Interpreting NMR data for beta-peptides using molecular dynamics simulations

NMR is one of the most used techniques to resolve structure of proteins and peptides in solution. However, inconsistencies may occur due to the fact that a polypeptide may adopt more than one conformation. Since the NOE distance bounds and (3)J-values used in such structure determination represent a nonlinear average over the total ensemble of conformers, imposition of NOE or (3)J-value restraints to obtain one unique conformation is not an appropriate procedure in such cases. Here, we show that unrestrained MD simulation of a solute in solution using a high-quality force field yields a conformational ensemble that is largely compatible with the experimental NMR data on the solute. Four 100 ns MD simulations of two forms of a nine-residue beta-peptide in methanol at two temperatures produced conformational ensembles that were used to interpret the NMR data on this molecule and resolve inconsistencies between the experimental NOEs. The protected and unprotected forms of the beta-peptide adopt predominantly a 12/10-helix in agreement with the qualitative interpretation of the NMR data. However, a particular NOE was not compatible with this helix indicating the presence of other conformations. The simulations showed that 3(14)()-helical structures were present in the ensemble of the unprotected form and that their presence correlates with the fulfillment of the particular NOE. Additionally, all inter-hydrogen distances were calculated to compare NOEs predicted by the simulations to the ones observed experimentally. The MD conformational ensembles allowed for a detailed and consistent interpretation of the experimental data and showed the small but specific conformational differences between the protected and unprotected forms of the peptide.     

A novel approach for designing simple point charge models for liquid water with three interaction sites

A simultaneous improvement of the diffusion and dielectric properties of the simple point charge (SPC) model for liquid water appears to be very difficult with conventional reparametrization of the commonly used Lennard-Jones and Coulomb interaction functions and without including a self-energy correction in the effective pair-potential as is done in the SPC/E model. Here, a different approach to circumvent this problem is presented. A short-range interaction term, which corrects the oxygen-oxygen energy at small distances by small amounts of energy, was introduced in the nonbonded interaction function. This additional force-field term allows to derive new parameter sets for SPC-like water models that yield better agreement with experimental data on liquid water. Based on previous investigations of the force-field parameter dependence of the water properties of SPC-like models, the necessary parameter changes to obtain a lower diffusion coefficient and a larger dielectric permittivity were specified and accordingly six new models were developed. They all represent an improvement over SPC in terms of structural and diffusional properties, four of them show better dielectric properties also. One model, SPC/S, has been characterized in more detail, and represents most properties of liquid water better than SPC while avoiding the larger discrepancies with experimental values regarding density, thermal compressibility, energy, and free energy of the SPC/E model. We conclude that the use of a simple, short-ranged additional oxygen-oxygen interaction term makes a simultaneous improvement of the diffusion coefficient and the dielectric properties of water feasible.     

Arthrobacter sp. JS443‐Based Whole Cell Amperometric Biosensor for p‐Nitrophenol

An amperometric microbial biosensor for highly sensitive and selective determination of p‐nitrophenol (PNP) is reported. The biosensor consisted of PNP‐degrader Arthrobacter sp. JS443 immobilized by entrapment in Nafion polymer deposited on the top of the carbon paste electrode transducer. The biosensor was based on the measurement of the oxidation current of the intermediates 4‐nitrocatechol and 1,2,4‐benzenetriol formed by the highly selective oxidation of PNP by Arthrobacter sp. The sensor signal and response time were optimized with applied potential of +0.4 V (vs. Ag/AgCl reference electrode) and 0.03 mg of cells and operating in pH 7.5, 50 mM citrate‐phosphate buffer at room temperature. When operated at optimized conditions, the Arthrobacter sp.‐based biosensor measured as low as 5 nM (0.7 ppb) of PNP. The biosensor demonstrated excellent selectivity with no interference from phenolic compounds such as 2‐nitrophenol, phenol and 3‐chlorophenol but was interfered by 3‐nitrophenol and 3‐methyl‐4‐nitrophenol. It had good precision and intra‐ and inter‐day reproducibility, accuracy and was stable up to 3 days when stored in buffer at 4 °C. When applied for measurement in water from Lake Elsinore, CA, the results obtained were in excellent agreement with the amounts determined spectrophotometrically.     

