Protein Radicals in Enzyme Catalysis

Selenocysteine Substitution in a Class I Ribonucleotide Reductase

Ribonucleotide reductases (RNRs) employ a complex radical-based mechanism during nucleotide reduction involving multiple active site cysteines that both activate the substrate and reduce it. Using an engineered allo-tRNA, we substituted two active site cysteines with distinct function in the class Ia RNR of Escherichia coli for selenocysteine (U) via amber codon suppression, with efficiency and selectivity enabling biochemical and biophysical studies. Examination of the interactions of the C₄₃₉U α₂ mutant protein with nucleotide substrates and the cognate β₂ subunit demonstrates that the endogenous Y₁₂₂^• of β₂ is reduced under turnover conditions, presumably through radical transfer to form a transient U₄₃₉^• species. This putative U₄₃₉^• species is formed in a kinetically competent fashion but is incapable of initiating nucleotide reduction via 3'-H abstraction. An analogous C₂₂₅U α₂ protein is also capable of radical transfer from Y₁₂₂^•, but the radical-based substrate chemistry partitions between turnover and stalled reduction akin to the reactivity of mechanism-based inhibitors of RNR. The results collectively demonstrate the essential role of cysteine redox chemistry in the class I RNRs and establish a new tool for investigating thiyl radical reactivity in biology.

A Diruthenium Complex of an N-Pyridyl-o-aminophenol Derivative: A Route to Mixed Valency

An N-pyridyl-o-aminophenol derivative that stabilises mixed-valence states of ruthenium ions is disclosed. A diruthenium complex, [(L_IQ ⁰ )Ru₂ Cl₅ ]⋅MeOH (1⋅MeOH) is successfully isolated, in which L_IQ ⁰ is the o-iminobenzoquinone form of 2-[(3-nitropyridin-2-yl)amino]phenol (L_AP H₂ ). In 1, L_IQ ⁰ oriented towards one ruthenium centre is a non-innocent NO-donor redox ligand, whereas another oriented towards another ruthenium centre is an innocent pyridine-donor redox ligand. Complex 1 is a diruthenium(II,III) mixed-valence complex, [Ru^II (L_IQ ⁰ )(μ-Cl)₂ Ru^III ], with a minor contribution from the diruthenium(III,III) state. [Ru^III (L_ISQ ^.- )(μ-Cl)₂ Ru^III ] contains L_ISQ ^.- , which is the o-iminobenzosemiquinonate anion radical form of the ligand. Complexes 1^- and 1⁺ are diruthenium(II,II), [Ru^II (L_IQ ⁰ )(μ-Cl)₂ Ru^II ], and diruthenium(III,III), [Ru^III (L_IQ ⁰ )(μ-Cl)₂ Ru^III ], complexes, respectively, of L_IQ ⁰ . Complex 1^2- is a diruthenium(II,II) complex of the o-iminobenzosemiquinonate anion radical (L_ISQ ^.- ), [Ru^II (L_ISQ ^.- )(μ-Cl)₂ Ru^II ], with a minor contribution from the diruthenium(III,II) form, [Ru^III (L_AP ^2- )(μ-Cl)₂ Ru^II ]. Complex 1²⁺ is a diruthenium(III,IV) mixed-valence complex of L_IQ ⁰ , [Ru^III (L_IQ ⁰ )(μ-Cl)₂ Ru^IV ]. Complexes 1 and 1²⁺ exhibit inter-valence charge-transfer transitions at λ=1300 and 1370 nm, respectively.

Uno Ferro, a de novo Designed Protein, Binds Transition Metals with High Affinity and Stabilizes Semiquinone Radical Anion

Metalloenzymes often utilize radicals in order to facilitate chemical reactions. Recently, DeGrado and co-workers have discovered that model proteins can efficiently stabilize semiquinone radical anion produced by oxidation of 3,5-di-tert-butylcatechol (DTBC) in the presence of two zinc ions. Here, we show that the number and the nature of metal ions have relatively minor effect on semiquinone stabilization in model proteins, with a single metal ion being sufficient for radical stabilization. The radical is stabilized by both metal ion, hydrophobic sequestration, and interactions with the hydrophilic residues in the protein interior resulting in a remarkable, nearly 500 mV change in the redox potential of the SQ^{. -} /catechol couple compared to bulk aqueous solution. Moreover, we have created 4G-UFsc, a single metal ion-binding protein with pm affinity for zinc that is higher than any other reported model systems and is on par with many natural zinc-containing proteins. We expect that the robust and easy-to-modify DFsc/UFsc family of proteins will become a versatile tool for mechanistic model studies of metalloenzymes.

