Study on the bioactivity changes of hydroxylated sulfonylureas derivatives: A possible metabolism

Some new sulfonylureas and their hydroxylation products had been synthesized from 2-amino-4-methylpyrimidine. Their bioactivities against E. coli AHAS II in vitro were tested and the results indicated that the hydroxylation decreased the inhibition activities of sulfonylureas significantly. Subsequently herbicidal tests against stem-growth of barnyard grass and root-growth of rape confirmed the above conclusion. The preliminary molecular docking studies were also carried out to investigate the binding modes of non-hydroxylated and hydroxylated sulfonylureas with AHAS.     

Conformational changes of DNA γ-irradiated in the presence of aliphatic alcohols in solution

The conformational changes of DNA in aqueous solutions containing ethanol and iso- and n-propanol having concentrations of 0–23 wt.% and ionic strength μ = 0.003 NaCl and exposed to γ radiation at doses from 0 Gy to 30 Gy were studied by low-gradient viscosimetry and circular dichroism. The dependence of the specific volume (V _sp) of DNA on the radiation dose changed at different contents of alcohol. There is a critical concentration (C _cr) at which the structure of the mixed solvent is rearranged. The V _sp of DNA decreased as the radiation dose increased at C _alc = 12 wt.% < C _cr and increased at C _alc = 23 wt.% > C _cr. In both cases, the largest V _sp of DNA was observed in water ethanol solutions. The secondary structure of the macromolecule in the systems corresponds to the form. It was shown that the observed conformational changes in irradiated DNA at C _alc < C _cr and C _alc > C _cr could not be explained only by the ability of alcohols to intercept the radicals formed in radiolysis of water.     

Molecular recognition: minimizing the acid–base interaction of a tunable host–guest system changes the selectivity of binding

Two new receptors incorporating a 4-n-butyl aniline moiety has been designed, synthesized and evaluated for their binding properties towards a series of ureido-glycine derivatives. The host design is based on an urea adamantyl host motif known from large generations of poly(propylene imine) dendrimers functionalized with urea adamantyl moieties on the periphery. The design of the host molecules was directed towards a study of the effects of basicity of an amine function versus the effect of molecular recognition on the binding strength as seen from comparing the results obtained in the present work with previously guest–host studies. The guest–host interaction features an electrostatic interaction and multiple hydrogen binding interactions, where the main difference between the hosts described here and previously described is a substitution from an amine to aniline. Anilines are weaker bases than aliphatic amines and they generally give lower binding constants when treated with acidic guest molecules. The association constants have been measured using NMR titrations and the nature of the guest–host system is discussed based on these results. A general decrease in binding affinities is observed upon changing from the trialkyl amine hosts to the dialkyl aniline based hosts. One exception was observed where the weaker base host had stronger affinity to one of the guests. Thus, when the basicity of the host is decreased other factors influence the binding such as a better geometric fit. A crystal structure of one of the receptors has been solved and it shows no intramolecular hydrogen bonding.     

How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ significantly in regard to the nonbonded parameters for polar functional groups and their ability to reproduce the correct solvation and partitioning behavior of small molecular analogues of the amino acid side chains. Despite the differences in the force field parameters no major differences could be detected in a wide range of structural properties such as the root-mean-square deviation from the experimental structure, radii of gyration, solvent accessible surface, secondary structure, or hydrogen bond propensities on a 5 to 10 ns time scale. The small differences that were observed correlated primarily with the presence of charged residues as opposed to residues that differed most between the parameter sets. The work highlights the variation that can be observed in nanosecond simulations of protein systems and implications of this for force field validation, as well as for the analysis of protein simulations in general.     

Blue shifts and unusual intensity changes in the infrared spectra of the enflurane···acetone complexes: spectroscopic and theoretical studies

Blue-shifting C-H···O hydrogen-bonded complexes between enflurane (CHFCl-CF(2)-O-CHF(2)) and deuterated acetone have been identified in CCl(4) solution by FT-IR spectroscopy. For the two ν(C-H) stretching vibrations of enflurane the observed blue shifts are +17 and +11 cm(-1). The corresponding two infrared ν(C-H) bands show the opposite changes of their intensity, one is decreasing, and the other is significantly increasing, upon formation of the hydrogen bonding. The structures, binding energies, and theoretical infrared spectra of the enflurane-acetone complexes were calculated by MP2 and B3LYP methods using the 6-311++G(d,p) basis set. The interaction energies were evaluated by the complete basis set limit (CBS) calculations at the HF, MP2, and CCSD(T) levels of theory. Although the MP2 method slightly overestimates the blue shifts, the MP2 predicted frequency difference and the relative IR intensities of two ν(C-H) stretching bands for the enflurane-acetone complexes show good agreement with experiment. Unfortunately, the B3LYP method predicts incorrect IR intensities of these hydrogen-bonded systems. The NBO analysis was performed to unravel the origin of the unusual intensity changes of two ν(C-H) stretching bands, in enflurane complexes.     

