Factors affecting gas-phase deuterium scrambling in peptide ions and their implications for protein structure determination

In this report, we evaluate the validity of using hydrogen/deuterium exchange in combination with collision-induced dissociation mass spectrometry (CID MS) for the detailed structural and conformational investigation of peptides and proteins. This methodology, in which partly deuterated peptide ions are subjected to collision-induced dissociation in the vacuum of a mass spectrometer, has emerged as a useful tool in structural biology. It may potentially provide quantitatively the extent of deuterium incorporation per individual amino acid in peptides and proteins, thus providing detailed structural information related to protein structure and folding. We report that this general methodology has limitations caused by the fact that the incorporated deuterium atoms migrate prior or during the CID MS analysis. Our data are focused on a variety of transmembrane peptides, incorporated in a lipid bilayer, in which the near-terminal amino acids that anchor at the lipid-water interface are systematically varied. Our findings suggest that, under the experimental conditions we use, the extent of intramolecular hydrogen scrambling is strongly influenced by experimental factors, such as the exact amino acid sequence of the peptide, the nature of the charge carrier, and therefore most likely by the gas-phase structure of the peptide ion. Moreover, the observed scrambling seems to be independent of the nature of the peptide fragment ions (i.e., protonated B and Y' ' ions, and sodiated A and Y' ions). Our results strongly suggest that scrambling may be reduced by using alkali metal cationization instead of protonation in the ionization process.     

Site-selective labeling strategies for screening by NMR

NMR based screening has become an important tool in the pharmaceutical industry. Methods that provide information on the location of small molecule binding sites on the surface of a drug target (e. g. SAR-by-NMR and related techniques) are of particular interest. In order to extend the applicability of such techniques to drug targets of higher molecular weight, selective labeling strategies may be employed. Dual-amino acid selective labeling and site directed non-native amino acid replacement (SNAAR) allow for the selective detection of NMR resonances of a specific amino acid residue. This results in significantly reduced spectral complexity, which not only enables application to higher molecular weight systems, but also eliminates the need for sequential resonance assignment in order to identify the binding site. Regio-selective (or segmental) labeling of an entire protein domain of a multi domain protein may also be achieved. Labeling only a selected part of a multi domain protein (e. g. a catalytic or ligand binding domain) is an attractive way to simplify the spectral interpretation without disturbing the system under study.     

Solvent effects on charge transport through solid deposits of [Os(4,4'-diphenyl-2,2'-dipyridyl)2Cl2

Mechanically attached, solid-state films of [Os(4,4'-diphenyl-2,2'-dipyridyl)2Cl2] have been formed on gold macro- and microelectrodes and their voltammetric properties investigated. The voltammetric response of these films associated with the Os(2+/3+) redox reaction is reminiscent of that observed for an ideal reversible, solution phase redox couple only when the contacting electrolyte contains of the order of 40% v/v of acetonitrile (ACN). The origin of this effect appears to involve preferential solvation of the redox centres by acetonitrile which facilitates the incorporation of charge compensating counterions. Scanning electron microscopy reveals that voltammetric cycling in 40:60 ACN-H2O containing 1.0 M LiClO4 as the electrolyte induces the formation of microcrystals. Voltammetry conducted under semi-infinite linear diffusion conditions has been used to determine the apparent diffusion coefficient, Dapp, for homogeneous charge transport through the deposit. The dynamics of charge transport decrease with increasing film thickness but appear to increase with increasing electrolyte concentration. These observations suggest that ion transport rather than the rate of electron self-exchange limit the overall rate of charge transport through these solids. When in contact with 40:60 ACN-H2O containing 1.0 M LiClO4 as electrolyte, Dapp values for oxidation and reduction are identical at 1.7 +/- 0.4 x 10(-12) cm2 s(-1). In the same electrolyte, the standard heterogeneous electron transfer rate constant, k(o), determined by fitting the full voltammogram using the Butler-Volmer formalism, is 8.3 +/- 0.5 x 10(-7) cm s(-1). The importance of these results for the rational design of solid state redox active materials for battery, display and sensor applications is considered.     

