Towards the chiral metabolomics: Liquid chromatography–mass spectrometry based dl-amino acid analysis after labeling with a new chiral reagent, (S)-2,5-dioxopyrrolidin-1-yl-1-(4,6-dimethoxy-1,3,5-triazin-2-yl)pyrrolidine-2-carboxylate,and the application to saliva of healthy volunteers

A novel triazine-type chiral derivatization reagent, i.e., (S)-2,5-dioxopyrrolidin-1-yl-1-(4,6-dimethoxy-1,3,5-triazin-2-yl) pyrrolidine-2-carboxylate (DMT-(S)-Pro-OSu), was developed for the highly sensitive and selective detection of chiral amines and amino acids by UPLC–MS/MS analysis. The enantiomers of amino acids were easily labeled with the reagents at room temperature within 40 min in an alkaline medium containing triethylamine. The diastereomers derived from proteolytic amino acids, except serine, were well separated under isocratic elution conditions by reversed-phase chromatography using an ODS column (R_s = 1.2–9.0). dl-Serine was separated by use of an ADME column which has relatively higher polar surface than the conventional ODS column. The characteristic product ions, i.e., m/z 195.3 and m/z 209.3, were detected from all the diastereomers by the collision-induced dissociation of the protonated molecule. A highly sensitive detection on the amol–fmol level was obtained from the selected reaction monitoring (SRM) chromatogram. The chiral amines (e.g., adrenaline and noradrenaline) labeled with DMT-(S)-Pro-OSu were also well separated and sensitively detected by the present procedure. The method using DMT-(S)-Pro-OSu was used for the determination of dl-amino acids in the human saliva from healthy volunteers. Various l-amino acids were identified in the saliva. Furthermore, d-alanine (d-Ala) and d-proline (d-Pro) were also detected in relatively high concentrations (>5%). The ratio was higher in male saliva than in female saliva. However, the difference in the ratio of d-Ala for one day was not very high and the effect of foods and beverage seemed to be negligible. Based on the results using l-Ala-d₃, the d-Ala in saliva seemed to be produced due to the racemization with some enzymes such as racemase. The racemization reaction was reversible, i.e., d-Ala-d₃ was also racemized to l-Ala-d₃ in saliva. Thus, care should be taken during the analysis of dl-amino acids in saliva. The present method using DMT-(S)-Pro-OSu may be applicable for the determination of chiral amine metabolomics, because the resulting derivatives produce the same product ions without relation to the compounds and show highly sensitive detection in the SRM mode of MS/MS. Consequently, DMT-(S)-Pro-OSu seems to be a useful chiral derivatization reagent for the determination of amines and amino acids in biological samples.     

Parallel distributed block coordinate descent methods based on pairwise comparison oracle

The aim of this paper is to find the global solutions of uncertain optimization problems having a quadratic objective function and quadratic inequality constraints. The bounded epistemic uncertainties in the constraint coefficients are represented using either universal or existential quantified parameters and interval parameter domains. This approach allows to model non-controlled uncertainties by using universally quantified parameters and controlled uncertainties by using existentially quantified ones. While existentially quantified parameters could be equivalently considered as additional variables, keeping them as parameters allows maintaining the quadratic problem structure, which is essential for the proposed algorithm. The branch and bound algorithm presented in the paper handles both universally and existentially quantified parameters in a homogeneous way, without branching on their domains, and uses some dedicated numerical constraint programming techniques for finding a robust, global solution. Several examples clarify the theoretical parts and the tests demonstrate the usefulness of the proposed method.     

Rotating Navier-Stokes Equations in $${\mathbb R}^{3}_{+}$$ with Initial Data Nondecreasing at Infinity: The Ekman Boundary Layer Problem

We prove time local existence and uniqueness of solutions to a boundary layer problem in a rotating frame around the stationary solution called the Ekman spiral. We choose initial data in the vector-valued homogeneous Besov space for 2 <  p <  ∞. Here the L ^p -integrability is imposed in the normal direction, while we may have no decay in tangential components, since the Besov space contains nondecaying functions such as almost periodic functions. A crucial ingredient is theory for vector-valued homogeneous Besov spaces. For instance we provide and apply an operator-valued bounded H ^∞-calculus for the Laplacian in for a general Banach space .     

