Peptide bond formation by aminolysin-A catalysis: a simple approach to enzymatic synthesis of diverse short oligopeptides and biologically active puromycins

A new S9 family aminopeptidase derived from the actinobacterial thermophile Acidothermus cellulolyticus was cloned and engineered into a transaminopeptidase by site-directed mutagenesis of catalytic Ser(491) into Cys. The engineered biocatalyst, designated aminolysin-A, can catalyze the formation of peptide bonds to give linear homo-oligopeptides, hetero-dipeptides, and cyclic dipeptides using cost-effective substrates in a one-pot reaction. Aminolysin-A can recognize several C-terminal-modified amino acids, including the l- and d-forms, as acyl donors as well as free amines, including amino acids and puromycin aminonucleoside, as acyl acceptors. The absence of amino acid esters prevents the formation of peptides; therefore, the reaction mechanism involves aminolysis and not a reverse reaction of hydrolysis. The aminolysin system will be a beneficial tool for the preparation of structurally diverse peptide mimetics by a simple approach.     

Core/shell Fe3O4 @SiO2 nanoparticles modified with PAH as a vector for EGFP plasmid DNA delivery into HeLa cells

Novel stable core/shell Fe(3)O(4)@SiO(2)/PAH nanoparticles are synthesized using 15 nm Fe(3)O(4) as the template that is modified with PAH. The resulting nanoparticles can absorb plasmid DNA to mediate gene transfer in cultured HeLa cells. An electrophoretic assay suggests that the Fe(3)O(4)@SiO(2)/PAH nanoparticles protect the plasmid DNA from serum and DNase I degradation. A cell viability assay shows that the Fe(3)O(4)@SiO(2)/PAH nanoparticles exhibit a low cytotoxicity toward endothelial cells. Qualitative analysis of transfection in HeLa cells by nanoparticles carrying a plasmid DNA encoding EGFP demonstrates a fairly high expression level, even in the presence of serum. Thus, Fe(3)O(4)@SiO(2)/PAH nanoparticles are biocompatible and suitable for nonviral delivery, and may find applications in cancer therapy.     

Distribution of phospholipid molecular species in autogenous access grafts for hemodialysis analyzed using imaging mass spectrometry

Arteriovenous fistulae (AVF) using vein grafts are frequently used for vascular access in hemodialysis. When superficial veins are used as autogenous access grafts for hemodialysis, atherosclerotic-like tissue degeneration often causes stenosis and obstruction. Although the differences between the pathology of degeneration in AVF and atherosclerosis (i.e., peripheral artery occlusive disease (PAD)) are known, their underlying molecular mechanisms are not. We determined the characteristic abnormal lipid metabolism of AVF. Oil red O staining clearly showed the accumulation of lipid molecules in AVF and PAD tissues. We found that the staining pattern was different between AVF and PAD tissues. The media and adventitia of AVF and the intima and media of PAD were intensely stained. Quantitative lipid analysis revealed that the amount of PL was significantly increased in AVF and PAD. Next, we performed matrix-assisted laser desorption/ionization imaging mass spectroscopy and determined the characteristic distribution of lysophosphatidylcholine (LPC) and phosphatidylcholine (PC) in AVF. The distribution patterns of LPC (1-acyl 16:0) and PC (diacyl 16:0/20:4) were consistent with the Oil red O staining images, suggesting that metabolisms related to LPC (1-acyl 16:0) and PC (diacyl 16:0/20:4) are altered in AVF.     

Recent developments and applications of hybrid surface plasmon resonance interfaces in optical sensing

Nanostructured noble metals exhibit an intense optical near field due to surface plasmon resonance, therefore promising widespread applications and being of interest to a broad spectrum of scientists, ranging from physicists, chemists, and materials scientists to biologists. A wealth of research is available discussing the synthesis, characterization, and application of noble metal nanoparticles in optical sensing. However, with respect to the sensitivity of the frequency and width of these surface plasmon resonance modes to the particle’s shape, size, and environment, in nearly every case, success strongly depends on the availability of highly stable, adhesive, and sensitive nanoparticles. This undoubtedly presents a challenging task to nanofabrication. The past decade has witnessed fascinating advances in this field, in particular, the construction of oxide-based hybrid plasmonic interfaces to overcome the problem addressed above by (1) coating the metallic nanostructures with thin overlayers to form sandwiched structures or (2) embedding metallic nanostructures in a dielectric matrix to obtain metal/dielectric matrix nanocomposite films. In this critical review, we focus on recent work related to this field, beginning with a presentation of hybrid films with enhanced structural and optical stability, readily and selectively designed using chemical and physical techniques. We then illustrate their interesting optical properties and demonstrate exciting evidence for the postulated application in surface plasmon sensing fields. Finally, we survey the work remaining to be done for that potential to be realized.     

Palladium-catalyzed cross coupling reaction of N-alkoxyimidoyl bromides and its application to one-pot synthesis of N-arylamines

The synthetic utility of N-alkoxyimidoyl halides is demonstrated using the palladium-catalyzed cross-coupling reaction. The Sonogashira and Suzuki-Miyaura coupling reactions of N-alkoxyimidoyl bromides produced versatile ketoxime ethers in good to excellent yields. A one-pot reaction of the imidoyl bromides with arylboronic acid and allylmagnesium bromide to produce N-arylamines via Suzuki-Miyaura coupling followed by domino reaction involving sequential addition-eliminative rearrangement-addition reactions was developed.     