A quantum-dot based protein module for in vivo monitoring of protease activity through fluorescence resonance energy transfer

Here, we present a new generation of nanoscale probes for in vivo monitoring of protease activity by fluorescence resonance energy transfer (FRET). The approach is based on a genetically programmable protein module carrying a fluorescently labeled, protease-specific sequence that can self-assemble onto quantum dots. The protein module was used for real-time detection of human immunodeficiency virus type-1 protease (HIV-1 Pr) activity as well as quantitative assessment of inhibitor efficiency.     

Effect of (L:D) Aspect Ratio on Single Polypyrrole Nanowire FET Device

Effect of different aspect ratio (length to diameter ratio, L:D) on single polypyrrole (Ppy) nanowire based field effect transistor (FET) sensor for real time pH monitoring was studied. Ppy nanowires with diameters of ~60, ~80 and ~200 nm were synthesized using electrochemical deposition inside anodized aluminium oxide (AAO) template and were assembled using AC dielectrophoretic alignment followed by maskless anchoring on a pair of gold electrodes separated with different gap lengths. Microfabricated gold electrode patterns with gap size between 1 - 4 μm were developed by means of MEMS technique (photolithography). Using field effect transistor geometry with pair of microfabricated gold contact electrodes serving as a source and a drain, and a platinum (Pt) mesh (anchored in a microfluidic channel) was used as a gate electrode. When effect of different aspect ratio of the nanowire were compared, higher sensitivity was recorded for higher aspect ratio. The sensitivity was further improved by modulating the gate potential. These FET sensors based on single polypyrrole nanowire exhibited excellent and tunable sensitivity towards pH variations.     

Radial distribution of the contributions to band broadening of a silica‐based semi‐preparative monolithic column

Using an on‐column local electrochemical microdetector operated in the amperometric mode, band elution profiles were recorded at different radial locations at the exit of a 10 mm id, 100 mm long silica‐based monolithic column. HETP plots were then acquired at each of these locations, and all these results were fitted to the Knox equation. This provided a spatial distribution of the values of the eddy diffusion (A), the molecular diffusion (B), and the resistance to the kinetics of mass transfer (C) terms. Results obtained indicate that the wall region yields higher A values and smaller C values than the central core region. Significant radial fluctuations of these contributions to band broadening occur throughout the exit column cross‐section. This phenomenon is due to the structural radial heterogeneity of the column.     

The Formation of Large‐Area Conducting Graphene‐Like Platelets

The treatment of a suspension of graphite oxide (GO) with sodium azide leads to a material that, after reduction, features amino groups at the top and bottom of the sheets. These groups react through microcontact printing with an isothiocyanate monolayer on a silicon oxide substrate to form covalent bonds that strongly attach to the particles on the surface. With ultrasonication it is possible to obtain exfoliation of the sheets that are not covalently bound to the surface leaving single‐layer platelets attached to the substrate. The azido derivative can be also used to functionalize the graphene oxide with long alkylic chains through a click chemistry approach. This functionalization results in the exfoliation of this material in dimethylformamide. The novel materials were fully characterized by different techniques including IR spectroscopy, thermogravimetric analysis (TGA), scanning and transmission electron microscopy (SEM and TEM), X‐Ray photoelectron spectroscopy (XPS), and solid state NMR spectroscopy. The material with amino groups, after the reduction step, is conductive with a resistivity only approximately seven times larger than that of unprocessed graphite. This implies that after reduction of the GO, the conjugated sp² network is largely restored. We consider this to be an important step towards a chemical approach for forming conducting large‐area platelet films of single‐layer graphene.     

Comparative evaluation on the thermal properties and stability of MWCNT nanofluid with conventional surfactants and ionic liquid

Journal of Thermal Analysis and Calorimetry - Conventional surfactants such as CTAB (cetrimonium bromide), SDS (sodium dodecyl sulphate), SDBS (sodium dodecyl sulphonate) are combined with...