Subtle pH differences trigger single residue motions for moderating conformations of calmodulin

This study reveals the essence of ligand recognition mechanisms by which calmodulin (CaM) controls a variety of Ca(2+) signaling processes. We study eight forms of calcium-loaded CaM each with distinct conformational states. Reducing the structure to two degrees of freedom conveniently describes main features of the conformational changes of CaM via simultaneous twist-bend motions of the two lobes. We utilize perturbation-response scanning (PRS) technique, coupled with molecular dynamics simulations. PRS is based on linear response theory, comprising sequential application of directed forces on selected residues followed by recording the resulting protein coordinates. We analyze directional preferences of the perturbations and resulting conformational changes. Manipulation of a single residue reproduces the structural change more effectively than that of single/pairs/triplets of collective modes of motion. Our findings also give information on how the flexible linker acts as a transducer of binding information to distant parts of the protein. Furthermore, by perturbing residue E31 located in one of the EF hand motifs in a specific direction, it is possible to induce conformational change relevant to five target structures. Independently, using four different pK(a) calculation strategies, we find this particular residue to be the charged residue (out of a total of 52), whose ionization state is most sensitive to subtle pH variations in the physiological range. It is plausible that at relatively low pH, CaM structure is less flexible. By gaining charged states at specific sites at a pH value around 7, such as E31 found in the present study, local conformational changes in the protein will lead to shifts in the energy landscape, paving the way to other conformational states. These findings are in accordance with Fluorescence Resonance Energy Transfer (FRET) measured shifts in conformational distributions towards more compact forms with decreased pH. They also corroborate mutational studies and proteolysis results which point to the significant role of E31 in CaM dynamics.     

The Optimization of Dilute Acid Hydrolysis of Cotton Stalk in Xylose Production

Cotton stalk, a lignocellulosic waste material, is composed of xylose that can be used as a raw material for production of xylitol, a high-value product. There is a growing interest in the use of lignocellulosic wastes for conversion into various chemicals because of their low cost and the fact that they are renewable and abundant. The objective of the study was to determine the effects of H₂SO₄ concentration, temperature, and reaction time on the production of sugars (xylose, glucose, and arabinose) and on the reaction by-products (furfural and acetic acid). Response surface methodology was used to optimize the hydrolysis process in order to obtain high xylose yield and selectivity. The optimum reaction temperature, reaction time, and acid concentration were 140 °C, 15 min, and 6%, respectively. Under these conditions, xylose yield and selectivity were found to be 47.88% and 2.26 g g⁻¹, respectively.     

Simultaneous determination of potassium guaiacolsulfonate, guaifenesin, diphenhydramine HCl and carbetapentane citrate in syrups by using HPLC-DAD coupled with partial least squares multivariate calibration

A simple and rapid analytical procedure was proposed for the determination of chromatographic peaks by means of partial least squares multivariate calibration (PLS) of high-performance liquid chromatography with diode array detection (HPLC-DAD). The method is exemplified with analysis of quaternary mixtures of potassium guaiacolsulfonate (PG), guaifenesin (GU), diphenhydramine HCI (DP) and carbetapentane citrate (CP) in syrup preparations. In this method, the area does not need to be directly measured and predictions are more accurate. Though the chromatographic and spectral peaks of the analytes were heavily overlapped and interferents coeluted with the compounds studied, good recoveries of analytes could be obtained with HPLC-DAD coupled with PLS calibration. This method was tested by analyzing the synthetic mixture of PG, GU, DP and CP. As a comparison method, a classsical HPLC method was used. The proposed methods were applied to syrups samples containing four drugs and the obtained results were statistically compared with each other. Finally, the main advantage of HPLC-PLS method over the classical HPLC method tried to emphasized as the using of simple mobile phase, shorter analysis time and no use of internal standard and gradient elution.     

Bright soliton in an expulsive potential in a dipolar condensate

We study the stability of matter-wave bright solitons for a dipolar Bose-Einstein condensate in a harmonic potential which is transversely attractive and longitudinally expulsive. We map the regimes of stability as a function of dipole-dipole interaction strength using sech-based variational ansatz. The critical points for collapse and explosion are presented.     

