Tripeptides adopt stable structures in water. A combined polarized visible Raman,FTIR, and VCD spectroscopy study

We have measured the band profile of amide I in the infrared, isotropic, and anisotropic Raman spectra of L-alanyl-D-alanyl-L-alanine, acetyl-L-alanyl-L-alanine, L-vanyl-L-vanyl-L-valine, L-seryl-L-seryl-L-serine, and L-lysyl-L-lysyl-L-lysine at acid, neutral, and alkaline pD. The respective intensity ratios of the two amide I bands depend on the excitonic coupling between the amide I modes of the peptide group. These intensity ratios were obtained from a self-consistent spectral decomposition and then were used to determine the dihedral angles between the two peptide groups by means of a recently developed algorithm (Schweitzer-Stenner, R. Biophys. J. 2002, 83, 523-532). The validity of the obtained structures were checked by measuring and analyzing the vibrational circular dichroism of the two amide I bands. Thus, we found two solutions for all protonation states of trialanine. Assuming a single conformer, one obtains a very extended beta-helix-like structure. Alternatively, the data can be explained by the coexistence of a 3(1)(PII) and a beta-sheet-like structure. Acetyl-L-alanyl-L-alanine exhibits a structure which is very similar to that obtained for trialanine. The tripeptide with the central D-alanine adopts an extended structure with a negative psi and a positive phi angle. Trivaline and triserine adopt single beta(2)-like structures such as that identified in the energy landscape of the alanine dipeptide. Trilysine appears different from the other investigated homopeptides in that it adopts a left-handed helix which at acid pD is in part stabilized by hydrogen bonding between the protonated carboxylate (donor) and the N-terminal peptide carbonyl. Our result provides compelling evidence for the capability of short peptides to adopt stable structures in an aqueous solution, which at least to some extent reflect the intrinsic structural propensity of the respective amino acids in proteins. Furthermore, this paper convincingly demonstrates that the combination of different vibrational spectroscopies provides a powerful tool for the determination of the secondary structure of peptides in solution.     

Synthesis of New Spirodifuranose Derivatives by Reduction of Stable Spiro-Endoperoxides

Synthesis of three new stable spirodifuranose derivatives (3, 5, and 7), which cannot be obtained easily using ordinary synthetic methods, has been achieved by reduction of 3-O-acetyl and 3-O-methyl derivatives of (4R)-1,2-O-alkylidene-5-eno-4,7-epidioxy-5,6,8-trideoxy-α-D-threo-1,4-furano-4,7-diulo-octoses (1, 4, and 6).     

The role of growth temperature in the adhesion and mechanics of pathogenic L. monocytogenes: an AFM study

The adhesion strengths of pathogenic L. monocytogenes EGDe to a model surface of silicon nitride were quantified using atomic force microscopy (AFM) in water for cells grown under five different temperatures (10, 20, 30, 37, and 40 °C). The temperature range investigated was chosen to bracket the thermal conditions in which L. monocytogenes survive in the environment. Our results indicated that adhesion force and energy quantified were at their maximum when the bacteria were grown at 30 °C. The higher adhesion observed at 30 °C compared to the adhesion quantified for bacterial cells grown at 37, 40, 20, and 10 °C was associated with longer and denser bacterial surface biopolymer brushes as predicted from fitting a model of steric repulsion to the approach distance-force data as well from the results of protein colorimetric assays. Theoretically predicted adhesion energies based on soft-particle DLVO theory agreed well with the adhesion energies computed from AFM force-distance retraction data (r(2) = 0.94); showing a minimum energy barrier to adhesion at 30 °C.     

