Using Gas-Phase Guest–Host Chemistry to Probe the Structures of b Ions of Peptides

Middle-sized b _n (n????5) fragments of protonated peptides undergo selective complex formation with ammonia under experimental conditions typically used to probe hydrogen?Cdeuterium exchange in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Other usual peptide fragments like y, a, a*, etc., and small b _n (n????4) fragments do not form stable ammonia adducts. We propose that complex formation of b _n ions with ammonia is characteristic to macrocyclic isomers of these fragments. Experiments on a protonated cyclic peptide and N-terminal acetylated peptides fully support this hypothesis; the protonated cyclic peptide does form ammonia adducts while linear b _n ions of acetylated peptides do not undergo complexation. Density functional theory (DFT) calculations on the proton-bound dimers of all-Ala b ₄ , b ₅ , and b ₇ ions and ammonia indicate that the ionizing proton initially located on the peptide fragment transfers to ammonia upon adduct formation. The ammonium ion is then solvated by N⁺-H??O H-bonds; this stabilization is much stronger for macrocyclic b _n isomers due to the stable cage-like structure formed and entropy effects. The present study demonstrates that gas-phase guest?Chost chemistry can be used to selectively probe structural features (i.e., macrocyclic or linear) of fragments of protonated peptides. Stable ammonia adducts of b ₉ , b ₉ -A, and b ₉ -2A of A₈YA, and b ₁₃ of A₂₀YVFL are observed indicating that even these large b-type ions form macrocyclic structures.     

Why do the Abundances of Ions Generated by MALDI Look Thermally Determined?

In a previous study (J. Mass Spectrom. 48, 299–305, 2013), we observed that the abundance of each ion in a matrix-assisted laser desorption ionization (MALDI) spectrum looked thermally determined. To find out the explanation for the phenomenon, we estimated the ionization efficiency and the reaction quotient (Q_A) for the autoprotolysis of matrix, M + M → [M + H]⁺ + [M ? H]^?, from the temperature-controlled laser desorption ionization spectra of α-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB). We also evaluated the equilibrium constants (K_A) for the autoprotolysis at various temperatures by quantum chemical calculation. Primary ion formation via various thermal models followed by autoprotolysis-recombination was compatible with the observations. The upper limit of the effective temperature of the plume where autoprotolysis-recombination occurs was estimated by equating Q_A with the calculated equilibrium constant.

What Is the Structure of Pterodonoic Acid?

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What is the structure of the RecA-DNA filament?

The bacterial RecA protein has been a model system for understanding how a protein can catalyze homologous genetic recombination. RecA-like proteins have now been characterized from many organisms, from bacteriophage to humans. Some of the RecA-like proteins, including human RAD51, appear to function as helical filaments formed on DNA. However, we currently have high resolution structures of inactive forms of the protein, and low resolution structures of the active complexes formed by RecA-like proteins on DNA in the presence of ATP or ATP analogs. Within a crystal of the E. coli RecA protein, a helical polymer exists, and it has been widely assumed that this polymer is quite similar to the active helical filament formed on DNA. Recent developments have suggested that this may not be the case.     

What is the enthalpy of formation of acrylonitrile?

Acrylonitrile is a key industrial compound with numerous uses. Despite its importance, its enthalpy of formation is still contentious. There is a 12 kJ mol⁻¹ range of values reported for the gas phase quantity: 173–185 kJ mol⁻¹. Quantum chemical calculations, using current methodologies and defining reactions, suggest values between 185 and 191 kJ mol⁻¹: the recommended value, an average, is 188 ± 7 kJ mol⁻¹.     

What is the mole?

The mole is a difficult concept. Surveys have shown that even many teachers do not have a proper understanding of it. To help to meet this problem, the SI/IUPAC formulation of the mole is carefully presented and explained. New SI proposals are also briefly discussed.     

What is the acidity of a plutonium solution?

The determination of the pH of a plutonium solution has traditionally depended on an electrode or a titration in the presence of a complexing agent. A new approach uses the equilibrium distribution of the Pu oxidation states to estimate the hydrogen ion concentration. The method is used to estimate the equilibrium constant of the first hydrolysis reaction of tetravalent plutonium.     

What is the mechanism of soap film entrainment?

Classical Frankel's law describes the formation of soap films and their evolution upon pulling, a model situation of film dynamics in foams (formation, rheology, and destabilization). With the purpose of relating film pulling to foam dynamics, we have built a new setup able to give an instantaneous measurement of film thickness, thus allowing us to determine film thickness profile during pulling. We found that only the lower part of the film is of uniform thickness and follows Frankel's law, provided the entrainment velocity is small. We show that this is due to confinement effects: there is not enough surfactant in the bulk to fully cover the newly created surfaces which results in immobile film surfaces. At large velocities, surfaces become mobile and then Frankel's law breaks down, leading to a faster drainage and thus to a nonstationary thickness at the bottom of the film. These findings should help in understanding the large dispersion of previous experimental data reported during the last 40 years and clarifying the pulling phenomenon of thin liquid films.     

What is the effective charge of TGA-stabilized CdTe nanocolloids?