Fluorescence response of hypocrellin B to the environmental changes in a mimic biological membrane——liposome

Hypocrellins (HA or HB) were well known as novel photosensitizers for photodynamic therapy (PDT). The investigations on their photophysical and photochemical properties have been carried out inten-sively in the past 20 years[1—4]. Intramolecular hydro-gen bonds are formed in a hypocrellin molecule, so are intramolecular proton transfers at the excited state, which has been proved to be essential for the fluores-cence emission of hypocrellins[5]. The two phenolic hydroxyl groups in a hypocr…     

Novel cotton cellulose by cationisation during the mercerisation process—part 1: chemical and morphological changes

Cationisation is the modification of cotton cellulose by using quaternary ammonium compounds that block negative OH groups, thus resulting in electropositive cotton cellulose. It is an alternative method for achieving better adsorption of chemical compounds and substances, such as dyestuffs, fluorescent whitening agents, and other textile auxiliaries. The cationisation of cotton cellulose changes the surface electrical charge (electrokinetic potential) by significantly increasing its adsorption properties. The presented article investigated the chemical and morphological changes in cotton cellulose when cationised with an epihalohydrin, 2,3-epoxypropyl trimethyl ammonium chloride, after and during the mercerisation process. When comparing mercerised cotton with cationised cotton, it was concluded that cationisation during the mercerisation process using short-chain cationic compounds would result in a novel cotton cellulose that would bring a new dimension to cotton pre-treatment and finishing. The modified cotton would retain all the beneficial properties of mercerised cotton with a change of surface charge that would ensure further improvement in quality.     

Cell electrophoresis on a chip: what can we know from the changes in electrophoretic mobility?

An overview of both experimental and theoretical studies of cell electrophoresis mobility (EPM) over the past fifty years and the relevance of cell EPM measurement are presented and discussed from the viewpoint of exploring the potential use of cell EPM as an index of the biological condition of cells. Physical measurements of the optical and/or electrical properties of cells have been attracting considerable attention as noninvasive cell-evaluation methods that are essential for the future of cell-based application technologies such as cell-based drug screening and cell therapy. Cell EPM, which can be measured in a noninvasive manner by cell electrophoresis, reflects the electrical and mechanical properties of the cell surface. Although the importance of cell EPM has been underestimated for a long time, mostly owing to the technical difficulties associated with its measurement, recent improvements in measurement technology using microcapillary chips have been changing the situation: cell EPM measurement has become more reliable and faster. Recent studies using the automated microcapillary cell electrophoresis system have revealed the close correlation between cell EPM and important biological phenomena including cell cycle, apoptosis, enzymatic treatment, and immune reaction. In particular, the converged EPM distribution observed for synchronized cells has altered the conventional belief that cell EPMs vary considerably. Finding a new significance of cell EPM is likely to lead to noninvasive cell evaluation methods essential for the next-generation of cell engineering.     

Effect of physicochemical conditions on the ultrafiltration of β-lactoglobulin: Fluorescence probing of induced structural changes

This work aims for determining the impact of different environmental conditions, such as pH, ionic strength (salt concentration) and the chemistry of the membrane surface (hydrophilic/hydrophobic character) on the structure of permeating proteins after ultrafiltration. In the permeation experiments reported in this paper, different solutions of a model protein – β-lactoglobulin – at pH 3, 5 and 8 and salt concentrations of 1, 10 and 100 mM were processed with membranes of different molecular weight cut-off (10 and 30 kDa) and materials (regenerated cellulose—RC, and polyethersulfone—PES).     

Are conformational changes, induced by osmotic pressure variations, the underlying mechanism of controlling the adhesive activity of mussel adhesive proteins?

