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Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [H-1, N-15]-HSQC-NOESY-[H-1, N-15]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign.
A promising replacement for the radioactive sources commonly encountered in ion mobility spectrometers is a miniaturized, energy-efficient photoionization source that produce the reactant ions via soft X-radiation (2.8 keV). In order to successfully apply the photoionization source, it is imperative to know the spectrum of reactant ions and the subsequent ionization reactions leading to the detection of analytes. To that end, an ionization chamber based on the photoionization source that reproduces the ionization processes in the ion mobility spectrometer and facilitates efficient transfer of the product ions into a mass spectrometer was developed. Photoionization of pure gasses and gas mixtures containing air, N-2, CO2 and N2O and the dopant CH2Cl2 is discussed. The main product ions of photoionization are identified and compared with the spectrum of reactant ions formed by radioactive and corona discharge sources on the basis of literature data. The results suggest that photoionization by soft X-radiation in the negative mode is more selective than the other sources. In air, adduct ions of O-2 - with H2O and CO2 were exclusively detected. Traces of CO2 impact the formation of adduct ions of O-2 - and Cl -(upon addition of dopant) and are capable of suppressing them almost completely at high CO2 concentrations. Additionally, the ionization products of four alkyl nitrates (ethylene glycol dinitrate, nitroglycerin, erythritol tetranitrate and pentaerythritol tetranitrate) formed by atmospheric pressure chemical ionization induced by X-ray photoionization in different gasses (air, N-2 and N2O) and dopants (CH2Cl2, C2H5Br and CH3I) are investigated. The experimental studies are complemented by density functional theory calculations of the most important adduct ions of the alkyl nitrates (M) used for their spectrometric identification. In addition to the adduct ions [M + NO3](-) and [M + Cl](-), adduct ions such as [M + N2O2](-), [M + Br](-) and [M+ I](-) were detected, and their gas-phase structures and energetics are investigated by density functional theory calculations. Copyright (C) 2016 John Wiley & Sons, Ltd.
An ellipsometric approach towards the description of inhomogeneous polymer-based Langmuir layers
(2016)
The applicability of nulling-based ellipsometric mapping as a complementary method next to Brewster angle microscopy (BAM) and imaging ellipsometry (IE) is presented for the characterization of ultrathin films at the air-water interface. First, the methodology is demonstrated for a vertically nonmoving Langmuir layer of star-shaped, 4-arm poly(omega-pentadecalactone) (PPDL-D4). Using nulling-based ellipsometric mapping, PPDL-D4-based inhomogeneously structured morphologies with a vertical dimension in the lower nm range could be mapped. In addition to the identification of these structures, the differentiation between a monolayer and bare water was possible. Second, the potential and limitations of this method were verified by applying it to more versatile Langmuir layers of telechelic poly[(rac-lactide)-co-glycolide]-diol (PLGA). All ellipsometric maps were converted into thickness maps by introduction of the refractive index that was derived from independent ellipsometric experiments, and the result was additionally evaluated in terms of the root mean square roughness, R-q. Thereby, a three-dimensional view into the layers was enabled and morphological inhomogeneity could be quantified.
This report describes the aggregation behavior of an ABC-type ampholytic block copolypeptide, poly(ethylene oxide)-block-poly(L-lysine)-block-poly(L-glutamate), in aqueous media in dependence of pH. Polypeptide secondary structures and self-assemblies are investigated by circular dichroism (CD), Fourier transform infrared (FT-IR) and NMR spectroscopy, zeta potential measurements, analytical ultracentrifugation (AUC), dynamic/static light scattering (DLS/SLS), and cryogenic transmission electron microscopy (cryoTEM). The polymer chains tend to form vesicles when the hydrophobic polypeptide helix is located at the chain end (acidic pH) and are existing as single chains when it is located in the center and flanked by the two hydrophilic segments (basic pH). Precipitation occurs in the intermediate pH range due to polyion complexation of the charged polypeptide segments.