Tuning Radical Relay Residues by Proton Management Rescues Protein Electron Hopping

Transient tyrosine and tryptophan radicals play key roles in the electron transfer (ET) reactions of photosystem (PS) II, ribonucleotide reductase (RNR), photolyase, and many other proteins. However, Tyr and Trp are not functionally interchangeable, and the factors controlling their reactivity are often unclear. Cytochrome c peroxidase (CcP) employs a Trp191^•+ radical to oxidize reduced cytochrome c (Cc). Although a Tyr191 replacement also forms a stable radical, it does not support rapid ET from Cc. Here we probe the redox properties of CcP Y191 by non-natural amino acid substitution, altering the ET driving force and manipulating the protic environment of Y191. Higher potential fluorotyrosine residues increase ET rates marginally, but only addition of a hydrogen bond donor to Tyr191^• (via Leu232His or Glu) substantially alters activity by increasing the ET rate by nearly 30-fold. ESR and ESEEM spectroscopies, crystallography, and pH-dependent ET kinetics provide strong evidence for hydrogen bond formation to Y191^• by His232/Glu232. Rate measurements and rapid freeze quench ESR spectroscopy further reveal differences in radical propagation and Cc oxidation that support an increased Y191^• formal potential of ∼200 mV in the presence of E232. Hence, Y191 inactivity results from a potential drop owing to Y191^•+ deprotonation. Incorporation of a well-positioned base to accept and donate back a hydrogen bond upshifts the Tyr^• potential into a range where it can effectively oxidize Cc. These findings have implications for the Y_Z/Y_D radicals of PS II, hole-hopping in RNR and cryptochrome, and engineering proteins for long-range ET reactions.

Non-heme iron enzyme-catalyzed complex transformations: Endoperoxidation, cyclopropanation, orthoester, oxidative C-C and C-S bond formation reactions in natural product biosynthesis

Non-heme iron enzymes catalyze a wide range of chemical transformations, serving as one of the key types of tailoring enzymes in the biosynthesis of natural products. Hydroxylation reaction is the most common type of reactions catalyzed by these enzymes and hydroxylation reactions have been extensively investigated mechanistically. However, the mechanistic details for other types of transformations remain largely unknown or unexplored. In this paper, we present some of the most recently discovered transformations, including endoperoxidation, orthoester formation, cyclopropanation, oxidative C-C and C-S bond formation reactions. In addition, many of them are multi-functional enzymes, which further complicate their mechanistic investigations. In this work, we summarize their biosynthetic pathways, with special emphasis on the mechanistic details available for these newly discovered enzymes.

The effect of π-π stacking interaction of the indole ring with the coordinated phenoxyl radical in a nickel(ii)-salen type complex. Comparison with the corresponding Cu(ii) complex

In order to gain new insights into the effect of the π-π stacking interaction of the indole ring with the phenoxyl radical moiety as seen in the active form of galactose oxidase, we have prepared Ni(ii) complexes of a methoxy substituted salen-type ligand containing a pendent indole ring on the dinitrogen chelate backbone and characterized their one-electron oxidized forms. The X-ray crystal structure analysis and the other physicochemical experiments of the Ni(ii) complex revealed no significant intramolecular interaction of the indole ring with the coordination plane. On the other hand, the X-ray crystal structures of the oxidized Ni(ii) complex exhibited the π-π stacking interaction of the indole ring mainly with one of the two phenolate moieties. While the phenoxyl radical electron was delocalized on the two phenolate moieties in the Ni(ii)-salen coordination plane, the phenolate moiety in close contact with the indole moiety was considered to be the initial oxidation locus, indicating that the indole ring interacted with the phenoxyl radical by π-π stacking. The UV-vis-NIR spectrum of the oxidized Ni(ii) complex with the pendent indole ring was different from that of the complex without the side chain indole ring, but the differences were rather small in comparison with the oxidized Cu(ii)-salen complexes with the π-π stacking interaction of the indole ring. Such differences are due to the electronic structure difference, the localized radical electron on one of the phenolate moieties in the oxidized Cu(ii) complexes being more favorable for the π-π stacking interaction.

Ultrafast Oxidation of a Tyrosine by Proton-Coupled Electron Transfer Promotes Light Activation of an Animal-like Cryptochrome

The animal-like cryptochrome of Chlamydomonas reinhardtii (CraCRY) is a recently discovered photoreceptor that controls the transcriptional profile and sexual life cycle of this alga by both blue and red light. CraCRY has the uncommon feature of efficient formation and longevity of the semireduced neutral form of its FAD cofactor upon blue light illumination. Tyrosine Y₃₇₃ plays a crucial role by elongating , as fourth member, the electron transfer (ET) chain found in most other cryptochromes and DNA photolyases, which comprises a conserved tryptophan triad. Here, we report the full mechanism of light-induced FADH^• formation in CraCRY using transient absorption spectroscopy from hundreds of femtoseconds to seconds. Electron transfer starts from ultrafast reduction of excited FAD to FAD^•- by the proximal tryptophan (0.4 ps) and is followed by delocalized migration of the produced WH^•+ radical along the tryptophan triad (∼4 and ∼50 ps). Oxidation of Y₃₇₃ by coupled ET to WH^•+ and deprotonation then proceeds in ∼800 ps, without any significant kinetic isotope effect, nor a pH effect between pH 6.5 and 9.0. The FAD^•-/Y₃₇₃^• pair is formed with high quantum yield (∼60%); its intrinsic decay by recombination is slow (∼50 ms), favoring reduction of Y₃₇₃^• by extrinsic agents and protonation of FAD^•- to form the long-lived, red-light absorbing FADH^• species. Possible mechanisms of tyrosine oxidation by ultrafast proton-coupled ET in CraCRY, a process about 40 times faster than the archetypal tyrosine-Z oxidation in photosystem II, are discussed in detail.

