HOUDINI: a new approach to computer-based structure generation

A new method of structure generation called convergent structure generation has been developed to address limitations of earlier methods. The features of the program (HOUDINI) based on this method include the following: a single integrated representation of the collective substructural information; the use of parallel atom groups for efficient processing of families of alternative substructural inferences; and a managed structure generation procedure designed to build required structural features early in the process.     

Computer-assisted chemical structure analysis

The new generation of the CASE system described in this paper offers a promising approach to both spectrum interpretation and structure generation that allows for a natural linkage between them. The approach takes full advantage of the information contained in available spectral libraries, yet is not limited by the substructural deficiencies of these data bases.     

Phase resetting and dynamics in isolated atrioventricular nodal cell clusters

In the heart, the AV node is the primary conduction pathway between the atria and ventricles and subserves an important function by virtue of its rate-dependent properties. Cell clusters isolated from the rabbit atrioventricular (AV) node beat with a stable rhythm (cycle length: 300-520 ms) and are characterized by slow action potential upstroke velocities (7 to 30 V/s). The goal of this study is to better characterize the phase resetting and the rhythms during periodic stimulation of this slow inward current system. Single or periodic depolarizing pulses (20 ms in duration) were injected into AV nodal cell clusters using glass microelectrodes. Phase resetting curves of both strong, weak as well as discontinuous types were obtained by applying single current pulses of different intensities and latencies following every ten action potentials. Graded responses were elicited in a wide range of stimulus phases and amplitudes. A single premature stimulus caused a transient prolongation of the cycle length. Sustained periodic stimulation, at rates faster than the intrinsic beat rate, resulted in various N:M (stimulus frequency: action potential frequency) entrainment rhythms as well as periodic or irregular changes in action potential morphology. The changes in action potential characteristics were evaluated by computing the area under the action potential trace and above a fixed threshold (-45 mV). We show that the variations in action potential morphology play a major role in the onset of complicated dynamics observed in this experimental preparation. In this context, the prediction of entrainment rhythms using techniques based on the iteration of phase resetting curves (PRCs) is inadequate since the PRC does not carry information directly related to the changes in action potential morphology. This study demonstrates the need to consider graded events which, though not propagated, have important implications in the understanding of dynamical diseases of the heart. (c) 1995 American Institute of Physics.     

Advances in contrast variation for macromolecular structure determination by polarized neutron scattering and anomalous dispersion of synchrotron X-rays

Contrast variation for macromolecular structure determination is usually achieved by isomorphous replacement of 1-H by 2-H (D) using small-angle neutron scattering (SANS). This is particularly easy in aqueous solvents. By adding heavy water the contrast of dissolved proteins, nucleic acids and membranes changes drastically. It is the region inaccesible to solvent molecules, which acts as a label. Measurements of the scattering intensity at three different scattering densities of a solvent yields the three basic scattering functions. The contrast dependence of the radius of gyration receives particular interest. More recently smaller labels have been used. Their dimensions are smaller than those of the total particle by an order of magnitude. They are used for in situ structure determination of the labelled region. Contrast variation of the labelled region can be achieved by gradual deuteration of the label. Again, the measurements have to be done at three different contrasts in order to separate the scattering function of the label. - By eliminating any intramolecular scattering density fluctuation (K. Nierhaus' principle of the ‘transparent’ ribosome) the structure of selectively labelled ribosomal proteins can be determined in situ by using only one derivative. Spin contrast variation of biomolecules relies on the nuclear spin dependence of neutron scattering by protons and, to a smaller extent, by deuterons. It is particularly well suited for labels rich in protons embedded in a deuterated matrix. Variation of the target polarization yields the three basic scattering functions from the same sample. In collaboration with CERN and ILL, a special set-up for spin contrast variation has been installed at the reactor FRG1 of the GKSS Research Centre at Geesthacht. The dynamic nuclear polarization of proton spins in proteins, nucleic acids and ribosomes is achieved in the presence of Cr(V) at T = 0.4 K, H = 2.5 T and 4 mm microwave irradiation. Within two hours, the proton polarization will reach more than 70 % in favourable cases. Measurements have been carried out with various proteins, transfer ribonucleic acid (tRNA) and the large subunit of E.coli ribosomes, the latter also with its total protein deuterated (i.e. ribosomal ribonucleic acid (rRNA) acts as a label). There is an agreement between the nuclear spin polarization of protons and deuterons measured by NMR and the nuclear spin dependent change of polarized small-angle neutron scattering. The results of spin contrast variation experiments are compared with those obtained from near-edge anomalous X-ray scattering using synchrotron radiation. Particular attention is given to the anomalous dispersion of light elements, like sulfur, which tend to show a strong dependence on the chemical bonding of the atom. In purple membrane, the anomalous scattering of sulfur in protein, bound to methionine and sulfates in the lipid matrix has been determined separately.     

