Temperature dependence of ligand-protein complex formation as reflected by saturation transfer difference NMR experiments

We show that temperature is an important parameter for the sensitivity of saturation transfer difference (STD) spectroscopy. A decreased intensity of STD signals is observed for lactose binding to growth-regulatory galectin7 (p53-induced gene 1), as well as for nucleotide binding to annexin A6, when the temperature is increased from 281 to 298-310 K. Opposite temperature effects on STD intensity are observed for S-peptide binding to S-protein to reconstitute RNase S. However, the STD signals for tryptophan binding to downstream regulatory element antagonist modulator of the human prodynorphin gene (DREAM)are relatively unaffected between 281 and 298 K. The known kinetics of the binding of ATP by the uncoupling protein from brown adipose tissue mitochondria (UCP1) predicted an observable STD at 310 K, but rapid sample degradation limits the experiments to much lower temperatures. Temperature strongly influences the kinetics and affinity constant of various types of complex formation and in so doing influences the observed STD effects. Therefore, temperature can be exploited to facilitate the optimization of STD-based applications, and at the same time minimize the number of test samples. STD-based screening protocols to detect new target-specific compounds may yield a larger number of potential ligands if screened at various temperatures.     

Similarities and differences between azomethines and ketimines: synthesis, materials characterization and structure of novel imines compounds

Imines (ketimines and azomethines) derived from p-dibenzoylbenzene (DB) and terephthalic aldehyde (TA) and two aromatic amines: aniline and 2,6-dimethylaniline have been investigated. Compounds were synthesized via condensation of amines with carbonyl monomers in DMA or amine solution. When using DMA as a solvent, azomethines with high yields were obtained. On the other hand, the amines used as a monomers served also as an effective solvent for the synthesis of the ketanils. This different reactivity of the aldehyde and ketone groups in DMA and in amine depends on the dehydration mechanism being dominated by a kinetic process or thermodynamic one. On the basis of FTIR, 13C and 1H NMR, UV-vis spectra, thermal characteristic and theoretical calculations conclusions are drawn regarding the similarities and differences between azomethines and ketimines.     

Automated high-throughput generation of droplets

We report a microfluidic technique for high-throughput generation of droplets of nanolitre volume in parallel channels with online control of the volumes, volume fraction and distribution of droplet volumes with the use of two external valves.     

Olefin epoxidation by molybdenum peroxo compound: molecular mechanism characterized by the electron localization function and catastrophe theory

The oxygen atom transfer reaction from the Mimoun-type complex MoO(η(2)-O(2))(2)OPH(3) to ethylene C(2)H(4) affording oxirane C(2)H(4)O has been investigated within the framework of the Bonding Evolution Theory in which the corresponding molecular mechanism is characterized by the topological analysis of the electron localization function (ELF) and Thom's catastrophe theory (CT). Topological analysis of ELF and electron density analysis reveals that all Mo-O bonds in MoO(η(2)-O(2))(2)OPH(3) and MoO(2)(η(2)-O(2))OPH(3) belong to closed-shell type interactions though negative values of total energy densities E(e)(r(BCP)) imply some covalent contribution. The peroxo O(i)-O(j) bonds are characterized as charge-shift or protocovalent species in which pairs of monosynaptic basins V(3)(O(i)), V(3)(O(j)) with a small electron population of ~0.25e each, are localized between core basins C(O(i)), C(O(j)). The oxygen transfer reaction from molybdenum diperoxo complex MoO(η(2)-O(2))(2)OPH(3) to C(2)H(4) system can be described by the following consecutive chemical events: (a) protocovalent peroxo O(2)-O(1) bond breaking, (b) reduction of the double C(1)=C(2) bond to single C(1)-C(2) bond in ethylene, (c) displacement of oxygen O(1) with two nonbonding basins, V(i=1,2)(O(1)), (d) increase of a number of the nonbonding basins to three (V(i=1,2,4)(O(1))); (e) reorganization and reduction in the number of nonbonding basis to two basins (V(i=1,4)(O(1))) resembling the ELF-topology of the nonbonding electron density in oxirane, (e) formation of the first O(1)-C(2) bond in oxirane, (f) C(2)-O(1)-C(2) ring closure, (g) formation of singular nonbonding basin V(O(2)) in new Mo=O(2) bond. The oxygen atom is transferred as an anionic moiety carrying a rather small electronic charge ranging from 0.5 to 0.7e.     

Application of Sugar Phosphonates for the Preparation of Higher Carbon Monosaccharides

ABSTRACT

Reaction of sugar derived phosphonates [Sug-C(O)CH₂P(O)(OMe)₂] with sugar aldehydes (Sug'-CHO) provides the higher enones of the general formula Sug-C(O)CH=CH-Sug' with the trans configuration of the double bond. The phosphonate method is superior to the previously used phosphorane methodology [Sug-C(O)CH=PPh₃ + Sug'-CHO] since sugar phosphonates can be prepared in much higher yields and are much more nucleophilic than corresponding phosphoranes. The sugar enones are reduced to appropriate allylic alcohols with zinc borohydride; the stereoselectivity of this process is >97:3 (with the D-glycero isomer predominating) when the carbonyl group is placed at the α-position to the sugar ring. CD spectroscopy was used for the determination of the configuration of higher sugar allylic alcohols.     