Synthesis of new transition metal complexes of 1H-perimidine derivatives having antimicrobial and anti-inflammatory activities

New series of 1H-perimidine-2-thiol derivatives and (2-substituted-1H-perimidin-1-yl)ethane-1,2-dione derivatives and their ligands (C₂₄H₁₄N₄S₂O₂) H₂L¹ and (C₂₆H₁₈N₄S₂O₂) H₂L² have been synthesized with transition metal ions, e.g., Copper (II), Silver (I), Cobalt (II) and Ruthenium (III) were prepared and evaluated for their antimicrobial, analgesic and anti-inflammatory activities. The synthesized compounds and their complexes were characterized by elemental analysis, ¹H NMR, IR, MS, molar conductance, thermal gravimetric analysis and electronic spectra. All results revealed that compounds 3 and 13 exhibited high inhibitory effects against some bacterial strains by the disc diffusion method. On the other hand, compounds 2, 3, 7 and 12 displayed potent anti-inflammatory activity.     

Purification and Properties of a Thermostable Xylanase GH 11 from Penicillium occitanis Pol6

An extracellular, endo-??-1,4-xylanase was purified to homogeneity from the culture filtrate of the filamentous fungus Penicillium occitanis Pol6, grown on oat spelt xylan. The purified enzyme (PoXyn2) showed a single band on SDS?CPAGE with an apparent molecular weight of 30?kDa. The xylanase activity was optimal at pH?3.0 and 65?°C. The specific activity measured for oat spelt xylan was 2,368?U?mg^?1. The apparent K _m and V _max values were 8.33?mg?ml^?1 and 58.82???mol?min^?1?ml^?1, respectively, as measured on oat spelt xylan. Thin-layer chromatography experiments revealed that purified PoXyn2 degrades xylan in an endo-fashion releasing xylobiose as main end product. The genomic DNA and cDNA encoding this protein were cloned and sequenced. This PoXyn2 presents an open reading frame of 962?bp, not interrupted by any introns and encoding for a mature protein of 320 amino acids and 29.88?kDa.     

Stable conformations of tripeptides in aqueous solution studied by UV circular dichroism spectroscopy

Determination of the precise solution structure of peptides is of utmost importance to the understanding of protein folding and peptide drugs. Herein, we have measured the UV circular dichroism (UVCD) spectra of tri-alanine dissolved in D(2)O, H(2)O, and glycerol. The results clearly show the coexistence of a polyproline II or 3(1)-helix and a somewhat disordered flat beta-strand conformation, in complete agreement with recent predictions from spectroscopic data (Eker et al. J. Am. Chem. Soc. 2002, 124, 14 330-14 341). A thermodynamic analysis revealed that enthalpic contributions of about 11 and 17 kJ/mol stabilize polyproline II in D(2)O and H(2)O, respectively, but at room temperature they are counterbalanced by entropic contributions, which clearly favor the more disordered beta-strand conformation. It is hypothesized that this delicate balance is the reason for the variety of structural propensities of amino acid residues in the absence of nonlocal interactions. The isotope effect yielding a higher occupation of polyproline II in H(2)O with respect to D(2)O strongly suggests that a hydrogen-bonding network involving the peptide and water molecules in the hydration shell plays a major role in stabilizing this conformation. The equilibrium between polyproline II and beta-strand is practically maintained in glycerol, which suggests that glycerol can substitute water as stabilizing solvent for the polyproline II conformation. We also measured the UVCD spectra of tri-valine and tri-lysine (both at acidic pD) in D(2)O and found them to adopt a flat beta-strand and left-handed turn structure, respectively, in accordance with recent analyses of vibrational spectroscopy data. Generally, the present study adds substantial evidence to the notion that the so-called random coil state of peptides is much more structured than generally assumed.     

Oxidation of cyclohexane catalyzed by metal-ion-exchanged zeolites

The ion-exchange rates and capacities of the zeolite NaY for the Cu(II), Co(II), and Pb(II) metal ions were investigated. Ion-exchange equilibria were achieved in approximately 72 h for all the metal ions. The maximum ion exchange of metal ions into the zeolite was found to be 120 mg Pb(II), 110 mg Cu(II), and 100 mg Co(II) per gram of zeolite NaY. It is observed that the exchange capacity of a zeolite varies with the exchanged metal ion and the amount of metal ions exchanged into zeolite decreases in the sequence Pb(II) > Cu(II) > Co(II). Application of the metal-ion-exchanged zeolites in oxidation of cyclohexane in liquid phase with visible light was examined and it is observed that the order of reactivity of the zeolites for the conversion of cyclohexane to cyclohexanone and cyclohexanol is CuY > CoY > PbY. It is found that conversion increases by increase of the empty active sites of a zeolite and the formation of cyclohexanol is favored initially, but the cyclohexanol is subsequently converted to cyclohexanone.     

