Hierarchical dynamics in allostery following ATP hydrolysis monitored by single molecule FRET measurements and MD simulations

We report on a study that combines advanced fluorescence methods with molecular dynamics (MD) simulations to cover timescales from nanoseconds to milliseconds for a large protein. This allows us to delineate how ATP hydrolysis in a protein causes allosteric changes at a distant protein binding site, using the chaperone Hsp90 as test system. The allosteric process occurs via hierarchical dynamics involving timescales from nano- to milliseconds and length scales from Ångstroms to several nanometers. We find that hydrolysis of one ATP is coupled to a conformational change of Arg380, which in turn passes structural information via the large M-domain α-helix to the whole protein. The resulting structural asymmetry in Hsp90 leads to the collapse of a central folding substrate binding site, causing the formation of a novel collapsed state (closed state B) that we characterise structurally. We presume that similar hierarchical mechanisms are fundamental for information transfer induced by ATP hydrolysis through many other proteins.

We report on a study that combines advanced fluorescence methods with molecular dynamics simulations to cover timescales from nanoseconds to milliseconds for a large protein, the chaperone Hsp90.     

Eliashberg theory for disordered superconductors. II. Tunneling into disordered two-dimensional Pb films

A series ofc-axis oriented YBa₂Cu₃O _x -films with different oxygen content were prepared by laser deposition. The oxygen contentx was determined by X-ray diffraction and by resonant Rutherford-back-scattering (RRBS) measurements. Thec-axis length in these films of YBa₂Cu₃O _x is about 0.5% larger compared to bulk values. We describe transport measurements in magnetic fields up to 7 Tesla between room temperature andT _c in samples with an oxygen content between the orthorhombic-to-tetragonal transition (x6.4) and full oxygenation (x7). The ratio /R _H was investigated with respect to the two-dimensional Luttinger liquid theory and the model of the two-dimensional ionic metal. We report on deviations from the expected quadratic temperature behaviour of /R _H , especially in films with high oxygen content.     

Prediction of aqueous solubility of drugs and pesticides with COSMO-RS

The COSMO-RS method, originally developed for the prediction of liquid-liquid and liquid-vapor equilibrium constants based on quantum chemical calculations, has been extended to solid compounds by addition of a heuristic expression for the Gibbs free energy of fusion. By this addition, COSMO-RS is now capable of a priori prediction of aqueous solubilities of a wide range of typical neutral drug and pesticide compounds. Only three parameters in the heuristic expression have been fitted on a data set of 150 drug-like compounds. On these data an rms deviation of 0.66 log-units was achieved. Later, the model was tested on a set of 107 pesticides, which have been critically selected based on two experimental data sources and by a crosscheck with an independent HQSAR model. On this data set an rms of 0.61 log-units was achieved, without any adjustments to the structurally extremely diverse pesticides. This result verifies the ability of this extended COSMO-RS to predict aqueous solubilities of drugs and pesticides of almost arbitrary structural classes. The new method is COSMO-RSol.     

First structural characterization of binary AsIII and SbIII azides

The highly explosive molecules As(N(3))(3) and Sb(N(3))(3) were obtained in pure form by the reactions of the corresponding fluorides with (CH(3))(3)SiN(3) in SO(2) and purification by sublimation. The crystal structures and (14)N NMR, infrared, and Raman spectra were determined, and the results compared to ab initio second-order perturbation theory calculations. Whereas Sb(N(3))(3) possesses a propeller-shaped, pyramidal structure with perfect C(3) symmetry, the As(N(3))(3) molecule is significantly distorted from C(3) symmetry due to crystal packing effects.     

Analysis of sulphonated polyphenols, synthetic tanning agents in heavily polluted tannery wastewaters

A method is presented for the analysis of sulphonated polyphenols, acting as synthetic tanning agents, in heavily polluted tannery wastewater. It consists of ion-pair solid-phase extraction (RP-18) with tetrabutylammonium bromide followed by reversed-phase ion-pair liquid chromatography on a C₁₈ stationary phase with UV detection. The detection limit is 15 μg/1. The influence of the wastewater matrix on extraction and the effects of pH and temperature on the HPLC separation are discussed. The procedure is not affected by the high contents of dissolved organic carbon and inorganic salts of tannery wastewater. The tannery effluents investigated contained around 40 mg/1 of sulphonated polyphenols. These compounds appear to be refractory against both anaerobic and aerobic biological wastewater treatment. They might, thus, contribute to the dissolved organic sulphur content of surface waters.     

Atomistic Simulation Study of Calcium,Phosphate and Fluoride Ion Association to the Teleopeptide‐Tails of Collagen – Initial Steps to Biomineral Formation

The attachment of single ions to putative adsorption sites in the tails of collagen fibers is investigated by means of molecular dynamics simulations and discussed with respect to the very early steps of apatite/collagen biomineral formation. Our studies clearly demonstrate an increased flexibility of the tails of the triple‐helical collagen protein. Apart from the termini of the backbone, several side chains were also observed to be freely accessible to ion attachment from aqueous solution. The teleopeptide was systematically scanned for suitable adsorption sites for calcium, phosphate and fluoride ions. Association of these ions was then explored from potential of mean force calculations. The resulting energy profiles reveal a variety of favorable protein‐ion bonds and hint at the suitability of the collagen tails to promote apatite aggregation.     

Total synthesis of two 12-nordrimanes and the pharmacological active sesquiterpene hydroquinone yahazunol

The synthesis of two 12-nordrimanes and yahazunol was achieved via 8-oxo-12-nordrimanic acid methyl ester. The cytotoxic activity of yahazunol and seven other sesquiterpene hydroquinones and sesquiterpene quinones has been determined.     

Neutron activation analysis of heavy rare earths

A method of nondestructive activation analysis of heavy rare earth elements (Sm−Lu) is described. Intensities of γ-ray peaks are compared to that of an internal reference after irradiations by both thermal and fission spectrum neutrons. Results are obtained from computer comparisons of peak areas. Work was performed at the Ames Laboratory of the U.S. Atomic Energy Commission. Contribution No. 2895.     

Voltammetric trace determination of ubiquinones at mercury electrodes

Summary Voltammetric methods were developed for the determination of ubiquinones on the basis of their adsorption and redox behaviour at mercury electrodes. Linear calibration plots were obtained in the concentration range between 10^–4 mol/l and 2.3·10^–5 mol/l from differential pulse voltammetric measurements under experimental conditions avoiding significant adsorption of the analyte. A remarkable decrease of the detection limit down to 10^–7 mol/l was achieved with the help of adsorptive accumulation of ubiquinone molecules at the mercury electrode followed by differential pulse detection. The resulting non-linear calibration plot was explained with a model, which takes into account both adsorption and diffusion of the analyte.