Fast Photochemical Oxidation of Proteins (FPOP) Maps the Epitope of EGFR Binding to Adnectin

Epitope mapping is an important tool for the development of monoclonal antibodies, mAbs, as therapeutic drugs. Recently, a class of therapeutic mAb alternatives, adnectins, has been developed as targeted biologics. They are derived from the 10th type III domain of human fibronectin (¹⁰Fn3). A common approach to map the epitope binding of these therapeutic proteins to their binding partners is X-ray crystallography. Although the crystal structure is known for Adnectin 1 binding to human epidermal growth factor receptor (EGFR), we seek to determine complementary binding in solution and to test the efficacy of footprinting for this purpose. As a relatively new tool in structural biology and complementary to X-ray crystallography, protein footprinting coupled with mass spectrometry is promising for protein–protein interaction studies. We report here the use of fast photochemical oxidation of proteins (FPOP) coupled with MS to map the epitope of EGFR-Adnectin 1 at both the peptide and amino-acid residue levels. The data correlate well with the previously determined epitopes from the crystal structure and are consistent with HDX MS data, which are presented in an accompanying paper. The FPOP-determined binding interface involves various amino-acid and peptide regions near the N terminus of EGFR. The outcome adds credibility to oxidative labeling by FPOP for epitope mapping and motivates more applications in the therapeutic protein area as a stand-alone method or in conjunction with X-ray crystallography, NMR, site-directed mutagenesis, and other orthogonal methods. Figure

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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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Mapping the Binding Interface of VEGF and a Monoclonal Antibody Fab-1 Fragment with Fast Photochemical Oxidation of Proteins (FPOP) and Mass Spectrometry

We previously analyzed the Fab-1:VEGF (vascular endothelial growth factor) system described in this work, with both native top-down mass spectrometry and bottom-up mass spectrometry (carboxyl-group or GEE footprinting) techniques. This work continues bottom-up mass spectrometry analysis using a fast photochemical oxidation of proteins (FPOP) platform to map the solution binding interface of VEGF and a fragment antigen binding region of an antibody (Fab-1). In this study, we use FPOP to compare the changes in solvent accessibility by quantitating the extent of oxidative modification in the unbound versus bound states. Determining the changes in solvent accessibility enables the inference of the protein binding sites (epitope and paratopes) and a comparison to the previously published Fab-1:VEGF crystal structure, adding to the top-down and bottom-up data. Using this method, we investigated peptide-level and residue-level changes in solvent accessibility between the unbound proteins and bound complex. Mapping these data onto the Fab-1:VEGF crystal structure enabled successful characterization of both the binding region and regions of remote conformation changes. These data, coupled with our previous higher order structure (HOS) studies, demonstrate the value of a comprehensive toolbox of methods for identifying the putative epitopes and paratopes for biotherapeutic antibodies.

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New Protein Footprinting: Fast Photochemical Iodination Combined with Top-Down and Bottom-Up Mass Spectrometry

We report a new approach for the fast photochemical oxidation of proteins (FPOP) whereby iodine species are used as the modifying reagent. We generate the radicals by photolysis of iodobenzoic acid at 248 nm; the putative iodine radical then rapidly modifies the target protein. This iodine-radical labeling is sensitive, tunable, and site-specific, modifying only histidine and tyrosine residues in contrast to OH radicals that modify 14 amino-acid side chains. We iodinated myoglobin (Mb) and apomyoglobin (aMb) in their native states and analyzed the outcome by both top-down and bottom-up proteomic strategies. Top-down sequencing selects a certain level (addition of one I, two I's) of modification and determines the major components produced in the modification reaction, whereas bottom-up reveals details for each modification site. Tyr146 is found to be modified for aMb but less so for Mb. His82, His93, and His97 are at least 10 times more modified for aMb than for Mb, in agreement with NMR studies. For carbonic anhydrase and its apo form, there are no significant differences of the modification extents, indicating their similarity in conformation and providing a control for this approach. For lispro insulin, insulin-EDTA, and insulin complexed with zinc, iodination yields are sensitive to differences in insulin oligomerization state. The iodine radical labeling is a promising addition to protein footprinting methods, offering higher specificity and lower reactivity than ?OH and SO(4)(-?), two other radicals already employed in FPOP.     

