EPR Spectroscopic Studies of Lipoxygenases

Polyunsaturated fatty acids are sources of diverse natural, and chemically designed products. The enzyme lipoxygenase selectively oxidizes fatty acid acyl chains using controlled free radical chemistry; the products are regio‐ and stereo‐chemically unique hydroperoxides. A conserved structural fold of ≈600 amino acids harbors a long and narrow substrate channel and a well‐shielded catalytic iron. Oxygen, a co‐substrate, is blocked from the active site until a hydrogen atom is abstracted from substrate bis‐allylic carbon, in a non‐heme iron redox cycle. EPR spectroscopy of ferric intermediates in lipoxygenase catalysis reveals changes in the metal coordination and leads to a proposal on the nature of the reactive intermediate. Remarkably, free radicals are so well controlled in lipoxygenase chemistry that spin label technology can be applied as well. The current level of understanding of steps in lipoxygenase catalysis, from the EPR perspective, will be reviewed.     

Spectroscopic analysis of immobilised redox enzymes under direct electrochemical control

This article reviews recent developments in spectroscopic analysis of electrode-immobilised enzymes under direct, unmediated electrochemical control. These methods unite the suite of spectroscopic methods available for characterisation of structural, electronic and coordination changes in proteins with the exquisite control over complex redox enzymes that can be achieved in protein film electrochemistry in which immobilised protein molecules exchange electrons directly with an electrode. This combination is particularly powerful in studies of highly active enzymes where redox states can be controlled even under fast electrocatalytic turnover. We examine examples in which UV-visible, IR, Raman and MCD spectroscopy have been combined with direct electrochemistry to probe redox-dependent chemistry, and consider future opportunities for 'direct' spectroelectrochemistry of immobilised enzymes.     

Tripyrrindione as a Redox‐Active Ligand: Palladium(II) Coordination in Three Redox States

The tripyrrin‐1,14‐dione scaffold of urinary pigment uroerythrin coordinates divalent palladium as a planar tridentate ligand. Spectroscopic, structural and computational investigations reveal that the tripyrrindione ligand binds as a dianionic radical, and the resulting complex is stable at room temperature. One‐electron oxidation and reduction reactions do not alter the planar coordination sphere of palladium(II) and lead to the isolation of two additional complexes presenting different redox states of the ligand framework. Unaffected by stability problems common to tripyrrolic fragments, the tripyrrindione ligand offers a robust platform for ligand‐based redox chemistry.     

Artificial cytochrome b: computer modeling and evaluation of redox potentials.

We generated atomic coordinates of an artificial protein that was recently synthesized to model the central part of the native cytochrome b (Cb) subunit consisting of a four-helix bundle with two hemes. Since no X-ray structure is available, the structural elements of the artificial Cb were assembled from scratch using all known chemical and structural information available and avoiding strain as much as possible. Molecular dynamics (MD) simulations applied to this model protein exhibited root-mean-square deviations as small as those obtained from MD simulations starting with the crystal structure of the native Cb subunit. This demonstrates that the modeled structure of the artificial Cb is relatively rigid and strain-free. The model structure of the artificial Cb was used to determine the redox potentials of the two hemes by calculating the electrostatic energies from the solution of the linearized Poisson-Boltzmann equation (LPBE). The calculated redox potentials agree within 20 meV with the experimentally measured values. The dependence of the redox potentials of the hemes on the protein environment was analyzed. Accordingly, the total shift in the redox potentials is mainly due to the low dielectric medium of the protein, the protein backbone charges, and the salt bridges formed between the arginines and the propionic acid groups of the hemes. The difference in the shift of the redox potentials is due to the interactions with the hydrophilic side chains and the salt bridges formed with the propionic acids of the hemes. For comparison and to test the computational procedure, the redox potentials of the two hemes in the native Cb from the cytochrome bc(1) (Cbc(1)) complex were also calculated. Also in this case the computed redox potentials agree well with experiments.     

