NMR distinction of single- and multiple-mode binding of small-molecule protein ligands

Identifying and characterizing small-molecule inhibitors of protein-protein interactions is of high interest for drug discovery and for chemical genetics studies of biological pathways. Very often, initial hits or first-generation compounds have low micromolar dissociation constants and cause line broadening in NMR spectra. It is very important for subsequent structure-based compound optimization to know if this line broadening is caused by intermediate exchange of the dissociation kinetics only or in addition by multiple binding modes. Here, we present an approach of how to distinguish these two situations and demonstrate its experimental application. Two very similar small-molecule ligands of Bcl-xL are considered that cause both severe line broadening of interface residues. We show that one compound exhibits single-mode binding, and broadening is just due to dissociation kinetics in the intermediate exchange regime, and the line broadening can be overcome by providing excess ligand. In the other case, line broadening is due to dissociation kinetics and exchange between multiple bound conformations, and broadening cannot be overcome by providing excess ligand. The procedures used are very general and can also be applied to characterizing protein-protein and protein-nucleic acid interactions.     

A general polymer-based process to prepare mixed metal oxides: the case of Zn1-xMgxO nanoparticles

Nanometer-sized mixed metal oxide (MMO) particles (Zn1-xMgxO) with very precise stoichiometry are prepared employing a polymer-based method. The precursor is formed by loading a polyacrylate with metal ions followed by purification of the polymer metal ion complex via repeated precipitation/redissolution cycles. Calcination of the polymer precursor at 550 degrees C gives particles of the metastable solid solution of the ZnO/MgO system in the composition range (x<0.2 and x>or=0.82). The MMO crystal particles are typically 20-50 nm in diameter. Doping of the ZnO by Mg2+ causes a shrinkage of lattice parameter c. Effects of band gap engineering on the optical band gap are reported. The photoluminescence in the visible is also affected, and its maximum shifts from 2.12 eV (pure ZnO) to 2.32 eV at x=0.21. The crystalline MMO particles start to undergo segregation into hexagonal and cubic phases upon annealing at 800 degrees C.     

Effects of electric fields on proton transport through water chains

Molecular dynamics simulations on quantum energy surfaces are carried out to study the effects of perturbing electric fields on proton transport (PT) in protonated water chains. As an idealized model of a hydrophobic cavity in the interior of a protein the water molecules are confined into a carbon nanotube (CNT). The water chain connects a hydrated hydronium ion (H3O+) at one end of the CNT and an imidazole molecule at the other end. Without perturbing electric fields PT from the hydronium proton donor to the imidazole acceptor occurs on a picosecond time scale. External perturbations to PT are created by electric fields of varying intensities, normal to the CNT axis, generated by a neutral pair of charges on the nanotube wall. For fields above approximately 0.5 VA, the hydronium ion is effectively trapped at the CNT center, and PT blocked. Fields of comparable strength are generated inside proteins by nearby polar/charged amino acids. At lower fields the system displays a rich dynamic behavior, where the excess charge shuttles back and forth along the water chain before reaching the acceptor group on the picosecond time scale. The effects of the perturbing field on the proton movement are analyzed in terms of structural and dynamic properties of the water chain. The implications of these observations on PT in biomolecular systems and its control by external perturbing fields are discussed.     

Comparison of different separation technologies for proteome analyses: isoform resolution as a prerequisite for the definition of protein biomarkers on the level of posttranslational modifications

In this article we evaluate methods used to reveal the molecular complexity, which is generated in biological samples by posttranslational modifications (PTM) of proteins. We show how distinct molecular differences on the level of phosphorylation sites in a single protein (ovalbumin) can be resolved with different success using 1D and 2D gel-electrophoresis and reversed-phase liquid chromatography (LC) with monolithic polystyrol-divinylbenzol (PS-DVB) columns for protein separation, and matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS) for protein identification. Phosphorylation site analysis was performed using enzymatic dephosphorylation in combination with differential peptide mass mapping. Liquid chromatography-MALDI-TOF MS coupling with subsequent on-target tryptic protein digestion turned out to be the fastest method tested but yielded low resolution for the analysis of PTM, whereas 2D gel-electrophoresis, due to its unique capability of resolving highly complex isoform pattern, turned out to be the most suitable method for this purpose. The evaluated methods complement one another and in connection with efficient technologies for differential and quantitative analysis, these approaches have the potential to reveal novel molecular details of protein biomarkers.     

Phase behavior of a symmetrical binary fluid mixture

We have investigated the phase behavior of a symmetrical binary fluid mixture for the situation where the chemical potentials mu(1) and mu(2) of the two species differ. Attention is focused on the set of interparticle interaction strengths for which, when mu(1)=mu(2), the phase diagram exhibits both a liquid-vapor critical point and a tricritical point. The corresponding phase behavior for the case mu(1) not equalmu(2) is investigated via integral-equation theory calculations within the mean spherical approximation and grand canonical Monte Carlo (GCMC) simulations. We find that two possible subtypes of phase behavior can occur, these being distinguished by the relationship between the triple lines in the full phase diagram in the space of temperature, density, and concentration. We present the detailed form of the phase diagram for both subtypes and compare with the results from GCMC simulations, finding good overall agreement. The scenario via which one subtype evolves into the other is also studied, revealing interesting features.     

