Influences of Proline and Cysteine Residues on Fragment Yield in Matrix-Assisted Laser Desorption/Ionization In-Source Decay Mass Spectrometry

Matrix-assisted laser desorption/ionization in-source decay produces highly informative fragments for the sequencing of peptides/proteins. Among amino acids, cysteine and proline residues were found to specifically influence the fragment yield. As they are both frequently found in small peptide structures for which de novo sequencing is mandatory, the understanding of their specific behaviors would allow useful fragmentation rules to be established. In the case of cysteine, a c?/w fragment pair originating from Xxx–Cys is formed by side-chain loss from the cysteine residue. The presence of a proline residue contributes to an increased yield of ISD fragments originating from N–C_α bond cleavage at Xxx₁–Xxx₂Pro, which is attributable to the cyclic structure of the proline residue. Our results suggest that the aminoketyl radical formed by MALDI-ISD generally induces the homolytic N–C_α bond cleavage located on the C–terminal side of the radical site. In contrast, N–C_α bond cleavage at Xxx–Pro produces no fragments and the N–C_α bond at the Xxx₁–Xxx₂Pro bond is alternatively cleaved via a heterolytic cleavage pathway.      

Estimation of peptide N–Cα bond cleavage efficiency during MALDI‐ISD using a cyclic peptide

Matrix‐assisted laser desorption/ionization in‐source decay (MALDI‐ISD) induces N–C_α bond cleavage via hydrogen transfer from the matrix to the peptide backbone, which produces a c′/z? fragment pair. Subsequently, the z? generates z′ and [z + matrix] fragments via further radical reactions because of the low stability of the z?. In the present study, we investigated MALDI‐ISD of a cyclic peptide. The N–C_α bond cleavage in the cyclic peptide by MALDI‐ISD produced the hydrogen‐abundant peptide radical [M + 2H]⁺? with a radical site on the α‐carbon atom, which then reacted with the matrix to give [M + 3H]⁺ and [M + H + matrix]⁺. For 1,5‐diaminonaphthalene (1,5‐DAN) adducts with z fragments, post‐source decay of [M + H + 1,5‐DAN]⁺ generated from the cyclic peptide showed predominant loss of an amino acid with 1,5‐DAN. Additionally, MALDI‐ISD with Fourier transform‐ion cyclotron resonance mass spectrometry allowed for the detection of both [M + 3H]⁺ and [M + H]⁺ with two ¹³C atoms. These results strongly suggested that [M + 3H]⁺ and [M + H + 1,5‐DAN]⁺ were formed by N–C_α bond cleavage with further radical reactions. As a consequence, the cleavage efficiency of the N–C_α bond during MALDI‐ISD could be estimated by the ratio of the intensity of [M + H]⁺ and [M + 3H]⁺ in the Fourier transform‐ion cyclotron resonance spectrum. Because the reduction efficiency of a matrix for the cyclic peptide cyclo(Arg‐Gly‐Asp‐D‐Phe‐Val) was correlated to its tendency to cleave the N–C_α bond in linear peptides, the present method could allow the evaluation of the efficiency of N–C_α bond cleavage for MALDI matrix development. Copyright © 2016 John Wiley & Sons, Ltd.     

Mass spectrometric characterization of phosphorylated peptides using MALDI in‐source decay via redox reactions

Matrix‐assisted laser desorption/ionization in‐source decay (MALDI‐ISD) has been used for characterization of a phosphorylated peptides and proteins because labile phosphate group is not lost during the MALDI‐ISD process. The conventional MALDI‐ISD is initiated by the hydrogen transfer from reducing matrix molecules to peptide backbone, leading to c′‐ and z′‐series ions. In contrast, when an oxidizing chemical 5‐nitrosalicylic acid (5‐NSA) is served as the MALDI‐ISD matrix, a‐ and x‐series ions are specifically generated by hydrogen abstraction from peptide backbone to matrix molecule. The 5‐NSA provides useful complementary information to the conventional MALDI‐ISD for the analysis of amino acid sequencing and site localization of phosphorylation in peptides. The MALDI‐ISD with reducing and oxidizing matrix could be a useful method for the de novo peptide sequencing. Copyright © 2012 John Wiley & Sons, Ltd.     