Ultrafast spectroscopy and coherent acoustic phonons of Au-Ag core-shell nanorods

We performed the first investigations of coherent acoustic phonons in Au-Ag core-shell nanorods, which were compared with the results of parental Au nanorods. Both breathing and extensional modes were observed in Au-Ag core-shell nanorods with ~11 nm Ag shell while only extensional modes were detected in other core-shell nanorods with 4-7 nm Ag shell. Young's modulus estimated from the oscillation period of extensional modes was found to be larger for Au-Ag core-shell nanorods with ~4 nm Ag shell, as compared with that of Au nanorods. The value of Young's modulus decreases with the increase of the Ag shell thickness and finally becomes smaller than that of Au nanorods. This phenomenon is interpreted in terms of the surface effects and the existence of grain boundaries in the lattice structure of Ag shell.     

Geminate charge recombination in liquid alkane with concentrated CCl4: effects of CCl4 radical anion and narrowing of initial distribution of Cl-

Dynamics of radical cations and electrons in an admixture of a linear saturated hydrocarbon (n-dodecane) and halocarbon (carbon tetrachloride, CCl(4)) were investigated by picosecond electron beam pulse radiolysis. The decay of thermalized electrons (e(th)(-)) observed in infrared transient photoabsorption were simply accelerated by the addition of CCl(4), giving a high rate constant of 2.3 × 10(11) mol(-1) dm(3) s(-1). The decrease of the initial yield of e(th)(-) was quantified by C(37) (50 mmol), which is linked to the reaction of epithermal electrons (e(-)) with CCl(4). In contrast, the n-dodecane radical cation (RH(2)(?+)) monitored in the near-infrared indicated a convex-type dependence of the decay rate on CCl(4) concentration, although the initial yield of RH(2)(?+) remained almost constant up to a much higher CCl(4) concentration. The decay of RH(2)(?+) was analyzed by Monte Carlo simulations of geminate ion recombination with e(th)(-), chlorine anion (Cl(-)) formed via dissociative electron attachment, and CCl(4) radical anion. The results showed a good agreement with the experiments by considering two assumptions: (1) CCl(4) radical anion formed via e(th)(-) attachment and (2) narrowing of the initial distribution of Cl(-). The decrease in the initial yield of RH(2)(?+) at high CCl(4) concentration was well explained by immediate decomposition of CCl(4)(?+) to CCl(3)(+) and hole transfer from CCl(4)(?+) to adjacent RH(2) without diffusive motion of the reactants. Time-dependent density functional theory supported the spectroscopic assignment of intermediate species in the n-dodecane/CCl(4) system. The present results would be of help in understanding the electron capture reaction in multicomponent systems such as a chemically amplified resist in lithography.     

Kinetics and mechanisms of the allyl + allyl and allyl + propargyl recombination reactions

The kinetics and mechanisms of the self-reaction of allyl radicals and the cross-reaction between allyl and propargyl radicals were studied both experimentally and theoretically. The experiments were carried out over the temperature range 295-800 K and the pressure range 20-200 Torr (maintained by He or N(2)). The allyl and propargyl radicals were generated by the pulsed laser photolysis of respective precursors, 1,5-hexadiene and propargyl chloride, and were probed by using a cavity ring-down spectroscopy technique. The temperature-dependent absorption cross sections of the radicals were measured relative to that of the HCO radical. The rate constants have been determined to be k(C(3)H(5) + C(3)H(5)) = 1.40 × 10(-8)T(-0.933) exp(-225/T) cm(3) molecule(-1) s(-1) (Δ log(10)k = ± 0.088) and k(C(3)H(5) + C(3)H(3)) = 1.71 × 10(-7)T(-1.182) exp(-255/T) cm(3) molecule(-1) s(-1) (Δ log(10)k = ± 0.069) with 2σ uncertainty limits. The potential energy surfaces for both reactions were calculated with the CBS-QB3 and CASPT2 quantum chemical methods, and the product channels have been investigated by the steady-state master equation analyses based on the Rice-Ramsperger-Kassel-Marcus theory. The results indicated that the reaction between allyl and propargyl radicals produces five-membered ring compounds in combustion conditions, while the formations of the cyclic species are unlikely in the self-reaction of allyl radicals. The temperature- and pressure-dependent rate constant expressions for the important reaction pathways are presented for kinetic modeling.     

Systematic computational study on the unimolecular reactions of alkylperoxy (RO2), hydroperoxyalkyl (QOOH), and hydroperoxyalkylperoxy (O2QOOH) radicals

Unimolecular isomerization and decomposition reactions of alkylperoxy (RO(2)), hydroperoxyalkyl (QOOH), and hydroperoxyalkylperoxy (O(2)QOOH) radicals play important roles in the low-temperature oxidation of hydrocarbons. In this study, these reactions have been investigated by the CBS-QB3 quantum chemical method, and the variation of the rate parameters by the structural change of alkyl groups has been studied systematically for the rule-based construction of the low-temperature oxidation mechanisms of arbitrary noncyclic alkanes. The results can be well-interpreted in terms of the group additivity and the ring-strain effect of the cyclic transition states. To extract the important processes needed for the chemical kinetic modeling, the competing reaction channels were compared in detail by steady-state analysis with the high-pressure limiting rate constants. The importance of some reactions of O(2)QOOH radicals, which have not been considered in the previous modeling studies, such as the hydrogen exchange reactions between -OOH and -OO(?) groups and hydrogen shift reactions from non-OOH sites, is suggested.     

Preparation of carbon quantum dots with tunable photoluminescence by rapid laser passivation in ordinary organic solvents

A simple approach to prepare carbon quantum dots is presented in this communication by laser rapid passivation of nano carbon particles in ordinary organic solvent. The as-prepared carbon dots exhibited visible, tunable and stable photoluminescence (PL). XPS analysis showed that the increased oxygen concentration might be concerned with the origin of PL.