Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides

A method to facilitate the characterization of stapled or cyclic peptides is reported via an arginine-selective derivatization strategy coupled with MS/MS analysis. Arginine residues are converted to ornithine residues through a deguanidination reaction that installs a highly selectively cleavable site in peptides. Upon activation by CID or UVPD, the ornithine residue cyclizes to promote cleavage of the adjacent amide bond. This Arg-specific process offers a unique strategy for site-selective ring opening of stapled and cyclic peptides. Upon activation of each derivatized peptide, site-specific backbone cleavage at the ornithine residue results in two complementary products: the lactam ring-containing portion of the peptide and the amine-containing portion. The deguanidination process not only provides a specific marker site that initiates fragmentation of the peptide but also offers a means to unlock the staple and differentiate isobaric stapled peptides.

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Characterization of the Cysteine Content in Proteins Utilizing Cysteine Selenylation with 266 nm Ultraviolet Photodissociation (UVPD)

Characterization of the cysteine content of proteins is a key aspect of proteomics. By defining both the total number of cysteines and their bound/unbound state, the number of candidate proteins considered in database searches is significantly constrained. Herein we present a methodology that utilizes 266 nm UVPD to count the number of free and bound cysteines in intact proteins. In order to attain this goal, proteins were derivatized with N-(phenylseleno)phthalimide (NPSP) to install a selectively cleavable Se–S bond upon 266 UVPD. The number of Se–S bonds cleaved upon UVPD, a process that releases SePh moieties, corresponds to the number of cysteine residues per protein.

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Statistical Examination of the <Emphasis Type="Italic">a</Emphasis> and <Emphasis Type="Italic">a</Emphasis> + 1 Fragment Ions from 193 nm Ultraviolet Photodissociation Reveals Local Hydrogen Bonding Interactions

Dissociation of proteins and peptides by 193 nm ultraviolet photodissociation (UVPD) has gained momentum in proteomic studies because of the diversity of backbone fragments that are produced and subsequent unrivaled sequence coverage obtained by the approach. The pathways that form the basis for the production of particular ion types are not completely understood. In this study, a statistical approach is used to probe hydrogen atom elimination from a + 1 radical ions, and different extents of elimination are found to vary as a function of the identity of the C-terminal residue of the a product ions and the presence or absence of hydrogen bonds to the cleaved residue.

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Trapping Nanostructures on Surfaces through Weak Interactions

The assembly of imidazole‐functionalized phenanthroline‐strapped zinc porphyrins (ZnPorphen) with alkyl or polyethylene glycol (PEG) side chains was studied in solution and by AFM after casting on highly oriented pyrolytic graphite (HOPG) or mica. The nature of the solvent and its evaporation time influenced the morphology of the objects observed. On HOPG, short rods of about 100 nm were observed after fast evaporation of solutions of the alkyl derivatives in CHCl₃, THF, or pyridine, whereas islands of aligned rows of longer wires were obtained from methylcyclohexane (MCH). Slow evaporation of MCH led to a three‐dimensional assembly. The PEG porphyrin assembled into short wires on HOPG or fibers on mica after slow evaporation of solutions in THF. This study shows the role of surface–molecule interactions in the interfacial assembly of ZnPorphen derivatives and contributes to understanding the parameters that control their noncovalent assembly into molecular wires on a surface.     

An efficient data format for mass spectrometry-based proteomics

The diverse range of mass spectrometry (MS) instrumentation along with corresponding proprietary and nonproprietary data formats has generated a proteomics community driven call for a standardized format to facilitate management, processing, storing, visualization, and exchange of both experimental and processed data. To date, significant efforts have been extended towards standardizing XML-based formats for mass spectrometry data representation, despite the recognized inefficiencies associated with storing large numeric datasets in XML. The proteomics community has periodically entertained alternate strategies for data exchange, e.g., using a common application programming interface or a database-derived format. However, these efforts have yet to gain significant attention, mostly because they have not demonstrated significant performance benefits over existing standards, but also due to issues such as extensibility to multidimensional separation systems, robustness of operation, and incomplete or mismatched vocabulary. Here, we describe a format based on standard database principles that offers multiple benefits over existing formats in terms of storage size, ease of processing, data retrieval times, and extensibility to accommodate multidimensional separation systems.     

