Influence of amino acid side chain packing on Fe-methionine coordination in thermostable cytochrome C

Paramagnetic NMR and optical studies of the oxidized forms of mesophile Pseudomonas aeruginosa cytochrome c(551) and its quintuple mutant (F7A/V13M/F34Y/E43Y/V78I), and thermophile Hydrogenobacter thermophilus cytochrome c(552) demonstrated that the amino acid side chain packings in the protein interior influence the coordination bond between the heme iron and the axial methionine in the proteins. The strength of heme axial coordinations was found to correlate with the overall protein thermostability.     

Synthesis and applications of [1-(15)N]-labeled 4,6-dimethyl-4H-[1,2,5]oxadiazolo[3,4-d]pyrimidine-5,7-dione 1-oxide as a useful tool for mechanistic investigations

[1-(15)N]-Labeled 4,6-dimethyl-4H-[1,2,5]oxadiazolo[3,4-d]pyrimidine-5,7-dione 1-oxide (1-(15)N1) was easily prepared by nitration of commercially available 6-amino-1,3-dimethyl-1H-pyrimidine-2,4-dione using 15N-enriched nitric acid followed by an intramolecular oxidative cyclization with iodosylbenzene diacetate under mild conditions. On the basis of the experimental results using 1-(15)N1, the formation of 8-phenyltheophylline (3), the 1,3-dimethylalloxazines (4: n = 0, 1), and 1,3,7,9-tetramethyl-1H,9H-pyrimido[5,4-g]pteridine-2,4,6,8-tetraone++ + (5) in the thermal reaction of the N-oxide 1 with benzylamine, aniline, or piperidine, and the generation of NO or NO-related species in the reaction with N-acetylcysteamine were reasonably explained by considering the initial attack of the employed nucleophiles on the 3a-position of 1.     

Ultraviolet derivatization of steroidal saponin in garlic and commercial garlic products as p-nitrobenzoate for liquid chromatographic determination

A method is described for determination of the steroidal saponin, eruboside B, originating in garlic and garlic products as the p-nitrobenzoyl chloride (PNBC) derivative by reversed-phase liquid chromatography (with ultraviolet detection at 260 nm. Proto-eruboside B was extracted from garlic (Allium sativum L.); subjected to solid-phase extraction (SPE) with a C18 cartridge, Florisil column chromatography, and silica gel column chromatography; and then enzymatically converted to eruboside B, which was applied as an external standard. Steroidal saponins in garlic and commercial garlic products were extracted with methanol and purified by SPE cartridges, followed by enzymatic treatment. A frostanol saponin such as proto-eruboside B is enzymatically transformed to a spirostanol saponin, eruboside B. After the derivatization with PNBC, the saponin derivative was chromatographed on a C8 column with a gradient elution of (A) 80% aqueous acetonitrile and (B) 100% acetonitrile. The detection limit of the developed method was 1 microg/g for the samples. The method was applied to the analysis of garlic and garlic health food products available in Japan.     

Regioselective synthesis and biological activity of oxidized chitosan derivatives

Oxidized chitosan derivatives with various degrees of oxidation (DS, 0.1–1.0) were prepared by the treatment of chitosan with CrO₃/aq HClO₄ or by the oxidation of ­3‐O‐ and N‐protected chitosan with 30% aq H₂O₂/Na₂WO₄ followed by 3‐O‐ and N‐deprotection. The oxidized products were then N‐acetylated with Ac₂O in order to improve their water‐solubility. Although the oxidized chitosan derivative of DS 0.28 and the degree of N‐acetylation of chitosan (DA) 38% was insoluble in the pH 3–8 region, that of DS 0.26 and DA 76% was soluble in the neutral pH range. The newly‐prepared acetylated and oxidized chitosan derivatives were found to suppress the chemiluminescence response of inflammatory cells such as canine polymorphonuclear cells (PMNs). Analysis by the surface plasmon resonance method revealed that the bind and release behavior of PMNs to acetylated oxidized chitosan derivatives was similar to that against carboxymethylated chitosan derivatives. The amount of water‐soluble chitosan derivative bound to cytokine IL‐8 was found to be affected by the structural and electronic features of the chitosan substituents in the chitosan chain. Copyright © 2003 John Wiley & Sons, Ltd.     

