Epsilon -N,N,N-trimethyllysine-specific ions in matrix-assisted laser desorption/ionization-tandem mass spectrometry

Epsilon -N,N,N-trimethyllysine (K(me3)) is a component of a number of proteins and plays an important role in the expression of their biological functions. Trimethylation, which causes an incremental increase in mass of 42.0470 Da from that of the corresponding MH(+) ion, cannot be distinguished from the acetylation (+42.0106 Da), which also occurs on epsilon-amino groups of Lys or alpha-amino groups in many proteins, without high-accuracy mass measurement which is accurate to within the second decimal place. MALDI-MS and MS/MS have been applied for the analyses of post-translational modifications of histone H3, which is known to contain both multiple acetylation and methylation sites in its sequence. During the measurements of the modified peptides, a novel fragmentation which involves the loss of trimethylamine from K(me3) was found. This characteristic fragmentation, which was observed to produce ions separated by 59 Da from the conventional precursor ion or sequence ions, would be useful for probing K(me3) units in the sequence.     

Chain length effect of the counterion on the partial molal volume of alkanesulfonates

The partial molal volumes of two series of homologous surfactants, n-alkylammonium decanesulfonates and a, ?-alkanediammonium nonanesulfonates, were measured below and above their CMC in aqueous solution. Their counterions were n-alkylammonium and a, ?-alkanediammonium. The relationship between the partial molal volume and the chain length of the counterion below the CMC had an inflection point. The relationship between them, above the CMC, was almost linear. In the case of the alkylammonium salts, the values of the volume change of micellization were almost the same when the chain length of the counterions was shorter than the butyl, and increased with an increase in the chain length when it was longer than the propyl. In the case of the alkanediammonium salts, the volume change of micellization showed a small decrease with the chain length when it was shorter than octane, and was very large for the nonane ammonium salt. The large positive increase in the volume change with the increase in the chain length of the counterion can be explained by the hydrophobic interaction between the alkyl chain of the counterion and the hydrophobic core of the micelle.     

Conformational studies of sequential polypeptides of L-Alanine and β-Alanine

Summary In order to investigate the effect of the -alanine residue on the conformational stability of -helical poly(L-alanine), studies have been made on the conformations of sequential copolypeptides having the following repeating sequences: (L-Ala--Ala) _n , (L-Ala-L-Ala--Ala) _n , (L-Ala--Ala-L-Ala-L-Ala) _n and (L-Ala-L-Ala-X) _n , where X is D,L--amino-isobutyric acid residue. Conformations of these polypeptides were measured both in the solution and solid states by means of optical rotatory dispersion, infrared and far-infrared spectroscopies and X-ray diffractions. All the copolypeptides studied here did not give the -helix. It may be, therefore, concluded that the -alanine residue is not incorporated in but impairs the -helix of poly(L-alanine), since the hydrogen bond periodicity in the -helical chain is disturbed by the introduction of such a -amino acid as -alanine.With 5 figures and 2 tables     

Surface-potential reversibility of an amino-terminated self-assembled monolayer based on nanoprobe chemistry

Nanoprobe chemistry offers a promising approach for the construction of nanostructures consisting of organic molecules by employing the tip of a scanning probe microscope. In a previous report, we demonstrated that a nitroso-terminated surface on an organosilane self-assembled monolayer could be converted into an amino-terminated surface by applying such a nanoprobe electrochemical technique. This paper reports on surface-potential reversibility originating from a reversible chemical reaction between amino and nitroso groups. In addition, we demonstrate surface-potential memory based on this chemical reversibility. Amino-terminated SAMs were prepared from p-aminophenyl-trimethoxysilane through chemical vapor deposition. Surface potentials were acquired by Kelvin force microscopy. When scanning probe lithography was conducted with a gold tip at positive-bias voltages, the surface potential of the scanned area shifted dramatically in the negative direction. Scanning with negative-bias voltages led to positive shift in the surface potential of the scanned area. The surface potential could be recovered even after multiple scannings with positive and negative applied bias voltages. On the basis of this discovery, we also succeeded in demonstrating surface-potential memory via our nanoprobe electrochemical technique.     

Lifetime regulation of the charge-separated state in DNA by modulating the oxidation potential of guanine in DNA through hydrogen bonding

A series of naphthalimide (NI)- and 5-bromocytosine ((br)C)-modified oligodeoxynucleotides (ODNs) were prepared, and their lifetimes of the charge-separated states during the photosensitized one-electron oxidation of DNA were measured. Various lifetimes of the charge-separated states were observed depending on the sequence and the incorporation sites of (br)C, and the oxidation potential of G in the (br)C:G base-pair relative to that of G in the C:G base-pair and in the GGG sequence was determined by comparing the lifetimes of the charge-separated states. The change in the cytosine C5 hydrogen to bromine resulted in a 24 mV increase in the oxidation potential of G in the (br)C:G base-pair as compared to that of G in the C:G base-pair, the value of which is comparable to a 58 mV decrease in the oxidation potential of G in the GGG sequence. These results clearly demonstrate that hole transfer in DNA can be controlled through hydrogen bonding by introducing a substituent on the cytosine.     