Aldol condensations over reconstructed Mg-Al hydrotalcites: structure-activity relationships related to the rehydration method

Two different rehydration procedures in the liquid or gas phase have been applied to reconstruct mixed oxides derived from calcined hydrotalcite-like materials to be used as catalysts for aldol condensation reactions. The as-synthesized hydrotalcite, its decomposition product, as well as the reconstructed solids upon rehydration were characterized by XRD, N(2) adsorption, He pycnometry, FTIR, SEM, TEM, (27)Al MAS-NMR and CO(2)-TPD (TPD=temperature-programmed desorption). Compared to the Mg-Al mixed oxide rehydrated in the gas phase (HT-rg), that rehydrated in the liquid phase (HT-rl) exhibits a superior catalytic performance with respect to the aldol condensation of citral with ketones to yield pseudoionones and in the self-aldolization of acetone. The textural properties of HT-rl and HT-rg differ strongly and determine the catalytic behavior. A memory effect led to a higher degree of reconstruction of the lamellar structure when the mixed oxide was rehydrated in the gas phase rather than in the liquid phase, although liquid-phase rehydration under fast stirring produced a surface area that was 26 times greater. This contrasts to typical statements in the literature claiming a higher degree of reconstruction in the presence of large amounts of water in the medium. CO(2)-TPD shows that the number of OH(-) groups and their nature are very similar in HT-rg and HT-rl, and cannot explain the markedly different catalytic behavior. Accordingly, only a small fraction of the available basic sites in the rehydrated samples is active in liquid-phase aldol condensations. Our results support the model in which only basic sites near the edges of the hydrotalcite platelets are partaking in aldol reactions. Based on this, reconstructed materials with small crystallites (produced by exfoliation during mechanical stirring), that is, possessing a high external surface area, are beneficial in the reactions compared to larger crystals with a high degree of intraplatelet porosity.     

The rate of homolysis of adducts of peroxynitrite to the C=O double bond.

Nucleophilic addition of the peroxynitrite anion, ONOO(-), to the two prototypical carbonyl compounds, acetaldehyde and acetone, was investigated in the pH interval 7.4-14. The process is initiated by fast equilibration between the reactants and the corresponding tetrahedral adduct anion, the equilibrium being strongly shifted to the reactant side. The adduct anion also undergoes fast protonation by water and added buffers. Consequently, the rate of the bimolecular reaction between ONOO(-) and the carbonyl is strongly dependent on the pH and on the concentration of the buffer. The pK(a) of the carbonyl-ONOO adduct was estimated to be approximately 11.8 and approximately 12.3 for acetone and acetaldehyde, respectively. It is shown that both the anionic and the neutral adducts suffer fast homolysis along the weak O-O bond to yield free alkoxyl and nitrogen dioxide radicals. The yield of free radicals was determined to be about 15% with both carbonyl compounds at low and high pH, while the remainder collapses to molecular products in the solvent cage. The rate constants for the homolysis of the adducts vary from ca. 3 x 10(5) to ca. 5 x 10(6) s(-1), suggesting that they cannot act as oxidants in biological systems. This small variation around a mean value of about 10(6) s(-1) suggests that the O-O bond in the adduct is rather insensitive to its protonation state and to the nature of its carbonyl precursor. An overall reaction scheme was proposed, and all the corresponding rate constants were evaluated. Finally, thermokinetic considerations were employed to argue that the formation of dioxirane as an intermediate in the reaction of ONOO(-) with acetone is an unlikely process.     

Selection rules for helicate ligand component self-assembly: steric, pH, charge, and solvent effects

The reaction between 1,10-phenanthroline-2,9-dicarboxaldehyde, copper(I), and certain primary amines was found to give quantitatively a dicopper double-helicate product (two of which were crystallographically characterized) by imine self-assembly around Cu(I) templates. The parameters of this reaction were investigated, and important roles were found to be played by (i) the steric bulk of the amine, (ii) the charge of the amine, (iii) the solvent used, and (iv) the pH of the solution. Water was found to allow the broadest range of structures to form, and ligand-component exchange reactions (involving the substitution of an aromatic for an aliphatic amine) were demonstrated to proceed readily in this solvent.     

