Biomedical subjects

Dietmar Schwahn

Publications and source records attributed to Dietmar Schwahn.

7 recordsLinked to original sources

PubMed2006

Dynamic flexibility of double-stranded RNA activated PKR in solution.

PKR, an interferon-induced double-stranded RNA activated serine-threonine kinase, is a component of signal transduction pathways mediating cell growth control and responses to stress and viral infection. Analysis of separate PKR functional domains by NMR and X-ray crystallography has revealed details of PKR RNA binding domains and kinase domain, respectively. Here, we report the structural characteristics, calculated from biochemical and neutron scattering data, of a native PKR fraction with a high level of autophosphorylation and constitutive kinase activity. The experiments reveal association of the protein monomer into dimers and tetramers, in the absence of double-stranded RNA or other activators. Low-resolution structures of the association states were obtained from the large angle neutron scattering data and reveal the relative orientation of all protein domains in the activated kinase dimer. Low-resolution structures were also obtained for a PKR tetramer-monoclonal antibody complex. Taken together, this information leads to a new model for the structure of the functioning unit of the enzyme, highlights the flexibility of PKR and sheds light on the mechanism of PKR activation. The results of this study emphasize the usefulness of low-resolution structural studies in solution on large flexible multiple domain proteins.

Biopolymers↗

PubMed2005

Composition fluctuations in a homopolymer-diblock copolymer mixture covering the three-dimensional Ising, isotropic Lifshitz, and Brasovskiĭ classes of critical universality.

The phase behavior of a three-component polymer blend consisting of a critical mixture of polybutadiene and polystyrene (PB/PS) with varying amount of a symmetric PB-PS diblock copolymer was explored with small-angle neutron scattering. Our focus were thermal composition fluctuations which we discuss in terms of mean field, three-dimensional Ising, isotropic Lifshitz, and Brasovskiĭ classes of critical universality. Particular attention is spent to the observation of a narrow reentrant two-phase regime and double critical point in the Lifshitz critical regime as well as the Lifshitz line. Critical exponents of the isotropic Lifshitz case are proposed in spite of the demonstrated nonexistence of the isotropic Lifshitz critical point. The Ginzburg number (Gi) and Flory-Huggins parameter were determined over the whole diblock concentration range; Gi changes by three orders of magnitude, two orders of magnitude of that change over a 0.03 diblock concentration interval within the isotropic Lifshitz regime.

Journal Article↗

PubMed2005

Behavior of tri(n-butyl)ammonium bis[citrato(3-)-O1,O3,O6]silicate in aqueous solution: analysis of a sol-gel process by small-angle neutron scattering.

The racemic hexacoordinate silicon(IV) complex tri(n-butyl)ammonium bis[citrato(3-)-O1,O3,O6]silicate (1) was synthesized by treatment of Si(OMe)4 with 2 molar equiv of citric acid and 2 molar equiv of N(n-Bu)3. The corresponding germanium analogue, tri(n-butyl)ammonium bis[citrato(3-)-O1,O3,O6]germanate (5; structurally characterized by single-crystal X-ray diffraction), was obtained analogously, starting from Ge(OMe)4. Upon dissolution in water, the lambda6Si-silicate dianion of 1 hydrolyzes spontaneously (formation of Si(OH)4 and citric acid), whereas the lambda6Ge-germanate dianion of 5 was found to be stable in water. Aqueous "solutions" of 1, with concentrations that are significantly higher than the saturation concentration of Si(OH)4, look absolutely clear over a period of several weeks; however, in reality, these solutions are sols with very small particles that slowly grow with time and finally form a gel that precipitates. This sol-gel process was monitored by small-angle neutron scattering (SANS). For reasons of comparison, an aqueous solution of the hydrolytically stable germanium compound 5 was also studied by the SANS technique.

Journal Article↗

PubMed2005

Ginzburg number of a homopolymer-diblock copolymer mixture covering the 3D-Ising, isotropic Lifshitz, and Brasovskii classes of critical universality.

The Ginzburg number Gi of deuterated poly(butadiene) (dPB) and poly(styrene) (PS) homopolymer blend of critical composition mixed with a dPB-PS symmetric diblock copolymer was determined from small angle neutron scattering. A 3 orders of magnitude change of Gi was determined between binary polymer blend and diblock copolymer melt. The strongest change of Gi is observed within the isotropic Lifshitz regime of critical universality occurring over a 3% range of diblock concentration and interpolates the corresponding Gi of the 3D-Ising and Brasovskii regimes. A Lifshitz critical point was not observed consistent with the proposed lower critical dimension d(LCP)=4.

Journal Article↗

PubMed2004

Concentration fluctuations in polymer gel investigated by neutron scattering: static inhomogeneity in swollen gel.