ATNRC and SET‐NRC synthesis of PtBA‐g‐PEO well‐defined amphiphilic graft copolymers

A series of new well‐defined amphiphilic graft copolymers containing hydrophobic poly(tert‐butyl acrylate) backbone and hydrophilic poly(ethylene oxide) side chains were reported. Reversible addition‐fragmentation chain transfer homopolymerization of tert‐butyl 2‐((2‐bromopropanoyloxy)methyl)acrylate was first performed to afford a well‐defined backbone with a narrow molecular weight distribution (M_w/M_n = 1.07). The target poly(tert‐butyl acrylate)‐g‐poly(ethylene oxide) (PtBA‐g‐PEO) graft copolymers with low polydispersities (M_w/M_n = 1.18–1.26) were then synthesized by atom transfer nitroxide radical coupling or single electron transfer‐nitroxide radical coupling reaction using CuBr(Cu)/PMDETA as catalytic system. Fluorescence probe technique was employed to determine the critical micelle concentrations (cmc) of the obtained amphiphilic graft copolymers in aqueous media. Furthermore, PAA‐g‐PEO graft copolymers were obtained by selective acidic hydrolysis of hydrophobic PtBA backbone while PEO side chains kept inert. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Top‐down mass spectrometry of intact phosphorylated β‐casein: Correlation between the precursor charge state and internal fragments

Phosphorylated proteins play essential roles in many cellular processes, and identification and characterization of the relevant phosphoproteins can help to understand underlying mechanisms. Herein, we report a collision‐induced dissociation top‐down approach for characterizing phosphoproteins on a quadrupole time‐of‐flight mass spectrometer. β‐casein, a protein with two major isoforms and five phosphorylatable serine residues, was used as a model. Peaks corresponding to intact β‐casein ions with charged states up to 36⁺ were detected. Tandem mass spectrometry was performed on β‐casein ions of different charge states (12⁺, and 15⁺ to 28⁺) in order to determine the effects of charge state on dissociation of this protein. Most of the abundant fragments corresponded to y, b ions, and internal fragments caused by cleavage of the N‐terminal amide bond adjacent to proline residues (Xxx‐Pro). The abundance of internal fragments increased with the charge state of the protein precursor ion; these internal fragments predominantly arose from one or two Xxx‐Pro cleavage events and were difficult to accurately assign. The presence of abundant sodium adducts of β‐casein further complicated the spectra. Our results suggest that when interpreting top‐down mass spectra of phosphoproteins and other proteins, researchers should consider the potential formation of internal fragments and sodium adducts for reliable characterization.     

Laser‐induced decomposition of 2,2‐dimethoxy‐2‐phenylacetophenone and benzoin in methyl methacrylate homopolymerization studied via matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry

Pulsed laser polymerization (PLP) experiments were performed on the bulk polymerization of methyl methacrylate (MMA) at ?34 °C. The aim of this study was to investigate the polymer end groups formed during the photoinitiation process of MMA monomer using 2,2‐dimethoxy‐2‐phenylacetophenone (DMPA) and benzoin as initiators via matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry. Analysis of the MALDI‐TOF spectra indicated that the two radical fragments generated upon pulsed laser irradiation show markedly different reactivity toward MMA: whereas the benzoyl fragment—common to both DMPA and benzoin—clearly participates in the initiation process, the acetal and benzyl alcohol fragments cannot be identified as end groups in the polymer. The complexity of the MALDI‐TOF spectrum strongly increased with increasing laser intensity, this effect being more pronounced in the case of benzoin. This indicates that a cleaner initiation process is at work when DMPA is used as the photoinitiator. In addition, the MALDI‐TOF spectra were analyzed to extract the propagation‐rate coefficient, k_p, of MMA at ?34 °C. The obtained value of k_p = 43.8 L mol^?1 s^?1 agrees well with corresponding numbers obtained via size exclusion chromatography (k_p = 40.5 L mol^?1 s^?1). © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 675–681, 2002; DOI 10.1002/pola.10150     

