Effects of glycosylation on peptide conformation: a synergistic experimental and computational study

Asparagine-linked glycosylation, the co-translational covalent attachment of carbohydrates to asparagine side chains, has a major effect on the folding, stability, and function of many proteins. The carbohydrate composition in mature glycoproteins is heterogeneous due to modification of the initial oligosaccharide by glycosidases and glycosyltransferases during the glycoprotein passage through the endoplasmic reticulum and Golgi apparatus. Despite the diversity of carbohydrate structures, the core beta-D-(GlcNAc)(2) remains conserved in all N-linked glycoproteins. Previously, results from our laboratory showed that the molecular composition of the core disaccharide has a critical and unique conformational effect on the peptide backbone. Herein, we employ a synergistic experimental and computational approach to study the effect of the stereochemistry of the carbohydrate--peptide linkage on glycopeptide structure. A glycopeptide derived from a hemagglutinin protein fragment was synthesized, with the carbohydrate attached to the peptide with an alpha-linked stereochemistry. Computational and biophysical analyses reveal that the conformations of the peptide and alpha- and beta-linked glycopeptides are uniquely influenced by the attached saccharide. The value of computational approaches for probing the influence of attached saccharides on polypeptide conformation is highlighted.     

Synthesis and Solution Studies of Silver(I)‐Assembled Porphyrin Coordination Cages

The synthesis and the characterization of two porphyrin coordination cages are reported. The design of the cage formation is based on the coordination of silver(I) ions to the pyridyl units of 3‐pyridyl appended porphyrins. ¹H/¹⁰⁹Ag NMR spectroscopy, and diffusion‐ordered spectroscopy (DOSY) experiments demonstrate that both the free base porphyrin 2H‐TPyP and the Zn‐porphyrin Zn‐TPyP form the closed cages, [ Ag₄(2H‐TPyP)₂ ]⁴⁺ and [ Ag₄(Zn‐TPyP)₂ ]⁴⁺, respectively, upon addition of two equivalents of Ag⁺. The complexation processes are characterized in details by means of absorption and emission spectroscopy in diluted CH₂Cl₂ solutions. The data are discussed in the frame of the point‐dipole exciton coupling theory; the two porphyrin monomers, in fact, experience a rigid face‐to‐face geometry in the cages and a weak inter‐porphyrin exciton coupling. An intermediate species is observed, for Zn‐TPyP , in a porphyrin/Ag⁺ stoichiometric ratio of about 1:0.5 and is tentatively ascribed to an oblique open form. The occurrence of a photoinduced electron‐transfer reaction within the cages is excluded on the basis of the experimental outcomes and thermodynamic evaluations. Photophysical experiments evidence different reactivities of singlet and triplet excited states in the assemblies. A lower fluorescence quantum yield and triplet formation is discussed in relation to the constrained geometry of the complexes. Unusually long triplet excited state lifetimes are measured for the assemblies.     

Separation and detection of peroxynitrite and its metabolites by capillary electrophoresis with UV detection

A method for the separation and direct detection of peroxynitrite (ONOO(-)) and two of its degradation products, nitrite (NO(2)(-)) and nitrate (NO(3)(-)), using capillary electrophoresis with ultraviolet detection is described. The separation parameters were optimized and included electrokinetic injection, a run buffer consisting of 25 mM K(2)HPO(4) 7.5 mM DTAB, pH 12, and a field strength of -323 V/cm. A diode array UV detector was employed in these studies as it allowed the determination of all three species simultaneously. Nitrate and nitrite provided the maximum response at 214 nm while peroxynitrite generated the best response at 302 nm. All three species could be detected at 214 nm, while simultaneous detection at 214 and 302 nm positively identified each peak.     

Optimization of N‐methyl‐N‐[tert‐butyldimethylsilyl]trifluoroacetamide as a derivatization agent for determining isotopic enrichment of glycerol in very‐low density lipoproteins