A tailor‐made polymethacrylate bearing a reactive diene in reversible diels–alder reaction

A tailor‐made polymethacrylate bearing a pendant furfuryl group was prepared by atom transfer radical polymerization (ATRP), an important method of recent advances in controlled radical polymerization. It was otherwise difficult to prepare via conventional radical polymerization, because of several side reactions involving the reactive diene functionality of the furfuryl group. Successful Diels–Alder (DA) chemistry was carried out using this reactive furfuryl group of the tailor‐made polymer as diene and a bismaleimide as a dienophile. Interestingly, the resultant material was observed to be thermoreversible as evidenced by FT‐IR and DSC studies. This example of application of a tailor‐made polymer having controlled molecular architecture and with reactive diene functionality in DA chemistry will open new possibilities to prepare newer tailor‐made reversible materials. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4441–4449, 2007     

Control of the stoichiometry in host-guest complexation by redox chemistry of guests: inclusion of methylviologen in cucurbit[8]uril

The binding stoichiometry of a host-guest complex can be effectively controlled by the redox chemistry of the guest: a 1:1 inclusion complex of methylviologen dication (MV2+) in cucurbit[8]uril (CB[8]) converts completely and reversibly to a 2:1 inclusion complex of cation radical (MV+.) in CB[8] upon the reduction of the guest.     

Effects of surface curvature and surface chemistry on the structure and activity of proteins adsorbed in nanopores

The interactions of proteins with the surface of cylindrical nanopores are systematically investigated to elucidate how surface curvature and surface chemistry affect the conformation and activity of confined proteins in an aqueous, buffered environment. Two globular proteins, lysozyme and myoglobin, with different catalytic functions, were used as model proteins to analyze structural changes in proteins after adsorption on ordered mesoporous silica SBA-15 and propyl-functionalized SBA-15 (C(3)SBA-15) with carefully controlled pore size. Liquid phase ATR-FTIR spectroscopy was used to study the amide I and II bands of the adsorbed proteins. The amide I bands showed that the secondary structures of free and adsorbed protein molecules differ, and that the secondary structure of the adsorbed protein is influenced by the local geometry as well as by the surface chemistry of the nanopores. The conformation of the adsorbed proteins inside the nanopores of SBA-15 and C(3)SBA-15 is strongly correlated with the local geometry and the surface properties of the nanoporous materials, which results in different catalytic activities. Adsorption by electrostatic interaction of proteins in nanopores of an optimal size provides a favorably confining and protecting environment, which may lead to considerably enhanced structural stability and catalytic activity.     

DOPA Residues Endow Collagen with Radical Scavenging Capacity**

Here we uncover collagen, the main structural protein of all connective tissues, as a redox-active material. We identify dihydroxyphenylalanine (DOPA) residues, post-translational oxidation products of tyrosine residues, to be common in collagen derived from different connective tissues. We observe that these DOPA residues endow collagen with substantial radical scavenging capacity. When reducing radicals, DOPA residues work as redox relay: they convert to the quinone and generate hydrogen peroxide. In this dual function, DOPA outcompetes its amino acid precursors and ascorbic acid. Our results establish DOPA residues as redox-active side chains of collagens, probably protecting connective tissues against radicals formed under mechanical stress and/or inflammation.     

Dark Photocatalysis: Storage of Solar Energy in Carbon Nitride for Time‐Delayed Hydrogen Generation

While natural photosynthesis serves as the model system for efficient charge separation and decoupling of redox reactions, bio‐inspired artificial systems typically lack applicability owing to synthetic challenges and structural complexity. We present herein a simple and inexpensive system that, under solar irradiation, forms highly reductive radicals in the presence of an electron donor, with lifetimes exceeding the diurnal cycle. This radical species is formed within a cyanamide‐functionalized polymeric network of heptazine units and can give off its trapped electrons in the dark to yield H₂, triggered by a co‐catalyst, thus enabling the temporal decoupling of the light and dark reactions of photocatalytic hydrogen production through the radical′s longevity. The system introduced here thus demonstrates a new approach for storing sunlight as long‐lived radicals, and provides the structural basis for designing photocatalysts with long‐lived photo‐induced states.     