Tetraalkylammonium Picrates in the Dichloromethane–Water System: Ion-Pair Formation and Liquid–Liquid Distribution of Free Ions and Ion Pairs

Equilibria concerning picrates of tetraalkylammonium ions (Me₄N⁺, Et₄N⁺, Pr₄N⁺, Bu₄N⁺, Bu₃MeN⁺) in a dichloromethane−water system have been investigated at 25 ^∘C. The 1:1 ion-pair formation constants (K _IP,o ^o) in dichloromethane at infinite dilution were conductometrically determined. The distribution constants (K _D ^o) of the ion pairs and the free cations between the solvents were determined by a batch-extraction method. The K _IP,o ^o value varies in the cation sequence, Bu₄N⁺ ≈ Pr₄N⁺ ≈ Et₄N⁺ < Bu₃MeN⁺ < < Me₄N⁺; this trend is explained by the electrostatic cation−anion interaction taking into account the structures of the ion pairs determined by density functional theory calculations. For the ion pairs of the symmetric R₄N⁺ cations, there is a linear positive relationship between log₁₀ K _D ^o and the number of methylene groups in the cation (N _{CH 2}). The ion pair of asymmetric Bu₃MeN⁺ has a higher distribution constant than that expected from the above log₁₀ K _D ^o versus N _{CH 2} relationship. These cation dependencies of log₁₀ K _D ^o for the ion pairs are explained theoretically by using the Hildebrand-Scatchard equation. For all the cations, the log₁₀ K _D ^o value of the free cation increases linearly with N _{CH 2}; the variation of log₁₀ K _D ^o is discussed by decomposing the distribution constant into the Born-type electrostatic contribution and the non-Born one, and attributed to the latter that is governed by the differences in the molar volumes of the cations. The cation dependencies of the ion-pair extractability and ion pairing in water are also discussed. An erratum to this article can be found at     

Trapping effect of eugenol on hydroxyl radicals induced by L-DOPA in vitro

Many researchers have stated that eugenol might inhibit lipid peroxidation at the stage of initiation, propagation, or both, and many attempts have been made to elucidate the mechanism of its antioxidant activity. Nevertheless, details of its mechanism are still obscure. This study was carried out to investigate the trapping effect of eugenol on hydroxyl radical generated from L-3,4-dihydroxyphenylalanine (DOPA) in MiliQ water and the generation mechanism of the hydroxyl radical by this system which uses no metallic factor. This was studied by adding L-DOPA and 5,5-dimethyl-1-pyrroline N-oxide (DMPO) to phosphate buffered saline (PBS) or MiliQ water, and the generation of hydroxyl radical was detected on an ESR spectrum. By this method, the effect of antioxidants was detected as a modification of ESR spectra. We found that the eugenol trapped hydroxyl radicals directly, because it had no iron chelating action, did not trap L-DOPA semiquinone radical and inhibited hydroxyl radicals with or without iron ion.     

Catalytic specificity exhibited by p-sulfonatocalix[n]arenes in the methanolysis of N-acetyl-l-amino acids

Specific acid catalysis of p-sulfonatocalix[n]arenes (n = 4, Calix-S4; n = 6, Calix-S6; n = 8, Calix-S8) was observed in the alcoholysis of N-acetyl-l-amino acids in methanol. The methanolysis rates of basic amino acid substrates (His, Lys, and Arg) were markedly enhanced in the presence of Calix-Sn, as compared with rates observed with p-hydroxybenzenesulfonic acid (pHBS), which is a noncyclic analogue of Calix-Sn. This catalytic effect of Calix-Sn was not observed for the methanolysis of Phe, Tyr, and Trp substrates. On the other hand, (1)H NMR experiments following the effect of Calix-Sn on N-acetyl-l-amino acid substrates in CD(3)OD showed that the spectrum of a mixture of the His substrate with Calix-Sn was significantly different from the combined spectra of the respective compounds. These changes in spectra support the formation of an inclusion complex of Calix-Sn with basic amino acids. Furthermore, it was obvious that methanolysis of the His substrate catalyzed by Calix-S4 and Calix-S6 obeyed Michaelis-Menten kinetics. These results indicate that the catalytic activity of Calix-Sn originates from its forming a complex with specific substrates (basic amino acids), similar to enzymatic reactions.     