Stable isotope kinetic studies play an important role in the study of very‐low density lipoprotein (VLDL) metabolism, including basic and clinical research. Today, [1,1,2,3,3‐²H₅]glycerol is the most cost‐effective alternative to measure glycerol and triglyceride kinetics. Recycling of glycerol from glycolysis and gluconeogenesis may lead to incompletely labelled tracer molecules. Many existing methods for the measurement of glycerol isotopic enrichment involve the production of glycerol derivatives that result in fragmentation of the glycerol molecule after ionization. It would be favourable to measure the intact tracer molecule since incompletely labelled tracer molecules may be measured as fully labelled. The number of methods available to measure the intact tracer in biological samples is limited. The aim of this project was to develop a gas chromatography/mass spectrometry (GC/MS) method for glycerol enrichment that measures the intact glycerol backbone and is suitable for electron ionization (EI), which is widely available. A previously published method for N‐methyl‐N‐[tert‐butyldimethylsilyl]trifluoroacetamide (MTBSTFA) derivatization was significantly improved; we produced a stable derivative and increased recovery 27‐fold in standards. We used the optimized MTBSTFA method in VLDL‐triglyceride and found that further modification was required to take matrix effects into account. We now have a robust method to measure glycerol isotopic enrichment by GC/EI‐MS that can be used to rule out the known problem of tracer recycling in studies of VLDL kinetics. Copyright © 2010 John Wiley & Sons, Ltd.     

Diastereoselective formation of homochiral flexible perylene bisimide cyclophanes and their hybrids with fullerenes

Cyclophanes of different ring sizes featuring perylene-3,4:9,10-tetracarboxylic acid bisimide (PBI) linked by flexible malonates were designed, synthesized, and investigated with respect to their structural, chemical and photo-physical properties. It is predominantly the number of PBIs and their geometric arrangement, which influence dramatically their properties. For example, two-PBI containing cyclophanes reveal physico-chemical characteristics that are governed by strong co-facial π–π interactions. This is in stark contrast to cyclophanes with either three or four PBIs. Key to co-facial π–π stackings are the flexible malonate linkers, which, in turn, set up the ways and means for diastereoselectivity of the homochiral PBIs at low temperatures, on one hand. In terms of selectivity, diastereomeric (M,M)/(P,P) : (M,P)/(P,M) pairs with a ratio of approximately 10 : 1 are discernible in the ¹H NMR spectra in C₂D₂Cl₄ and a complete diastereomeric excess is found in CD₂Cl₂. On the other hand, symmetry-breaking charge transfer as well as charge separation at room temperature are corroborated in steady-state and time-resolved photo-physical investigations. Less favourable are co-facial π–π stackings in the three-PBI containing cyclophanes. For statistical reasons, the diastereoisomers (M,M,M)/(P,P,P) and (M,M,P)/(P,P,M) occur here in a ratio of 1 : 3. In this case, symmetry-breaking charge transfer as well as charge separation are both slowed down. The work was rounded-off by integrating next to the PBIs, for the first time, hydrophobic or hydrophilic fullerenes into the resulting cyclophanes. Our novel fullerene–PBI cyclophanes reveal unprecedented diastereoselective formation of homochiral (M,M)/(P,P) pairs exceeding the traditional host–guest approach. Hybridization with fullerenes allows us to modulate the resulting solubility, stacking, cavity and chirality, which is of tremendous interest in the field.

Perylene bisimide (PBI) cyclophanes linked by flexible malonates were functionalized with fullerenes. Modulation of the chemical environment enhances the chiral self-sorting, leading exclusively to the homochiral diastereomeric pair (M,M)/(P,P).     

Two-dimensional correlation spectroscopy and multivariate curve resolution for the study of lipid oxidation in edible oils monitored by FTIR and FT-Raman spectroscopy

Accelerate oxidative degradation of six vegetable oils was monitored using FTIR and FT-Raman spectroscopy. Two-dimensional correlation spectroscopy and multivariate curve resolution alternating least squares (MCR-ALS) were applied to the analysis of the data. The use of hetero-spectral two-dimensional correlation of FTIR and FT-Raman data allowed the use of well established band assignments to interpret less clearly assigned spectral features. With a moving window approach it was possible to obtain simplified two-dimensional correlation maps and to detect compounds evolving with different kinetic. Simultaneous analysis of the oxidation experiments of the six different oils monitored by both spectroscopic techniques was performed using MCR-ALS. Although a complete resolution of the data was not possible, the spectral changes occurring during the oxidative degradation of the oils were described with a five-component model. The two fundamentally different chemometric approaches lead to coincident results.     