By using small-angle neutron scattering (SANS) and neutron spin echo (NSE), we have quantitatively investigated the static inhomogeneity in poly (N-isopropyl acrylamide) gel (PNIPA) in microscopic length scales of 0.015<q<0.16 A(-1), where q is a wave number of scattered neutrons. NSE revealed that at lower q( congruent with 0.015 A(-1)), the concentration fluctuations in the PNIPA gel decays more slowly as compared to the PNIPA solution without crosslinks. According to our scenario that the slower decay found for the PNIPA gel is due to the static inhomogeneity coexisting in the swollen gel, small-angle scattering S(q) obtained by SANS has been quantitatively decomposed into thermal and static scattering components, respectively, S(th)(q) and S(st)(q). It was further revealed that (i) the q-region where S(st)(q) becomes dominant is closely related to that for the abnormal butterfly scattering under stretching, and (ii) as the temperature increases toward the temperature for volume phase transition, S(st)(q) of a squared Lorentzian shape increases more drastically than S(th)(q) of a Lorentzian shape. These findings were quantitatively understood in the theoretical framework by Panyukov and Rabin [Macromolecules 29, 7960 (1996)] or by Onuki [J. Phys. II. France 2, 45 (1992)], taking into account stress-fluctuation coupling under coexistence of the inherent structural heterogeneity in the real gel. We further found that the static inhomogeneity showing S(st)(q) seems to relate to the necklacelike microstructure, appearing after a shallow quench into the collapsed phase.

Journal Article↗

PubMed2004

On the role of block copolymer additives for calcium carbonate crystallization: small angle neutron scattering investigation by applying contrast variation.

The role of the double-hydrophilic block copolymer poly(ethylen glycol)-block-poly(methacrylic acid) (PEG-b-PMAA) on the morphogenesis of calcium carbonate (CaCO3) was studied by applying the contrast variation small angle neutron scattering technique. The morphology and size of CaCO3 crystals is strongly affected by the addition of PEG-b-PMAA. In order to determine the partial scattering functions of the polymer and CaCO3 mineral, we developed both an experimental and theoretical approach with a sophisticated method of their determination from the scattering intensity. Partial scattering functions give detailed information for each component. In particular, the partial scattering function of the polymer, Spp, shows a monotonic slope with Q(-2 to -3) where the scattering vector Q is low (Q < 0.01 Angstrom(-1)), which is a clear evidence that the polymer within the CaCO3 mineral has a mass fractal dimension. The other partial scattering functions reflected the geometry of the CaCO3 particles or the "interaction" of polymer and CaCO3 on a microscopic scale, which leads to a coherent view with Spp.

Journal Article↗

PubMed2002

Structure and properties of the dendron-encapsulated polyoxometalate (C(52)H(60)NO(12))(12)[(Mn(H(2)O))(3)(SbW(9)O(33))(2)], a first generation dendrizyme.

Combining analytical and theoretical methods, we present a detailed study of a heteropolytungstate cluster encapsulated in a shell of dendritically branching surfactants, namely (C(52)H(60)NO(12))(12)[(Mn(H(2)O))(3)(SbW(9)O(33))(2)], 3. This novel surfactant-encapsulated cluster (SEC) self-assembles spontaneously from polyoxometalate-containing solutions treated with a stoichiometric amount of dendrons. Compound 3 exhibits a discrete supramolecular architecture in which a single polyoxometalate anion resides in a compact shell of dendrons. Our approach attempts to combine the catalytic activity of polyoxometalates with the steric properties of tailored dendritic surfactants into size-selective catalytic systems. The structural characterization of the SEC is based on analytical ultracentrifugation (AUC) and small-angle neutron scattering (SANS). The packing arrangement of dendrons at the cluster surface is gleaned from molecular dynamics (MD) simulations, which suggests a highly porous shell structure due to the dynamic formation of internal clefts and cavities. From analysis of the MD trajectory of 3, a theoretical neutron-scattering function is derived that is in good agreement with experimental SANS data. Force field parameters used in MD simulations are partially derived from a quantum mechanical geometry optimization of [(Zn(H(2)O))(3)(SbW(9)O(33))(2)](12)(-), 2b, at the density functional theory (DFT) level. DFT calculations are corroborated by X-ray structure analysis of Na(6)K(6)[(Zn(H(2)O))(3)(SbW(9)O(33))(2)].23H(2)O, which is isostructural with the catalytically active Mn derivative 2a. The combined use of theoretical and analytical methods aims at rapidly prototyping smart catalysts ("dendrizymes"), which are structurally related to naturally occurring metalloproteins.

Journal Article↗