Nickel(II) Complexes with Redox Noninnocent Octaazamacrocycles as Catalysts in Oxidation Reactions

Nickel(II) complexes with 15-membered (1-5) and 14-membered (6) octaazamacrocyclic ligands derived from 1,2- and 1,3-diketones and S-methylisothiocarbohydrazide were prepared by template synthesis. The compounds were characterized by elemental analysis, electrospray ionization mass spectrometry, IR, UV-vis, ¹H NMR spectroscopies, and X-ray diffraction. The complexes contain a low-spin nickel(II) ion in a square-planar coordination environment. The electrochemical behavior of 1-6 was investigated in detail, and the electronic structure of 1e-oxidized and 1e-reduced species was studied by electron paramagnetic resonance, UV-vis-near-IR spectroelectrochemistry, and density functional theory calculations indicating redox noninnocent behavior of the ligands. Compounds 1-6 were tested in the microwave-assisted solvent-free oxidation of cyclohexane by tert-butyl hydroperoxide to produce the industrially significant mixture of cyclohexanol and cyclohexanone (i.e., A/K oil). The results showed that the catalytic activity was affected by several factors, namely, reaction time and temperature or amount and type of catalyst. The best values for A/K oil yield (23%, turnover number of 1.1 × 10²) were obtained with compound 6 after 2 h of microwave irradiation at 100 °C.

Raman and Quantum Yield Studies of Trp48-d5 in Azurin: Closed-Shell and Neutral Radical Species

Isotopologues are valuable vibrational probes that shift features in a vibrational spectrum while preserving the electronic structure of the molecule. We report the vibrational and electronic spectra of perdeuterated tryptophan in solution (l-Trp-d₅), as Trp48-d₅ in azurin, and as the photogenerated neutral tryptophan radical, Trp48-d₅^•, in azurin. The UV resonance Raman bands of the perdeuterated closed-shell tryptophan in solution and in azurin are lower in frequency relative to the protiated counterpart. The observed decrease in frequencies of l-Trp-d₅ bands relative to l-Trp-h₅ enables the analysis of vibrational markers of other amino acids, e.g., phenylalanine, that overlap with some modes of l-Trp-h₅. The Raman intensities vary between l-Trp-d₅ and l-Trp-h₅; these differences likely reflect modifications in normal mode composition upon perdeuteration. Analysis of the W3, W6, and W17 modes suggests that the W3 mode retains its utility as a conformational marker; however, the H-bond markers W6 and W17 appear to be less sensitive upon perdeuteration. The neutral tryptophan radical, Trp48-d₅^•, was generated in azurin with a slightly lower radical quantum yield than for Trp48-h₅^•. The visible resonance Raman spectrum of Trp48-d₅^• is different from that of Trp48-h₅^•, especially in terms of relative intensities, and all assignable peaks decreased in frequency upon perdeuteration. The absorption and emission spectra of the perdeuterated closed-shell and radical species exhibited hypsochromic shifts of less than 1 nm relative to the protiated species. The data presented here indicate that l-Trp-d₅ is a valuable probe of vibrational structure, with minimal modification of photoreactivity and photophysics compared to l-Trp-h₅.

Solution structure and biochemical characterization of a spare part protein that restores activity to an oxygen-damaged glycyl radical enzyme

Glycyl radical enzymes (GREs) utilize a glycyl radical cofactor to carry out a diverse array of chemically challenging enzymatic reactions in anaerobic bacteria. Although the glycyl radical is a powerful catalyst, it is also oxygen sensitive such that oxygen exposure causes cleavage of the GRE at the site of the radical. This oxygen sensitivity presents a challenge to facultative anaerobes dwelling in areas prone to oxygen exposure. Once GREs are irreversibly oxygen damaged, cells either need to make new GREs or somehow repair the damaged one. One particular GRE, pyruvate formate lyase (PFL), can be repaired through the binding of a 14.3 kDa protein, termed YfiD, which is constitutively expressed in E. coli. Herein, we have solved a solution structure of this 'spare part' protein using nuclear magnetic resonance spectroscopy. These data, coupled with data from circular dichroism, indicate that YfiD has an inherently flexible N-terminal region (residues 1-60) that is followed by a C-terminal region (residues 72-127) that has high similarity to the glycyl radical domain of PFL. Reconstitution of PFL activity requires that YfiD binds within the core of the PFL barrel fold; however, modeling suggests that oxygen-damaged, i.e. cleaved, PFL cannot fully accommodate YfiD. We further report that a PFL variant that mimics the oxygen-damaged enzyme is highly susceptible to proteolysis, yielding additionally truncated forms of PFL. One such PFL variant of ~ 77 kDa makes an ideal scaffold for the accommodation of YfiD. A molecular model for the rescue of PFL activity by YfiD is presented.

