Probing the Time Scale of FPOP (Fast Photochemical Oxidation of Proteins): Radical Reactions Extend Over Tens of Milliseconds

Hydroxyl radical (?OH) labeling with mass spectrometry detection reports on protein conformations and interactions. Fast photochemical oxidation of proteins (FPOP) involves ?OH production via H₂O₂ photolysis by UV laser pulses inside a flow tube. The experiments are conducted in the presence of a scavenger (usually glutamine) that shortens the ?OH lifetime. The literature claims that FPOP takes place within 1 μs. This ultrafast time scale implies that FPOP should be immune to labeling-induced artifacts that may be encountered with other techniques. Surprisingly, the FPOP time scale has never been validated in direct kinetic measurements. Here we employ flash photolysis for probing oxidation processes under typical FPOP conditions. Bleaching of the reporter dye cyanine-5 (Cy5) served as readout of the time-dependent radical milieu. Surprisingly, Cy5 oxidation extends over tens of milliseconds. This time range is four orders of magnitude longer than expected from the FPOP literature. We demonstrate that the glutamine scavenger generates metastable secondary radicals in the FPOP solution, and that these radicals lengthen the time frame of Cy5 oxidation. Cy5 and similar dyes are widely used for monitoring the radical dose experienced by proteins in solution. The measured Cy5 kinetics thus strongly suggest that protein oxidation in FPOP extends over a much longer time window than previously thought (i.e., many milliseconds instead of one microsecond). The optical approach developed here should be suitable for assessing the performance of future FPOP-like techniques with improved temporal labeling characteristics.

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碱性溶液中甲醇分子诱导的肌血球素构象变化

考察了不同pH值的碱性溶液中甲醇分子对诱导肌血球素构象变化的影响. 电喷雾电离质谱(ESI-MS)测量结果表明, 当pH分别为11.0, 11.4, 12.0时, 不同体积分数的甲醇(30%, 50%, 70%及90%)和水混合溶液将诱导肌血球素的构象变化. 当pH=11.0时, 肌血球素在溶液中均以hMb为主要形态存在(即血红素稳定存在于肌红蛋白中); 当pH=11.4时, 30%甲醇中的肌血球素仍以hMb为主, 但升高甲醇比例会导致hMb上的辅基脱落生成aMb(蛋白质分子); 当pH=12.0时, 溶液中的肌血球素均以aMb为主. 但当应用负离子质谱测量模式时, 检测出的肌血球素负离子均以aMb构象为主. 同时采用圆二色谱(CD)及紫外-可见(UV-Vis)光谱等研究发现, pH值和甲醇含量分别决定蛋白质分子的二级和三级结构的变化.     

Temperature jump and fast photochemical oxidation probe submillisecond protein folding

We report a new mass-spectrometry-based approach for studying protein-folding dynamics on the submillisecond time scale. The strategy couples a temperature jump with fast photochemical oxidation of proteins (FPOP), whereby folding/unfolding is followed by changes in oxidative modifications by OH radical reactions. Using a flow system containing the protein barstar as a model, we altered the protein's equilibrium conformation by applying the temperature jump and demonstrated that its reactivity with OH free radicals serves as a reporter of the conformational change. Furthermore, we found that the time-dependent increase in mass resulting from free-radical oxidation is a measure of the rate constant for the transition from the unfolded to the first intermediate state. This advance offers the promise that, when extended with mass-spectrometry-based proteomic analysis, the sites and kinetics of folding/unfolding can also be followed on the submillisecond time scale.     

Laser flash photochemical oxidation to locate heme binding and conformational changes in myoglobin

Fast photochemical oxidation of proteins (FPOP), a means of protein footprinting, uses OH radicals to oxidize the solvent-exposed residues of proteins on a short time scale (∼1 μs). A 248 nm pulsed laser beam dissociates H₂O₂ (15 mM) into hydroxyl radicals. The radicals react with exposed and reactive amino acid residues (e.g., C, M, W, Y, F, H, L, I) in competition with quenching with a glutamine scavenger present in solution. We report here the use of FPOP to confirm that the F-helix is conformationally constrained in the holo form of myoglobin, whereas it is conformationally free in the apo form. The interpretation finds support in the differences in oxidation of various residues in the apo versus holo forms. The differential reactivity of leucine 137 suggests that it is part of a hinge region on the H-helix, enabling the binding pocket to close in the apo form. This is our second study that offers support that FPOP is capable of elucidating the conformational dynamics of proteins by obtaining information that may not be accessible by other methods.     

