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.     

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.     

The enthalpies of combustion and formation of <Emphasis Type="Italic">L</Emphasis>-α-glutamic and 6-aminohexanoic acids

Summary The energies of combustion of crystalline L-α-glutamic and 6-aminohexanoic acids were measured in a static bomb adiabatic calorimeter, in pure oxygen at 3040 kPa. Corrections were made for the heats due to the ignition of sample and for the nitric acid formation. The derived enthalpies of formation for L-α -glutamic and 6-aminohexanoic acids are Δ_fH_cr⁰= -1002.6±1.1 kJ mol^-1and Δ_fH_cr⁰= -641.6±1.2 kJ mol^-1, respectively. The data of enthalpy of formation are compared with literature values and with estimated values by means of group additivity, using parameters recommended by Domalski and Hearing.     

New instanton and meron solutions of a generally covariant four-dimensional sigma model

We construct new solutions of the fourdimensional sigma model coupled to the metric tensor field and having an internalO invariance. Our solutions interpolate continuously between the known instanton and meron solutions depending upon a parameterf. We find that the typical domain for the instantons is 2<f≦3 while for the merons is 0≦f≦2.     

Diterpenoid Alkaloids of Delphinium buschianum Grossh.

From the aerial parts of Delphinium buschianum Grossh ., collected in Turkey, a new diterpenoid alkaloid 1 , named budelphine, was isolated along with the known diterpenoid alkaloids karakoline ( 2 ), 18‐hydroxy‐14‐O‐methylgadesine ( 3 ), delsoline ( 4 ), lapaconidine ( 5 ), columbianine ( 6 ), 14‐benzoylneoline ( 7 ), and hetisine ( 9 ). The structure of 1 was established on the basis of ¹H‐, ¹³C‐, DEPT, ¹H,¹H‐COSY, NOESY, HSQC, and HMBC NMR studies.