Eleonora V. Shtykova

Structural Analysis of Influenza A Virus Matrix Protein M1 and Its Self-Assemblies at Low pH

Influenza A virus matrix protein M1 is one of the most important and abundant proteins in the virus particles broadly involved in essential processes of the viral life cycle. The absence of high-resolution data on the full-length M1 makes the structural investigation of the intact protein particularly important. We employed synchrotron small-angle X-ray scattering (SAXS), analytical ultracentrifugation and atomic force microscopy (AFM) to study the structure of M1 at acidic pH. The low-resolution structural models built from the SAXS data reveal a structurally anisotropic M1 molecule consisting of a compact NM-fragment and an extended and partially flexible C-terminal domain. The M1 monomers co-exist in solution with a small fraction of large clusters that have a layered architecture similar to that observed in the authentic influenza virions. AFM analysis on a lipid-like negatively charged surface reveals that M1 forms ordered stripes correlating well with the clusters observed by SAXS. The free NM-domain is monomeric in acidic solution with the overall structure similar to that observed in previously determined crystal structures. The NM-domain does not spontaneously self assemble supporting the key role of the C-terminus of M1 in the formation of supramolecular structures. Our results suggest that the flexibility of the C-terminus is an essential feature, which may be responsible for the multi-functionality of the entire protein. In particular, this flexibility could allow M1 to structurally organise the viral membrane to maintain the integrity and the shape of the intact influenza virus.

The crystal structure of the MPN domain from the COP9 signalosome subunit CSN6

CSN6 and CSN6 bind by x ray scattering ( View interaction )

Low-resolution structure of immunoglobulins IgG1, IgM and rheumatoid factor IgM-RF from solution X-ray scattering data

Low-resolution structures of immunoglobulins IgG, IgM and rheumatoid factor IgM-RF in solution were analyzed using synchrotron radiation small-angle X-ray scattering and the macromolecular shapes were restored ab initio from the scattering data. The shape of IgG agrees well with the distorted Y-type crystallographic model but has a swollen appearance reflecting flexibility of the molecule in solution. The structures of pentameric IgM and IgM-RF were reconstructed assuming a five-fold symmetry. The IgM displays a flat star-like shape with observable F(ab)2 regions. The overall shape of the IgM-RF is similar to that of the IgM but with distinctly asymmetric F(ab)2 regions. This result agrees with the earlier observed functional dissimilarity of the Fab fragments in the rheumatoid factor and points to their structural dissimilarity.

Structural and SAXS analysis of the budding yeast SHU-complex proteins

PSY3 and CSM2 bind by X‐ray crystallography ( View interaction ) PSY3 , CSM2 , Shu 1 and Shu 2 physically interact by x ray scattering (View interaction)

SAXS-data-based structural modeling of DNA–gadolinium complexes fixed in particles of cholesteric liquid-crystalline dispersions

Structure of cholesteric liquid-crystalline dispersions (CLCDs) formed by double-stranded DNA molecules and treated with gadolinium salts was studied by small-angle X-ray scattering (SAXS). The obtained SAXS data open the way for structural modeling of these complexes to obtain a reasonable explanation for the correlated decrease in amplitude of an abnormal negative band in the circular dichroism (CD) spectra and the characteristic Bragg peak in the experimental small-angle X-ray scattering curves observed on treatment of CLCD by gadolinium salts. Model simulations of different kinds of structural organizations of the DNA–gadolinium complex were performed using novel SAXS data analysis methods in combination with several new, complementary modeling techniques, enabling us to build low-resolution three-dimensional structural models of DNA–gadolinium complexes fixed in CLCD particles. The obtained models allow us to suggest that a change takes place in the helical twist of quasinematic layers formed by these molecules at high concentrations of gadolinium salt. This change in the twist can be used to explain the experimentally observed increase in amplitude of an abnormal band in the CD spectra of DNA CLCD.

Small-angle X-ray scattering reveals hollow nanostructures in iota- and kappa-carrageenan/surfactant complexes

Complexes of polyelectrolyte gels with oppositely charged surfactants form ordered polymer matrices with unique structure properties, which can be used in a wide range of medical, chemical and physical applications. Ordered matrices made of natural components are of special interest for medical and biological purposes. In the present study, self-organised complexes of native - and -carrageenans formed with oppositely charged cetylpyridinium chloride (CPC) are prepared and structurally characterised using small-angle X-ray scattering (SAXS). Starting from the molar ratio CPC/(charge of carrrageenan) of 0.2, the carrageenan gel shrinks and ordered motifs in its internal structure are formed. The internal order in the sample is reflected by the Bragg peaks in the scattering patterns which permit to compute periodicity and characteristic sizes of the ordered regions. Moreover, strong central scattering appears and the calculated fractal dimensions indicate that these regions are organised in well defined clusters. The periodicity of the ordered motifs computed from the Bragg peaks in the scattering patterns corresponds to the width of the surfactant bilayer (about 4.0 nm) for all the complexes. The crystallite size ranges from 25 nm to 40 nm depending on the type of carrageenan and on the amount of CPC. A model of the ordered fragments is proposed whereby the carrageenan/surfactant bilayers are regularly packed at the walls of hollow cylindric clusters with the outer radius of about 8 nm and height 40 nm. More detailed ab initio models indicate that these particles are formed by bent worm-like substructures with the cross-section coinciding to the thickness of the carrageenan/CPC bilayer. Thanks to a higher charge density per monomer, -carrageenans form more regular structures than -carrageenans.