Determination of hydroxyl radical photoproduction rates in natural waters.

The photochemical formation rates of hydroxyl radicals (OH radicals) in river water and seawater were determined by a simple, rapid and sensitive benzene probe method, in which phenol formed by the reaction between benzene and photochemically-generated OH radicals was analyzed by on-line preconcentration HPLC. The OH radical formation rates from well-known OH radical sources, such as nitrate, nitrite and hydrogen peroxide, were in good agreement with those reported previously. River water samples containing high concentrations of nitrate and nitrite were found to show high OH radical formation rates. Ten to 80% of the OH radical formation in river water and seawater was due to the photolysis of nitrate and nitrite, but OH radical formation from hydrogen peroxide was negligible. The OH radical formation from unknown sources other than nitrate, nitrite and hydrogen peroxide was strongly correlated to the amount of fluorescent matter.     

A long-lived luminescence and EPR bimodal lanthanide-based probe for free radicals

We developed a novel spin-labeled terbium complex Tb(3+)/cs124-DTPA-TEMPO (1) by covalently labeling a nitroxide radical on the terbium complex for monitoring free radicals of various areas. This lanthanide complex probe shows a high EPR signal which resulted from the nitroxide radical moiety, and is weakly luminescent which resulted from the intramolecular quenching effect of the nitroxide radical on sensitised terbium luminescence. The intensity of both the EPR and luminescence can be modulated by eliminating the paramagnetism of the nitroxide radical through recognition of a carbon-centered radical analyte and thus gives a quantification of the analyte. We have preliminarily applied this probe in the luminescent detection of model carbon-centered radicals and hydroxyl radicals (·OH). This probe is water-soluble and contains lanthanide-luminescence properties, favorable for the time-resolved luminescence technique. The investigation of the intramolecular quenching process has showed that the labeled nitroxide radical quenches multiple excited states of the terbium complex, resulting in highly efficient quenching of terbium luminescence. This probe is the first example of intramolecular modulation of lanthanide luminescence by a nitroxide radical.     

Direct measurements of HOx radicals in the marine boundary layer: testing the current tropospheric chemistry mechanism

OH and HO(2) radicals, atmospheric detergents, and the reservoir thereof, play central roles in tropospheric chemistry. In spite of their importance, we had no choice but to trust their concentrations predicted by modeling studies based on known chemical processes. However, recent direct measurements of these radicals have enabled us to test and revise our knowledge of the processes by comparing the predicted and observed values of the radical concentrations. We developed a laser-induced fluorescence (LIF) instrument and successfully observed OH and HO(2) at three remote islands of Japan (Oki Island, Okinawa Island, and Rishiri Island). At Okinawa Island, the observed daytime level of HO(2) agreed closely with the model estimates, suggesting that the photochemistry at Okinawa is well described by the current chemistry mechanism. At Rishiri Island, in contrast, the observed daytime level of HO(2) was consistently much lower than the calculated values. We proposed that iodine chemistry, usually not incorporated into the mechanism, is at least partly responsible for the discrepancy in the results. At night, HO(2) was detected at levels greater than 1 pptv at all three islands, suggesting the presence of processes in the dark that produce radicals. We showed that ozone reactions with unsaturated hydrocarbons, including monoterpenes, could significantly contribute to radical production.     

Microcalorimetric Study of Methanol Adsorption on Initial Silica and Silica Modified with Polyfluoroalkyl Groups

The adsorption of methanol on initial silica and modified silica samples containing large mesopores is studied by the adsorption–calorimetric method. The grafted tridecylfluoroalkyl groups have a tilted orientation on the silica and physically screen the part of the surface OH groups that have not been involved in the reaction with a modifier. Adsorbed methanol makes the modifying layer looser, thus facilitating the accessibility of methanol molecules to these hydrophilic adsorption sites. Concentrations of OH groups involved in the chemical interaction with molecules of the modifier, OH groups physically screened by its organofluoric radicals, and OH groups located on the surface areas free of the modifier are quantitatively estimated. An additional silanization of the modified silica leads to coverage of silica surface areas that are free of organofluoric modifier with trimethylsilyl radicals. The heat of interaction between the methanol molecules and silica surface hydroxyl groups is determined; it is equal to 60 kJ/mol. The structure of the modifying organofluoric layer and changes in this structure that resulted from additional silanization of the surface and from the methanol adsorption are discussed.     