One‐step synthesis of poly(lactic‐co‐glycolic acid)‐g‐poly‐1‐vinylpyrrolidin‐2‐one copolymers

The radical polymerization of 1‐vinylpyrrolidin‐2‐one (NVP) in poly(lactic‐co‐glycolic acid) (PLGA) 50:50 at 100 °C leads to amphiphilic PLGA‐g‐PVP copolymers. Their composition is determined by FT‐IR spectroscopy. Thermogravimetric analyses agree with FT‐IR determinations. Saponification of the PLGA‐g‐PVP polyester portion allows isolating the PVP side chains and measuring their molecular weight, from which the average chain transfer constant (C_T) of the PLGA units is estimated. The MALDI‐TOF spectra of PVP reveal the presence at one chain end of residues of either glycolic acid‐ or lactic acid‐ or lactic/glycolic acid dimers, trimers and one tetramer, the other terminal being hydrogen. This unequivocally demonstrates that grafting occurred. Accordingly, the orthogonal solvent pair ethyl acetate—methanol, while separating the components of PLGA/PVP intimate mixtures, fails to separate pure PVP or PLGA from the reaction products. All PLGA‐g‐PVP and PLGA/PLGA‐g‐PVP blends, but not PLGA/PVP blends, give long‐time stable dispersions in water. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 1919–1928     

Synthesis of twin‐tail tadpole‐shaped (cyclic polystyrene)‐ block‐[linear poly (tert‐butyl acrylate)]2 by combination of glaser coupling reaction with living anionic polymerization and atom transfer radical polymerization

The twin‐tail tadpole‐shaped (cyclic polystyrene)‐block‐[linear poly (tert‐butyl acrylate)]₂ [(c‐PS)‐b‐(l‐PtBA)₂] was synthesized by combination of Glaser coupling reaction with atom transfer radical polymerization (ATRP) and living anionic polymerization (LAP). First, the telechelic PS with an active and an ethoxyethyl‐protected hydroxyl groups at both ends was prepared by LAP of St monomers using lithium naphthalenide as initiator and terminated by 1‐ethoxyethyl glycidyl ether. And the alkyne groups were introduced onto each PS end by selectively reaction of active hydroxy group with propargyl bromide in NaH/tetrahydrofuran (THF) system. Then, the intramolecular cyclization was carried out by Glaser coupling reaction in pyridine/Cu(I)Br system in air atmosphere. Finally, the macroinitiator of c‐PS with two bromine groups at the junction point was synthesized via the cleavage of ethoxyethyl group and the subsequent esterification of the deprotected hydroxyl groups with 2‐bromoisobutyryl bromide. The copolymer of (c‐PS)‐b‐(l‐PtBA)₂ was obtained by ATRP of tBA monomers, and the PtBA segment was also hydrolyzed for (cyclic polystyrene)‐block‐(linear polyacrylic acid)₂ [(c‐PS)‐b‐(l‐PAA)₂]. The target copolymers and all intermediates were well characterized by GPC, MALDI‐TOF MS, and ¹H NMR in detail. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Synthesis of well‐defined naphthalene and photo‐labile group‐labeled polystyrene via ATRP