Generation of Carbenes by Photochemical Cycloelimination

A wide variety of shelf stable substrates undergo photochemical cycloelimination under relatively mild conditions. Suitable substrates include cyclopropanes, oxiranes, aziridines, and diazirines, as well as 3 H-pyrazoles and 1,3-dioxolanes. Carbenes prepared from these substrates as well as certain cyclic carbonates, sulfites, and phosphoranes behave chemically in a manner similar to divalent carbon species produced from conventional diazo precursors, namely, they react with alkenes to give cyclopropanes and undergo insertion into C? H bonds of alkanes. In many cases the carbenes formed may also be detected by EPR and optical spectroscopic methods.     

Improved Identification and Relative Quantification of Sites of Peptide and Protein Oxidation for Hydroxyl Radical Footprinting

Protein oxidation is typically associated with oxidative stress and aging and affects protein function in normal and pathological processes. Additionally, deliberate oxidative labeling is used to probe protein structure and protein–ligand interactions in hydroxyl radical protein footprinting (HRPF). Oxidation often occurs at multiple sites, leading to mixtures of oxidation isomers that differ only by the site of modification. We utilized sets of synthetic, isomeric “oxidized” peptides to test and compare the ability of electron-transfer dissociation (ETD) and collision-induced dissociation (CID), as well as nano-ultra high performance liquid chromatography (nanoUPLC) separation, to quantitate oxidation isomers with one oxidation at multiple adjacent sites in mixtures of peptides. Tandem mass spectrometry by ETD generates fragment ion ratios that accurately report on relative oxidative modification extent on specific sites, regardless of the charge state of the precursor ion. Conversely, CID was found to generate quantitative MS/MS product ions only at the higher precursor charge state. Oxidized isomers having multiple sites of oxidation in each of two peptide sequences in HRPF product of protein Robo-1 Ig1-2, a protein involved in nervous system axon guidance, were also identified and the oxidation extent at each residue was quantified by ETD without prior liquid chromatography (LC) separation. ETD has proven to be a reliable technique for simultaneous identification and relative quantification of a variety of functionally different oxidation isomers, and is a valuable tool for the study of oxidative stress, as well as for improving spatial resolution for HRPF studies.

(L)2C2P2: Dicarbondiphosphide Stabilized by N-Heterocyclic Carbenes or Cyclic Diamido Carbenes

Carbon phosphides, C_nP_m, may have highly promising electronic, optical, and mechanical properties, but they are experimentally almost unexplored materials. Phosphaheteroallenes stabilized by N-heterocyclic carbenes undergo a one-electron reduction to yield compounds of the type (L)₂C₂P₂ with diverse structures. The use of imidazolylidenes as ligands L give complexes with a central four-membered ring C₂P₂, while more electrophilic cyclic diamidocarbenes (DAC) give a compound with an acyclic π-conjugated CP−PC unit. Cyclic C₂P₂ compounds are best described as non-Kekulé molecules that are stabilized by coordination to the NHC ligands NHC→(C₂P₂)←NHC. These species can be easily oxidized to give stable radical cations [(NHC)₂C₂P₂]^+.. The remarkably stable molecules with an acylic C₂P₂ core are best described with electron-sharing bonds (DAC)=C=P−P=C=(DAC).     

硝基酚类化合物在海水中的光化学氧化研究

酚类化合物尤其是硝基苯酚属于国家严格控制排放的有毒物质 .由于工业排污等原因 ,在近岸水体中能检测到许多酚类化合物 .我国胶州湾和杭州湾表层海水中酚的含量分别高达 3和 9mg/L[1] .酚的毒性会影响海水生物的生长和繁殖 ,危及人类健康 .由于硝基苯酚难于生化降解 ,因此研究其在水体中的光降解十分重要 [2～ 6 ] .文献中关于有机污染物的光化学研究大多侧重于废水处理 ,且降解方法也多采用 Ti O2 催化降解 [7,8] .对于硝基苯酚在天然水体中的光降解则知之甚少 .本文通过模拟海水条件下硝基苯酚的光化学反应及其影响因素 ,更加深入地了…     

Carbene Footprinting Reveals Binding Interfaces of a Multimeric Membrane‐Spanning Protein

Mapping the interaction sites between membrane‐spanning proteins is a key challenge in structural biology. In this study a carbene‐footprinting approach was developed and applied to identify the interfacial sites of a trimeric, integral membrane protein, OmpF, solubilised in micelles. The diazirine‐based footprinting probe is effectively sequestered by, and incorporated into, the micelles, thus leading to efficient labelling of the membrane‐spanning regions of the protein upon irradiation at 349 nm. Areas associated with protein–protein interactions between the trimer subunits remained unlabelled, thus revealing their location.     