Photochromism of triangle terthiophene derivatives as molecular re-router

2,2[prime or minute]-3,3[double prime]-Terthiophene derivatives undergo photochemically reversible cyclization and cycloreversion reactions. The absorption peak wavelength changed systematically with substitution of the phenyl rings at 5-, 5[prime or minute]- and 5[double prime]-positions of the thiophene rings, which indicates re-routing of the [small pi]-conjugation system.     

The role of the putative catalytic base in the phosphoryl transfer reaction in a protein kinase: first-principles calculations

Protein kinases are important enzymes controlling the majority of cellular signaling events via a transfer of the gamma-phosphate of ATP to a target protein. Even after many years of study, the mechanism of this reaction is still poorly understood. Among many factors that may be responsible for the 1011-fold rate enhancement due to this enzyme, the role of the conserved aspartate (Asp166) has been given special consideration. While the essential presence of Asp166 has been established by mutational studies, its function is still debated. The general base catalyst role assigned to Asp166 on the basis of its position in the active site has been brought into question by the pH dependence of the reaction rate, isotope measurements, and pre-steady-state kinetics. Recent semiempirical calculations have added to the controversy surrounding the role of Asp166 in the catalytic mechanism. No major role for Asp166 has been found in these calculations, which have predicted the reaction process consisting of an early transfer of a substrate proton onto the phosphate group. These conclusions were inconsistent with experimental observations. To address these differences between experimental results and theory with a more reliable computational approach and to provide a theoretical platform for understanding catalysis in this important enzyme family, we have carried out first-principles structural and dynamical calculations of the reaction process in cAPK kinase. To preserve the essential features of the reaction, representations of all of the key conserved residues (82 atoms) were included in the calculation. The structural calculations were performed using the local basis density functional (DFT) approach with both hybrid B3LYP and PBE96 generalized gradient approximations. This kind of calculation has been shown to yield highly accurate structural information for a large number of systems. The optimized reactant state structure is in good agreement with X-ray data. In contrast to semiempirical methods, the lowest energy product state places the substrate proton on Asp166. First-principles molecular dynamics simulations provide additional support for the stability of this product state. The latter also demonstrate that the proton transfer to Asp166 occurs at a point in the reaction where bond cleavage at the PO bridging position is already advanced. This mechanism is further supported by the calculated structure of the transition state in which the substrate hydroxyl group is largely intact. A metaphoshate-like structure is present in the transition state, which is consistent with the X-ray structures of transition state mimics. On the basis of the calculated structure of the transition state, it is estimated to be 85% dissociative. Our analysis also indicates an increase in the hydrogen bond strength between Asp166 and substrate hydroxyl and a small decrease in the bond strength of the latter in the transition state. In summary, our calculations demonstrate the importance of Asp166 in the enzymatic mechanism as a proton acceptor. However, the proton abstraction from the substrate occurs late in the reaction process. Thus, in the catalytic mechanism of cAPK protein kinase, Asp166 plays a role of a "proton trap" that locks the transferred phosphoryl group to the substrate. These results resolve prior inconsistencies between theory and experiment and bring new understanding of the role of Asp166 in the protein kinase catalytic mechanism.     

Lipid-soluble and water-soluble arsenic compounds in blubber of ringed seal (Pusa hispida)

High concentrations of arsenic were observed in the blubber of ringed seals (Pusa hispida) in our previous study. To better understand the arsenic accumulation in blubber of marine mammals, arsenicals in the blubber of ringed seal were characterized using high performance liquid chromatography–inductively coupled plasma mass spectrometry (HPLC–ICPMS). The most predominant water-soluble arsenical in the blubber was dimethylarsinic acid (DMA), in spite of the predominance of arsenobetaine in other tissues. Lipid-soluble fraction was hydrolyzed under mild (tetraethylammonium hydroxide (TEAH) hydrolysis) and strong (NaOH hydrolysis) conditions, and then an aliquot of hydrolysate was injected onto HPLC–ICPMS. Both TEAH-labile and TEAH-stable/NaOH-labile lipid-soluble fractions contained precursors of DMA. These results suggest that the blubber might be the pool of DMA and DMA-containing precursors in ringed seals.     

Synthesis of the common left-half part of pectenotoxins

The common left-half [C31-C33(OC1-C7)-C40] part of pectenotoxins has been synthesized convergently from the C31-C35, C36-C40, and C1-C7 parts. The C31-C35 part, prepared via a new route shorter than our previous route, was coupled with the C36-C40 part through reductive lithiation and addition reactions to give an adduct stereoselectively, which was converted to a cyclic acetal corresponding to the C31-C40 part. The left-half was synthesized by a three-step process including esterification of the C31-C40 part with the C1-C7 part.