The mussel adhesive protein Mefp-1, under physiological conditions, presumably has a self-avoiding random walk conformation with helix-like or turned deca-peptide segments. Such a conformation may coil up under osmotic pressure induced by surrounding macromolecules. As a consequence, the orientation of the 3,4-dihydroxy-phenylalanine groups (dopa), essential for the adhesive strength as well as the cohesive strength in Mefp-1, will be altered. Changing the concentration of the protein itself or of different-type surrounding macromolecules may therefore be a tool to control the protein's adhesive activity. The effect of osmotic pressure on the conformation and dopa reactivity of Mefp-1 is studied by the addition of (poly)ethylene oxide (PEO) as a model macromolecule (Mw = 100 kD). From UV-spectroscopy measurements, it can be concluded that dopa reactivity in Mefp-1 changes with increasing PEO concentration. Fitting of the measured absorbance intensity data of the oxidation product dopaquinone versus time with a kinetic model points to the decreased accessibility of dopa groups in the Mefp-1 structure, a faster oxidation, and diminished cross linking under the influence of increasing PEO concentration up to 2.4 g/L, corresponding to an osmotic pressure of approximately 73 Pa. At higher PEO concentrations, the accessibility of the dopa groups for oxidation as well as cross-link formation decreases until about 20% of the dopa groups are oxidized at a PEO concentration of 3.8 g/L, corresponding to an osmotic pressure of approximately 113 Pa. FTIR measurements on the basis of amide I shifts qualitatively point to a transition to a more continuously turned structure of Mefp-1 in the presence of PEO. Therefore, it seems that conformational changes caused by variations of osmotic pressure determine the extent of steric hindrance of the dopa groups and hence the adhesive reactivity of Mefp-1.     

The influence of structural changes of the N‐substituent on liquid crystalline behaviour of ester imides

Several new ester imide derivatives with different N‐substituents in the imide ring were synthesized and their mesogenic properties investigated by thermal analysis, optical microscopy and X‐ray diffraction. All the esters of N‐4‐[(4′‐decyloxybiphenyl‐4‐yl)oxycarbonyl]phthalimideacetic acid and aliphatic alcohols exhibited monolayer SmA and SmC phases. In addition, for the ethyl and propyl esters a monotropic hexatic (F or I) phase was observed. The introduction of additional substituents at the carbon atom in the methylenemethoxycarbonyl group (in the vicinity of the nitrogen atom) substantially influenced liquid crystalline properties: the compounds with a flexible chain exhibited monotropic SmA–SmB dimorphism, but liquid crystalline properties vanished for the substituent containing the more rigid phenyl ring.     

Recognition of DNA based on changes in the fluorescence intensity of CdSe/CD QDs–phenanthroline systems

The CdSe quantum dots (QDs) modified by mercapto-β-cyclodextrin (CD) were synthesized and characterized by transmission electron microscopy, powder X-ray diffraction, excitation and emission spectra, and fluorescence lifetime. When λ_ex = 370 nm, the fluorescence peak of CdSe/CD QDs is at 525 nm. Phenanthroline (Phen) is able to quench their fluorescence, which can be recovered by the addition of DNA. The quenching and restoration of fluorescence intensity were found to be linearly proportional to the amount of Phen and DNA, respectively. The variation of the fluorescence intensity of the CdSe/CD QDs–Phen system was studied, and it was demonstrated to result from a static mechanism due to the formation of a Phen inclusion complex with the CdSe QDs modified by mercapto-β-cyclodextrin. The fluorescence recovery was due to the binding of DNA with Phen in the inclusion complex, leading to the freeing of the CdSe/CD QDs. The binding constants and sizes of the binding sites of the Phen–DNA interaction were calculated to be 1.33 × 10⁷ mol^?1 L and 10.79 bp.     

Prediction of changes in the heat capacity of the liquid–vapor phase transition based on modified Randič indices. Alkanes and oxygen-containing compounds

The work proposes a method to predict changes in the heat capacity of the liquid—vapor phase transition Δ _l ^g Ср ⁰ (298.2) based on modified Randi? indices for alkanes and acyclic oxygen-containing compounds: alcohols, aldehydes, ketones, ethers, and esters. Based on the obtained Δ _l ^g Ср ⁰ (298.2) values heat capacities in the liquid phase Cp _liq ⁰ (298.2) are calculated for the compounds under study.     

Demystifying the pH dependent conformational changes of human heparanase pertaining to structure–function relationships: an in silico approach

Heparanase (HPSE) is an endo-β-d-glucuronidase that has diverse functions in mammals which includes cell survival, cell adhesion and cell migration. HPSE features both enzymatic and non-enzymatic functionalities in a pH dependent manner. Hence, in this study, an extensive molecular dynamics simulation, molecular docking, protein Angular dispersion analysis were performed for apo form and holo forms to understand its conformational changes at varied pH conditions. On comparative conformational analysis of apo and holo forms, it was inferred that the HSPE has undergone pH dependent structural changes, thereby affecting the binding of Heparan sulfate proteoglycan (HSPG). Moreover, HPSE also showed favourable structural changes for optimal binding of HSPG at pH 5.0 and 6.0, as inferred from functional flap displacements within HPSE. Thus, this study provides significant insights on optimal pH for HPSE to exhibit its enzymatic activity. The outcome of this study shall aid in ideal lead generation for targeting HPSE mediated disease conditions.     

