Focused grid‐based resampling for protein docking and mapping

The fast Fourier transform (FFT) sampling algorithm has been used with success in application to protein‐protein docking and for protein mapping, the latter docking a variety of small organic molecules for the identification of binding hot spots on the target protein. Here we explore the local rather than global usage of the FFT sampling approach in docking applications. If the global FFT based search yields a near‐native cluster of docked structures for a protein complex, then focused resampling of the cluster generally leads to a substantial increase in the number of conformations close to the native structure. In protein mapping, focused resampling of the selected hot spot regions generally reveals further hot spots that, while not as strong as the primary hot spots, also contribute to ligand binding. The detection of additional ligand binding regions is shown by the improved overlap between hot spots and bound ligands. © 2016 Wiley Periodicals, Inc.     

Plasma-enhanced synthesis of bactericidal quaternary ammonium thin layers on stainless steel and cellulose surfaces

We have investigated bottom-up chemical synthesis of quaternary ammonium (QA) groups exhibiting antibacterial properties on stainless steel (SS) and filter paper surfaces via nonequilibrium, low-pressure plasma-enhanced functionalization. Ethylenediamine (ED) plasma under suitable conditions generated films rich in secondary and tertiary amines. These functional structures were covalently attached to the SS surface by treating SS with O 2 and hexamethyldisiloxane plasma prior to ED plasma treatment. QA structures were formed by reaction of the plasma-deposited amines with hexyl bromide and subsequently with methyl iodide. Structural compositions were examined by electron spectroscopy for chemical analysis and Fourier transform infrared spectroscopy, and surface topography was investigated with atomic force microscopy and water contact angle measurements. Modified SS surfaces exhibited greater than a 99.9% decrease in Staphylococcus aureus counts and 98% in the case of Klebsiella pneumoniae. The porous filter paper surfaces with immobilized QA groups inactivated 98.7% and 96.8% of S. aureus and K. pneumoniae, respectively. This technique will open up a novel way for the synthesis of stable and very efficient bactericidal surfaces with potential applications in development of advanced medical devices and implants with antimicrobial surfaces.     

Copper complexes of mono- and ditopic [(methylthio)methyl]borates: missing links and linked systems en route to copper enzyme models

TMEDA-free (TMEDA: tetramethylethylenediamine) LiCH(2)SMe is a suitable reagent for the selective introduction of (methylthio)methyl groups into PhBBr(2) and its p-silylated derivative Me(3)Si--C(6)H(4)--BBr(2). The resulting compounds, R*--C(6)H(4)--B(Br)(CH(2)SMe) (R*=H: 2; R*=SiMe(3): 7) and PhB(CH(2)SMe)(2) (3), form cyclic dimers through B--S adduct bonds in solution and in the solid state. Compounds 2 and 3 have successfully been used for preparing the (N(2)S) scorpionate [PhBpz(2)(CH(2)SMe)](-) ([5](-)) (pz: pyrazol-1-yl) and the (NS(2)) scorpionate [PhBpz(CH(2)SMe)(2)](-), respectively. Compound 7 proved to be an excellent building block for the heteroditopic poly(pyrazol-1-yl)borate p-[pz(3)B--C(6)H(4)--Bpz(2)(CH(2)SMe)](2-) ([10](2-)) that mimics the two ligation sites of the copper enzymes peptidylglycine alpha-hydroxylating monooxygenase and dopamine beta-monooxygenase. Treatment of the monotopic tripod [5](-) with CuCl and CuBr(2) results in the formation of complexes K[Cu(5)(2)] and [Cu(5)(2)]. An X-ray crystallography study of K[Cu(5)(2)] revealed a tetrahedral (N(2)S(2)) coordination environment for the Cu(I) ion, whereas the Cu(II) ion of [Cu(5)(2)] possesses a square-pyramidal (N(4)S) ligand sphere (S-atom in the axial position). The remarkable redox properties of K[Cu(5)(2)] and [Cu(5)(2)] have been assessed by cyclic voltammetry and quantum chemical calculations. The reaction of K[Cu(5)(2)] with dry air leads to the Cu(II) species [Cu(5)(2)] and to a tetranuclear Cu(II) complex featuring [PhB(O)pz(2)](2-) ligands. Addition of CuCl to K(2)[10] gives the complex K(3)[Cu(10)(2)] containing two ligand molecules per Cu(I) center. The Cu(I) ion binds to both heteroscorpionate moieties and thereby establishes a coordination environment similar to that of the Cu(I) ion in K[Cu(5)(2)].     