2-Fluoroadenine ((2F)A) is a therapeutic agent, which is suggested for application in cancer radiotherapy. The molecular mechanism of DNA radiation damage can be ascribed to a significant extent to the action of low-energy (<20 eV) electrons (LEEs), which damage DNA by dissociative electron attachment. LEE induced reactions in (2F)A are characterized both isolated in the gas phase and in the condensed phase when it is incorporated into DNA. Information about negative ion resonances and anion-mediated fragmentation reactions is combined with an absolute quantification of DNA strand breaks in (2F)A-containing oligonucleotides upon irradiation with LEEs. The incorporation of (2F)A into DNA results in an enhanced strand breakage. The strand-break cross sections are clearly energy dependent, whereas the strand-break enhancements by (2F)A at 5.5, 10, and 15 eV are very similar. Thus, (2F)A can be considered an effective radiosensitizer operative at a wide range of electron energies.
Templates of complex nanopatterns in a form of hierarchically sequenced dots and stripes can be generated in block copolymer films on lithography-free 3D topographic substrates. The approach exploits thickness- and swelling-responsive morphological behavior of block copolymers, and demonstrates novel possibilities of topography-guided registration of nanopatterns due to periodic confinement and spontaneous orthogonal flow-fields.
The enzymatic degradation of oligo(epsilon-caprolactone) (OCL) based films at the air-water interface is investigated by Langmuir monolayer degradation (LMD) experiments to elucidate the influence of the molecular architecture and of the chemical structure on the chain scission process. For that purpose, the interactions of 2D monolayers of two star-shaped poly(epsilon-caprolactone)s (PCLs) and three linear OCL based copolyesterurethanes (P(OCL-U)) with the lipase from Pseudomonas cepacia are evaluated in comparison to linear OCL. While the architecture of star-shaped PCL Langmuir layers slightly influences their degradability compared to OCL films, significantly retarded degradations are observed for P(OCL-U) films containing urethane junction units derived from 2, 2 (4), 4-trimethyl hexamethylene diisocyanate (TMDI), hexamethylene diisocyanate (HDI) or lysine ethyl ester diisocyanate (LDI). The enzymatic degradation of the OCL based 2D structures is related to the presence of hydrophilic groups within the macromolecules rather than to the packing density of the film or to the molecular weight. The results reveal that the LMD technique allows the parallel analysis of both the film/enzyme interactions and the degradation process on the molecular level. (C) 2016 Elsevier Ltd. All rights reserved.
In recent simulations of femtosecond laser induced desorption of molecular oxygen from the Ag(110) surface, it has been shown that depending on the properties (depth and electronic environment) of the well in which 02 is adsorbed, the desorption can be either induced dominantly by hot electrons or via excitations of phonons. In this work we explore whether the ratios between the desorption yields from different adsorption wells can be tuned by changing initial surface temperature and laser pulse properties. We show that the initial surface temperature is an important parameter, and that by using low initial surface temperatures the electronically mediated process can be favored. In contrast, laser properties seem to have only a modest influence on the results. (C) 2016 Elsevier B.V. All rights reserved.
Cryogenic transmission electron microscopy (cryo-TEM) studies suggest that TTBC molecules self-assemble in aqueous solution to form single-walled tubes with a diameter of about 35 A. In order to reveal the arrangement and mutual orientations of the individual molecules in the tube, we combine information from crystal structure data of this dye with a calculation of linear absorbance and linear dichroism spectra and molecular dynamics simulations. We start with wrapping crystal planes in different directions to obtain tubes of suitable diameter. This set of tube models is evaluated by comparing the resulting optical spectra with experimental data. The tubes that can explain the spectra are investigated further by molecular dynamics simulations, including explicit solvent molecules. From the trajectories of the most stable tube models, the short-range ordering of the dye molecules is extracted and the optimization of the structure is iteratively completed. The final structural model is a tube of rings with 6-fold rotational symmetry, where neighboring rings are rotated by 30 and the-transition dipole moments of the chromophores form an angle of 74 with respect to the symmetry axis of the tube. This model is in agreement with cryo-TEM images and can explain the optical spectra, consisting of a sharp red-shifted J-band that is polarized parallel to to the symmetry axis of the tube and a broad blue-shifted H-band polarized perpendicular to this axis. The general structure of the homogeneous spectrum of this hybrid HJ-aggregate is described by an analytical model that explains the difference in redistribution of oscillator strength inside the vibrational manifolds of the J- and H-bands and the relative intensities and excitation energies of those bands. In addition to the-particular system investigated here, the present methodology can be expected to aid the structure prediction for a wide range of self-assembled dye aggregates.