Synthesis of polyenamines by vinylogous nucleophilic substitution polymerization of 2,2′-disubstituted bis(4-ethoxymethylene-5-oxazolone) with diamines

A new class of polyenamines was synthesized by the vinylogous nucleophilic substitution polymerization of 2,2′-p-phenylenebis(4-ethoxymethylene-5-oxazolone) with diamines in polar aprotic solvents under very mild conditions. The polymers derived from aliphatic diamines were soluble in these solvents and had inherent viscosities in the range of 0.3–0.9. The dilute solutions showed marked decrease in viscosity with time, presumably due to hydrolytic chain scission of the enamine structures in the polymer backbone. The polymers exhibited no melting temperature, and onset of breakdown under thermogravimetric analysis in a nitrogen atmosphere occurred at 250–300°C.     

1.1-GHz continuous-wave EPR spectroscopy with a frequency modulation method

Continuous-wave EPR spectroscopy using a frequency modulation (FM) scheme was developed. An electronically tunable resonator and an automatic tuning control (ATC) system were used. Using the FM scheme instead of magnetic field modulation, we detected EPR absorption at the first derivative mode. We used a microwave frequency of 1.1 GHz in the present experiment. Similar signal-to-noise ratios were obtained with conventional field modulation and the FM method, and a low-quality factor EPR resonator was not necessary to suppress the significant microwave reflection from the resonator. The FM method with a tunable resonator may be an alternative solution to achieving phase-sensitive detection, when the side-effects of magnetic field modulation, such as microphonic noise and mechanical vibration, are detrimental for EPR detection.     

Shotgun Proteomics Revealed Preferential Degradation of Misfolded In Vivo Obligate GroE Substrates by Lon Protease in Escherichia coli

The Escherichia coli chaperonin GroEL/ES (GroE) is one of the most extensively studied molecular chaperones. So far, ~80 proteins in E. coli are identified as GroE substrates that obligately require GroE for folding in vivo. In GroE-depleted cells, these substrates, when overexpressed, tend to form aggregates, whereas the GroE substrates expressed at low or endogenous levels are degraded, probably due to misfolded states. However, the protease(s) involved in the degradation process has not been identified. We conducted a mass-spectrometry-based proteomics approach to investigate the effects of three ATP-dependent proteases, Lon, ClpXP, and HslUV, on the E. coli proteomes under GroE-depleted conditions. A label-free quantitative proteomic method revealed that Lon protease is the dominant protease that degrades the obligate GroE substrates in the GroE-depleted cells. The deletion of DnaK/DnaJ, the other major E. coli chaperones, in the ∆lon strain did not cause major alterations in the expression or folding of the obligate GroE substrates, supporting the idea that the folding of these substrates is predominantly dependent on GroE.     

Radiation-induced polymerization of glass-forming systems. VII. Polymerization in supercooled state under high pressure

Radiation-induced polymerization of glass-forming monomers such as 2-hydroxyethyl methacrylate and glycidyl methacrylate under high pressure was studied. The glass transition temperature of these monomers was heightened by increased pressure. The temperature dependence of polymerizability showed a characteristic relation; similar to those in supercooled-phase polymerization under normal pressure, that had a maximum at T_v which shifted to higher levels of temperature as well as to T_g under high pressure. Polymerizability in the supercooled state also increased under increased pressure.     

Roles of K151 and D180 in L‐2‐haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and ab initio fragment molecular orbital calculations