Synthesis, acidity and antioxidant properties of some novel 3,4-disubstituted-4,5-dihydro-1H-1,2,4-triazol-5-one derivatives

3-Alkyl(aryl)-4-amino-4,5-dihydro-1H-1,2,4-triazol-5-ones 2a-g reacted with 4-diethylaminobenzaldehyde to afford the corresponding 3-alkyl(aryl)-4-(4-diethyl-aminobenzylidenamino)-4,5-dihydro-1H-1,2,4-triazol-5-ones 3a-g. The acetylation reactions of compounds 3a-e were investigated and compounds 4a-e were thus obtained. The new compounds were characterized using IR, (1)H-NMR, (13)C-NMR, UV and MS spectral data. In addition, the newly synthesized compounds 3a-g were titrated potentiometrically with tetrabutylammonium hydroxide in four non-aqueous solvents such as isopropyl alcohol, tert-butyl alcohol, acetone and N,N-dimethylformamide (DMF), and the half-neutralization potential values and the corresponding pKa values were determined for all cases. Moreover, 3 and 4 type compounds were also screened for their antioxidant activities.     

Determination of the LO phonon energy by using electronic and optical methods in AlGaN/GaN

The longitudinal optical (LO) phonon energy in AlGaN/GaN heterostructures is determined from temperature-dependent Hall effect measurements and also from Infrared (IR) spectroscopy and Raman spectroscopy. The Hall effect measurements on AlGaN/GaN heterostructures grown by MOCVD have been carried out as a function of temperature in the range 1.8-275 K at a fixed magnetic field. The IR and Raman spectroscopy measurements have been carried out at room temperature. The experimental data for the temperature dependence of the Hall mobility were compared with the calculated electron mobility. In the calculations of electron mobility, polar optical phonon scattering, ionized impurity scattering, background impurity scattering, interface roughness, piezoelectric scattering, acoustic phonon scattering and dislocation scattering were taken into account at all temperatures. The result is that at low temperatures interface roughness scattering is the dominant scattering mechanism and at high temperatures polar optical phonon scattering is dominant.     

A new triterpene from Scorzonera latifolia (Fisch. and Mey.) DC

A novel triterpene 1 (3-β-hydroxy-fern-7-en-6-one-acetate) together with four known compounds, urs-12-en-11-one-3-acetyl (2), 3-β-hydroxy-fern-8-en-7-one-acetate (3), olean-12-en-11-one-3-acetyl (4) and leucodin (5) were obtained from the S. latifolia roots. All compounds were isolated from the n-hexane extract of S. latifolia roots using several chromatographic techniques. The structure of the isolated compounds was elucidated on the basis of (1)H-NMR, (13)C-NMR and 2D NMR data (HMBC, HMQC, COSY, TOCSY, NOESY, DEPT) as well as GC EITOF-HRMS.     

Novel and enantioselective syntheses of (R)- and (S)-3-hydroxy-4-(2,4,5-trifluorophenyl)butanoic acid: a synthon for sitagliptin and its derivatives

A new synthetic strategy for (R)- and (S)-3-hydroxy-4-(2,4,5-trifluorophenyl)butanoic acid, a building block in the preparation of sitagliptin and its derivatives, was developed. Pd(OAc)₂ catalyzed coupling of 2,4,5-trifluoro-1-iodobenzene with allyl alcohol gave 3-(2,4,5-trifluorophenyl)propanal in a yield of 95%. l-Proline catalyzed reaction of the 3-phenylpropanal (in only 1.2 molar equiv) with nitrosobenzene followed by reduction with NaBH₄ and Pd/C catalyzed hydrogenation gave (R)-3-(2,4,5-trifluorophenyl)propane-1,2-diol with >99% ee and 65% yield. Selective tosylation of primary hydroxyl group of the 1,2-propandiol unit followed by cyanide displacement afforded (R)-3-hydroxy-4-(2,4,5-trifluorophenyl)butanenitrile (80%). The nitrile was converted to the title β-hydroxy acid under basic hydrolysis in a yield of 90%. Thus, (R)-3-hydroxy-4-(2,4,5-trifluorophenyl)butanoic acid was prepared enantioselectively from the starting material in four steps and 45% overall yield. The reaction sequence was repeated with d-proline as the catalyst to give (S)-3-hydroxy-4-(2,4,5-trifluorophenyl)butanoic acid in 45% overall yield and >99% enantiomeric excess.