4-Azidoaniline,a Versatile Protein and Peptide Modifying Agent for Photo Affinity Labeling

A modified synthesis of 4-azidoaniline and the use of this compound as a protein and peptide modifying agent for photoaffinity labeling is described. 4-Azidoaniline was diazotized to 4-azidophenyldiazonium and coupled to N-acetyl-tyrosine-ethylester, and to a tyrosine containing analog of bradykinin. It is shown that the 4-azidoaniline reagent offers great advantages over other protein modifying agents for photoaffinity labeling, i.e., very high nitrene reactivity, possibility of tritium or iodine labeling, ligand-receptor complex can be cleaved after isolation. The biological activity of the modified bradykinin analog is measured on rabbit aorta strip in the dark and is similar to the unsubstituted analog. Under the influence of light the modified peptide is able to block partially the myotropic action of bradykinin.     

Characterization of ELISA Antibody-Antigen Interaction using Footprinting-Mass Spectrometry and Negative Staining Transmission Electron Microscopy

We describe epitope mapping data using multiple covalent labeling footprinting-mass spectrometry (MS) techniques coupled with negative stain transmission electron microscopy (TEM) data to analyze the antibody–antigen interactions in a sandwich enzyme-linked immunosorbant assay (ELISA). Our hydroxyl radical footprinting-MS data using fast photochemical oxidation of proteins (FPOP) indicates suppression of labeling across the antigen upon binding either of the monoclonal antibodies (mAbs) utilized in the ELISA. Combining these data with Western blot analysis enabled the identification of the putative epitopes that appeared to span regions containing N-linked glycans. An additional structural mapping technique, carboxyl group footprinting-mass spectrometry using glycine ethyl ester (GEE) labeling, was used to confirm the epitopes. Deglycosylation of the antigen resulted in loss of potency in the ELISA, supporting the FPOP and GEE labeling data by indicating N-linked glycans are necessary for antigen binding. Finally, mapping of the epitopes onto the antigen crystal structure revealed an approximate 90° relative spatial orientation, optimal for a noncompetitive binding ELISA. TEM data shows both linear and diamond antibody–antigen complexes with a similar binding orientation as predicted from the two footprinting-MS techniques. This study is the first of its kind to utilize multiple bottom-up footprinting-MS techniques and TEM visualization to characterize the monoclonal antibody-antigen binding interactions of critical reagents used in a quality control (QC) lot-release ELISA.

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Generation of Aryl Radicals through Reduction of Hypervalent Iodine(III) Compounds with TEMPONa: Radical Alkene Oxyarylation

A novel method for selective generation of aryl radicals from diaryliodonium salts and iodanylidene malonates with sodium 2,2,6,6‐tetramethylpiperidine‐1‐oxyl (TEMPONa) as a single‐electron transfer (SET) reducing reagent is described. In the presence of various alkenes, aryl radicals formed after SET‐reduction of hypervalent iodine compounds undergo alkene addition and the adduct radicals that are thus generated are efficiently trapped by the concomitantly generated TEMPO radical to eventually afford oxyarylated products in moderate to very good yields. The efficiency of aryl radical generation of various iodine(III) reagents is studied and the generation of an iodanylidene malonate aryl radical is also investigated by computational methods.     

Study on the Nitroxide-linked Naphthalene as a Probe for Hydroxyl Radicals

Reactive oxygen species (ROS),such as superoxide radical (O₂^-)and hydroxyl radical (OH), are thought to be involved in the action of many toxins and several human diseases. Among the various radicals,the hydroxyl radical is presumed to play a central role due to its strong activity. Several methods have been developed to detect hydroxyl radicals. Among them, one of the most commonly used is ESR method. Because of a high-cost instrument, this method is not suitable for routine analysis. Another method is aromatic hydroxylation. Though this method is highly sensitive, the multiple hydroxylation products make the quantitative detection of hydroxyl radical complex.     