Photochemical oxidation of hydrocarbons by a vanadium(V) peroxo complex

The oxidation of alkanes and benzene by VO(O₂)L·2H₂O (L=2-picolinate) in acetonitrile is accelerated upon irradiation with visible and, especially, UV light. Cyclohexyl hydroperoxide, cyclohexanol, and cyclohexanone in approximately 2:1:1 ratio are formed from cyclohexane both in the dark and photochemical reactions. Benzene is oxidized to phenol.Istituto di Teoria e Struttura Elettronica dei Composti di Coordinazione, CNR, Area della Ricerca di Roma, via Salaria km 29.5, C. P. 10, 00016 Monterotondo Stazione, Rome, Italy. N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, 117977 Moscow. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 8, pp. 1918–1921, August, 1992.     

Stabilization of High Oxidation State Upconversion Nanoparticles by N‐Heterocyclic Carbenes

The stabilization of high oxidation state nanoparticles by N‐heterocyclic carbenes is reported. Such nanoparticles represent an important subset in the field of nanoparticles, with different and more challenging requirements for suitable ligands compared to elemental metal nanoparticles. N‐Heterocyclic carbene coated NaYF₄:Yb,Tm upconversion nanoparticles were synthesized by a ligand‐exchange reaction from a well‐defined precursor. This new photoactive material was characterized in detail and employed in the activation of photoresponsive molecules by low‐intensity near‐infrared light (λ =980 nm).     

Synthesis of Platinum(II) N-Heterocyclic Carbenes Based on Adenosine

Organometallic derivatization of nucleosides is a highly promising strategy for the improvement of the therapeutic profile of nucleosides. Herein, a methodology for the synthesis of metalated adenosine with a deprotected ribose moiety is described. Platinum(II) N-heterocyclic carbene complexes based on adenosine were synthesized, namely N-heterocyclic carbenes bearing a protected and unprotected ribose ring. Reaction of the 8-bromo-2′,3′,5′-tri-O-acetyladenosine with Pt(PPh₃)₄ by C8−Br oxidative addition yielded complex 1, with a Pt^II centre bonded to C-8 and an unprotonated N7. Complex 1 reacted at N7 with HBF₄ or methyl iodide, yielding protic carbene 2 or methyl carbene 3, respectively. Deprotection of 1 to yield 4 was achieved with NH₄OH. Deprotected compound 4 reacted at N7 with HCl solutions to yield protic NHC 5 or with methyl iodide yielding methyl carbene 6. Protic N-heterocyclic carbene 5 is not stable in DMSO solutions leading to the formation of compound 7, in which a bromide was replaced by chloride. The cis-influence of complexes 1–7 was examined by ³¹P{¹H} and ¹⁹⁵Pt NMR. Complexes 2, 3, 5, 6 and 7 induce a decrease of ¹J_Pt,P of more than 300 Hz, as result of the higher cis-influence of the N-heterocyclic carbene when compared to the azolato ligand in 1 and 4.     

Laser‐Initiated Radical Trifluoromethylation of Peptides and Proteins: Application to Mass‐Spectrometry‐Based Protein Footprinting

Described is a novel, laser‐initiated radical trifluoromethylation for protein footprinting and its broad residue coverage. ^.CF₃ reacts with 18 of the 20 common amino acids, including Gly, Ala, Ser, Thr, Asp, and Glu, which are relatively silent with regard to ^.OH. This new approach to footprinting is a bridge between trifluoromethylation in materials and medicinal chemistry and structural biology and biotechnology. Its application to a membrane protein and to myoglobin show that the approach is sensitive to protein conformational change and solvent accessibility.     

Carbenes in the synthesis of heterocycles (review)

The syntheses of heterocyclic compounds by reactions of carbenes with carbon-heteroatom multiple bonds, isomerization of unstable adducts of carbenes to carbon-carbon bonds, and the incorporation of carbenes in C-H, C-N, and C-O bonds are examined.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1443–1464, November, 1976.     

