Single-site mutation and secondary structure stability: an isodesmic reaction approach. The case of unnatural amino acid mutagenesis Ala-->Lac

A method is described to evaluate backbone interactions in proteins via computational unnatural amino acid mutagenesis. Several N-acetyl polyalanyl amides (AcA(n)NH(2)) were optimized in the representative helical (3(10)-, 4(13)-, and a "hybrid" kappa-helix, n = 7, 9, 10, 14) and hairpin (two- and three-stranded antiparallel beta-sheets with type I turns betaalphaalphaepsilon, n = 6, 9, 10) conformations, and extended conformers of N-acetyl polyalanyl methylamides (n = 2, 3) were used to derive multistranded beta-sheet fragments. Subsequently, each residue of every model structure was substituted, one at a time, with l-lactic acid. The resulting mutant structures were again optimized, and group-transfer energies DeltaE(GT) were obtained as heats of the isodesmic reactions: AcA(n)NHR + AcOMe --> AcA(x)LacA(y)NHR + AcNHMe (R = H, CH(3)). These group-transfer energies correlate with the degree of charge polarization of the substituted peptide linkages as measured by the difference Deltae in H and O Mulliken populations in HN-C=O and with the H-bond distances in the "wild-type" structures. A good correlation obtains for the HF/3-21G and B3LYP/6-31G* group-transfer energies. The destabilization effects are interpreted in terms of loss of interstrand and intrastrand H-bonds, decrease in Lewis basicity of the C=O group, and O...O repulsion. On the basis of several comparisons of Ala --> Lac DeltaE(GT)'s with heats of the NH --> CH(2) substitutions, the latter contribution is estimated (B3LYP/6-31G*) to range between 1.5 and 2.4 kcal mol(-1), a figure close to the recent experimental DeltaDeltaG(o) value of 2.6 kcal mol(-1) (McComas, C. C.; Crowley, B. M.; Boger, D. L. J. Am.Chem. Soc. 2003, 125, 9314). The partitioning yields the following maximum values of the electronic association energy of H-bonds in the examined sample of model structures (B3LYP/6-31G* estimates): 3(10)-helix D(e) = -1.7 kcal mol(-1), alpha-helix D(e) = -3.8 kcal mol(-1), beta-sheet D(e) = -6.1 kcal mol(-1). The premise of experimental evaluations of the backbone-backbone H-bonding that Ala --> Lac substitution in proteins is isosteric (e.g., Koh, J. T.; Cornish, V. W.; Schultz, P. G. Biochemistry 1997, 36, 11314) is often but not always corroborated. Examination of the integrity of H-bonding pattern and phi(i), psi(i) distribution identified several mutants with significant distortions of the "wild-type" structure resulting inter alia from the transitions between i, i + 3 and i, i + 4 H-bonding in helices, observed previously in the crystallographic studies of depsipeptides (Ohyama, T.; Oku, H.; Hiroki, A.; Maekawa, Y.; Yoshida, M.; Katakai, R. Biopolymers 2000, 54, 375; Karle, I. L.; Das, C.; Balaram, P. Biopolymers 2001, 59, 276). Thus, the isodesmic reaction approach provides a simple way to gauge how conformation of the polypeptide chain and dimensions of the H-bonding network affect the strength of backbone-backbone C=O...HN bonds. The results indicate that the stabilization provided by such interactions increases on going from 3(10)-helix to alpha-helix to beta-sheet.     

Structure of starch-bentonite gels

Mixed gels of starch and bentonite are investigated in the interval 0.056–0.089 of total solids/water ratio and 0-100% starch in the solids. The bentonite was a sodium calcium bentonite with a Na/Ca ratio of 1.76. In water it forms gels consisting of a network of band-type structures. Starch forms gels through hydrogen bonds between granules and/or amylose and amylopectin present on the external surfaces of granules and/or in fully stretched form. Mixed gels of bentonite and starch were obtained by adding corn starch granules to the already formed bentonite gels and heating the mixture above the Kofler gelatinization temperature. Amylose and amylopectin were adsorbed on strands of band-type structures of mont-morillonite lamellae. Starch gellation, e.g. diffusion of amylose out of the granule, was facilitated in the presence of bentonite. On the other hand, the presence of starch favored delamination of the montmorillonite particle into thinner lamellae. Maximum gelatinization and polymer adsorption were observed for gels with 20% starch and 80% bentonite. Montmorillonite networks formed the continuous phase for 0-80% starch. At higher starch concentrations, montmorillonite flakes were dispersed within the polymer network. Increase in the water content of the gels caused segregation of the bentonite and starch.     

