Label Scrambling During CID of Covalently Labeled Peptide Ions

Covalent labeling along with mass spectrometry is finding more use as a means of studying the higher order structure of proteins and protein complexes. Diethylpyrocarbonate (DEPC) is an increasingly used reagent for these labeling experiments because it is capable of modifying multiple residues at the same time. Pinpointing DEPC-labeled sites on proteins is typically needed to obtain more resolved structural information, and tandem mass spectrometry after protein proteolysis is often used for this purpose. In this work, we demonstrate that in certain instances, scrambling of the DEPC label from one residue to another can occur during collision-induced dissociation (CID) of labeled peptide ions, resulting in ambiguity in label site identity. From a preliminary study of over 30 labeled peptides, we find that scrambling occurs in about 25% of the peptides and most commonly occurs when histidine residues are labeled. Moreover, this scrambling appears to occur more readily under non-mobile proton conditions, meaning that low charge-state peptide ions are more prone to this reaction. For all peptides, we find that scrambling does not occur during electron transfer dissociation, which suggests that this dissociation technique is a safe alternative to CID for correct label site identification. Graphical Abstract

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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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Evidence for ion–ion interactions between peptides and anions (HSO4− or ClO4−) derived from high‐acidity acids

The existence of gas‐phase electrostatic ion–ion interactions between protonated sites on peptides ([Glu] Fibrinopeptide B, Angiotensin I and [Asn¹, Val⁵]‐Angiotensin II) and attaching anions (ClO₄^? and HSO₄^?) derived from strong inorganic acids has been confirmed by CID MS/MS. Evidence for ion–ion interactions comes especially from the product ions formed during the first dissociation step, where, in addition to the expected loss of the anion or neutral acid, other product ions are also observed that require covalent bond cleavage (i.e. H₂O loss when several carboxylate groups are present, or NH₃ loss when only one carboxylate group is present). For [[Glu] Fibrinopeptide B + HSO₄]^?, under CID, H₂O water loss was found to require less energy than H₂SO₄ departure. This indicates that the interaction between HSO₄^? and the peptide is stronger than the covalent bond holding the hydroxyl group, and must be an ion–ion interaction. The strength and stability of this type of ion‐pairing interaction are highly dependent on the accessibility of additional mobile charges to the site. Positive mobile charges such as protons from the peptide can be transferred to the attaching anion to possibly form a neutral that may depart from the complex. Alternatively, an ion–ion interaction can be disrupted by a competing proximal additional negatively charged site of the peptide that can potentially form a salt bridge with the positively charged site and thereby facilitate the attaching anion's departure. Copyright © 2014 John Wiley & Sons, Ltd.     

Resistance of composite materials based on BaCeO3 against the corrosive effects of carbon dioxide and water vapour at intermediate fuel cell operating temperatures

The objective of this work is to analyse the chemical stability of BaCe_0.85Y_0.15O_3?δ –Ce_0.85Y_0.15O_2?δ (BCY15–YDC15) composite materials at 600 °C and to compare the aforementioned chemical stability with that of pure BCY15. The composite powders were obtained by mixing together powders of BCY15 and YDC15 in the following volume fractions: 90 % BCY15 + 10 % YDC15, 70 % BCY15 + 30 % YDC15, 30 % BCY15 + 70 % YDC15, 20 % BCY15 + 80 % YDC15 and 10 % BCY15 + 90 % YDC15. After that both powders and sintered samples of the BCY15 and the BCY15–YDC15 composites were saturated in two different atmospheres at 600 °C: CO₂/H₂O (3.1 mol% H₂O) and N₂/H₂O (46.8 mol% H₂O). The effects of the previously mentioned atmospheres on the physicochemical properties of the samples were investigated via differential thermal analysis (DTA) combined with thermogravimetric analysis (TG). Furthermore, mass spectrometry was used to analyse the chemical composition of the gases released from the samples during the DTA–TG heating process. The surface and cross-section morphology of the samples were examined by scanning electron microscopy. Moreover, the phase composition of each sample was studied via X-ray Diffraction. From the combined analysis, it can be concluded that the addition of YDC15 in the composite samples leads to an increase in resistance against the corrosive effects of CO₂. Furthermore, it was determined that all samples maintain stability in the presence of H₂O at 600 °C.     