Multiple time step update schemes for dissipative particle dynamics

In dynamical simulations of coarse-grained models of soft matter in a solvent a considerable amount of the total simulation time is generically spent on updating the solvent particles, although their dynamics is in most cases not of primary interest. In order to speed up such simulations and as a consequence allow to extend them to cover larger system sizes, we propose and examine various multiple, specifically dual, time step update algorithms for dissipative particle dynamics simulations that are based on the velocity-Verlet scheme [Phys. Rev. 159, 98 (1967)]. Common to all update variants is that the solvent beads are updated with a lower frequency than the bonded interactions within the solute. As a test case we consider a coarse-grained model of a lipid bilayer in water. Our results demonstrate that a considerable saving of simulation time can be gained, while the obtained simulation data are within error brackets virtually identical to those obtained for the reference single time step update scheme.     

Ancistrocladinium A and B, the first N,C-coupled naphthyldihydroisoquinoline alkaloids, from a Congolese ancistrocladus species

The isolation and structural elucidation of three novel-type naphthylisoquinoline alkaloids, ancistrocladinium A and B (the latter along with its atropisomer), from a Congolese Ancistrocladus species collected in the habitat Yeteto is reported. Their structures, including all stereochemical features, were elucidated by spectroscopic, chemical, and chiroptical methods. Ancistrocladinium A and B are the first N,C-coupled naphthyldihydroisoquinoline alkaloids found in nature, i.e., with an iminium-aryl axis. Although ancistrocladinium A, which is N,8'-coupled, is configurationally stable at this axis, ancistrocladinum B and its rotational isomer are based on a hitherto unprecedented N,6'-coupling type, with a slow rotation about the hetero biaryl axis at room temperature; they thus occur as a 46:54 mixture of two configurationally semistable atropo-diastereomers. For the isomerization of (P)-ancistrocladinium B to its (M)-diastereomer and for the opposite direction, the Gibbs free energies of activation were determined to be DeltaG double dagger1 = 105.8 kJ mol-1 and DeltaG double dagger2 = 105.7 kJ mol-1, respectively. In addition, the compounds were shown to have promising antileishmanial activities.     

Contributions of the different water sources to the Elqui river runoff (northern Chile) evaluated by H/O isotopes

We present the results of an isotope (2H and 18O) and hydrogeochemical study in order to constrain the origin, recharge, and evolution of the surface and groundwater in the arid Andean realm of the Elqui watershed. The results of 2H and18O analyses of water samples obtained during our summer and winter campaigns indicate a generally meteoric origin of the river and spring waters of the watershed. The isotope signature of water of the Elqui river and its tributaries as well as that of groundwater in the coastal region fits the 2H-18O relation of delta2H =7.61delta18O+6.1. A relatively fast discharge and a quasi-closed catchment area can be asserted for water along the river flow path. The tributaries from the more arid coastal area, north of the Elqui river, differ in their isotopic signature due to evaporation and hydrochemically due to interactions with the strongly altered and fractured volcanic rocks of the basement. In the Andean zone, the18O-enriched hydrothermal spring of Ba?os del Toro exhibits the influence of water-rock interaction processes. The chemistry of the river water changes from sulphate- to chloride-rich along the river course from the high Andean mountains to the coast. The sulphate-rich character of these Andean waters reflects their passage through sulphide-rich rock massifs that were subjected to strong oxidation processes in the near superficial environment. This sulphate signature is enforced by past and present mining of precious metal epithermal deposits (e.g. those of El Indio-Tambo Au-Cu-As district), in which mineralised zones were developed during a series of Miocene magmatic-hydrothermal episodes in the Andean realm. Owing to the proximity of the lower Elqui river waters and its tributaries to the Pacific coast, the chloride character may be induced by agricultural and marine (sea spray, fog) sources. Generally, the main source of the Elqui river water is mainly attributed to surface runoff and less to contributions from the basement fractured aquifer.     

Sulphur and oxygen isotopic characters of dissolved sulphate in groundwater from the Pleistocene aquifer in the southern Jordan Valley (Jericho area, Palestine)

Sulphate and chloride concentrations in the shallow Pleistocene aquifer systems in the lower Jordan valley area indicate a general trend of increasing salinity eastward and southward. This study was conducted in one of the important sub-basins feeding the Pleo-Pleistocene aquifer in the Jericho area in the southern part of the valley using S and O isotopes of dissolved sulphate. The results show that sulphate has mainly two contributions to the groundwater. One is the surface seepage, which is present as a salty leachate form with the positive delta34Ssulphate values of primary gypsum in Lisan and Samara formations, and the second is the upwelling saline water which was in contact with a deep secondary gypsum, aragonites and salty rocks and rose up under heavy abstraction with depleted 34S in sulphate and relatively high sulphate and chloride content. The latest was clearly shown in the Arab Project wells to the east that is undergoing a continuous heavy abstraction. The isotopic signatures of S and O in these wells to the east show that this depleted 34S and highly concentrated sulphate might also indicate a dissolved sulphate originating from pyrite oxidation that results from the interaction with a pyrite-rich aquifer, which can well up with salty water under heavy abstraction and is oxidised in the upper aerobic shallow aquifer.