π-π Stacking Interaction in an Oxidized CuII -Salen Complex with a Side-Chain Indole Ring: An Approach to the Function of the Tryptophan in the Active Site of Galactose Oxidase

In order to gain new insights into the effect of the π-π stacking interaction of the indole ring with the Cu^II -phenoxyl radical as seen in the active form of galactose oxidase, we have prepared a Cu^II complex of a methoxy-substituted salen-type ligand, containing a pendent indole ring on the dinitrogen chelate backbone, and characterized its one-electron-oxidized forms. The X-ray crystal structures of the oxidized Cu^II complex exhibited the π-π stacking interaction of the indole ring mainly with one of the two phenolate moieties. The phenolate moiety in close contact with the indole moiety showed the characteristic phenoxyl radical structural features, indicating that the indole ring favors the π-π stacking interaction with the phenoxyl radical. The UV/Vis/NIR spectra of the oxidized Cu^II complex with the pendent indole ring was significantly different from those of the complex without the side-chain indole ring, and the absorption and CD spectra exhibited a solvent dependence, which is in line with the phenoxyl radical-indole stacking interaction in solution. The other physicochemical results and theoretical calculations strongly support that the indole ring, as an electron donor, stabilizes the phenoxyl radical by the π-π stacking interaction.

Enzymatic Reactions Involving Ketyls: From a Chemical Curiosity to a General Biochemical Mechanism

Ketyls are radical anions with nucleophilic properties. Ketyls obtained by enzymatic one-electron reduction of thioesters were proposed as intermediates for the dehydration of (R)-2-hydroxyacyl-CoA to (E)-2-enoyl-CoA. This concept was extended to the Birch-like reduction of benzoyl-CoA to 1,5-cyclohexadienecarboxyl-CoA. Nature uses two methods to achieve the therefore required low reduction potentials of less than -600 mV, either by an ATP-driven electron transfer similar to that catalyzed by the iron protein of nitrogenase or by electron bifurcation. Ketyls formed by thiyl radical-initiated oxidation of alcohols followed by deprotonation are involved in coenzyme B₁₂-independent diol dehydratases, other glycyl radical enzymes mediating key reactions in the degradations of choline, taurine, and 4-hydroxyproline, and all three classes of ribonucleotide reductases. A special case is the dehydration of 4-hydroxybutyryl-CoA to crotonyl-CoA, which most likely proceeds via an oxidation to an allylic ketyl but requires neither a strong reductant nor an external radical generator.

(Spectro)electrochemical and Electrocatalytic Investigation of 1,1'-Dithiolatoferrocene-Hexacarbonyldiiron

Hexacarbonyldiiron bridged by a 1,1'-dithiolatoferrocene, [Fe(C₅H₄S)₂{Fe(CO)₃}₂] (1), was synthesized, and the electrochemistry showed reversible oxidation at the Fe(C₅H₄S)₂ site and quasi-reversible reduction at the hexacarbonyldiiron site. Spectroelectrochemical techniques showed reduction-induced ligand isomerization, where the thiolate ligand went from bridging to terminal and one carbon monoxide ligand moved to a quasi-bridging position; this mechanism was further supported by cyclic voltammetry simulation and density functional theory calculations. Complex 1 showed electrocatalytic activity toward hydrogen-evolving reaction.

Modulating lifetimes and relaxation times of phenoxyl radicals through their incorporation into different hybrid nanostructures

Playing with the structural features of various hybrid materials enables to adjust physical properties of phenoxyl radicals.