TBAF Promoted Formation of Symmetrical Trisulfides

We have developed a new method for the synthesis of functionalized symmetrical trisulfides based on (5,5‐dimethyl‐2‐thioxo‐1,3,2‐dioxa‐phosphorin‐2‐yl)disulfanyl derivatives prepared from readily available 5,5‐dimethyl‐2‐sul‐fanyl‐2‐thioxo‐1,3,2‐dioxaphosphorinane or bis(5,5‐dimethyl‐2‐thioxo‐1,3,2‐dioxaphosphorinan‐2‐yl) disulfide. The symmetrical trisulfides can be obtained from aliphatic and aromatic thiols and l ‐cysteine derivatives under mild conditions with high yield and purity.     

Intermolecular interactions in electron transfer through stretched helical peptides

The helical peptide Cys-Ala-Lys-(Glu-Ala-Ala-Ala-Lys)(2)-Ala-NH-(CH(2))(2)-SH has been organized forming a self-assembled monolayer on gold (0.602 peptides per nm(2)), its conductance behavior under stretching conditions being studied using scanning tunnelling microscopy and current sensing atomic force microscopy. The helical conformation of the peptide has been found to play a fundamental role in the conductance. Moreover, variation of the current upon molecular stretching indicates that peptides can be significantly elongated before the conductance drops to zero, the critical elongation being 1.22 ± 0.47 nm. Molecular dynamics simulations of a single peptide in the free state and of a variable number of peptides tethered to a gold surface (i.e. densities ranging from 0.026 to 1.295 peptides per nm(2)) have indicated that the helical conformation is intrinsically favored in solvated environments while in desolvated environments it is retained because of the fundamental role played by peptide-peptide intermolecular interactions. The structure obtained for the system with 24 tethered peptides, with a density of 0.634 peptides per nm(2) closest to the experimental one, is in excellent agreement with experimental observations. On the other hand, simulations in which a single molecule is submitted to different compression and stretching processes while the rest remain in the equilibrium have been used to mimic the variation of the tip-substrate distance in experimental measures. Results allowed us to identify the existence, and in some cases coexistence, of intermolecular and intramolecular ionic ladders, suggesting that peptide-mediated electron transfer occurs through the hopping mechanism. Finally, quantum mechanical calculations have been used to investigate the variation of the electronic structure upon compression and stretching deformations.     

Rapid screening of antibiotic toxicity in an automated microdroplet system

We report an automated microfluidic platform for 'digitally' screening the composition space of droplets containing cocktails of small molecules and demonstrate the features of this system by studying epistatic interactions between antibiotics and Escherichia coli ATCC 25922. This system has several key characteristics: (i) it uses small (<100 μL) samples of liquids and suspensions of bacteria that are introduced directly into the chip; (ii) it generates a sequence of droplets with compositions, including reagents and bacterial cell suspensions that are programmed by the user; (iii) it exports the sequence of droplets to an external segment of tubing that is subsequently disconnected for incubation and storage; and (iv) after incubation of bacteria in droplets, the droplets are injected into a second device equipped with an in-line fiber optic spectrophotometer that measures cell growth. The system generates and fuses droplets with precise (<1% in standard deviation) control of liquid volumes and of the concentrations of input substrates. We demonstrate the application of this technology in determining the minimum inhibitory concentration and pair-wise interactions of ampicillin, tetracycline, and chloramphenicol against E. coli. The experiments consumed small volumes of reagents and required minutes to create the droplets and several hours for their incubation and analysis.     

Influence of wood mercerization on the crystallization of polypropylene in wood/PP composites

Mercerization process is very significant because the alkali treatment facilitates reactivity of lignocellulosic fillers, thus allowing better response to chemical modification. In the present study, the effect of mercerization of pine wood on the nucleation ability of polypropylene was investigated by means of differential scanning calorimetry. We discovered that for the composites with wood containing cellulose II, the decrease in the crystal conversion of the polymer matrix and increase in the half-time of crystallization values are significant. It can be concluded that the amount of cellulose II formed upon alkalization of lignocellulosic fillers determines their nucleation ability. To evaluate the transcrystalline effects caused by various woods, which were untreated or treated with sodium hydroxide, the polarized optical microscopy was also performed. The nucleation of polypropylene on the surface of wood was investigated by induction time measurement. It was found that surfaces of the unmodified wood generate epitaxial nucleation, whereas the mercerized wood generates nonepitaxial nucleation. The differences in the type of nucleation suggest that the effectiveness of formation of transcrystalline structures depends on the contribution of cellulose I and cellulose II. Moreover, the presence of epitaxy is not necessary for the appearance of transcrystalline structures. The results showed that the transcrystalline structures appeared in each system, even with wood containing significant contribution of cellulose II. The only difference noted was the change in the nucleation abilities of the wood surface. Results of this study imply the necessity of quantitative determination of the contributions of cellulose I and cellulose II, whose presence determine the type of nucleation and nucleation ability of the filler surface.     

Projective Fraïssé limits and the pseudo-arc

The aim of the present work is to develop a dualization of the Fraïssé limit construction from model theory and to indicate its surprising connections with the pseudo-arc. As corollaries of general results on the dual Fraïssé limits, we obtain Mioduszewski's theorem on surjective universality of the pseudo-arc among chainable continua and a theorem on projective homogeneity of the pseudo-arc (which generalizes a result of Lewis and Smith on density of homeomorphisms of the pseudo-arc among surjective continuous maps from the pseudo-arc to itself). We also get a new characterization of the pseudo-arc via the projective homogeneity property.