One‐Electron Oxidation of a Disilicon(0) Compound: An Experimental and Theoretical Study of [Si2]+ Trapped by N‐Heterocyclic Carbenes

One‐electron oxidation of the disilicon(0) compound Si₂(Idipp)₂ ( 1 , Idipp=1,3‐bis(2,6‐diisopropylphenyl)imidazolin‐2‐ylidene) with [Fe(C₅Me₅)₂][B(Ar^F)₄] (Ar^F=C₆H₃‐3,5‐(CF₃)₂) affords selectively the green radical salt [Si₂(Idipp)₂][B(Ar^F)₄] ( 1 ‐[B(Ar^F)₄). Oxidation of the centrosymmetric 1 occurs reversibly at a low redox potential (E_1/2=?1.250 V vs. Fc⁺/Fc), and is accompanied by considerable structural changes as shown by single‐crystal X‐ray structural analysis of 1 ‐B(Ar^F)₄. These include a shortening of the Si?Si bond, a widening of the Si‐Si‐C_NHC angles, and a lowering of the symmetry, leading to a quite different conformation of the NHC substituents at the two inequivalent Si sites in 1⁺ . Comparative quantum chemical calculations of 1 and 1⁺ indicate that electron ejection occurs from the symmetric (n₊) combination of the Si lone pairs (HOMO). EPR studies of 1 ‐B(Ar^F)₄ in frozen solution verified the inequivalency of the two Si sites observed in the solid‐state, and point in agreement with the theoretical results to an almost equal distribution of the spin density over the two Si atoms, leading to quite similar ²⁹Si hyperfine coupling tensors in 1⁺ . EPR studies of 1 ‐B(Ar^F)₄ in liquid solution unraveled a topomerization with a low activation barrier that interconverts the two Si sites in 1⁺ .     

Metal-Free Electrochemical Reduction of Carbon Dioxide Mediated by Cyclic(Alkyl)(Amino) Carbenes

Carbenes are known to activate carbon dioxide to form zwitterionic adducts. Their inherent metal-free redox activity remains understudied. Herein, we demonstrate that zwitterionic adducts of carbon dioxide formed with cyclic(alkyl)(amino) carbenes are not only redox active, but they can mediate the stoichiometric reductive disproportionation of carbon dioxide to carbon monoxide and carbonate. Infrared spectroelectrochemical experiments show that the reaction proceeds through an intermediate radical anion formed by one-electron reduction, ultimately generating a ketene product and carbonate in the absence of additional organic or inorganic reagents.     

Chemical and Photochemical Water Oxidation Catalyzed by Mononuclear Ruthenium Complexes with a Negatively Charged Tridentate Ligand

Two mononuclear ruthenium complexes [RuL(pic)₃] ( 1 ) and [RuL(bpy)(pic)] ( 2 ) (H₂L=2,6‐pyridinedicarboxylic acid, pic=4‐picoline, bpy=2,2′‐bipyridine) have been synthesized and fully characterized. Both complexes could promote water oxidation chemically and photochemically. Compared with other known ruthenium‐based water oxidation catalysts using [Ce(NH₄)₂(NO₃)₆] (Ce^IV) as the oxidant in solution at pH 1.0, complex 1 is one of the most active catalysts yet reported with an initial rate of 0.23 turnover s^?1. Under acidic conditions, the equatorial 4‐picoline in complex 1 dissociates first. In addition, ligand exchange in 1 occurs when the Ru^III state is reached. Based on the above observations and MS measurements of the intermediates during water oxidation by 1 using Ce^IV as oxidant, [RuL(pic)₂(H₂O)]⁺ is proposed as the real water oxidation catalyst.     

氟改变了醇在镍(100)表面上的氧化机理

利用程序热脱附(TPD)实验研究了2-丙醇和三氟-2-丙醇在Ni(100)表面的吸附和热反应过程. 实验结果表明, 电负性大的氟原子取代丙醇中γ-位氢原子后, 使丙醇从脱氢反应转化为脱水反应. 在这两种化合物的TPD 实验产物中发现, 有以脱水反应生成的烯烃(丙烯, 三氟丙烯), 脱氢反应产生的酮类(丙酮, 三氟丙酮)等分子析出. 实验结果表明, 氟原子取代γ-H后阻止了产生中间产物醇盐的β-H 脱氢反应, 打开了γ-H脱氢反应的通道, 导致烯烃的产生. 在2-丙醇吸附于镍表面的TPD实验中观察到了消去β-H产生丙酮的脱氢反应, 而1,1,1-三氟-2-丙醇在镍表面上经过脱水反应则产生了3,3,3-三氟丙烯.