Photochemical Rescue of a Conformationally Inactivated Ribonucleotide Reductase

Class Ia ribonucleotide reductase (RNR) of Escherichia coli contains an unusually stable tyrosyl radical cofactor in the β₂ subunit (Y₁₂₂^•) necessary for nucleotide reductase activity. Upon binding the cognate α₂ subunit, loaded with nucleoside diphosphate substrate and an allosteric/activity effector, a rate determining conformational change(s) enables rapid radical transfer (RT) within the active α₂β₂ complex from the Y₁₂₂^• site in β₂ to the substrate activating cysteine residue (C₄₃₉) in α₂ via a pathway of redox active amino acids (Y₁₂₂[β] ↔ W₄₈[β]? ↔ Y₃₅₆[β] ↔ Y₇₃₁[α] ↔ Y₇₃₀[α] ↔ C₄₃₉[α]) spanning >35 Å. Ionizable residues at the α₂β₂ interface are essential in mediating RT, and therefore control activity. One of these mutations, E₃₅₀X (where X = A, D, Q) in β₂, obviates all RT, though the mechanism of control by which E₃₅₀ mediates RT remains unclear. Herein, we utilize an E₃₅₀Q-photoβ₂ construct to photochemically rescue RNR activity from an otherwise inactive construct, wherein the initial RT event (Y₁₂₂^• → Y₃₅₆) is replaced by direct photochemical radical generation of Y₃₅₆^•. These data present compelling evidence that E₃₅₀ conveys allosteric information between the α₂ and β₂ subunits facilitating conformational gating of RT that specifically targets Y₁₂₂^• reduction, while the fidelity of the remainder of the RT pathway is retained.

NADPH-dependent and -independent disulfide reductase systems

Over the past seven decades, research on autotrophic and heterotrophic model organisms has defined how the flow of electrons ("reducing power") from high-energy inorganic sources, through biological systems, to low-energy inorganic products like water, powers all of Life's processes. Universally, an initial major biological recipient of these electrons is nicotinamide adenine dinucleotide-phosphate, which thereby transits from an oxidized state (NADP+) to a reduced state (NADPH). A portion of this reducing power is then distributed via the cellular NADPH-dependent disulfide reductase systems as sequential reductions of disulfide bonds. Along the disulfide reduction pathways, some enzymes have active sites that use the selenium-containing amino acid, selenocysteine, in place of the common but less reactive sulfur-containing cysteine. In particular, the mammalian/metazoan thioredoxin systems are usually selenium-dependent as, across metazoan phyla, most thioredoxin reductases are selenoproteins. Among the roles of the NADPH-dependent disulfide reductase systems, the most universal is that they provide the reducing power for the production of DNA precursors by ribonucleotide reductase (RNR). Some studies, however, have uncovered examples of NADPH-independent disulfide reductase systems that can also support RNR. These systems are summarized here and their implications are discussed.

Orthometalated N-(Benzophenoxazine)-o-aminophenol: Phenolato versus Phenoxyl States

The molecular and electronic structures of the orthometalated ruthenium(III) and osmium(III) complexes of N-(benzophenoxazine)-o-aminophenol (^OXLH₂) that exhibits versatile redox activities are reported. The redox chemistry of ^OXLH₂ is remarkably different from that of N-(aryl)-o-aminophenol (^APLH₂). The study established that ^OXLH₂ is redox noninnocent and is a precursor of a phenoxyl radical. One of the C-H bonds of ^OXLH₂ is activated by ions, and ^OXLH₂ reveals three different redox states as dianionic phenolato (^OXL^2-), monoanionic phenoxyl radical (^OXL^•-), and zwitterionic phenoxium cation (^OXL^±) states. The reaction of ^OXLH₂ with [Ru^II(PPh₃)₃Cl₂] in boiling toluene in air affords an orthometalated ^OXL^2- complex of ruthenium(III), trans-[(^OXL^2-)Ru^III(PPh₃)₂(Cl)] (1), whereas the similar reaction with [Os^II(PPh₃)₃Br₂] yields an orthometalated ^OXL^•- complex, cis-[(^OXL^•-)Os^III(PPh₃)Br₂] (2). 1 and 2 exhibit ligand-based reversible redox waves due to ^OXL^•-/^OXL^2-, ^OXL^±/^OXL^•-, and M^III/M^II couples. The 1 ⁺ ion is a ^OXL^•- complex of ruthenium(III). 2 ^- exhibits temperature-dependent valence tautomerism due to [Os^II(^OXL^•-) ↔ Os^III(^OXL^2-)] equilibrium. 2 ^2- is a ^OXL^2- complex of osmium(II), while 1 ²⁺ and 2 ⁺ are ^OXL^± complexes of metal(III). 2 is an oxidant and effective catalyst for oxidation of 3,5-di-tert-butylcatechol to the corresponding quinone, and the turnover number is 119.7 h^-1. The UV-vis-NIR absorption spectrum of 1 displays an NIR band at 800 nm due to an intra-ligand-charge-transfer transition, which is absent in 2 incorporating a ^OXL^•- radical. The molecular and electronic structures of 1 and 2 and their oxidized and reduced analogues were confirmed by single-crystal X-ray crystallography, variable-temperature electron paramagnetic resonance spectroscopy, spectroelectrochemical measurements, and density functional theory calculations.

