initiates nucleotide reduction. This oxidation occurs over 35 Å and involves a specific pathway of redox active amino acids (Y122 ↔ [W48?] ↔ Y356 in β2 to Y731 ↔ Y730 ↔ C439 in α2). The mechanisms of the PCET steps at the interface of the α2β2 complex remain puzzling due to a lack of structural information for this region. Recently, DFT calculations on the 3-aminotyrosyl radical (NH2Y731˙)-α2 trapped by incubation of NH2Y731-α2/β2/CDP(substrate)/ATP(allosteric effector) suggested that R411-α2, a residue close to the α2β2 interface, interacts with NH2Y731˙ and accounts in part for its perturbed EPR parameters. To examine its role, we further modified NH2Y731-α2 with a R411A substitution. NH2Y731˙/R411A generated upon incubation of NH2Y731/R411A-α2/β2/CDP/ATP was investigated using multi-frequency (34, 94 and 263 GHz) EPR, 34 GHz pulsed electron-electron double resonance (PELDOR) and electron-nuclear double resonance (ENDOR) spectroscopies. The data indicate a large conformational change in NH2Y731˙/R411A relative to the NH2Y731˙ single mutant. Particularly, the inter-spin distance from NH2Y731˙/R411A in one αβ pair to Y122˙ in a second αβ pair decreases by 3 Å in the presence of the R411A mutation. This is the first experimental evidence for the flexibility of pathway residue Y731-α2 in an α2β2 complex and suggests a role for R411 in the stacked Y731/Y730 conformation involved in collinear PCET. Furthermore, NH2Y731˙/R411A serves as a probe of the PCET process across the subunit interface.

Charge-Transfer Dynamics at the α/β Subunit Interface of a Photochemical Ribonucleotide Reductase

Ribonucleotide reductase (RNR) catalyzes the conversion of ribonucleotides to deoxyribonucleotides to provide the monomeric building blocks for DNA replication and repair. Nucleotide reduction occurs by way of multistep proton-coupled electron transfer (PCET) over a pathway of redox active amino acids spanning ∼35 Å and two subunits (α2 and β2). Despite the fact that PCET in RNR is rapid, slow conformational changes mask examination of the kinetics of these steps. As such, we have pioneered methodology in which site-specific incorporation of a [Re(I)] photooxidant on the surface of the β2 subunit (photoβ2) allows photochemical oxidation of the adjacent PCET pathway residue β-Y356 and time-resolved spectroscopic observation of the ensuing reactivity. A series of photoβ2s capable of performing photoinitiated substrate turnover have been prepared in which four different fluorotyrosines (FnYs) are incorporated in place of β-Y356. The FnYs are deprotonated under biological conditions, undergo oxidation by electron transfer (ET), and provide a means by which to vary the ET driving force (ΔG°) with minimal additional perturbations across the series. We have used these features to map the correlation between ΔG° and kET both with and without the fully assembled photoRNR complex. The photooxidation of FnY356 within the α/β subunit interface occurs within the Marcus inverted region with a reorganization energy of λ ≈ 1 eV. We also observe enhanced electronic coupling between donor and acceptor (HDA) in the presence of an intact PCET pathway. Additionally, we have investigated the dynamics of proton transfer (PT) by a variety of methods including dependencies on solvent isotopic composition, buffer concentration, and pH. We present evidence for the role of α2 in facilitating PT during β-Y356 photooxidation; PT occurs by way of readily exchangeable positions and within a relatively "tight" subunit interface. These findings show that RNR controls ET by lowering λ, raising HDA, and directing PT both within and between individual polypeptide subunits.

Proton-coupled electron hopping in Ru-modified P. aeruginosa azurin

We constructed two artificial multiple-step electron transfer (hopping) systems based on Pseudomonas aeruginosa azurin where a tyrosine (YOH) is situated between Ru(2,2'-bipyridine)2(imidazole)(histidine) and the native copper site: RuH107YOH109 and RuH124-YOH122. We investigated the rates of Cu(I) oxidation by flash-quench generated Ru(III) over a range of conditions that probed the role of proton-coupled oxidation/reduction of YOH in the reaction. Rates of Cu(I) oxidation were enhanced over single-step electron transfer by factors between 3 and 80, depending on specific scaffold and buffer conditions.

Demonstration of intramolecular energy transfer in asymmetric bimetallic ruthenium(ii) complexes

Asymmetric bimetallic Ru(ii) complexes exhibit photo-induced intramolecular energy transfer with rate constant values on the order of 10⁷ s⁻¹.

Proton-coupled electron transfer in the reduction of carbonyls using SmI2–H2O: implications for the reductive coupling of acyl-type ketyl radicals with SmI2–H2O

The feasibility of concerted PCET in the reduction of carbonyl groups using SmI₂–H₂O is quantitatively assessed.

Electron transfer mechanisms of DNA repair by photolyase

Photolyase is a flavin photoenzyme that repairs two DNA base damage products induced by ultraviolet (UV) light: cyclobutane pyrimidine dimers and 6-4 photoproducts. With femtosecond spectroscopy and site-directed mutagenesis, investigators have recently made significant advances in our understanding of UV-damaged DNA repair, and the entire enzymatic dynamics can now be mapped out in real time. For dimer repair, six elementary steps have been characterized, including three electron transfer reactions and two bond-breaking processes, and their reaction times have been determined. A unique electron-tunneling pathway was identified, and the critical residues in modulating the repair function at the active site were determined. The dynamic synergy between the elementary reactions for maintaining high repair efficiency was elucidated, and the biological nature of the flavin active state was uncovered. For 6-4 photoproduct repair, a proton-coupled electron transfer repair mechanism has been revealed. The elucidation of electron transfer mechanisms and two repair photocycles is significant and provides a molecular basis for future practical applications, such as in rational drug design for curing skin cancer.