Towards catenanes using π-stacking interactions and their influence on the spin-state of a bis(2,2':6',2"terpyridine)iron(II) domain

The ligand 6,6"bis(4-methoxyphenyl)-4'-phenyl-2,2':6',2"terpyridine (2) has been prepared and characterized; deprotection using pyridinium chloride leads to the formation of 6,6"bis(4-hydroxyphenyl)-4'-phenyl-2,2':6',2"terpyridinium chloride ([H3]Cl). Treatment of the latter with 3-(2-(2-bromoethoxy)ethoxy)prop-1-ene under basic conditions yields ligand 4 containing pendant, alkene-terminated chains. Whereas direct complexation of 4 with ruthenium(II) proved problematical, the homoleptic complexes [Fe(2)(2)][PF(6)](2) and [Ru(2)(2)][PF(6)](2) were prepared in good to moderate yields. In the solid state, both complexes exhibit multiple face-to-face π-stacking of arene and pyridine rings which influences the coordination geometry about the metal ion. Consequential weakening of the ligand field results in [Fe(2)(2)][PF(6)](2) being high-spin. Variable temperature solution (1)H NMR spectroscopic studies confirm the iron(ii) centre remains high-spin between 200 and 295 K. The paramagnetically shifted (1)H NMR spectrum exhibits signals in the range δ 109.7 to -66.5 ppm and has been fully assigned. Paramagnetic relaxation enhancement (PRE) has been used to correlate the observed proton line-widths to the distances of the protons from the metal centre and these are in good agreement with the Fe···H separations observed in the solid state. The [Fe(2)(2)](2+) ion undergoes two dynamic processes (i) rotation of the pendant phenyl rings which is fast on the NMR timescale at 200 K, and (ii) twisting and sliding of the aromatic rings of the tpy and anisyl units which interconverts the two enantiomers of [Fe(2)(2)](2+) at 295 K.     

ULTRAVIOLET ACTION SPECTRA FOR PHOTOBIOLOGICAL EFFECTS IN CULTURED HUMAN LENS EPITHELIAL CELLS

Abstract— The action spectrum for cell killing by UV radiation in human lens epithelial (HLE) cells is not known. Here we report the action spectrum in the 297–365 nm region in cultured HLE cells with an extended lifespan (HLE B-3 cells) and define their usefulness as a model system for photobiological studies. Cells were irradiated with monochromatic radiation at 297, 302, 313, 325, 334 and 365 nm. Cell survival was determined using a clonogenic assay. Analysis of survival curves showed that radiation at 297 nm was six times more effective in cell killing than 302 nm radiation; 297 nm radiation was more than 260, 590, 1400 and 3000 times as effective in cell killing as 313, 325, 334 and 365 nm radiation, respectively. The action spectrum was similar in shape to that for other human epithelial cell lines and rabbit lens epithelial cells. The effect of UV radiation on crystallin synthesis was also determined at different wavelengths. To determine whether exposure to UV radiation affects the synthesis of β-crystallin, cells were exposed to sublethal fluences of UV radiation at 302 and 313 nm, labeled with [³⁵S]methionine and the newly synthesized βY-crystallin was analyzed by immunoprecipitation and western blotting using an antibody to β-crystallin. The results show a decrease in crystallin synthesis in HLE cells irradiated at 302 and 313 nm at fluences causing low cytotoxicity. The effect of radiation on membrane perturbation was determined by measuring enhancement of synthesis of prostaglandin E₂ (PGE₂). Synthesis of PGE₂ occurs at all UV wavelengths tested in the 297–365 nm region. The slope of the PGE₂ response curves was higher than that of cell killing curves in cultured HLE cells. These data show that cultured HLE cells with extended lifespan are a suitable system for investigating photobiological responses of cells to UV radiation.