The atom transfer radical polymerizations of styrene were successfully carried out in bulk and solution, respectively, at 115 °C, with a novel photoiniferter reagent, (1‐naphthyl)methyl N,N‐diethyldithiocarbamate (NMDC), as an initiator in the presence of copper (I) bromide and N,N,N′,N″,N″‐pentamethyldiethylenetriamine. The results showed that NMDC was an effective initiator with high initiation efficiency for ATRP of St. The polymerization rate was first‐order with respect to the monomer concentration and the molecular weights of the obtained polystyrene (PS) increased linearly with the monomer conversion, with very narrow molecular weight distributions (M_w/M_n = 1.07–1.29). The functionalized naphthalene‐labeled PS bearing N,N‐(diethylamino)dithiocarbamoyl group which was confirmed by ¹H NMR analysis, and chain extension of the PS exhibited fluorescence and ultraviolet absorption in chloroform (CHCl₃). © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 510–518, 2006     

Facile one‐pot/one‐step technique for preparation of side‐chain functionalized polymers: Combination of SET‐RAFT polymerization of azide vinyl monomer and click chemistry

An azido‐containing functional monomer, 11‐azido‐undecanoyl methacrylate, was successfully polymerized via ambient temperature single electron transfer initiation and propagation through the reversible addition–fragmentation chain transfer (SET‐RAFT) method. The polymerization behavior possessed the characteristics of “living”/controlled radical polymerization. The kinetic plot was first order, and the molecular weight of the polymer increased linearly with the monomer conversion while keeping the relatively narrow molecular weight distribution (M_w/M_n ≤ 1.22). The complete retention of azido group of the resulting polymer was confirmed by ¹H NMR and FTIR analysis. Retention of chain functionality was confirmed by chain extension with methyl methacrylate to yield a diblock copolymer. Furthermore, the side‐chain functionalized polymer could be prepared by one‐pot/one‐step technique, which is combination of SET‐RAFT and “click chemistry” methods. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Star polymers by cross‐linking of linear poly(benzyl‐L‐glutamate) macromonomers via free‐radical and RAFT polymerization. A simple route toward peptide‐stabilized nanoparticles

Poly(benzyl‐L ‐glutamate) (PBLG) macromonomers were synthesized by N‐carboxyanhydride (NCA) polymerization initiated with 4‐vinyl benzylamine. MALDI‐ToF analysis confirmed the presence of styrenic end‐groups in the PBLG. Free‐radical and RAFT polymerization of the macromonomer in the presence of divinyl benzene produced star polymers of various molecular weights, polydispersity, and yield depending on the reaction conditions applied. The highest molecular weight (M_w) of 10,170,000 g/mol was obtained in a free‐radical multibatch approach. It was shown that the PBLG star polymers can be deprotected to obtain poly(glutamic acid) star polymers, which form water soluble pH responsive nanoparticles. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

Selective cleavage enhanced by acetylating the side chain of lysine

Selective cleavage is of great interest in mass spectrometry studies as it can help sequence identification by promoting simple fragmentation pattern of peptides and proteins. In this work, the collision‐induced dissociation of peptides containing internal lysine and acetylated lysine residues were studied. The experimental and computational results revealed that multiple fragmentation pathways coexisted when the lysine residue was two amino acid residues away from N‐terminal of the peptide. After acetylation of the lysine side‐chain, ions were the most abundant primary fragment products and the Lys_(Ac)–Gly amide bond became the dominant cleavage site via an oxazolone pathway. Acetylating the side‐chain of lysine promoted the selective cleavage of Lys–Xxx amide bond and generated much more information of the peptide backbone sequence. The results re‐evaluate the selective cleavage due to the lysine basic side‐chain and provide information for studying the post‐translational modification of proteins and other bio‐molecules containing Lys residues. Copyright © 2013 John Wiley & Sons, Ltd.     

Free‐Radical Termination Kinetics Studied Using a Novel SP‐PLP‐ESR Technique

Summary: A novel method for measuring termination rate coefficients, k_t, in free‐radical polymerization is presented. A single laser pulse is used to instantaneously produce photoinitiator‐derived radicals. During subsequent polymerization, radical concentration is monitored by time‐resolved electron spin resonance (ESR) spectroscopy. The size of the free radicals, which exhibits a narrow distribution increases linearly with time t, which allows the chain‐length dependence of k_t to be deduced. The method will be illustrated using dodecyl methacrylate polymerization as an example.