Characterization and kinetics analysis of the thermal decomposition of the humic substance from hazelnut husk

A humic substance was obtained from hazelnut husk using an alkali extraction. The chemical and morphological structure of the humic matter was characterized via elemental analysis, Fourier transform infrared spectrometry (FTIR), nuclear magnetic resonance, Brunauer-Emmet-Teller (BET) analysis, scanning electron microscopy (SEM), and thermogravimetric-FTIR (TG-FTIR). In addition, thermal analysis measurements TG analysis-differential thermogravimetry/differential scanning calorimetry (TGA-DTG/DSC) were performed under dynamic air conditions to better determine the origin, physical and chemical structure, and decomposition process of the humic matter. The Kissinger-Akahira-Sunose (KAS) and Flynn-Wall-Ozawa (FWO) methods were used to calculate the kinetic parameters of the high-temperature decomposition process. It was observed that the activation energy values were almost constant at certain conversion and temperature intervals. In addition, the structure of the humic substance at different temperatures was also investigated via FTIR analysis. It was found that the obtained humic substance had a very stable structure and decomposed at a high temperature. The stability of the humic matter can be a useful tool in the environmental quality research of soil.     

Reconstruction and crosstalk of protein-protein interaction networks of Wnt and Hedgehog signaling in Drosophila melanogaster

In the last few years, researchers have an intense interest in the evolutionarily conserved signaling pathways which have crucial roles during embryonic development. The most intriguing factor of this interest is that malfunctioning of these signaling pathways (Hedgehog, Notch, Wnt etc.) leads to several human diseases, especially to cancer. This study deals with the β-catenin dependent branch of Wnt signaling and the Hedgehog signaling pathways which offer potential targeting points for cancer drug development. The identification of all proteins functioning in these signaling networks is crucial for the efforts of preventing tumor formation. Here, through integration of protein-protein interaction data and Gene Ontology annotations, Wnt/β-catenin and Hedgehog signaling networks consisting of proteins that have statistically high probability of being biologically related to these signaling pathways were reconstructed in Drosophila melanogaster. Next, by the structural network analyses, the crucial components functioning in these pathways were identified. The proteins Arm, Frizzled receptors (Fz and Fz2), Arr, Apc, Axn, Ci and Ptc were detected as the key proteins in these networks. Futhermore, the hub protein Mer having tumor suppressor function may be proposed as a putative drug target for cancer and deserves further investigation via experimental methods. Finally, the crosstalk analysis between the reconstructed networks reveals that these two signaling networks crosstalk to each other.     

Experimental investigation of radiocesium sorption on ceramic clay using a batch method

In this study, radiocesium sorption on ceramic clay was investigated as a function of particle size and initial ¹³⁷Cs concentration using a batch method. Ceramic clay samples taken from the Sö?üt(?nisar) clay deposit were composed of kaolinite, dickite and quartz. The equilibrium time and the liquid–solid ratio were determined as 60 min and 250 mL g^?1, respectively. The distribution coefficients (K _d) for variable liquid–solid ratio and the percentage adsorption (P _Ad) were calculated. The values of K _d and P _Ad ranged from 483 to 3165 mL g^?1 and 34–93%, respectively. The K _d and P _Ad values increased with increasing particle size, but decreased with increasing initial concentration. The sorption data were interpreted in terms of a Langmuir isotherm. The results indicated that the Sö?üt(?nhisar) ceramic clay has good sorption capacity for cesium.