L ‐2‐haloacid dehalogenase (L ‐DEX) catalyzes the hydrolytic dehalogenation of L ‐2‐haloalkanoic acids to produce the corresponding D ‐2‐hydroxyalkanoic acids. This enzyme is expected to be applicable to the bioremediation of environments contaminated with halogenated organic compounds. We analyzed the reaction mechanism of L ‐DEX from Pseudomonas sp. YL (L ‐DEX YL) by using molecular modeling. The complexes of wild‐type L ‐DEX YL and its K151A and D180A mutants with its typical substrate, L ‐2‐chloropropionate, were constructed by docking simulation. Subsequently, molecular dynamics (MD) and ab initio fragment molecular orbital (FMO) calculations of the complexes were performed. The ab initio FMO method was applied at the MP2/6‐31G level to estimate interfragment interaction energies. K151 and D180, which are experimentally shown to be important for enzyme activity, interact particularly strongly with L ‐2‐chloropropionate, catalytic water, nucleophile (D10), and with each other. Our calculations suggest that K151 stabilizes substrate orientation and balances the charge around the active site, while D180 stabilizes the rotation of the nucleophile D10, fixes catalytic water around D10, and prevents K151 from approaching D10. Further, D180 may activate catalytic water on its own or with K151, S175, and N177. These roles are consistent with the previous results. Thus, MD and ab initio FMO calculations are powerful tools for the elucidation of the mechanism of enzymatic reaction at the molecular level and can be applied to other catalytically important residues. The results obtained here will play an important role in elucidating the reaction mechanism and rational design of L ‐DEX YL with improved enzymatic activity or substrate specificity. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

A nanocarbon film electrode as a platform for exploring DNA methylation

We describe the quantitative nonlabel electrochemical detection of both cytosine (C) and methylcytosine (mC) in oligonucleotides using newly developed nanocarbon film electrodes. The film consists of nanocrystalline sp2 and sp3 mixed bonds formed by employing the electron cyclotron resonance (ECR) sputtering method. We successfully used this film to develop a simple electrochemical DNA methylation analysis technique based on the measurement of the differences between the oxidation currents of C and mC since our ECR nanocarbon film electrode can directly measure all DNA bases more quantitatively than conventional glassy carbon or boron-doped diamond electrodes. The excellent properties of ECR nanocarbon film electrodes result from the fact that they have a wide potential window while maintaining the high electrode activity needed to oxidize oligonucleotides electrochemically. Proof-of-concept experiments were performed with synthetic oligonucleotides including different numbers of C and mC. This film allowed us to perform both C- and mC-positive assays solely by using the electrochemical oxidation of oligonucleotides without bisulfite or labeling processes.     

Line-Mixing Calculations for the 5.3 μm NO Band

Line-mixing coefficients of the NO-N₂ system are calculated within the infinite-order sudden (IOS) and energy-corrected sudden (ECS) approximations. The so-called sum rule between the line width and the line-mixing coefficients is used for line-mixing calculation. Line widths calculated from the ECS model are in good agreement with experimental data for the 5.3 μm NO band. The band-correction function of NO, which characterizes the deviations from the superposition of Lorentz profiles, is also calculated. The ECS results as well as experimental data indicate strong sub-Lorentzian behavior in the wing of the R branch of the 5.3 μm NO band.     

Synthesis of a stable iminium salt and propellane derivatives

The treatment of morphinan 1 with NaH and MsCl provided very stable iminium salt 7 possessing propellane skeleton. One of the synthesized iminium salts 7, isobutyl derivative 7b, was crystallized and its structure was determined by X-ray crystallography. The natural bond orbital analysis suggested that the stability of the iminium should result from the stereoelectronic effect (hyperconjugation) attributed to their own structures.     

Diastereo- and enantioselective synthesis of nitroso Diels-Alder-type bicycloketones using dienamine: mechanistic insight into sequential nitroso Aldol/Michael reaction and application for optically pure 1-amino-3,4-diol synthesis

This article presents complete diastereo- and highly enantioselective synthesis of nitroso Diels-Alder-type bicycloketones using dienamine. With the hydrogen bonding of two hydroxyls in the bulky binaphthol 1c, high enantioselectivities and complete diastereoselectivity are realized in 2-oxa-3-aza-bicycloketone synthesis. On the other hand, alpha,beta-unsaturated ketone can be employed as diene precursor, utilizing readily available tetrazole catalyst 3b, to provide the 3-oxa-2-aza-bicycloketones in moderate yields with complete enantioselectivities. Investigation into the reaction utilizing 2-morpholino-4,4-diphenylcyclohexadiene 2d clearly indicated that cyclization with the bulky binaphthol 1c is involved in the sequential process, the N-nitroso aldol reaction, followed by Michael addition. In addition, optically pure 1-amino-3,4-diol is synthesized from 2-oxa-3-aza-bicycloketones. Use of p-phenoxynitrosobenzene allows access to protected amino diol via cleavage of the N-Ph bond.