A flow system for hydrogen peroxide production at reticulated vitreous carbon via electroreduction of oxygen

In this work, a reticulated vitreous carbon electrode (RVCE, 96.5 % porosity, 24 cm^?1) was modified with 2-anthraquinonyl groups to electrocatalytically reduce dissolved oxygen in neutral aqueous solution (0.1 M phosphate buffer solution supported with 3 M potassium chloride, pH of 6.7) to hydrogen peroxide (H₂O₂) at 25 °C under atmospheric pressure. The obtained current density was ca. 3 mA cm^?2. For the first time, the oxygen reduction was investigated on a novelly designed RVCE housed in a gravity-feed flow system. Fractional current conversions obtained on the RVC flow cell were compared and contrasted with those on a two-dimensional electrode, viz. a tubular flow electrode. The modified-on catalyst has the benefit in terms of easy separation of the product from the catalyst. The in situ generated low concentration of H₂O₂ provides potential applications to water purification processes and disinfection for water and food.     

Gold Carbenoids: Lessons Learnt from a Transmetalation Approach

Carbophilic catalysts that are based on Au^I allow a host of different nucleophiles to be added across various π systems. 1 – 3 Although many of these reactions are thought to proceed via gold carbenoids, the challenge to observe and characterize these putative intermediates has basically been unmet. 4 The current mechanistic interpretation therefore largely relies on indirect evidence and computational data, some of which are subject to debate. 5 In an attempt to fill this gap, we pursued a potential route to gold carbenoids by formal transmetalation of chromium or tungsten Fischer carbene complexes with [LAu]⁺. Whereas this transformation proceeds with exceptional ease as long as a stabilizing heteroelement is present on the carbene center, it stops half‐way in its absence. Rather unusual bimetallic arrays are formed, which allow the charge density to delocalize over several positions. The obvious difficulty of releasing an “unstabilized” gold carbenoid has potential mechanistic implications for the understanding of π‐acid catalysis in general.     

Mechanistic Insights into the Interface‐Directed Transformation of Thiols into Disulfides and Molecular Hydrogen by Visible‐Light Irradiation of Quantum Dots

Quantum dots (QDs) offer new and versatile ways to harvest light energy. However, there are few examples involving the utilization of QDs in organic synthesis. Visible‐light irradiation of CdSe QDs was found to result in virtually quantitative coupling of a variety of thiols to give disulfides and H₂ without the need for sacrificial reagents or external oxidants. The addition of small amounts of nickel(II) salts dramatically improved the efficiency and conversion through facilitating the formation of hydrogen atoms, thereby leading to faster regeneration of the ground‐state QDs. Mechanistic studies reveal that the coupling reaction occurs on the QD surfaces rather than in solution and offer a blueprint for how these QDs may be used in other photocatalytic applications. Because no sacrificial agent or oxidant is necessary and the catalyst is reusable, this method may be useful for the formation of disulfide bonds in proteins as well as in other systems sensitive to the presence of oxidants.     

Redox‐Neutral α,β‐Difunctionalization of Cyclic Amines

In contrast to the continuously growing number of methods that allow for the efficient α‐functionalization of amines, few strategies exist that enable the direct functionalization of amines in the β‐position. A general redox‐neutral strategy is outlined for amine β‐functionalization and α,β‐difunctionalization that utilizes enamines generated in situ. This concept is demonstrated in the context of preparing polycyclic N,O‐acetals from simple 1‐(aminomethyl)‐β‐naphthols and 2‐(aminomethyl)‐phenols.     

Mixed‐Metal MIL‐100(Sc,M) (M=Al,Cr, Fe) for Lewis Acid Catalysis and Tandem CC Bond Formation and Alcohol Oxidation

The trivalent metal cations Al³⁺, Cr³⁺, and Fe³⁺ were each introduced, together with Sc³⁺, into MIL‐100(Sc,M) solid solutions (M=Al, Cr, Fe) by direct synthesis. The substitution has been confirmed by powder X‐ray diffraction (PXRD) and solid‐state NMR, UV/Vis, and X‐ray absorption (XAS) spectroscopy. Mixed Sc/Fe MIL‐100 samples were prepared in which part of the Fe is present as α‐Fe₂O₃ nanoparticles within the mesoporous cages of the MOF, as shown by XAS, TGA, and PXRD. The catalytic activity of the mixed‐metal catalysts in Lewis acid catalysed Friedel–Crafts additions increases with the amount of Sc present, with the attenuating effect of the second metal decreasing in the order Al>Fe>Cr. Mixed‐metal Sc,Fe materials give acceptable activity: 40 % Fe incorporation only results in a 20 % decrease in activity over the same reaction time and pure product can still be obtained and filtered off after extended reaction times. Supported α‐Fe₂O₃ nanoparticles were also active Lewis acid species, although less active than Sc³⁺ in trimer sites. The incorporation of Fe³⁺ into MIL‐100(Sc) imparts activity for oxidation catalysis and tandem catalytic processes (Lewis acid+oxidation) that make use of both catalytically active framework Sc³⁺ and Fe³⁺. A procedure for using these mixed‐metal heterogeneous catalysts has been developed for making ketones from (hetero)aromatics and a hemiacetal.