Development of 1,3-acetonedicarboxylate-derived glucoside amphiphiles (ACAs) for membrane protein study

Detergents are extensively used for membrane protein manipulation. Membrane proteins solubilized in conventional detergents are prone to denaturation and aggregation, rendering downstream characterization of these bio-macromolecules difficult. Although many amphiphiles have been developed to overcome the limited efficacy of conventional detergents for protein stabilization, only a handful of novel detergents have so far proved useful for membrane protein structural studies. Here, we introduce 1,3-acetonedicarboxylate-derived amphiphiles (ACAs) containing three glucose units and two alkyl chains as head and tail groups, respectively. The ACAs incorporate two different patterns of alkyl chain attachment to the core detergent unit, generating two sets of amphiphiles: ACA-As (asymmetrically alkylated) and ACA-Ss (symmetrically alkylated). The difference in the attachment pattern of the detergent alkyl chains resulted in minor variation in detergent properties such as micelle size, critical micelle concentration, and detergent behaviors toward membrane protein extraction and stabilization. In contrast, the impact of the detergent alkyl chain length on protein stability was marked. The two C11 variants (ACA-AC11 and ACA-SC11) were most effective at stabilizing the tested membrane proteins. The current study not only introduces new glucosides as tools for membrane protein study, but also provides detergent structure–property relationships important for future design of novel amphiphiles.

Newly developed amphiphiles, designated ACAs, are not only efficient at extracting G protein-coupled receptors from the membranes, but also conferred enhanced stability to the receptors compared to the gold standards (DDM and LMNG).     

Newton methods for nonlinear inverse problems with random noise

We study the convergence of regularized Newton methods applied to nonlinear operator equations in Hilbert spaces if the data are perturbed by random noise. We show that under certain conditions it is possible to achieve the minimax rates of the corresponding linearized problem if the smoothness of the solution is known. If the smoothness is unknown and the stopping index is determined by Lepskij's balancing principle, we show that the rates remain the same up to a logarithmic factor due to adaptation. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Block copolymer micelles in aqueous media

Polystyrene-block-poly(methacrylic acid) and poly(methacrylic acid)-block-polystyrene-block-poly(methacrylic acid) di- and triblock copolymers form micelles with polystyrene cores and poly(methacrylic acid) shells when dissolved in water/1, 4-dioxane mixtures, rich in dioxane. These micelles can be transferred into water rich mixtures, into water, and into aqueous buffers by stepwise dialysis. Quasielastic light scattering and sedimentation velocity experiments show that in dioxane rich mixtures exists a dynamic micellization equilibrium, while in dioxane poor solutions and in aqueous buffers the equilibrium is frozen. The process of mixed micelles formation was observed in dioxane rich solutions.     

Structural characterization of ether lipids from the archaeon Sulfolobus islandicus by high‐resolution shotgun lipidomics

The molecular structures, biosynthetic pathways and physiological functions of membrane lipids produced by organisms in the domain Archaea are poorly characterized as compared with that of counterparts in Bacteria and Eukaryota. Here we report on the use of high‐resolution shotgun lipidomics to characterize, for the first time, the lipid complement of the archaeon Sulfolobus islandicus. To support the identification of lipids in S. islandicus, we first compiled a database of ether lipid species previously ascribed to Archaea. Next, we analyzed the lipid complement of S. islandicus by high‐resolution Fourier transform mass spectrometry using an ion trap‐orbitrap mass spectrometer. This analysis identified five clusters of molecular ions that matched ether lipids in the database with sub‐ppm mass accuracy. To structurally characterize and validate the identities of the potential lipid species, we performed structural analysis using multistage activation on the ion trap‐orbitrap instrument as well as tandem mass analysis using a quadrupole time‐of‐flight machine. Our analysis identified four ether lipid species previously reported in Archaea, and one ether lipid species that had not been described before. This uncharacterized lipid species features two head group structures composed of a trisaccharide residue carrying an uncommon sulfono group (?SO₃) and an inositol phosphate group. Both head groups are linked to a glycerol dialkyl glycerol tetraether core structure having isoprenoid chains with a total of 80 carbon atoms and 4 cyclopentane moieties. The shotgun lipidomics approach deployed here defines a novel workflow for exploratory lipid profiling of Archaea. Copyright © 2015 John Wiley & Sons, Ltd.     

Demonstration of a single-layer meanderline phase retarder at infrared

Meanderline wave plates are in common use at radio frequencies as polarization retarders. We present initial results of a gold meanderline structure on a silicon substrate that functions at a wavelength of 10.6 microm in the IR. The measured results show a distinct change in the polarization state of the incident beam after passing through the device, inducing a 74 degrees phase retardance between horizontal and vertical components. A high degree of polarization (88%) is maintained in the transmitted beam with an overall power transmittance of 38% and a beam profile that remains essentially unchanged.