Development of novel active acceptors possessing a positively charged structure for the transglycosylation reaction with Endo-M and their application to oligosaccharide analysis

With Boc-Asn-GlcNAc as a basic structure, four permanently positively charged kinds of new acceptors (GP-Boc-Asn-GlcNAc, GT-Boc-Asn-GlcNAc, HMP-Boc-Asn-GlcNAc, MPDPZ-Boc-Asn-GlcNAc) and five kinds of similar structure acceptors (2-PA-Boc-Asn-GlcNAc, 3-PA-Boc-Asn-GlcNAc, 4-PA-Boc-Asn-GlcNAc, HP-Boc-Asn-GlcNAc, PDPZ-Boc-Asn-GlcNAc) were synthesized as acceptors for the resolution of oligosaccharides in glycopeptides. The synthesized acceptors enzymatically reacted with Disialo-Asn (donor) in the presence of Endo-M. The reaction yields of each transglycosylation product were not obvious, because we do not have all the authentic Disialo-Asn-Boc-acceptors. Therefore, we used the peak area of the transglycosylation product detected by mass spectrometry and evaluated the utility of each acceptor. Among the Boc-Asn-GlcNAc acceptors, the positively charged MPDPZ derivative peak area was the highest, MPDPZ-Boc-Asn-GlcNAc with a positively charged structure showed about a 2.2 times greater sensitivity of the transglycosylation product compared to the conventional fluorescence acceptor DBD-PZ-Boc-Asn-GlcNAc. As a result, the MPDPZ-Boc-Asn-GlcNAc acceptor was suitable for the transglycosylation reaction with Endo-M. The development of a qualitative determination method for the N-linked oligosaccharides in glycoproteins was attempted by combination of the transglycosylation reaction and semi-micro high-performance liquid chromatography/electrospray ionization quadrupole time-of-flight tandem mass spectrometry (HPLC/ESI-QTOF-MS/MS). The asparaginyl-oligosaccharides in glycoproteins, liberated by treatment with Pronase E, were separated, purified and labeled with positively charged MPDPZ. The resulting derivatives were separated by a semi-micro HPLC system. The eluted N-linked oligosaccharide derivatives were then introduced into a QTOF-MS instrument and sensitively detected in the ESI(+) mode. Various fragment ions based on the carbohydrate units appeared in the MS/MS spectra. Among the peaks, m/z 782.37 corresponding to MPDPZ-Boc-Asn-GlcNAc is the most important one for identifying the asparaginyl-oligosaccharides. Disialo-Asn-Boc-MPDPZ was easily identified by the selected-ion chromatogram at m/z 782.37 by MS/MS detection. Therefore, the identification of N-linked oligosaccharides in glycoproteins seems to be possible by the proposed semi-micro HPLC separations followed by the QTOF-MS/MS detection. Furthermore, several oligosaccharides in ovalbumin and ribonuclease B were successfully identified by the proposed procedure.     

Proton transport properties of poly(aspartic acid) with different average molecular weights

We synthesized seven partially protonated poly(aspartic acids)/sodium polyaspartates (P-Asp) with different average molecular weights to study their proton transport properties. The number-average degree of polymerization (DP) for each P-Asp was 30 (P-Asp30), 115 (P-Asp115), 140 (P-Asp140), 160 (P-Asp160), 185 (P-Asp185), 205 (P-Asp205), and 250 (P-Asp250). The proton conductivity depended on the number-average DP. The maximum and minimum proton conductivities under a relative humidity of 70% and 298 K were 1.7 · 10^?3 S cm^?1 (P-Asp140) and 4.6 · 10^?4 S cm^?1 (P-Asp250), respectively. Differential thermogravimetric analysis (TG-DTA) was carried out for each P-Asp. The results were classified into two categories. One exhibited two endothermic peaks between t = (270 and 300) °C, the other exhibited only one peak. The P-Asp group with two endothermic peaks exhibited high proton conductivity. The high proton conductivity is related to the stability of the polymer. The number-average molecular weight also contributed to the stability of the polymer.     