Extraction Equilibria between Benzene and Water of Uni- and Bivalent Metal Picrates with Lariat 16-Crown-5: Effect of the Side Arms on the Extraction Ability and Selectivity

The overall extraction constants (K_ex) of uni- andbivalent metal picrates with 15-(2,5-dioxahexyl)-15-methyl-16-crown-5(L16C5) were determined between benzene and water at 25°C. TheK_ex values were analyzed into the constituent equilibriumconstants, i.e., the extraction constant of picric acid, the distributionconstant of the crown ether, the stability constant of the metalion–crown ether complex in water, and the ion-pair extraction constantof the complex cation with the picrate anion. The K_ex valuedecreases in the orders Ag⁺ > Na⁺ >Tl⁺ > K⁺ > Li⁺ andPb²⁺ > Ba²⁺ > Sr²⁺ for theuni- and bivalent metals, respectively, which are the same as those observedfor 16C5. The extraction selectivity was found to be governed by theselectivity of the ion-pair extraction of the L16C5–metal picratecomplex rather than by that of the complex formation in water. Theextraction ability of L16C5 is smaller for all the metals than that of 16C5,which is mostly attributed to the higher lipophilicity of L16C5. Differencesin the extraction selectivity between L16C5 and 16C5 were observed for thebivalent metals but little for the univalent metals. The side-arm effect onthe extraction selectivity was interpreted on the basis of the negativecorrelation between the effect on the complex stability constant in waterand that on the ion-pair extraction constant.     

Neural Networks for Financial Time Series Forecasting

Financial and economic time series forecasting has never been an easy task due to its sensibility to political, economic and social factors. For this reason, people who invest in financial markets and currency exchange are usually looking for robust models that can ensure them to maximize their profile and minimize their losses as much as possible. Fortunately, recently, various studies have speculated that a special type of Artificial Neural Networks (ANNs) called Recurrent Neural Networks (RNNs) could improve the predictive accuracy of the behavior of the financial data over time. This paper aims to forecast: (i) the closing price of eight stock market indexes; and (ii) the closing price of six currency exchange rates related to the USD, using the RNNs model and its variants: the Long Short-Term Memory (LSTM) and the Gated Recurrent Unit (GRU). The results show that the GRU gives the overall best results, especially for the univariate out-of-sample forecasting for the currency exchange rates and multivariate out-of-sample forecasting for the stock market indexes.     

Single-component nanodiscs via the thermal folding of amphiphilic graft copolymers with the adjusted flexibility of the main chain

Nanodiscs have attracted considerable attention as structural scaffolds for membrane-protein research and as biomaterials in e.g. drug-delivery systems. However, conventional disc-fabrication methods are usually laborious, and disc fabrication via the self-assembly of amphiphiles is difficult. Herein, we report the formation of polymer nanodiscs based on the self-assembly of amphiphilic graft copolymers by adjusting the persistence length of the main chain. Amphiphilic graft copolymers with a series of different main-chain persistence lengths were prepared and these formed, depending on the persistence length, either rods, discs, or vesicles. Notably, polymer nanodiscs were formed upon heating a chilled polymer solution without the need for any additives, and the thus obtained nanodiscs were used to solubilize a membrane protein during cell-free protein synthesis. Given the simplicity of this disc-fabrication method and the ability of these discs to solubilize membrane proteins, this study considerably expands the fundamental and practical scope of graft-copolymer nanodiscs and demonstrates their utility as tools for studying the structure and function of membrane proteins.

A strategy for the fabrication of nanodiscs via the self-assembly of thermoresponsive amphiphilic graft copolymers is demonstrated.