Learning from B12 enzymes: biomimetic and bioinspired catalysts for eco-friendly organic synthesis

Cobalamins (B₁₂) play various important roles in vivo. Most B₁₂-dependent enzymes are divided into three main subfamilies: adenosylcobalamin-dependent isomerases, methylcobalamin-dependent methyltransferases, and dehalogenases. Mimicking these B₁₂ enzyme functions under non-enzymatic conditions offers good understanding of their elaborate reaction mechanisms. Furthermore, bio-inspiration offers a new approach to catalytic design for green and eco-friendly molecular transformations. As part of a study based on vitamin B₁₂ derivatives including heptamethyl cobyrinate perchlorate, we describe biomimetic and bioinspired catalytic reactions with B₁₂ enzyme functions. The reactions are classified according to the corresponding three B₁₂ enzyme subfamilies, with a focus on our recent development on electrochemical and photochemical catalytic systems. Other important reactions are also described, with a focus on radical-involved reactions in terms of organic synthesis.

Nuclear RNR-α antagonizes cell proliferation by directly inhibiting ZRANB3

Since the origins of DNA-based life, the enzyme ribonucleotide reductase (RNR) has spurred proliferation because of its rate-limiting role in de novo deoxynucleoside-triphosphate (dNTP) biosynthesis. Paradoxically, the large subunit, RNR-α, of this obligatory two-component complex in mammals plays a context-specific antiproliferative role. There is little explanation for this dichotomy. Here, we show that RNR-α has a previously unrecognized DNA-replication inhibition function, leading to growth retardation. This underappreciated biological activity functions in the nucleus, where RNR-α interacts with ZRANB3. This process suppresses ZRANB3's function in unstressed cells, which we show to promote DNA synthesis. This nonreductase function of RNR-α is promoted by RNR-α hexamerization-induced by a natural and synthetic nucleotide of dA/ClF/CLA/FLU-which elicits rapid RNR-α nuclear import. The newly discovered nuclear signaling axis is a primary defense against elevated or imbalanced dNTP pools that can exert mutagenic effects irrespective of the cell cycle.

Uncoupled Redox-Inactive Lewis Acids in the Secondary Coordination Sphere Entice Ligand-Based Nitrite Reduction

Metal complexes composed of redox-active pyridinediimine (PDI) ligands are capable of forming ligand-centered radicals. In this Forum article, we demonstrate that integration of these types of redox-active sites with bioinspired secondary coordination sphere motifs produce direduced complexes, where the reduction potential of the ligand-based redox sites is uncoupled from the secondary coordination sphere. The utility of such ligand design was explored by encapsulating redox-inactive Lewis acidic cations via installation of a pendant benzo-15-crown-5 in the secondary coordination sphere of a series of Fe(PDI) complexes. Fe(15bz5PDI)(CO)2 was shown to encapsulate the redox-inactive alkali ion, Na+, causing only modest (31 mV) anodic shifts in the ligand-based redox-active sites. By uncoupling the Lewis acidic sites from the ligand-based redox sites, the pendant redox-inactive ion, Na+, can entice the corresponding counterion, NO2-, for reduction to NO. The subsequent initial rate analysis reveals an acceleration in anion reduction, confirming this hypothesis.

Fragmentation of a dioxolanyl radical via nonstatistical reaction dynamics: characterization of the vinyloxy radical by ns time-resolved laser flash photolysis

The photochemistry of two Barton esters, one derived from a dioxolane carboxylic acid and the other from pivalic acid, was investigated by product analysis and nanosecond laser flash photolysis (LFP). As expected, photolysis of the pivalate ester resulted in formation of the pyridine-2-thiyl and the t-butyl radical. Photolysis of the Barton ester of 2,2-dimethyl-1,3-dioxolane-4-carboxylic acid, on the other hand, revealed a complex multi-step fragmentation. In addition to the pyridine-2-thiyl and dioxolanyl radical, we gained evidence for the formation of the vinyloxy radical, CH2[double bond, length as m-dash]CHO˙. The latter was identified in the LFP by its π-complexes with benzene and diphenylether, its rapid quenching by electron-rich arenes and tri-n-butyl tin hydride, and its oxidative power in presence of trifluoroacetic acid as demonstrated by the oxidation of ferrocene to ferrocenium. Formation of CH2[double bond, length as m-dash]CHO˙ can be rationalized via fragmentation of the dioxolanyl radical. As the calculated barriers are too high for the reaction sequence to occur on the LFP time scale, we investigated the fragmentation of the photoexcited Barton ester via Born-Oppenheimer molecular dynamics simulations. In one trajectory, we could observe all reaction steps including ring opening of the dioxolanyl radical, suggesting that the excess energy gained in the ester cleavage and decarboxylation may lead to fragmentation of the hot dioxolanyl radical.