Two-dimensional high-performance liquid chromatographic determination of day–night variation of d-alanine in mammals and factors controlling the circadian changes

d-Alanine (d-Ala) is one of the naturally occurring d-amino acids in mammals, and its amount is known to have characteristic circadian changes. It is a candidate for a novel physiologically active substance and/or a biomarker, and the regulation mechanisms of the intrinsic amounts of d-Ala are expected to be clarified. In the present study, the effects of the possible factors controlling the d-Ala amounts, e.g., diet, d-amino acid oxidase (DAO) and intestinal bacteria, on the day–night changes in the intrinsic d-Ala amounts have been investigated using a highly sensitive and selective two-dimensional high-performance liquid chromatographic system combining a reversed-phase column and an enantioselective column. The circadian rhythm was not changed under fasting conditions. In the mice lacking d-amino acid oxidase activity (ddY/DAO^- mice), clear day–night changes were still observed, suggesting that the factors controlling the d-Ala rhythm were not their food and DAO activity. On the other hand, in the germ-free mice, quite low amounts of d-Ala were detected compared with those in the control mice, indicating that the main origin of d-Ala in the mice is intestinal bacteria. Because the d-Ala amounts in the digesta containing intestinal bacteria did not show the day–night changes, the controlling factor of the circadian changes of the d-Ala amount was suggested to be the intestinal absorption.     

Raman study of the variation in anatase structure of TiO<Subscript>2</Subscript> nanopowders due to the changes of sol–gel synthesis conditions

TiO₂ nanopowders were produced by sol–gel technique under different synthesis conditions. XRD results have shown that obtained nanopowders are in anatase phase, with the presence of a small amount of highly disordered brookite phase, whereas nanocrystallite size and amount of brookite slightly depend on sol–gel synthesis conditions. Raman measurements confirm these results. The analyses of the shift and width of the most intensive anatase E _g Raman mode by phonon confinement model suggest that anatase crystallite size should be in the range between 11 and 15 nm, what is in excellent correlation with XRD results. Obtained results have shown that Raman spectroscopy is a highly sensitive method for the estimation of anatase crystallite size as well as brookite content in TiO₂ nanopowders synthesized by variable sol–gel synthesis conditions.     

Identifying conformational changes of the β2 adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators

The new β₂ Adrenoceptor (β₂AR) crystal structures provide a high-resolution snapshot of receptor interactions with two particular partial inverse agonists, (−)-carazolol and timolol. However, both experimental and computational studies of GPCR structure are significantly complicated by the existence of multiple conformational states coupled to ligand type and receptor activity. Agonists and antagonists induce or stabilize distinct changes in receptor structure that mediate a range of pharmacological activities. In this work, we (1) established that the existing β₂AR crystallographic conformers can be extended to describe ligand/receptor interactions for additional antagonist types, (2) generated agonist-bound receptor conformations, and (3) validated these models for agonist and antagonist virtual ligand screening (VLS). Using a ligand directed refinement protocol, we derived a single agonist-bound receptor conformation that selectively retrieved a diverse set of full and partial β₂AR agonists in VLS trials. Additionally, the impact of extracellular loop two conformation on VLS was assessed by docking studies with rhodopsin-based β₂AR homology models, and loop-deleted receptor models. A general strategy for constructing and selecting agonist-bound receptor pocket conformations is presented, which may prove broadly useful in creating agonist and antagonist bound models for other GPCRs. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The role of disclinations in two phase changes induced by temperature and pressure in crystalline solids: melting and the brittle–ductile transition

It has long been known that the melting temperature T _m of close-packed metals correlates well with the mono-vacancy formation energy. However, with the possible exception of the face-centered-cubic metals, there is a prior phase transition from a mechanically brittle solid phase to a ductile phase. Here the likely role of disclinations in the brittle-ductile phase change is stressed. The present picture may help to understand the brittle–ductile transition not only in crystalline materials but also in amorphous phases. The structure of such phases can probably be characterized in terms of a disordered disclination network. As examples of elemental crystalline solids, Si and graphite are finally discussed, with the melting under pressure of graphite being quantified.