Stereoselective vinylogous Mukaiyama aldol reaction of α-haloenals

We have developed a high-yielding and stereoselective vinylogous Mukaiyama aldol reaction (VMAR) of α-haloenals. Contrary to the simple α,β-unsaturated aldehyde, α-haloenals were found to be reactive affording the corresponding VMAR adducts in excellent yields. Some transformations of VMAR adducts by Pd-mediated cross-coupling were also examined in order to demonstrate the synthetic utility of VMAR of α-haloenals.     

A probable hydrogen-bonded Meisenheimer complex: an unusually high S(N)Ar reactivity of nitroaniline derivatives with hydroxide ion in aqueous media

Observations show that nitroanilines exhibit an unusually high S(N)Ar reactivity with OH(-) in aqueous media in reactions that produce nitrophenols. S(N)Ar reaction of 4-nitroaniline (2a) in aqueous NaOH for 16 h yields 4-nitrophenol (4a) quantitatively, whereas a similar reaction of 4-nitrochlorobenzene (1a) gave 4a in 2% yield together with recovered 1a in 97%, suggesting that the leaving ability of the NH(2) group far surpasses that of Cl under these conditions. An essential feature of S(N)Ar reactions of nitroanilines is probably that the NH(2) leaving group participates in a hydrogen-bonding interaction with H(2)O. Density functional theory (DFT) calculations for a set of 4-nitroaniline, OH(-), and H(2)O suggest a possible formation of a Meisenheimer complex stabilized by hydrogen-bonding interactions and a six-membered ring structure. The results obtained here contrast with conventional S(N)Ar reactivity profiles in which nitroanilines are nearly unreactive with nucleophiles in organic solvents.     

Theoretical study on reaction scheme of silver(I) containing 5-substituted uracils bridge formation

We present a reaction scheme of silver containing 5-substituted uracils (N) bridge formation with two silver ions to a silver-mediated base pair [N-Ag(2)-N] by using the conductor-like polarizable continuum model (CPCM)-B3LYP/aug-cc-pVDZ level of theory. The whole reaction scheme is divided into the following three steps: (1) silver ion binding and deprotonation, (2) silver ion transfer, and (3) dimer formation and structural fluctuation. With a new pK(a) computing scheme proposed in our previous studies, it is found that a silver coordination decreases the pK(a) of N by 2.5-3.0 pK(a) units, which is an important clue for silver-ion selectivity by N. Judging from the calculation, we revealed that the silver ion transfer reaction and the dimerization reaction occur spontaneously. Moreover, both reactions are independent of the C5 ligand in N so that the deprotonation reaction, which is the first step of this scheme, plays a key role in forming the [N-Ag(2)-N] pairing.     

An MD simulation of the decoy action of Epstein�CBarr virus LMP1 protein mimicking the CD40 interaction with TRAF3

The Epstein?CBarr virus (EBV) is associated with a variety of malignancies and chronic active EBV infection is a severe systemic disease associated with high rates of mortality and morbidity. In this paper, the dynamics of the interaction of EBV-expressed latent membrane protein 1 (LMP1) with cellular signaling intermediate tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) is simulated using standard classical molecular dynamics (MD) protocols. For comparison, the dynamics of the interaction of TRAF3 with CD40, a TNFR mimicked by LMP1 to effect EBV infection is also calculated under similar conditions. Essential dynamics (ED) analysis is carried out to identify important degrees of vibrational freedom that relate to protein function and virus infection. Both the MD simulation and ED analysis reveal novel interactions that help explain the structural decoy action of LMP1 over CD40. These interactions involve the consensus sequence PXQXTXX shared by CD40 and LMP1. In LMP1, we have found novel interaction of Asp 209 with TRAF3 and the interaction is crucial although the adjacent Asp 210 was suggested to be essential by the X-ray analysis. In CD40, it is found that the hairpin formation is not indispensable for the interaction with TRAF3.