Future directions of structural mass spectrometry using hydroxyl radical footprinting

Hydroxyl radical protein footprinting coupled to mass spectrometry has been developed over the last decade and has matured to a powerful method for analyzing protein structure and dynamics. It has been successfully applied in the analysis of protein structure, protein folding, protein dynamics, and protein–protein and protein–DNA interactions. Using synchrotron radiolysis, exposure of proteins to a ‘white’ X‐ray beam for milliseconds provides sufficient oxidative modification to surface amino acid side chains, which can be easily detected and quantified by mass spectrometry. Thus, conformational changes in proteins or protein complexes can be examined using a time‐resolved approach, which would be a valuable method for the study of macromolecular dynamics. In this review, we describe a new application of hydroxyl radical protein footprinting to probe the time evolution of the calcium‐dependent conformational changes of gelsolin on the millisecond timescale. The data suggest a cooperative transition as multiple sites in different molecular subdomains have similar rates of conformational change. These findings demonstrate that time‐resolved protein footprinting is suitable for studies of protein dynamics that occur over periods ranging from milliseconds to seconds. In this review, we also show how the structural resolution and sensitivity of the technology can be improved as well. The hydroxyl radical varies in its reactivity to different side chains by over two orders of magnitude, thus oxidation of amino acid side chains of lower reactivity are more rarely observed in such experiments. Here we demonstrate that the selected reaction monitoring (SRM)‐based method can be utilized for quantification of oxidized species, improving the signal‐to‐noise ratio. This expansion of the set of oxidized residues of lower reactivity will improve the overall structural resolution of the technique. This approach is also suggested as a basis for developing hypothesis‐driven structural mass spectrometry experiments. Copyright © 2010 John Wiley & Sons, Ltd.     

Ab initio and QM/MM study of electron addition on the disulfide bond in thioredoxin

Thioredoxin controls the intracellular redox potential through a disulfide/dithiol couple. Under conditions of oxidative stress, this protein functions via one-electron exchange, in which formation of the disulfide radical anion occurs. Combined quantum mechanical (QM) and molecular mechanical (MM) calculations using two- and three-level ONIOM schemes were performed on the thioredoxin (Trx) protein of Chlamydomonas reinhardtii in its oxidized-disulfide and one-electron-reduced forms. In both cases, the active site disulfide moiety was described at the MP2(fc)/6-31+G(d) level, and larger regions of varying sizes around the active site were described at the B3LYP/6-31+G(d) level. The remainder of the 112 residues and 33 water molecules of the crystal structure (PDB entry 1EP7) were described by the AMBER force field. Adiabatic electron affinities were calculated for the disulfide bond in all systems. Separate QM or QM/QM calculations were performed on the QM regions to establish the role of the remainder of the protein on the active site properties. The radical anion species becomes more stable as the number of amide groups in the vicinity increases. One-electron reduction potentials were calculated for the small molecule models, and approximated for the protein for which the values are similar to the experimental one (approximately 0 V). This high reduction potential is due to interaction with the charged end of Lys40, as indicated by mutation in silico to norleucine. The inclusion of the protonated Asp30 side chain and a water molecule in the QM region leads to an increase in the electron affinity. Proton transfer from the Asp30 side chain to the Cys39 sulfur in the radical anion species is strongly disfavored. The radical anion is more stable than the protonated form, which is consistent with experimental results.     

