Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide

We report here an advanced approach for the characterization of the folding pattern of a de novo designed antiparallel coiled coil peptide by high-resolution methods. Incorporation of two fluorescence labels at the C- and N-terminus of the peptide chain as well as modification of two hydrophobic core positions by Phe/[15N,13C]Leu enable the study of the folding characteristics and of distinct amino acid side chain interactions by fluorescence resonance energy transfer (FRET) and NMR spectroscopy. Results of both experiments reveal the antiparallel alignment of the helices and thus prove the design concept. This finding is also supported by molecular dynamics simulations. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) in combination with NMR experiments was used for verification of the oligomerization equilibria of the coiled coil peptide.     

Harmonic oscillator tensors in contact transformation theory

The application of contact transformation theory to the perturbed harmonic oscillator is reexamined in the light of the harmonic oscillator tensors previously presented. It is found that the recasting of the formalism of this problem in terms of harmonic oscillator tensors results in great simplifications, most of which stem from the introduction of the additional algebraic quantum numbers (l, m). The order of magnitude of each fragment of the Hamiltonian is easily recognizable, and the diagonal and nondiagonal parts contained therein are readily identifiable. The determination of the contact transformation operator is reduced to a simple formula. First, an analysis is made for a single mode of vibration, and it is subsequently extended to a multimode case. The perturbed diatomic vibrator is presented as an example.     

Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin

The binding of a set of 10 triphenoxypyridine derivatives to two serine proteases, factor Xa and trypsin, has been used to analyze factors related to sampling and convergence in free energy calculations based on molecular dynamics simulation techniques. The inhibitors investigated were initially proposed as part of the Critical Assessment of Techniques for Free Energy Evaluation (CATFEE) project for which no experimental results nor any assessment of the predictions submitted by various groups have ever been published. The inhibitors studied represent a severe challenge for explicit free energy calculations. The mutations from one compound to another involve up to 19 atoms, the creation and annihilation of net charge and several alternate binding modes. Nevertheless, we demonstrate that it is possible to obtain highly converged results (+/- 5-10 kJ/mol) even for such complex multi-atom mutations by simulating on a nanosecond time scale. This is achieved by using soft-core potentials to facilitate the creation and deletion of atoms and by a careful choice of mutation pathway. The results show that given modest computational resources, explicit free energy calculations can be successfully applied to realistic problems in drug design.     

Calculation of the free energy of solvation for neutral analogs of amino acid side chains

The ability of the GROMOS96 force field to reproduce partition constants between water and two less polar solvents (cyclohexane and chloroform) for analogs of 18 of the 20 naturally occurring amino acids has been investigated. The estimations of the solvation free energies in water, in cyclohexane solution, and chloroform solution are based on thermodynamic integration free energy calculations using molecular dynamics simulations. The calculations show that while the force field reproduces the experimental solvation free energies of nonpolar analogs with reasonable accuracy the solvation free energies of polar analogs in water are systematically overestimated (too positive). The dependence of the calculated free energies on the atomic partial charges was also studied.     

High-performance liquid chromatographic determination of acetone in blood and urine in the clinical diagnostic laboratory.

A method for the determination of acetone in plasma or urine by high-performance liquid chromatography (HPLC) was developed. Plasma specimens are deproteinized with acetonitrile (1:1, v/v) 2,4-dinitrophenylhydrazine (DNPH) is added to the supernatant or to filtered urine samples, similarly treated with acetonitrile (2:1, v/v) to prevent crystallization of the synthesized phenylhydrazone. An aliquot (20 microliters) of the reaction mixture was subjected to HPLC at ambient temperature using a reversed-phase Pecosphere 3 x 3 C18 column with acetonitrile-water (45:55, v/v) as eluent at a flow-rate of 1 ml/min and detection at 365 nm. Hydroxyacetone and acetoacetate phenylhydrazone derivatives do not interfere. The identification of acetone by its retention time was confirmed by comparison with a laboratory-synthesized acetone DNPH derivative. The concentration of acetone, eluted within 3 min, was determined by the peak-height method. The detection limit was 0.034 mmol/l; the relative standard deviations were less than 5% within run (n = 20) and less than 10% between run (n = 20).     

Mathematics: a means of collaboration between industry and university

This paper is divided into two distinct but connected parts. In the first one we look for the best approach to the Mathematics teaching of the future engineer. This approach should have an eminently pragmatic character and should be directed towards teaching engineers to know and manage Mathematics at a tool. In the second part we illustrate how a collaboration with industry can be obtained from this kind of teaching.

Finally the conditions and consequences which should produce this cooperation are analysed, and some particular examples are mentioned.     

John’s Ellipsoid and the Integral Ratio of a Log-Concave Function

We extend the notion of John’s ellipsoid to the setting of integrable log-concave functions. This will allow us to define the integral ratio of a log-concave function, which will extend the notion of volume ratio, and we will find the log-concave function maximizing the integral ratio. A reverse functional affine isoperimetric inequality will be given, written in terms of this integral ratio. This can be viewed as a stability version of the functional affine isoperimetric inequality.     

Versatile carbon supported mono and bimetallic nanocomposites: synthesis,characterization and their potential application for furfural reduction

Biomass conversion has been developed by testing various metal based carbon catalysts. Most of the reported catalysts either use very expensive metals or support that provides lower selectivity. In this context, we fabricated new carbon based nanocomposites and studied their catalytic application for furfural reduction – a promising biomass derived molecule. The mono (Cu, Co and Ni) and bimetallic (CuCo and CuNi) nanoparticle supported on commercial graphite (CG) were prepared and characterized by TEM, EDS, XRD and Raman spectroscopy. The analysis revealed that the nanocomposites are made up of metallic nanoparticles with average particle size of 5–13 nm on the graphite matrix. The obtained results indicated that the Cu+Ni@CG catalyst exhibited high catalytic activity for furfural reduction, thus leaving Cu+Ni as the finest and cost effective catalyst for this study.     

Sensing the Anti-Epileptic Drug Perampanel with Paper-Based Spinning SERS Substrates

The applications of SERS in therapeutic drug monitoring, or other fields of analytical chemistry, require the availability of sensitive sensors and experimental approaches that can be implemented in affordable ways. In this contribution, we show the production of cost-effective SERS sensors obtained by depositing Lee-Meisel Ag colloids on filter paper either by natural sedimentation or centrifugation. We have characterized the morphological and plasmonic features of the sensors by optical microscopy, SEM, and UV-Vis spectroscopy. Such sensors can be used to quantify by SERS the anti-epileptic drug Perampanel (in the concentration range 1 × 10⁻⁴–5 × 10⁻⁶ M) by spinning them during the micro-Raman measurements on the top of a custom device obtained from spare part hard disk drives. This approach minimizes laser-induced heating effects and allows averaging over the spatial non-uniformity of the sensor.