Characterization of metal-labelled peptides by matrix-assisted laser desorption/ionization mass spectrometry and tandem mass spectrometry

Metal labelling of peptides and proteins using high-affinity metal-chelating compounds has found widespread applications in the medical and bioanalytical fields. In the present study we investigated the analysis of peptides derivatized either with cysteine- or amino group-directed metal-bound DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) chelators in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The metal complexes of DOTA were shown to be stable under MALDI-MS conditions. The introduction of the metal label led in a number of cases to significantly increased signal-to-noise (S/N) values and thus improved sensitivity of the labelled peptides compared to their unlabelled counterparts, especially for multiply labelled peptides. The presence of the labels did alter the tandem mass spectrometric (MS/MS) behaviour, namely the formation of sequence specific a-, b- and y-ion series, in dependence of the position of the label within the peptide sequence. For cysteine-derivatized peptides several label-specific reporter ions and characteristic immonium ions could be identified. Amino-directed labelling led only to the formation of characteristic immonium ions in ε-amino groups of lysine, whereas N-terminal labelling in some cases led to the formation of a(1)- and b(1)-ions. The results clearly show that MALDI-MS is suitable for the analysis of metal-labelled peptides, which was also confirmed in liquid chromatography (LC)/MALDI-based identification of proteins in a model protein mixture labelled with Cys-reactive DOTA. Here, in comparison to a run with alkylated cysteines, more than 50% more cysteine-containing peptides were identified.     

Room-temperature kinetics of short-chain alkanethiol film growth on Ag(111) from the vapor phase

We have used time-of-flight (TOF) direct recoiling spectroscopy (DRS) to follow propanethiol adsorption at 300 K from the vapor phase on an Ag(111) surface, for exposures ranging from 10(-1) to 10(5) L. Results show that the adsorption proceeds with changes in the sticking coefficient, consistent with at least three phases. At low exposures, the alkanethiol molecules adsorb with high probability at defect sites, followed by a slower growth mode that essentially covers the whole surface. A third change in the sticking coefficient is associated with the final saturation stage, corresponding to a thicker layer related to molecules in a more upright orientation. The adsorption kinetics for hexanethiol is similar to that of propanethiol but taking place at higher rates, stressing the importance of the hydrocarbon chain length in the growth process. ISS-TOF measurements during thermal desorption show that most of the C, H, and S go away together, suggesting that the molecules adsorb and desorb from flat regions without S-C bond cleavage. Fitting the desorption maximum at 450 K with a first-order desorption curve gives a desorption energy of 1.43 eV. A small final S content that is correlated with the initial Ag(111) surface roughness is observed after desorption.     

Li2EuSiO4, ein Europium(II)-dilithosilicat: Eu[(Li2Si)O4]

Li₂EuSiO₄, an Europium(II) Litho-Silicate: Eu[(Li₂Si)O₄] Single crystals of Li₂EuSiO₄ were first obtained by reaction of Eu₂SiO₄ with a melt of LiCl at 800 °C in a sealed tantalum tube. It crystallizes with the trigonal space group P3₁21, Z = 3, with a = 502.70(5), c = 1247.0(2) pm. The tetrahedra [LiO₄] and [SiO₄] are connected via common corners and thereby build up a three-dimensional network that leaves space for Eu²⁺ which is in an eightfold coordination. Li₂SrSiO₄ is isotypic with a = 502.59(4) and c = 1247.1(1) pm.     

Regioselective Dichlorination of a Non‐Activated Aliphatic Carbon Atom and Phenolic Bismethylation by a Multifunctional Fungal Flavoenzyme

The regioselective functionalization of non‐activated carbon atoms such as aliphatic halogenation is a major synthetic challenge. A novel multifunctional enzyme catalyzing the geminal dichlorination of a methyl group was discovered in Aspergillus oryzae (Koji mold), an important fungus that is widely used for Asian food fermentation. A biosynthetic pathway encoded on two different chromosomes yields mono‐ and dichlorinated polyketides (diaporthin derivatives), including the cytotoxic dichlorodiaporthin as the main product. Bioinformatic analyses and functional genetics revealed an unprecedented hybrid enzyme (AoiQ) with two functional domains, one for halogenation and one for O‐methylation. AoiQ was successfully reconstituted in vivo and in vitro, unequivocally showing that this FADH₂‐dependent enzyme is uniquely capable of the stepwise gem‐dichlorination of a non‐activated carbon atom on a freestanding substrate. Genome mining indicated that related hybrid enzymes are encoded in cryptic gene clusters in numerous ecologically relevant fungi.