Conformational preferences of N-acetyl-L-leucine-N'-methylamide. Gas-phase and solution calculations on the model dipeptide

A DFT study of N-acetyl-l-leucine-N'-methylamide conformers in the gas phase and in solution was carried out. The theoretical computational analysis revealed 43 different conformations at the B3LYP/6-31G(d) level of theory in the gas phase. In addition, the effects of three solvents (water, acetonitrile, and chloroform) were included in the calculations using the isodensity polarizable continuum model (IPCM) and the Poisson-Boltzmann self-consistent reaction field (PB-SCRF) method. The stability order of the different conformers in solution has been analyzed. The theoretical results were compared with some experimental data (X-ray, IR, and NMR).     

Effect of the solvatation shell exchange on the formation of malvidin-3-O-glucoside-ellagic acid complexes

The interaction of malvidin-3-O-glucoside with ellagic acid was studied in aqueous solutions in dependence of the ethanol content of the samples. The results show significant changes of the thermodynamic parameters when the ethanol content exceeds 8%vol. The quantum chemical calculations and the solvent relaxation measurements validate that the solvatation shell of the malvidin-ellagic acid complexes changes from water to ethanol around this critical alcoholic concentration. The change of the solvate shell is accompanied by increasing copigmentation; i.e., higher "multi-sandwich" complexes are formed. According to the considerable role of this interaction (namely copigmentation) in the formation of color in red wines, our results have several consequences for the winemaking process with regard to the stabilization of wine color.     

Phase Coexistence in a Dynamic Phase Diagram

Metastability and phase coexistence are important concepts in colloidal science. Typically, the phase diagram of colloidal systems is considered at the equilibrium without the presence of an external field. However, several studies have reported phase transition under mechanical deformation. The reason behind phase coexistence under shear flow is not fully understood. Here, multilamellar vesicle (MLV)‐to‐sponge (L₃) and MLV‐to‐L_α transitions upon increasing temperature are detected using flow small‐angle neutron scattering techniques. Coexistence of L_α and MLV phases at 40 °C under shear flow is detected by using flow NMR spectroscopy. The unusual rheological behavior observed by studying the lamellar phase of a non‐ionic surfactant is explained using ²H NMR and diffusion flow NMR spectroscopy with the coexistence of planar lamellar–multilamellar vesicles. Moreover, a dynamic phase diagram over a wide range of temperatures is proposed.     

A weak cation-exchange monolith as stationary phase for the separation of peptide diastereomers by CEC

A CEC weak cation-exchange monolith has been prepared by in situ polymerization of acrylamide, methylenebisacrylamide and 4-acrylamidobutyric acid in a decanol-dimethylsulfoxide mixture as porogen. The columns were evaluated by SEM and characterized with regard to the separation of diastereomers and α/β-isomers of aspartyl peptides. Column preparation was reproducible as evidenced by comparison of the analyte retention times of several columns prepared simultaneously. Analyte separation was achieved using mobile phases consisting of acidic phosphate buffer and ACN. Under these conditions the peptides migrated due to their electrophoretic mobility but the EOF also contributed as driving force as a function of the pH of the mobile phase due to increasing dissociation of the carboxyl groups of the polymer. Raising the pH of the mobile phase also resulted in deprotonation of the peptides reducing analyte mobility. Due to these mechanisms each pair of diastereomeric peptides displayed the highest resolution at a different pH of the buffer component of the mobile phase. Comparing the weak-cation exchange monolith to an RP monolith and a strong cation-exchange monolith different elution order of some peptide diastereomers was observed, clearly illustrating that interactions with the stationary phase contribute to the CEC separations.     

AFM nanoindentation to determine Young’s modulus for different EPDM elastomers

AFM nanoindentation was investigated as a method for determining the micromechanical properties of polymer materials. It is generally accepted that the shape of the tip of the cantilever undergoes a change in a standard AFM setup. The shape defines the projected contact area, so it is a parameter directly proportional to the elastic modulus; any change in the shape thus affects the accuracy of the results. The method suggested in this paper relies on the introduction of an experimentally determined tip-area function. Values for Young’s modulus were calculated for EPDM samples with different degrees of cure and crystallinity. The degree of crystallinity has a greater impact on the mechanical properties of the material than the degree of cure. Depending on the amplitude of the indentation, the E-moduli determined by AFM are systematically higher. When studying different regions of polymer materials, the values of the E-modulus determined by AFM become identical to those measured by means of DMA on extrapolation of the modulus at zero indentation.