Recent Development of Genetic Code Expansion for Posttranslational Modification Studies

Nowadays advanced mass spectrometry techniques make the identification of protein posttranslational modifications (PTMs) much easier than ever before. A series of proteomic studies have demonstrated that large numbers of proteins in cells are modified by phosphorylation, acetylation and many other types of PTMs. However, only limited studies have been performed to validate or characterize those identified modification targets, mostly because PTMs are very dynamic, undergoing large changes in different growth stages or conditions. To overcome this issue, the genetic code expansion strategy has been introduced into PTM studies to genetically incorporate modified amino acids directly into desired positions of target proteins. Without using modifying enzymes, the genetic code expansion strategy could generate homogeneously modified proteins, thus providing powerful tools for PTM studies. In this review, we summarized recent development of genetic code expansion in PTM studies for research groups in this field.

A new strategy to efficiently cleave and form C-H bonds using proton-coupled electron transfer

Oxidative activation and reductive formation of C-H bonds are crucial in many chemical, industrial, and biological processes. Reported here is a new strategy for these transformations, using a form of proton-coupled electron transfer (PCET): intermolecular electron transfer coupled to intramolecular proton transfer with an appropriately placed cofactor. In a fluorenyl-benzoate, the positioned carboxylate facilitates rapid cleavage of a benzylic C-H bond upon reaction with even weak 1e- oxidants, for example, decamethylferrocenium. Mechanistic studies establish that the proton and electron transfer to disparate sites in a single concerted kinetic step, via multi-site concerted proton-electron transfer. This work represents a new elementary reaction step available to C-H bonds. This strategy is extended to reductive formation of C-H bonds in two systems. Molecular design considerations and possible utility in synthetic and enzymatic systems are discussed.

Cleavage of a carbon-fluorine bond by an engineered cysteine dioxygenase

Cysteine dioxygenase (CDO) plays an essential role in sulfur metabolism by regulating homeostatic levels of cysteine. Human CDO contains a post-translationally generated Cys93-Tyr157 cross-linked cofactor. Here, we investigated this Cys-Tyr cross-linking by incorporating unnatural tyrosines in place of Tyr157 via a genetic method. The catalytically active variants were obtained with a thioether bond between Cys93 and the halogen-substituted Tyr157, and we determined the crystal structures of both wild-type and engineered CDO variants in the purely uncross-linked form and with a mature cofactor. Along with mass spectrometry and ¹⁹F NMR, these data indicated that the enzyme could catalyze oxidative C-F or C-Cl bond cleavage, resulting in a substantial conformational change of both Cys93 and Tyr157 during cofactor assembly. These findings provide insights into the mechanism of Cys-Tyr cofactor biogenesis and may aid the development of bioinspired aromatic carbon-halogen bond activation.

Biological hydropersulfides and related polysulfides - a new concept and perspective in redox biology

The chemical biology of thiols (RSH, e.g., cysteine and cysteine-containing proteins/peptides) has been a topic of extreme interest for many decades due to their reported roles in protein structure/folding, redox signaling, metal ligation, cellular protection, and enzymology. While many of the studies on thiol/sulfur biochemistry have focused on thiols, relatively ignored have been hydropersulfides (RSSH) and higher order polysulfur species (RSS_n H, RSS_n R, n > 1). Recent and provocative work has alluded to the prevalence and likely physiological importance of RSSH and related RSS_n H. RSSH of cysteine (Cys-SSH) has been found to be prevalent in mammalian systems along with Cys-SSH-containing proteins. The RSSH functionality has not been examined to the extent of other biologically relevant sulfur derivatives (e.g., sulfenic acids, disulfides, etc.), whose roles in cell signaling are strongly indicated. The recent finding of Cys-SSH biosynthesis and translational incorporation into proteins is an unequivocal indication of its fundamental importance and necessitates a more profound look into the physiology of RSSH. In this Review, we discuss the currently reported chemical biology of RSSH (and related species) as a prelude to discussing their possible physiological roles.

Properties of Site-Specifically Incorporated 3-Aminotyrosine in Proteins To Study Redox-Active Tyrosines: Escherichia coli Ribonucleotide Reductase as a Paradigm

3-Aminotyrosine (NH₂Y) has been a useful probe to study the role of redox active tyrosines in enzymes. This report describes properties of NH₂Y of key importance for its application in mechanistic studies. By combining the tRNA/NH₂Y-RS suppression technology with a model protein tailored for amino acid redox studies (α₃X, X = NH₂Y), the formal reduction potential of NH₂Y₃₂(O^•/OH) ( E°' = 395 ± 7 mV at pH 7.08 ± 0.05) could be determined using protein film voltammetry. We find that the Δ E°' between NH₂Y₃₂(O^•/OH) and Y₃₂(O^•/OH) when measured under reversible conditions is ∼300-400 mV larger than earlier estimates based on irreversible voltammograms obtained on aqueous NH₂Y and Y. We have also generated D₆-NH₂Y₇₃₁-α2 of ribonucleotide reductase (RNR), which when incubated with β2/CDP/ATP generates the D₆-NH₂Y₇₃₁^•-α2/β2 complex. By multifrequency electron paramagnetic resonance (35, 94, and 263 GHz) and 34 GHz ¹H ENDOR spectroscopies, we determined the hyperfine coupling (hfc) constants of the amino protons that establish RNH₂^• planarity and thus minimal perturbation of the reduction potential by the protein environment. The amount of Y in the isolated NH₂Y-RNR incorporated by infidelity of the tRNA/NH₂Y-RS pair was determined by a generally useful LC-MS method. This information is essential to the utility of this NH₂Y probe to study any protein of interest and is employed to address our previously reported activity associated with NH₂Y-substituted RNRs.

