Site‐Specific Investigation of the Steady‐State Kinetics and Dynamics of the Multistep Binding of Bile Acid Molecules to a Lipid Carrier Protein

The investigation of multi‐site ligand–protein binding and multi‐step mechanisms is highly demanding. In this work, advanced NMR methodologies such as 2D ¹H–¹⁵N line‐shape analysis, which allows a reliable investigation of ligand binding occurring on micro‐ to millisecond timescales, have been extended to model a two‐step binding mechanism. The molecular recognition and complex uptake mechanism of two bile salt molecules by lipid carriers is an interesting example that shows that protein dynamics has the potential to modulate the macromolecule–ligand encounter. Kinetic analysis supports a conformational selection model as the initial recognition process in which the dynamics observed in the apo form is essential for ligand uptake, leading to conformations with improved access to the binding cavity. Subsequent multi‐step events could be modelled, for several residues, with a two‐step binding mechanism. The protein in the ligand‐bound state still exhibits a conformational rearrangement that occurs on a very slow timescale, as observed for other proteins of the family. A global mechanism suggesting how bile acids access the macromolecular cavity is thus proposed.     

Microwave-assisted high-throughput acid hydrolysis in silicon carbide microtiter platforms--a rapid and low volume sample preparation technique for total amino acid analysis in proteins and peptides

An efficient microwave-assisted high-throughput protein hydrolysis protocol was developed utilizing strongly microwave absorbing silicon carbide-based microtiter platforms. The plates are equipped with 20 bore holes having the proper dimensions for holding standard screw-capped HPLC/GC vials. Due to the possibility of heating up to four heating platforms simultaneously (80 vials), parallel microwave-assisted acid hydrolyses can be performed under carefully controlled conditions significantly reducing the overall time required for protein hydrolysis and the subsequent evaporation step required for larger volumes of acid. An extensive optimization of the hydrolysis conditions has demonstrated that 5min irradiation at 160°C with 6N HCl leads to comparable results in terms of total and individual amino acid recovery as the traditional method requiring 24h heating at 110°C. Complete hydrolysis of several proteins and synthetic peptides was performed using 25μg of sample material and 100μL of 6N HCl in a dedicated low-volume HPLC/GC vial. Since the hydrolysis and subsequent analysis can be performed from the same vial, errors caused by sample transfer can be minimized. Control experiments have demonstrated that the observed rate enhancements are the result of a purely thermal/kinetic effect as a consequence of the considerable higher reaction temperatures.     

On the stability of Archimedean tilings formed by patchy particles

We have investigated the possibility of decorating, using a bottom-up strategy, patchy particles in such a way that they self-assemble in (two-dimensional) Archimedean tilings. Except for the trihexagonal tiling, we have identified conditions under which this is indeed possible. The more compact tilings, i.e., the elongated triangular and the snub square tilings (which are built up by triangles and squares only) are found to be stable up to intermediate pressure values in the vertex representation, i.e., where the tiling is decorated with particles at its vertices. The other tilings, which are built up by rather large hexagons, octagons and dodecagons, are stable over a relatively large pressure range in the centre representation where the particles occupy the centres of the polygonal units.     

Non-incremental interferometric displacement measurement using a laser Doppler sensor with phase coding

The inspection of fast rotating objects with rough surfaces is an important task in the emerging field of process control. However, this is challenging since fast and non-contact inspection techniques with a measurement uncertainty in the nanometer range are often required. We present a novel optical sensor allowing non-incremental interferometric displacement measurement of moving solid state objects with rough surfaces. It features three wavelength coded interference fringe systems which are superposed slightly tilted. The displacement is determined by evaluating the phase shift between the resulting scattered light signals. Experimentally, a measurement uncertainty of 660 nm was obtained. This displacement uncertainty is independent of the lateral object velocity in principle. Due to this unique feature, the sensor can be utilized advantageously for precise displacement and vibration measurements of high speed objects as demonstrated by vibration measurements at a turbo pump shaft rotating with 48 000 rpm.     

Application of nonlinear continuum dislocation theory to antiplane shear

We apply the nonlinear dislocation theory to the problem of antiplane constrained shear in a single crystal with one slip system. By taking dissipation into account, the relaxed energy functional has to be minimized. We show that, up to a threshold strain, no dislocations are nucleated and therefore the plastic slip is zero. Since this threshold value depends on the width of the specimen, a size effect takes place. The stress strain curve turns out to be a hysteresis loop exhibiting the work hardening due to the dislocation pile-up. It is shown that the Bauschinger effect holds true. (© 2014 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

On the discovery of events in EEG data utilizing information fusion

One way to tackle brain computer interfaces is to consider event related potentials in electroencephalography, like the well established P300 phenomenon. In this paper a multiple classifier approach to discover these events in the bioelectrical signal and with them whether or not a subject has recognized a particular pattern, is employed. Dealing with noisy data as well as heavily imbalanced target class distributions are among the difficulties encountered. Our approach utilizes partitions of electrodes to create robust and meaningful individual classifiers, which are then subsequently combined using decision fusion. Furthermore, a classifier selection approach using genetic algorithms is evaluated and used for optimization. The proposed approach utilizing information fusion shows promising results (over 0.8 area under the ROC curve).     

Pd‐Catalyzed Ring Assembly by Vinylation and Intramolecular Heck Coupling: A Versatile Strategy Towards Functionalized Azadibenzocyclooctynes

A new modular approach based on Pd‐catalyzed C? C bond formation is presented for the assembly of a benzannulated azocine scaffold, the key intermediate in the synthesis of functionalized azadibenzocyclooctynes (aza‐DIBOs). The intramolecular ring‐closing Heck coupling was investigated by variation of the C? X bond. The reaction rate is limited by the initial oxidative addition step and the regiochemistry strongly depends on the auxiliary phosphine. Under optimized conditions, the 8‐endo regioisomer was obtained in 71 % yield over two steps (with no protecting group chemistry) or in one pot, inclusive of C? N bond formation. The practical generation of the octyne triple bond of a prototypical N‐benzoyl aza‐DIBO, without the need for chromatographic purification, is also described. The structural features, including those of the ring‐strained cyclic octyne, were elucidated by NMR spectroscopy and X‐ray crystallographic analysis. The high reactivity of the N‐benzoyl aza‐DIBO synthesized is demonstrated in a strain‐promoted azide–alkyne cycloaddition reaction with an alkyl azide (k=0.38 M ^?1 s^?1).