Status Report on the High-Throughput Characterization of Complex Intact O-Glycopeptide Mixtures

A very complex mixture of intact, human N- and O-glycopeptides, enriched from the tryptic digest of urinary proteins of three healthy donors using a two-step lectin affinity enrichment, was analyzed by LC-MS/MS, leading to approximately 45,000 glycopeptide EThcD spectra. Two search engines, Byonic and Protein Prospector, were used for the interpretation of the data, and N- and O-linked glycopeptides were assigned from separate searches. The identification rate was very low in all searches, even when results were combined. Thus, we investigated the reasons why was it so, to help to improve the identification success rate. Focusing on O-linked glycopeptides, we noticed that in EThcD, larger glycan oxonium ions better survive the activation than those in HCD. These fragments, combined with reducing terminal Y ions, provide important information about the glycan(s) present, so we investigated whether filtering the peaklists for glycan oxonium ions indicating the presence of a tetra- or hexasaccharide structure would help to reveal all molecules containing such glycans. Our study showed that intact glycans frequently do not survive even mild supplemental activation, meaning one cannot rely on these oxonium ions exclusively. We found that ETD efficiency is still a limiting factor, and for highly glycosylated peptides, the only information revealed in EThcD was related to the glycan structures. The limited overlap of results delivered by the two search engines draws attention to the fact that automated data interpretation of O-linked glycopeptides is not even close to being solved.

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Synthesis and further transformations of 8-chloro-3,4-dihydroisoquinoline

Two procedures for the synthesis of barely accessible 8-chloro-3,4-dihydroisoquinoline were investigated. The first approach is based on a directed ortho-lithiation of N-pivaloyl meta-chlorophenylethylamine, followed by formylation and subsequent ring closure under acidic conditions. In the second, more advantageous variant, the N-hydroxyethyl ortho-chlorobenzylamine intermediate undergoes a Friedel-Crafts reaction, and the resulting tetrahydro derivative is oxidized with N-bromosuccinimide. The 8-chloro-3,4-dihydroisoquinoline key intermediate is then applied in Suzuki reactions to give various 8-aryl-3,4-dihydroisoquinolines, which are finally treated with alkyl or aryllithiums to give 1-substituted 8-aryl-1,2,3,4-tetrahydroisoquinolines. These novel 1,2,3,4-tetrahydroisoquinoline derivatives can be used as building blocks in the synthesis of potential drug candidates.     

DPPH-initiated oxygenation of 3-hydroxyflavone to O-benzoylsalicylic acid

Summary The oxidation of 3-hydroxyflavone (flaH) to O-benzoylsalicylic acid (O-bs) initiated by 2,2-diphenyl-1-picrylhydrazyl (DPPH) has been investigated in acetonitrile at ambient temperature. The kinetics was followed by monitoring the disappearance of DPPH spectrophotometrically at 520 nm and the rate constants were determined according to the rate law -d[DPPH]/dt = k [DPPH][Substrate]. The mean value of the rate constant k at 295 K is 1.21 ± 0.03 dm³ mol^-1 s^-1.     

Conformational analysis of melatonin at Hartree–Fock ab initio level

Melatonin is a hormone, which is synthesized and secreted by the pineal gland during darkness and has been implicated in the regulation of several neural and endocrine processes. Conformational analysis of melatonin was performed at Hartree–Fock ab initio level. With the help of STO-3G and 6-31G* basis sets, 192 and 128 conformers were obtained, respectively. In both cases, there were eight conformers with nearly planar 3-amido-side chain and the most stable conformation found had folded structure in accord with previously published results. The present paper compares the Hartree–Fock conformational space of melatonin with the results of active conformation models and conformational analyses published in the literature.     

HPLC determination of acidic d‐amino acids and their N‐methyl derivatives in biological tissues

d ‐Aspartate (d ‐Asp) and N‐methyl‐d ‐aspartate (NMDA) occur in the neuroendocrine systems of vertebrates and invertebrates, where they play a role in hormone release and synthesis, neurotransmission, and memory and learning. N‐methyl‐d ‐glutamate (NMDG) has also been detected in marine bivalves. Several methods have been used to detect these amino acids, but they require pretreatment of tissue samples with o‐phthaldialdehyde (OPA) to remove primary amino acids that interfere with the detection of NMDA and NMDG. We report here a one‐step derivatization procedure with the chiral reagent N‐α‐(5‐fluoro‐2,4‐dinitrophenyl)‐(d or l )‐valine amide, FDNP‐Val‐NH₂, a close analog of Marfey's reagent but with better resolution and higher molar absorptivity. The diastereomers formed were separated by HPLC on an ODS‐Hypersil column eluted with TFA/water–TFA/MeCN. UV absorption at 340 nm permitted detection levels as low as 5–10 pmol. d ‐Asp, NMDA and NMDG peaks were not obscured by other primary or secondary amino acids; hence pretreatment of tissues with OPA was not required. This method is highly reliable and fast (less than 40 min HPLC run). Using this method, we detected d ‐Asp, NMDA and NMDG in several biological tissues (octopus brain, optical lobe and bucchal mass; foot and mantle of the mollusk Scapharca broughtonii), confirming the results of other researchers. Copyright © 2009 John Wiley & Sons, Ltd.     

“Invisible” Conformers of an Antifungal Disulfide Protein Revealed by Constrained Cold and Heat Unfolding,CEST‐NMR Experiments,and Molecular Dynamics Calculations

Transition between conformational states in proteins is being recognized as a possible key factor of function. In support of this, hidden dynamic NMR structures were detected in several cases up to populations of a few percent. Here, we show by two‐ and three‐state analysis of thermal unfolding, that the population of hidden states may weight 20–40 % at 298 K in a disulfide‐rich protein. In addition, sensitive ¹⁵N‐CEST NMR experiments identified a low populated (0.15 %) state that was in slow exchange with the folded PAF protein. Remarkably, other techniques failed to identify the rest of the NMR “dark matter”. Comparison of the temperature dependence of chemical shifts from experiments and molecular dynamics calculations suggests that hidden conformers of PAF differ in the loop and terminal regions and are most similar in the evolutionary conserved core. Our observations point to the existence of a complex conformational landscape with multiple conformational states in dynamic equilibrium, with diverse exchange rates presumably responsible for the completely hidden nature of a considerable fraction.     

Small Delay Inertial Manifolds Under Numerics: A Numerical Structural Stability Result

In this paper we formulate a numerical structural stability result for delay equations with small delay under Euler discretization. The main ingredients of our approach are the existence and smoothness of small delay inertial manifolds, the C ¹-closeness of the small delay inertial manifolds and their numerical approximation and M.-C. Li's recent result on numerical structural stability of ordinary differential equations under the Euler method.     

Applications of the inverse infection problem on bank transaction networks

Central European Journal of Operations Research - The Domingos-Richardson model, along with several other infection models, has a wide range of applications in prediction. In most of these, a...     

Selective Reduction of Nitrones and Nitroxides to Functionalized Secondary Amines

Nitrones and nitroxides were selectively reduced with Fe/AcOH to secondary amines in the presence of different functional groups (aldehyde, nitrile, carboxylic ester, activated and nonactivated double or triple bonds).