The first bis(orotato–N,O) complex: Synthesis,crystal structure,spectroscopic and thermal characterization of (chaH)2[Cu(HOr–N,O)2(cha)] · 2H2O (cha = cyclohexylamine and HOr = orotate(2−))

The novel bis(cyclohexylaminium) cyclohexylaminebis(orotate–N,O)cuprate(II) dihydrate, (C₆H₁₅N)₂[Cu(C₅H₂N₂O₄)₂(C₆H₁₄N)] · 2H₂O, has been prepared and characterized by elemental analysis, magnetic measurements, FT-IR and UV–Vis spectroscopy, thermal analysis and X-ray diffraction. The Cu(II) complex crystallizes in the monoclinic space group P2₁/c. The copper atom in the five-coordinated (chaH)₂[Cu(HOr–N,O)₂(cha)] · 2H₂O is chelated by a deprotonated pyrimidine nitrogen atom and carboxylate oxygen atom as a bis(bidentate) ligand and the cyclohexylamine ligand completes the square-pyramidal coordination. The thermal decomposition of the complex has been predicted by the help of thermal analysis (TG, DTG and DTA).     

A survey of 222Rn concentrations in dwellings of Turkey

As part of a national program to determine public exposure to natural radiation, indoor air ²²²Rn concentrations were determined in dwellings of Turkey. The ²²²Rn concentrations were measured with time-integrating passive nuclear etched track detectors in 27 provincial centers. The indoor radon concentrations were found to be in the range of 10-380 Bq^.m^-3. This revised version was published online in August 2006 with corrections to the Cover Date.     

Phenolic compounds from the aerial parts of Clematis viticella L. and their in vitro anti-inflammatory activities*

Phytochemical investigations on the EtOH extract of Clematis viticella led to the isolation of six flavonoid glycosides, isoorientin (1), isoorientin 3′-O-methyl ether (2), quercetin 7-O-α-L-rhamnopyranoside (3), quercetin 3,7-di-O-α-L-rhamnopyranoside (4), manghaslin (5) and chrysoeriol 7-O-β-D-glucopyranoside (6), one phenylethanol derivative, hydroxytyrosol (7), along with three phenolic acids, caffeic acid (8), (E)-p-coumaric acid (9) and p-hydroxybenzoic acid (10). The structures of the isolates were elucidated on the basis of NMR and HR-MS data. All compounds were isolated from C. viticella for the first time. Compounds 7 and 8 showed significant anti-inflammatory activity at 100 μM by reducing the release of NO in LPS-stimulated macrophages comparable to positive control indomethacin. Compounds 3 and 7 exhibited anti-inflammatory activity through lowering the levels of TNF-α while 1, 3 and 5 decreased the levels of neopterin better than the positive controls.     

Kinetically controlled Ag+-coordinated chiral supramolecular polymerization accompanying a helical inversion

We report kinetically controlled chiral supramolecular polymerization based on ligand–metal complex with a 3 : 2 (L : Ag⁺) stoichiometry accompanying a helical inversion in water. A new family of bipyridine-based ligands (d-L1, l-L1, d-L2, and d-L3) possessing hydrazine and d- or l-alanine moieties at the alkyl chain groups has been designed and synthesized. Interestingly, upon addition of AgNO₃ (0.5–1.3 equiv.) to the d-L1 solution, it generated the aggregate I composed of the d-L1AgNO₃ complex (d-L1 : Ag⁺ = 1 : 1) as the kinetic product with a spherical structure. Then, aggregate I (nanoparticle) was transformed into the aggregate II (supramolecular polymer) based on the (d-L1)₃Ag₂(NO₃)₂ complex as the thermodynamic product with a fiber structure, which led to the helical inversion from the left-handed (M-type) to the right-handed (P-type) helicity accompanying CD amplification. In contrast, the spherical aggregate I (nanoparticle) composed of the d-L1AgNO₃ complex with the left-handed (M-type) helicity formed in the presence of 2.0 equiv. of AgNO₃ and was not additionally changed, which indicated that it was the thermodynamic product. The chiral supramolecular polymer based on (d-L1)₃Ag₂(NO₃)₂ was produced via a nucleation–elongation mechanism with a cooperative pathway. In thermodynamic study, the standard ΔG° and ΔH_e values for the aggregates I and II were calculated using the van''t Hoff plot. The enhanced ΔG° value of the aggregate II compared to that of the formation of aggregate I confirms that aggregate II was thermodynamically more stable. In the kinetic study, the influence of concentration of AgNO₃ confirmed the initial formation of the aggregate I (nanoparticle), which then evolved to the aggregate II (supramolecular polymer). Thus, the concentration of the (d-L1)₃Ag₂(NO₃)₂ complex in the initial state plays a critical role in generating aggregate II (supramolecular polymer). In particular, NO₃⁻ acts as a critical linker and accelerator in the transformation from the aggregate I to the aggregate II. This is the first example of a system for a kinetically controlled chiral supramolecular polymer that is formed via multiple steps with coordination structural change.

The nanoparticles were transformed into the supramolecular polymer as the thermodynamic product, involving a helical inversion from left-handed to right-handed helicity.     