Two straight lines provide a very satisfactory representation of the chain‐length dependence of k_t over the entire chain‐length region (c_R = radical concentration).     

Solid‐Phase Combinatorial Synthesis and Biological Evaluation of Destruxin E Analogues

The solid‐phase combinatorial synthesis of cyclodepsipeptide destruxin E has been demonstrated. The combinatorial synthesis of cyclization precursors 8 was achieved by using a split and pool method on SynPhase Lanterns. The products were successfully macrolactonized in parallel in the solution phase by using 2‐methyl‐6‐nitrobenzoic anhydride and 4‐(dimethylamino)pyridine N‐oxide to afford macrolactones 9 , and the subsequent formation of an epoxide in the side chain gave 18 member destruxin E analogues 6 . Biological evaluation of analogues 6 indicated that the N‐MeAla residue was crucial to the induction of morphological changes in osteoclast‐like multinuclear cells (OCLs). Based on structure–activity relationships, azido‐containing analogues 15 were then designed for use as a molecular probe. The synthesis and biological evaluation of analogues 15 revealed that 15 b , in which the Ile residue was replaced with a Lys(N₃) residue, induced morphological changes in OCLs at a sufficient concentration, and modification around the Ile residue would be tolerated for attachment of a chemical tag toward the target identification of destruxin E ( 1 ).     

Syntheses of N10‐substituted 7‐Arylpyrrolo[2,1‐c]‐[1,4]benzodiazepine‐5,11‐diones

Pyrrolo[2,1‐c][1,4]benzodiazepine‐5,11‐dione and its 7‐bromo derivative were alkylated at the N10 atom applying various methods. The resulting products were subjected to Suzuki–Miyaura reactions using a catalyst system consisting of Pd(Cl)₂(PPh₃)₂ and sodium tert‐butanolate in toluene. Results of an X‐ray single crystal analysis are presented.     

SET‐LRP of methyl methacrylate initiated with sulfonyl halides

Single electron transfer‐living radical polymerization (SET‐LRP) represents a robust and versatile method for the rapid synthesis of macromolecules with defined architecture. The present article describes the polymerization of methyl methacrylate by SET‐LRP in protic solvent mixtures. Herein, the polymerization process was catalyzed by a straightforward Cu(0)wire/Me₆‐TREN catalyst while initiation was obtained by toluenesulfonyl chloride. All experiments were conducted at 50 °C and the living polymerization was demonstrated by kinetic evaluation of the SET‐LRP. The process follows first order kinetic until all monomer is consumed which was typically achieved within 4 h. The molecular weight increased linearly with conversion and the molecular weight distributions were very narrow with M_w/M_n ～ 1.1. Detailed investigations of the polymer samples by MALDI‐TOF confirmed that no termination took place and that the chain end functionality is retained throughout the polymerization process. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 2236–2242, 2010     

SET‐LRP synthesis of PMHDO‐g‐PNIPAM well‐defined amphiphilic graft copolymer

A well‐defined amphiphilic graft copolymer, consisting of hydrophobic polyallene‐based backbone and hydrophilic poly(N‐isopropylacrylamide) (PNIPAM) side chains, was prepared by the combination of living coordination polymerization, single electron transfer‐living radical polymerization (SET‐LRP), and the grafting‐from strategy. First, the double‐bond‐containing backbone was prepared by [(η³‐allyl)NiOCOCF₃]₂‐initiated living coordination polymerization of 6‐methyl‐1,2‐heptadiene‐4‐ol (MHDO). Next, the pendant hydroxyls in every repeating unit of poly(6‐methyl‐1,2‐heptadiene‐4‐ol) (PMHDO) homopolymer were treated with 2‐chloropropionyl chloride to give PMHDO‐Cl macroinitiator. Finally, PNIPAM side chains were grown from PMHDO backbone via SET‐LRP of N‐isopropylacrylamide initiated by PMHDO‐Cl macroinitiator in N,N‐dimethylformamide/2‐propanol using copper(I) chloride/tris(2‐(dimethylamino)ethyl)amine as catalytic system to afford PMHDO‐g‐PNIPAM graft copolymers with a narrow molecular weight distribution (M_w/M_n = 1.19). The critical micelle concentration (cmc) in water was determined by fluorescence probe technique and the effects of pH and salinity on the cmc of PMHDO‐g‐PNIPAM were also investigated. The micellar morphology was found to be spheres using transmission electron microscopy. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013     