Sulfur and selenium: the role of oxidation state in protein structure and function

Sulfur and selenium occur in proteins as constituents of the amino acids cysteine, methionine, selenocysteine, and selenomethionine. Recent research underscores that these amino acids are truly exceptional. Their redox activity under physiological conditions allows an amazing variety of posttranslational protein modifications, metal free redox pathways, and unusual chalcogen redox states that increasingly attract the attention of biological chemists. Unlike any other amino acid, the "redox chameleon" cysteine can participate in several distinct redox pathways, including exchange and radical reactions, as well as atom-, electron-, and hydride-transfer reactions. It occurs in various oxidation states in the human body, each of which exhibits distinctive chemical properties (e.g. redox activity, metal binding) and biological activity. The position of selenium in the periodic table between the metals and the nonmetals makes selenoproteins ideal catalysts for many biological redox transformations. It is therefore apparent that the chalcogen amino acids cysteine, methionine, selenocysteine, and selenomethionine exhibit a unique biological chemistry that is the source of exciting research opportunities.     

Isolable Anion Radicals of Nitrosoarenes

Summary of main observation and conclusion The rich redox chemistry of nitrosoarenes has rendered these reactive molecules very useful in modern synthetic and material chemistry.Electrochemical studies have revealed the capability of nitrosoarenes to undergo one-electron oxidation or reduction reaction for a long time.However,the isolation and structural characterization of nitrosoarene radical compounds deviating the stabilization of transition-metal have not been achieved.Investigation on the reduction reaction of nitrosoarenes bearing steric demanding substituents has now revealed that the interaction of 2,6-dimesityl-1-nitroso-benzene(DmpNO)or 2,4,6-tri(tert-butyl)-1-nitroso-benzene(TtpNO)with KC8 and crypt-2,2,2 can produce the corresponding anion radical compound[K(crypt-2,2,2)][DmpNO](1)or[K(crypt-2,2,2)][TtpNO](2)in good isolated yield.Compounds 1 and 2 represent the first examples of isolable nitrosoarene radical compounds deviating the stabilization of transition-metal,and have been characterized by single-crystal X-ray diffraction study,electron paramagnetic resonance(EPR)spectroscopy,and elemental analysis.Theoretical study in collaboration with the characterization data revealed that the unpaired spin in[DmpNO]·-and[TtpNO]·-delocalizes on the nitroso and the central phenyl groups.     

Redox- and protonation-state driven substrate-protein dynamics in respiratory complex I

Respiratory complex I is a key enzyme in the electron transport chains of mitochondria and bacteria. It transfers two electrons to quinone and couples this redox reaction to proton pumping to electrically charge the membrane it is embedded in. The charge and pH gradient across the membrane drives the synthesis of ATP. The redox reaction and proton pumping in complex I are separated in space and time, which raises the question of how the two reactions are coupled so efficiently. Here, we focus on the unique ～35 Å long tunnel of complex I, which houses the binding site of quinone reduction. We discuss the redox and protonation reactions that occur in this tunnel and how they influence the dynamics of protein and substrate. On the basis of recent structural data and results from molecular simulations, we review how quinone reduction and dynamics may be coupled to proton pumping in complex I.     

Can Co(II) or Cd(II) substitute for Zn(II) in zinc fingers?

Zinc finger domains consist of sequences of amino acids containing cysteine and histidine residues tetrahedrally coordinated to a zinc ion. The role of zinc in a DNA binding finger was considered purely structural due to the absence of redox chemistry in zinc. However, whether other metals e.g. Co(II) or Cd(II) can substitute Zn(II) is not settled. For an answer the detailed interaction of Co(II) and Cd(II) with cysteine methylester and histidine methylester has been investigated as a model for the zinc core in zinc fingers. The study was extended to different temperatures to evaluate the thermodynamic parameters associated with these interactions. The results suggest that zinc has a unique role.     

Bismuth Compounds in Radical Catalysis: Transition Metal Bismuthanes Facilitate Thermally Induced Cycloisomerizations

The controlled radical chemistry of bismuth compounds is still in its infancy. Further developments are fueled by the properties of these complexes (e.g., low toxicity, high functional group tolerance, low homolytic bond dissociation energies, and reversible homolytic bond dissociations), which are highly attractive for applications in synthetic chemistry. Here we report the first catalytic application of transition metal bismuthanes (i.e. compounds with a Bi–TM bond; TM=transition metal). Using the catalyzed radical cyclo‐isomerization of δ‐iodo‐olefins as a model reaction, characteristics complementary or superior to known B, Mn, Cu, Zn, Sn, and alkali metal reagents are demonstrated (including a different crucial intermediate), establishing transition metal bismuthanes as a new class of (pre‐)catalysts for controlled radical reactions.     