The surface charge of semiconductor nanoparticles, Q, is an important parameter which determines their electrokinetic behavior, stability in water and polar solvents, functions of optical and electronic devices, self-assembly properties, and interactions with cell membranes. We have developed a simple method for quantitative determination of Q in their native aqueous environment. The method does not require the knowledge of exact atomic structure or make assumptions about effects of drying on charge distribution. The method is based on titration of nanoparticle dispersion with a solution of oppositely charged polyelectrolyte. The point of complete neutralization is recognized as an inflection point on the dependence of fluorescence intensity on the amount of polyelectrolyte added. Thioglycolic acid-stabilized CdTe nanoparticles 2 nm in diameter were found to carry an average Q from -2.6 to -5.5 for pH 7.5 to 10, respectively. This charge is found to be smaller than that calculated theoretically for an analogous structure (i.e., Q = -8), presumably due to adsorption of Cd(2+) ions on the stabilizer shell and on Te atoms with unsaturated valence located on the side planes of CdTe tetrahedrons.     

What is the first hydrolysis constant of tetravalent Plutonium?

A new method for estimating the numerical value of the first hydrolysis constant of tetravalent plutonium is illustrated by examples. It uses the pH and the equilibrium fractions of two of the Pu oxidation states. They are substituted into one or more of a choice of formulas that render explicit estimates of the hydrolysis constant.     

What is the initiation step of the Grubbs-Hoveyda olefin metathesis catalyst?

Density function theory calculations reveal that the Grubbs-Hoveyda olefin metathesis pre-catalyst is activated by the formation of a complex in which the incoming alkene substrate and outgoing alkoxy ligand are both clearly associated with the ruthenium centre. The computed energies for reaction are in good agreement with the experimental values, reported here.     

Non-Direct Sequence Ions in the Tandem Mass Spectrometry of Protonated Peptide Amides—an Energy-Resolved Study

The fragmentation reactions of the MH⁺ ions of Leu-enkephalin amide and a variety of heptapeptide amides have been studied in detail as a function of collision energy using a QqToF beam type mass spectrometer. The initial fragmentation of the protonated amides involves primarily formation of b_n ions, including significant loss of NH₃ from the MH⁺ ions. Further fragmentation of these b_n ions occurs following macrocyclization/ring opening leading in many cases to b_n ions with permuted sequences and, thus, to formation of non-direct sequence ions. The importance of these non-direct sequence ions increases markedly with increasing collision energy, making peptide sequence determination difficult, if not impossible, at higher collision energies.

A Comparative Study of the Separation of the Tryptic Peptides of the β-Chain of Normal and Abnormal Hemoglobins by Reversed Phase High Performance Liquid Chromatography

Abstract

The separation of the tryptic peptides of the human hemoglobin A β-chain by reversed phase high performance liquid chromatography under different elution conditions on several microparticulate alkylsilica supports is described. Similar methods have been used to separate the tryptic peptides of β-chain hemoglobin variants including HbC, HbE, and Hb (Kempsey). Selectivity differences which can be achieved under the different chromatographic conditions have been exploited to permit the assignment of all the anticipated peptide fragments derived from the tryptic digestion of these β-chain Hb-variants.     

What do Positrons Say about the Structure and Properties of Fluids?

Applications of positron annihilation spectroscopy to fluid state physics and chemistry are discussed. Special attention is paid to problems of surface (interface) layer structure, molecular orientations in the layer, and the effects of freesurface curvature and age on surface tension. Positron investigations of the structure of liquid mixtures, including microheterogeneity studies, are considered.     

What is the future of electrophoresis in large-scale genomic sequencing?

Although a finished human genome reference sequence is now available, the ability to sequence large, complex genomes remains critically important for researchers in the biological sciences, and in particular, continued human genomic sequence determination will ultimately help to realize the promise of medical care tailored to an individual's unique genetic identity. Many new technologies are being developed to decrease the costs and to dramatically increase the data acquisition rate of such sequencing projects. These new sequencing approaches include Sanger reaction-based technologies that have electrophoresis as the final separation step as well as those that use completely novel, nonelectrophoretic methods to generate sequence data. In this review, we discuss the various advances in sequencing technologies and evaluate the current limitations of novel methods that currently preclude their complete acceptance in large-scale sequencing projects. Our primary goal is to analyze and predict the continuing role of electrophoresis in large-scale DNA sequencing, both in the near and longer term.     

What is the flow activation volume of entangled polymer melts?

We evaluate the flow activation volume in polymer melts of isotactic polypropylene and atactic polystyrene with step-shear experiments at different melt temperatures. The melt is initially sheared with constant shear rate until the attainment of a melt state with nearly constant viscosity. Perturbations to this experiment, involving shear steps in short-time intervals with decreasing rates, are induced next. Measurements of the shear stress value at each shear rate step allow the evaluation of an experimental (apparent) flow activation volume. The true flow activation volume is evaluated by extrapolating the experimental data to infinite shear stress values. The value obtained is larger than the physical volume of the chain and agrees with the volume of a tube confining chains with a molecular weight between M _n and M _w. Besides supporting the validity of tube model, experiments based on this protocol may be used on model polymer samples, in composites with nanoparticles and in polymer blends to access the validity of mechanisms considered by flow models.