Admittance measurements of adsorption properties of 2,2′-bipyridine complexes: Part I. Cobalt(II) and nickel(II) complexes in aqueous solutions

The complex [Co bipy₃]²⁺ in aqueous perchlorate solution yields on the d.c. polarogramthree adsorption type pre-waves and a main reduction wave at ?1.2 V (SCE) corresponding to the reduction to monovalent complex. From admittance measurements and other results it can be concluded that two most positive pre-waves at ?0.2 V and ?0.5 V (SCE) are of non-faradaic nature being related to the adsorption of the complex with specifically adsorbed anions of the supporting electrolyte with the formation of a compact adsorbed layer of much lower interfacial capacity. The most negative pre-wave at ?0.9 V just preceding the main wave corresponds to the reduction of the adsorbed complex. The main wave at ?1.2 V is distorted by the adsorption of reaction products. Very similar and also strong adsorption-coupled interaction was found with divalent nickel trisbipyridine complex.     

Square wave adsorptive stripping voltammetric determination of famotidine in urine

Electrochemical studies of famotidine were carried out using voltammetric techniques: cyclic voltammetry, linear sweep and square wave adsorptive stripping voltammetry. The dependence of the current on pH, buffer concentration, nature of the buffer, and scan rate was investigated. The best results for the determination of famotidine were obtained in MOPS buffer solution at pH 6.7. This electroanalytical procedure enabled to determine famotidine in the concentration range 1 × 10⁻⁹–4 × 10⁻⁸ mol L⁻¹ by linear sweep adsorptive stripping voltammetry (LS AdSV) and 5 × 10⁻¹⁰–6 × 10⁻⁸ mol L⁻¹ by square wave adsorptive stripping voltammetry (SW AdSV). Repeatability, precision and accuracy of the developed methods were checked. The detection and quantification limits were found to be 1.8 × 10⁻¹⁰ and 6.2 × 10⁻¹⁰ mol L⁻¹ for LS AdSV and 4.9 × 10⁻¹¹ and 1.6 × 10⁻¹⁰ mol L⁻¹ for SW AdSV, respectively. The method was applied for the determination of famotidine in urine.     

Thermal degradation of some polymers based on ethylene glycol dimethacrylate

Thermogravimetric analysis and pyrolysis in combination with gas chromatography were used to study the thermal behaviour of some cross-linked polymers of ethylene glycol dimethacrylate. The investigated polymers show a complex thermal degradation mechanism. The complexity of the reaction increases together with increase of the ethylene glycol chain in the macromolecule and with increase of the pyrolysis temperature. At low temperature, the thermal decomposition products of the analyzed polymers are mainly the constituent monomers. At high temperatures, besides the monomer, other decomposition products are formed as a result of thermal cracking reactions, i.e. secondary reactions of decomposition and recombination.

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Zusammenfassung Zur Untersuchung des thermischen Verhaltens einiger quervernetzter Polymere auf Äthylenglykoldimetacrylatbasis wurden thermogravimetrische Analyse und Pyrolyse in Zusammenhang mit der Gaschromatographie angewendet. Die untersuchten Polymere zeigten einen komplexen thermischen Zersetzungsmechanismus. Die Komplexizität der Reaktion nimmt mit Zunahme der Anzahl der Äthylenglykolketten im Makromolekül und mit Zunahme der Pyrolysentemperatur gleichermaßen zu. Bei niedrigeren Temperaturen stellen die Hauptzerfallsprodukte der analysierten Polymere hauptsächlich deren Monomere dar. Bei höheren Temperaturen werden als Ergebnis thermischer Krackreaktionen, z. B. sekundäre Zersetzungs- und Rekombinationsreaktionen, neben den Monomeren auch andere Zersetzungsprodukte gebildet.

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Comparative study of the phenolic profile,antioxidant and antimicrobial activities of leaf extracts of five Juniperus L. (Cupressaceae) taxa growing in Turkey

Abstract

The purpose of this study was to conduct a comparative evaluation of some biological properties of methanol and water extracts of leaves of five Juniperus taxa growing in Turkey: J. communis L. var. communis (Jcc), J. communis L. var. saxatilis Pall. (Jcs), J. drupacea Labill. (Jd), J. oxycedrus L. subsp. oxycedrus (Joo), J. oxycedrus L. subsp. macrocarpa (Sibth. & Sm.) Ball. (Jom). The antioxidant properties were examined in vitro; both in the DPPH and in the reducing power tests, Joo methanol extract resulted the most active (IC₅₀?=?0.09?±?0.01mg/mL and ASE/mL?=?2.56?±?0.06). In the TBA assay, Jcs methanol extract exhibited the highest activity (IC₅₀?=?4.39?±?0.47?μg/mL). The extracts displayed bacteriostatic activity against Staphylococcus aureus, and Jd methanol extract resulted the most effective (MIC?=?19.53?μg/mL); no effect on the S. aureus biofilm formation was observed. The extracts resulted non-toxic in the Artemia salina lethality bioassay. Finally, the phenolic profile of the methanol extracts was characterized by HPLC-PDA/ESI-MS.