Phosphine Oxide-Functionalized Terthiophene Redox Systems

Main group systems capable of undergoing controlled redox events at extreme potentials are elusive yet highly desirable for a range of organic electronics applications including use as energy storage media. Herein we describe phosphine oxide-functionalized terthiophenes that exhibit two reversible 1e⁻ reductions at potentials below −2 V vs Fc/Fc⁺ (Fc=ferrocene) while retaining high degrees of stability. A phosphine oxide-functionalized terthiophene radical anion was synthesized in which the redox-responsive nature of the platform was established using combined structural, spectroscopic, and computational characterization. Straightforward structural modification led to the identification of a derivative that exhibits exceptional stability during bulk 2 e⁻ galvanostatic charge–discharge cycling and enabled characterization of a 2 e⁻ redox series. A new multi-electron redox system class is hence disclosed that expands the electrochemical cell potential range achievable with main group electrolytes without compromising stability.     

Impact of proximal and distal pocket site-directed mutations on the ferric/ferrous heme redox potential of yeast cytochrome c peroxidase

Cytochrome c peroxidase (CCP) contains a five-coordinate heme active site. The reduction potential for the ferric to ferrous couple in CCP is anomalously low and pH dependent (Eo?=?~?180?mV vs. S.H.E. at pH 7). The contribution of the protein environment to the tuning of the redox potential of this couple is evaluated using site-directed mutants of several amino acid residues in the environment of the heme. These include proximal pocket mutation of residues Asp-235, Trp-191, Phe-202, and His-175, distal pocket mutation of residues Trp-51, His-52, and Arg-48; and a heme edge mutation of Ala-147. Where unknown, the structural changes resulting from the amino acid substitution have been studied by X-ray crystallography. In most cases, ostensibly polar or charged residues are replaced by large hydrophobic groups or alternatively by Ala or Gly. These latter have been shown to generate large, solvent-filled cavities. Reduction potentials are measured as a function of pH by spectroelectrochemistry. Starting with the X-ray-derived structures of CCP and the mutants, or with predicted structures generated by molecular dynamics (MD), predictions of redox potential changes are modeled using the protein dipoles Langevin dipoles (PDLD) method. These calculations serve to model an electrostatic assessment of the redox potential change with simplified assumptions about heme iron chemistry, with the balance of the experimentally observed shifts in redox potential being thence attributed to changes in the ligand set and heme coordination chemistry, and/or other changes in the structure not directly evident in the X-ray structures (e.g., ionization states, specific roles played by solvent species, or conformationally flexible portions of the protein). Agreement between theory and experiment is good for all mutant proteins with the exception of the mutation Arg 48 to Ala, and His 52 to Ala. In the former case, the influence of phosphate buffer is adduced to account for the discrepancy, with evidence for phosphate binding in the distal pocket, and measurements made in a bis?Ctris propane/2-(N-morpholino)ethanesulfonic acid buffer system agree well with theory. For the latter case, an unknown structural element relevant to His-52 and/or solvent influence in the mutant akin to anion binding in the distal pocket (though lacking proof that it is, and in this case lacking a phosphate effect) manifests in this mutant. The use of exogenous (sixth) ligands in dissecting the contributions to control of redox potential is also explored as a pathway for model building.     

脑神经退行性疾病中的有机化学-朊病毒(疯牛病)中的蛋白物理有机化学和自由基化学

通过关于“普里昂”蛋白病毒疾病的已有临床、医学生理、免疫和化学等方面的现象，讨论了朊病毒当中的部分蛋白氧化损伤和蛋白自由基化学本质。