Radical identification by liquid chromatography/thermospray mass spectrometry

Radical adducts of 5,5-dimethyl-1-pyrroline N-oxide (DMPO) with hydroxyl, methanol-derived, and ethanol-derived radicals were detected by a combination of liquid chromatography with either electron paramagnetic resonance or thermospray mass spectrometry (LC/EPR or LC/TSP-MS) in the Fenton system (with methanol or ethanol). One radical adduct was observed in the reaction of DMPO with the hydroxyl radical or the methanol-derived radical, while two adducts were detected in the reaction of DMPO with ethanol-derived radicals. The LC/TSP-MS spectra showed quasi-molecular ions [M + H]+ at m/z 146 and m/z 160 for the methanol-derived and ethanol-derived radical adducts, respectively, and an apparent molecular ion M+ at m/z 130 for the hydroxyl radical adduct. Use of methyl-D3 alcohol (CD3OH) and ethyl-D5 alcohol (CD3CD2OH) indicated that carbon-centered radicals are formed. Experiments with partially deuterated ethanol (CD3CH2OH and CH3CD2OH) indicated that the two adducts observed in the reaction of DMPO with ethanol-derived radicals correspond to the two diastereomeric adducts of DMPO with the alpha-hydroxyethyl free radical.     

Surface Modification of Poly-ε-Caprolactone with an Atmospheric Pressure Plasma Jet

In this work, poly-ε-caprolactone samples are modified by an atmospheric pressure plasma jet in pure argon and argon/water vapour mixtures. In a first part of the paper, the chemical species present in the plasma jet are identified by optical emission spectroscopy and it was found that plasmas generated in argon/0.05 % water vapour mixtures show the highest emission intensity of OH (A–X) at 308 nm. In a subsequent section, plasma jet surface treatments in argon and argon/water vapour mixtures have been investigated using contact angle measurements and X-ray photoelectron spectroscopy. The polymer samples modified with the plasma jet show a significant decrease in water contact angle due to the incorporation of oxygen-containing groups, such as C–O, C=O and O–C=O. The most efficient oxygen inclusion was however found when 0.05 % of water vapour is added to the argon feeding gas, which correlates with the highest intensity of OH (X) radicals. By optimizing the OH (X) radical yield in the plasma jet, the highest polymer modification efficiency can thus be obtained.     

Variation in FPOP Measurements Is Primarily Caused by Poor Peptide Signal Intensity

Fast photochemical oxidation of proteins (FPOP) may be used to characterize changes in protein structure by measuring differences in the apparent rate of peptide oxidation by hydroxyl radicals. The variability between replicates is high for some peptides and limits the statistical power of the technique, even using modern methods controlling variability in radical dose and quenching. Currently, the root cause of this variability has not been systematically explored, and it is unknown if the major source(s) of variability are structural heterogeneity in samples, remaining irreproducibility in FPOP oxidation, or errors in LC-MS quantification of oxidation. In this work, we demonstrate that coefficient of variation of FPOP measurements varies widely at low peptide signal intensity, but stabilizes to ≈?0.13 at higher peptide signal intensity. We dramatically reduced FPOP variability by increasing the total sample loaded onto the LC column, indicating that the major source of variability in FPOP measurements is the difficulties in quantifying oxidation at low peptide signal intensities. This simple method greatly increases the sensitivity of FPOP structural comparisons, an important step in applying the technique to study subtle conformational changes and protein-ligand interactions.

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Electron transfer between a tyrosyl radical and a cysteine residue in hemoproteins: spin trapping analysis

We investigated electron transfer between a tyrosyl radical and cysteine residue in two systems, oxyhemoglobin (oxyHb)/peroxynitrite/5,5-dimethyl-1-pyrroline N-oxide (DMPO) and myoglobin (Mb)/hydrogen peroxide/DMPO, using a combination of techniques including ESR, immuno-spin trapping (IST), and ESI/MS. These techniques show that the nitrone spin trap DMPO covalently binds to one or more amino acid radicals in the protein. Treating oxyHb with peroxynitrite and Mb with H2O2 in the presence of a low DMPO concentration yielded secondary Cys-DMPO radical adduct exclusively, whereas in the presence of high DMPO, more of the primary Tyr-DMPO radical adduct was detected. In both systems studied, we found that, at high DMPO concentrations, mainly tyrosyl radicals (Hb-Tyr42/Tyr24 and Mb-Tyr103) are trapped and the secondary electron-transfer reaction does not compete, whereas in the presence of low concentrations of DMPO, the secondary reaction predominates over tyrosyl trapping, and a thiyl radical is formed and then trapped (Hb-Cys93 or Mb-Cys110). With increasing concentrations of DMPO in the reaction medium, primary radicals have an increasing probability of being trapped. MS/MS was used to identify the specific Tyr and Cys residues forming radicals in the myoglobin system. All data obtained from this combination of approaches support the conclusion that the initial site of radical formation is a Tyr, which then abstracts an electron from a cysteine residue to produce a cysteinyl radical. This complex phenomenon of electron transfer from one radical to another has been investigated in proteins by IST, ESR, and MS.     