Mixed Co/Fe Oxide Nanoparticles in Block Copolymer Micelles

Small iron oxide and Co-doped iron oxide nanoparticles (NPs) were synthesized in a commercial amphiphilic block copolymer, poly(ethylene oxide)-b-poly(methacrylic acid) (PEO 68-b-PMAA8), in aqueous solutions. The structure and composition of the micelles containing guest molecules (metal salts) or NPs (metal oxides) were studied using transmission electron microscopy, dynamic light scattering, X-ray photoelectron spectroscopy, and X-ray powder diffraction. The enlarged micelle cores after incorporation of metal salts are believed to be formed by both PMAA blocks containing metal species and penetrating PEO chains. The nanoparticle size distributions in PEO 68-b-PMAA8 were determined using small-angle X-ray scattering (SAXS) in bulk. Two independent methods for SAXS data interpretation for comprehensive analysis of volume distributions of metal oxide NPs showed presence of both small particles and larger entities containing metal species which are ascribed to organization of block copolymer micelles in bulk. The magnetometry measurements revealed that the NPs are superparamagnetic and their characteristics depend on the method of the NP synthesis. The important advantage of the PEO 68-b-PMAA8 stabilized magnetic nanoparticles described in this paper is their remarkable solubility and stability in water and buffers.

Linear clusters of gold nanoparticles in quasinematic layers of DNA liquid-crystalline dispersion particles

The effects of small size (∼2 nm) gold nanoparticles on the properties of particles of cholesteric liquid-crystalline dispersions formed by double-stranded DNA molecules were analyzed. It has been shown that gold nanoparticles induce two different processes. First, they facilitate reorganization of the spatial cholesteric structure of dispersion particles to nematic one. This process is accompanied by the fast decrease in the amplitude of abnormal band in the CD spectrum. Second, they can form ensembles consisting of gold nanoparticles. This process is accompanied by the development and displacement of surface plasmon resonance band in the visible region of the absorption spectrum. The appearance of this band is analyzed by considering two different models of the formation of ensembles consisting of gold nanoparticles. By small-angle X-ray scattering we performed structural analysis of phases formed by DNA cholesteric liquid-crystalline dispersion particles treated with gold nanoparticles. As a result of this study it was possible to prove the formation of linear clusters of gold nanoparticles in the “free space” between the adjacent DNA molecules fixed in the quasinematic layers of liquid-crystalline particles. It has been hypothesized that the formation of linear clusters of gold nanoparticles is most likely related to DNA molecules, ordered in the spatial structure of quasinematic layers, and the toxicity of these nanoparticles in biological systems hypothesized.

Crystal and solution structures of methyltransferase RsmH provide basis for methylation of C1402 in 16S rRNA

RsmH is a specific AdoMet-dependent methyltransferase (MTase) responsible for N(4)-methylation of C1402 in 16S rRNA and conserved in almost all species of bacteria. The methylcytidine interacts with the P-site codon of the mRNA and increases ribosomal decoding fidelity. In this study, high resolution crystal structure (2.25Å) of Escherichia coli RsmH in complex with AdoMet and cytidine (the putative rRNA binding site) was determined. The structural analysis demonstrated that the complex consists of two distinct but structurally related domains: the typical MTase domain and the putative substrate recognition and binding domain. A deep pocket was found in the conserved AdoMet binding domain. It was also found that the cytidine bound far from AdoMet with the distance of 25.9Å. It indicates that the complex is not in a catalytically active state, and structural rearrangement of RsmH or the nucleotides neighboring C1402 may be necessary to trigger catalysis. Although there is only one molecule in the asymmetric unit of the crystals, RsmH can form a compact dimer across a crystallographic twofold axis. Further analysis of RsmH by small-angle X-ray scattering (SAXS) also revealed the dimer in solution, but with a more flexible conformation than that in crystal, likely resulting from the absence of the substrate. It implies that an active status of RsmH in vivo is achieved by a formation of the dimeric architecture. In general, crystal and solution structural analysis provides new information on the mechanism of the methylation of the fine-tuning ribosomal decoding center by the RsmH.

Platinum nanoparticles generated in functionality-enhanced reaction media based on polyoctadecylsiloxane with long-chain functional modifiers.

Functionality-enhanced nanostructured matrices generated by intercalating polyoctadecylsiloxane (PODS) with octadecene (ODC) or octadecylamine (ODA) are employed as reaction media in which to grow Pt nanoparticles. Small-angle X-ray scattering (SAXS) signatures confirm that the amphiphilic PODS matrix orders into lamellae with a periodicity (d) of 5.24 nm, which corresponds to the siloxy bilayer and a double layer of alkyl tails. The regular packing of the hydrophobic tails becomes distorted upon introduction of ODC or ODA. Incorporation of K[(C2H4)PtCl3].H2O (a Zeise salt) into the PODS/ODC matrix, followed by reduction of the Pt ions by NaBH4 or H2, results in the localization of Pt compounds and nanoparticles along the siloxy bilayers, which remain dimensionally unchanged. Electron density profiles deduced from PODS/ODA, however, provide evidence for considerable structural reorganization upon metalation with H2PtCl6.6H2O. In this case, the siloxy bilayers broaden due to the presence of PtCl62- ions, and the hydrophobic layers become distorted due to the formation of (PtCl62-)(ODAH+)2 complexes. Subsequent reduction by NaBH4 restores the inherent PODS organization, while H2 reduction partially preserves the distorted matrix, indicating that some Pt nanoparticles form in close proximity to the siloxy bilayer. Transmission electron microscopy reveals that relatively monodisperse Pt nanoparticles measuring approximately 1 nm in diameter are located along the siloxy bilayers, whereas anomalous SAXS further indicates that nanoparticles form aggregates of comparable size to d within the PODS double layers.