Peptide‐poly(2‐(dimethylamino)ethyl methacrylate) conjugates: Synthesis and aqueous/nonaqueous self‐aggregation into nanostructures of dendritic and spherical morphologies

Peptide–polymer conjugate consisting of a sequence‐defined tripeptide and poly(2‐(dimethylamino)ethyl methacrylate) (PDMAEMA) is synthesized by a simple “grafting from” atom transfer radical polymerization (ATRP) approach. The ATRP of PDMAEMA using peptide‐macroinitiator and CuBr/1,1,4,7,10,10‐hexamethyltriethylenetetramine system in anisole follows pseudo first order kinetics up to a conversion of about 25% within a time span of 125 min. The attachment of peptide moiety at the end of PDMAEMA chain is confirmed from MALDI‐TOF‐MS and circular dichroism analyses. The self‐assembly of as‐synthesized peptide‐PDMAEMA conjugate in organic solvents leads to the formation of spherical nanoparticles as observed through FESEM. Peptide‐PDMAEMA conjugate become soluble in water due to the protonation of the pendent —N(CH₃)₂ moiety of DMAEMA group of the conjugate. Owing to the amphiphilic nature of the protonated conjugate (peptide‐PDMAEMAH), it also undergoes self‐aggregation in water into nanostructures of various morphologies such as dendrite, small sphere and large sphere at pHs of 2, 8, and 10, respectively. Peptide‐PDMAEMA‐IBu conjugate obtained by the post‐modification of —N(CH₃)₂ moiety of DMAEMA group of the conjugate with n‐butylbromide also undergoes self‐aggregation into dendritic nanostructures in water. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 3286–3297     

A Transformation of N‐Alkylated Anilines to N‐Aryloxamates

Transformation of N‐alkylated anilines to N‐aryloxamates was studied using ethyl 2‐diazoacetoacetate as an alkylating agent and dirhodium tetraacetate (Rh₂(OAc)₄) as the catalyst. The general applicability of the reaction as a synthetic method for N‐aryloxamates was studied with a number of substituted N‐alkylated anilines. The results revealed that the oxamate was formed by a radical reaction with molecular O₂ and Rh₂(OAc)₄ as initiator.     

Re‐formation Reaction of Cyclic Nitroxide‐Based Alkoxyamines: Steric and Polar/Stabilization Effects

In nitroxide‐mediated radical polymerization, the polymerization times decrease with the increasing re‐formation rate constant of the C? ON bond (→ alkoxyamine) between the growing polymer chain and the nitroxide radical. The factors influencing the re‐formation rate constant are of considerable interest, but up to now, the polar/stabilization effects have not been addressed thoroughly. The combination of new data with previously reported data now showed that the re‐formation rate constant k_c increases with the increasing polar character of the substituents attached to the nitroxide moiety. The polar/stabilization effects are weaker for the re‐formation than for the homolysis of the C? ON bond, and may be mainly attributed to the relocation of the odd electron onto the O‐atom of the N? O moiety, i.e., the stabilization of the nitroxide moiety. Hence, it is possible to predict the values of k_c by combining both the polar/stabilization (σ_I) and steric effects (E ), i.e., log(k_c/M ^?1 s^?1) = 9.86 + 0.57 ? σ_I + 0.40 ? E_s.