An intrinsic radical stability scale from the perspective of bond dissociation enthalpies: a companion to radical electrophilicities

Bond dissociation enthalpies (BDEs) of a large series of molecules of the type A-B, where a series of radicals A ranging from strongly electrophilic to strongly nucleophilic are coupled with a series of 8 radicals (CH2OH, CH3, NF2, H, OCH3, OH, SH, and F) also ranging from electrophilic to nucleophilic, are computed and analyzed using chemical concepts emerging from density functional theory, more specifically the electrophilicities of the individual radical fragments A and B. It is shown that, when introducing the concept of relative radical electrophilicity, an (approximately) intrinsic radical stability scale can be developed, which is in good agreement with previously proposed stability scales. For 47 radicals, the intrinsic stability was estimated from computed BDEs of their combinations with the strongly nucleophilic hydroxymethyl radical, the neutral hydrogen atom, and the strongly electrophilic fluorine atom. Finally, the introduction of an extra term containing enhanced Pauling electronegativities in the model improves the agreement between the computed BDEs and the ones estimated from the model, resulting in a mean absolute deviation of 16.4 kJ mol(-1). This final model was also tested against 82 experimental values. In this case, a mean absolute deviation of 15.3 kJ mol(-1) was found. The obtained sequences for the radical stabilities are rationalized using computed spin densities for the radical systems.     

Molecular description of indigo oxidation mechanisms initiated by OH and OOH radicals

In this work, we report a quantum chemistry mechanistic study of the hydroxyl (?OH) and hydroperoxyl (?OOH) radicals initiated oxidation of indigo, within the density functional theory framework. All possible hydrogen abstraction and radical addition reaction pathways have been considered. We find that the reaction between a free indigo molecule and an ?OH radical occurs mainly through two competing mechanisms: H-abstraction from an NH site and ?OH addition to the central C═C double bond. Although the latter is favored, both channels occur, the indigo chromophore group structure is modified, and thus the color is changed. This mechanism adequately accounts for the loss of chromophore in urban air, including indoor air such as in museums and in urban areas. Regarding the reactivity of indigo toward ?OOH radicals, only ?OOH-addition to the central double bond is thermodynamically feasible. The corresponding transition state free energy value is about 10 kcal/mol larger than the one for the ?OH initiated oxidation. Therefore, even considering that the ?OOH concentration is considerably larger than the one of ?OH, this reaction is not expected to contribute significantly to indigo oxidation under atmospheric conditions.     

A Polypyrrole Based Sensor for the Electrochemical Detection of OH Radicals

Polypyrrole was used as sensitive material in the development of a new device employed for the indirect detection of OH radicals. The polypyrrole film was electrosynthesized on glassy carbon. The modified electrode was exposed to the OH radicals generated by Fenton reaction. As a result of the overoxidation the conductivity of the polymer diminished very much. The overoxidation (%) was directly proportional to the ^.OH amount that reached the electrode surface. ABTS^.+, superoxide and alkylperoxy radicals did not interfere in the determination. The applicability of the device was demonstrated by estimating the ^.OH scavenging ability of ascorbic acid.     

Oxidation of organic films by beams of hydroxyl radicals

We have studied the oxidation of self-assembled monolayers (SAMs) of alkanes and alkenes with a thermal beam of OH radicals. The target films were produced by bonding alkane thiols and alkene thiols to a gold surface and the SAMs are mounted in a vacuum chamber at a base pressure of 10-9 Torr. Hydroxyl radicals were produced by a corona discharge in an Ar/H2O2/water mixture. The resultant molecular beam was scanned by an electrostatic hexapole and the OH radicals [4 (+/- 1) x 1011 OH radicals cm-2 sec-1] were focused onto the target SAM. All of the hydroxyl radicals impinging on the SAM surface are rotationally (J' ' 相似文献