Disulfide-Bridged Peptides That Mediate Enantioselective Cycloadditions through Thiyl Radical Catalysis

An enantioselective vinylcyclopropane ring-opening/cycloaddition cascade is described. The active thiyl radical catalysts are generated in situ via UV light-promoted homolysis of cystine-based dimers. Amide-functionalization of the peptide at the 4-proline position is essential for effective asymmetric induction. Stereochemical communication is dependent on steric interactions with this substituent that are enforced by H-bonding to the peptide backbone.

Superoxide dismutase protects ribonucleotide reductase from inactivation in yeast

Ribonucleotide reductase (RNR) catalyses the rate limiting step of DNA synthesis utilising a mechanism that requires a tyrosyl radical. We have previously shown that superoxide can quench protein tyrosyl radicals in vitro, either by oxidative addition, or reduction of the radical to tyrosine. Here, we observe that Saccharomyces cerevisiae strains lacking either copper-zincSOD (SOD1) or manganese SOD (SOD2) had decreased RNR activity compared to SOD-competent yeast. When superoxide production was increased by treatment with paraquat, RNR activity was further decreased, with yeast lacking SOD1 being the most sensitive. The growth of yeast lacking SOD1 was also the most sensitive to paraquat treatment. Using expressed recombinant RNR, superoxide addition was not detectable using mass-spectrometry. This suggests that oxidative addition is not the major route of inhibition in our system, but does not rule out reduction by superoxide as a possible mechanism. Our results demonstrate that protection of RNR from inactivation by superoxide is an important function of SOD, particularly cytoplasmic SOD1.

Redox-Active Ligand Assisted Multielectron Catalysis: A Case of CoIII Complex as Water Oxidation Catalyst

Water oxidation is the key step in both natural and artificial photosynthesis to capture solar energy for fuel production. The design of highly efficient and stable molecular catalysts for water oxidation based on nonprecious metals is still a great challenge. In this article, the electrocatalytic oxidation of water by Na[(L^4-)Co^III], where L is a substituted tetraamido macrocyclic ligand, was investigated in aqueous solution (pH 7.0). We found that Na[(L^4-)Co^III] is a stable and efficient homogeneous catalyst for electrocatalytic water oxidation with 380 mV onset overpotential in 0.1 M phosphate buffer (pH 7.0). Both ligand- and metal-centered redox features are involved in the catalytic cycle. In this cycle, Na[(L^4-)Co^III] was first oxidized to [(L^2-)Co^IIIOH] via a ligand-centered proton-coupled electron transfer process in the presence of water. After further losing an electron and a proton, the resting state, [(L^2-)Co^IIIOH], was converted to [(L^2-)Co^IV═O]. Density functional theory (DFT) calculations at the B3LYP-D3(BJ)/6-311++G(2df,2p)//B3LYP/6-31+G(d,p) level of theory confirmed the proposed catalytic cycle. According to both experimental and DFT results, phosphate-assisted water nucleophilic attack to [(L^2-)Co^IV═O] played a key role in O-O bond formation.

Modelling the Effect of Conformation on Hydrogen-Atom Abstraction from Peptides

Computational quantum chemistry is used to examine the effect of conformation on the kinetics of hydrogen-atom abstraction by HO• from amides of glycine and proline as peptide models. In accord with previous findings, it is found that there are substantial variations possible in the conformations and the corresponding energies, with the captodative effect, hydrogen bonding, and solvation being some of the major features that contribute to the variations. The ‘minimum-energy-structure-pathway’ strategy that is often employed in theoretical studies of peptide chemistry with small models certainly provides valuable fundamental information. However, one may anticipate different reaction outcomes in structurally constrained systems due to modified reaction thermodynamics and kinetics, as demonstrated explicitly in the present study. Thus, using a ‘consistent-conformation-pathway’ approach may indeed be more informative in such circumstances, and in this regard theory provides information that would be difficult to obtain from experimental studies alone.

New oxidovanadium(iv) complex with a BIAN ligand: synthesis, structure, redox properties and catalytic activity

The combination of a new oxidovanadium(iv) complex1with pyrazine-2-carboxylic acid (PCA; a cocatalyst) affords a catalytic system for the efficient oxidation of saturated hydrocarbons.