HPLC of synthetic polymers characterization of polystyrenes by high performance precipitation liquid chromatography (HPPLC)

Summary The advantages and disadvantages of high performance precipitation liquid chromatography have been demonstrated for polystyrene homopolymers. Depending on the mobile phase composition at the dissolution point of the polymeric sample and surface properties of the stationary phase, elution is governed either by a solution process or by adsorption. A contribution by adsorption was noticed on silica as well as on reversed phases based on silica with a normal phase gradient of increasing polarity (heptane to dichloromethane). Elution was solely governed by solubility of the polymers on both types of stationary phase for polystyrenes with a molecular weight above 35 000 and reversed phase gradient of decreasing polarity (methanol to dichloromethane). Under these conditions an identical dependence of elution solvent composition on sample size was found as for turbidity titrations. Due to differences in the velocity of the eluent front and the polymeric sample with porous stationary phases the polymers can be eluted as colloidal solutions Non-porous stationary phases are superior in this respect because the velocities of eluent and solutes are identical.     

The effect of minor-groove hydrogen-bond acceptors and donors on the stability and replication of four unnatural base pairs

The stability and replication of DNA containing self-pairs formed between unnatural nucleotides bearing benzofuran, benzothiophene, indole, and benzotriazole nucleobases are reported. These nucleobase analogues are based on a similar scaffold but have different hydrogen-bond donor/acceptor groups that are expected to be oriented in the duplex minor groove. The unnatural base pairs do not appear to induce major structural distortions and are accommodated within the constraints of a B-form duplex. The differences between these unnatural base pairs are manifest only in the polymerase-mediated extension step, not in base-pair stability or synthesis. The benzotriazole self-pair is extended with an efficiency that is only 200-fold less than a correct natural base pair. The data are discussed in terms of available polymerase crystal structures and imply that further modifications may result in unnatural base pairs that can be both efficiently synthesized and extended, resulting in an expanded genetic alphabet.     

Chemical studies on antioxidant mechanisms and free radical scavenging properties of lignans

The antioxidant activity, in terms of radical scavenging capacity, of altogether 15 different lignans was measured by monitoring the scavenging of the free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH). The effect of differences in skeletal arrangement or the degree of oxidation of the lignans was investigated in a structure-activity relationship study. A large variety in the radical scavenging capacities of the different lignans was observed and related to some structural features. Lignans with catechol (3,4-dihydroxyphenyl) moieties exhibited the highest radical scavenging capacity, while the corresponding guaiacyl (3-methoxy-4-hydroxyphenyl) lignans showed a slightly weaker scavenging capacity. In addition, the butanediol structure was found to enhance the activity, whereas a higher degree of oxidation at the benzylic positions decreased the activity. Additionally, the readily available lignans (-)-secoisolariciresinol, a mixture of hydroxymatairesinol epimers and (-)-matairesinol were studied in more detail, including kinetic measurements and identification of oxidation products in the reactions with DPPH and ABAP (2,2-azobis(2-methylpropionamidine) dihydrochloride. The identification of reaction products, by GC-MS, HPLC-MS and NMR spectroscopy, showed that dimerisation of the two aromatic moieties was the major radical termination reaction. Also, the formation of adducts was a predominant reaction in the experiments with ABAP. The kinetic data obtained from the reactions between the lignans and DPPH indicated a complex reaction mechanism.     

Studies on the distribution and concentration of thiamine in blood and urine

Studies are reported resulting in a reliable procedure for estimating the thiamine content in human blood and urine. For the determination in blood, heparinized blood is hemolyzed with 0.3 N hydrochloric acid at 100 °C. Cocarboxylase is then converted to free thiamine by means of wheat germ acid phosphatase at pH 5.0 in an acetate buffer. The liberated thiamine is adsorbed to a CG-50 (Rohm & Haas) carboxylic acid ion exchange acrylic resin column and then eluted with 1 N H₂SO₄. The thiamine is then oxidized to thiochrome and extracted with n-butyl alcohol, at pH 9.8–10.0, in the presence of disodium phosphate. Readout is by fluorometry at an excitation wavelength of 371 nm and an emission wavelength of 425 nm. The range found for thiamine in whole blood by this procedure on 18 normal adults was 1.9–3.9 μg/100 ml, with a mean value of 2.77 μg/100 ml of whole blood. The mean recovery of 12 recovery experiments was 94.1%. The same procedure is applicable to the determination of thiamine in urine. Conversion of cocarboxylase to free thiamine is not necessary since it was determined that practically all of the thiamine found in urine is not phosphorylated. Urine values were variable, the range for 11 healthy adults being 5.6–77.9 μg/100 ml with a mean value of 19.2 μg/100 ml. This corresponds to a value of 346 μg of thiamine/24 hours.