Synthetic polymers as substrates for a DNA-sliding clamp protein.

The clamp protein (gp45) of the DNA polymerase III of the bacteriophage T4 is known to bind to DNA and stay attached to it in order to facilitate the process of DNA copying by the polymerase. As part of a project aimed at developing new biomimetic data-encoding systems we have investigated the binding of gp45 to synthetic polymers, that is, rigid, helical polyisocyanopeptides. Molecular modelling studies suggest that the clamp protein may interact with the latter polymers. Experiments aimed at verifying these interactions are presented and discussed.

Investigation of neuroleptics and other aromatic compounds by laser-based ion mobility mass spectrometry.

Laser-based ion mobility (IM) spectrometry was used for the detection of neuroleptics and PAH. A gas chromatograph was connected to the IM spectrometer in order to investigate compounds with low vapour pressure. The substances were ionized by resonant two-photon ionization at the wavelengths λ = 213 and 266 nm and pulse energies between 50 and 300 µJ. Ion mobilities, linear ranges, limits of detection and response factors are reported. Limits of detection for the substances are in the range of 1-50 fmol. Additionally, the mechanism of laser ionization at atmospheric pressure was investigated. First, the primary product ions were determined by a laser-based time-of-flight mass spectrometer with effusive sample introduction. Then, a combination of a laser-based IM spectrometer and an ion trap mass spectrometer was developed and characterized to elucidate secondary ion-molecule reactions that can occur at atmospheric pressure. Some substances, namely naphthalene, anthracene, promazine and thioridazine, could be detected as primary ions (radical cations), while other substances, in particular acridine, phenothiazine and chlorprothixene, are detected as secondary ions (protonated molecules). The results are interpreted on the basis of quantum chemical calculations, and an ionization mechanism is proposed.

Electronic confinement and ordering instabilities in colossal magnetoresistive bilayer manganites.

We present angle-resolved photoemission studies of (La{1-z}Pr{z}){2-2x}Sr{1+2x}Mn{2}O{7} with x=0.4 and z=0.1, 0.2, and 0.4 along with density functional theory calculations and x-ray scattering data. Our results show that the bilayer splitting in the ferromagnetic metallic phase of these materials is small, if not completely absent. The charge carriers are therefore confined to a single MnO{2} layer, which in turn results in a strongly nested Fermi surface. In addition to this, the spectral function also displays clear signatures of an electronic ordering instability well below the Fermi level. The increase of the corresponding interaction strength with z and its magnitude of ∼400 meV make the coupling to a bare phonon highly unlikely. Instead we conclude that fluctuating order, involving electronic and lattice degrees of freedom, causes the observed renormalization of the spectral features.

Transition from a uni- to a bimodal interfacial charge distribution in [Formula: see text]/[Formula: see text] upon cooling.

We present a combined resonant soft X-ray reflectivity and electric transport study of [Formula: see text]/[Formula: see text] field effect devices. The depth profiles with atomic layer resolution that are obtained from the resonant reflectivity reveal a pronounced temperature dependence of the two-dimensional electron liquid at the [Formula: see text]/[Formula: see text] interface. At room temperature the corresponding electrons are located close to the interface, extending down to 4 unit cells into the [Formula: see text] substrate. Upon cooling, however, these interface electrons assume a bimodal depth distribution: They spread out deeper into the [Formula: see text] and split into two distinct parts, namely one close to the interface with a thickness of about 4 unit cells and another centered around 9 unit cells from the interface. The results are consistent with theoretical predictions based on oxygen vacancies at the surface of the [Formula: see text] film and support the notion of a complex interplay between structural and electronic degrees of freedom.

Insight into the complete substrate-binding pocket of ThiT by chemical and genetic mutations.

Energy-coupling factor (ECF) transporters are involved in the uptake of micronutrients in bacteria. The transporters capture the substrate by high-affinity binding proteins, the so-called S-components. Here, we present the analysis of two regions of the substrate-binding pocket of the thiamine-specific S-component in Lactococcus lactis, ThiT. First, interaction of the thiazolium ring of thiamine with residues Trp34, His125 and Glu84 by π-π-stacking and cation-π is studied, and second, the part of the binding pocket that extends from the hydroxyl group. We mutated either the transported ligand (chemically) or the protein (genetically). Surprisingly, modifications in the thiazolium ring by introducing substituents with opposite electronic effects had similar effects on the binding affinity. We hypothesize that the electronic effects are superseeded by steric effects of the added substituents, which renders the study of isolated interactions difficult. Amino acid substitutions in ThiT indicate that the electrostatic interaction facilitated by residue Glu84 of ThiT and thiamine is necessary for picomolar affinity. Deazathiamine derivatives that explore the subpocket of the binding site extending from the hydroxyl group of thiamine bind with high affinity to ThiT and may be developed into selective inhibitors of thiamine transport by ECF transporters. Molecular-dynamics simulations suggest that two of these derivatives may not only bind to ThiT, but could also be transported.