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PubMed2006

Strategies for data collection and calibration with a pinhole-geometry SAXS instrument on a synchrotron beamline.

Undulator X-ray sources on third-generation synchrotrons have pushed small-angle X-ray scattering (SAXS) to the forefront of techniques in nanoscience and technology. With higher X-ray fluxes and improved focusing, it is usually the scattered intensity detector that places the most serious limitations on the overall capabilities of the instrument. Incorporating relatively simple components like point detectors, scattering standards, masking filters and in-line sample visualization into the flight tube of a pinhole-geometry SAXS camera can do much to mitigate these limitations. How these enhancements can be incorporated into routine data collection is demonstrated on the ChemMatCARS SAXS instrument, which utilizes pinhole geometry with an undulator insertion device at sector 15 of the Advanced Photon Source. In addition, with an X-ray energy range of 6-32 keV (2.0-0.4 A) and an energy resolution of 10(-4) DeltaE/E, this instrument can measure anomalous SAXS over a wide variety of atom species, with reliable normalization of scattered data.

Calibration↗

PubMed2026

Cleavage region organizes the structural architecture of the SINE-derived B2 repressive ribozyme.

The SINE-encoded B2 retrotransposon is an RNA Polymerase III (POL-III)-derived transcript whose expression is substantially upregulated during various cellular stress responses. Beyond retrotransposition, the B2 non-coding RNA can directly bind and repress the activity of RNA Polymerase II (POL-II), leading to a significant downregulation of transcripts during stress. Notably, our recent findings have shown that B2 is a self-cleaving ribozyme whose activity can be induced by interactions with chromatin-modifying factors through non-canonical epigenetic mechanisms that co-regulate its function across distinct chromatin-binding target loci. Here, by integrating RNA chemical probing, small-angle X-ray scattering, and 3D motif modeling, we determine structural ensemble-to-function relations for the B2 SINE ribozyme RNA. Genetic perturbations of the RNA suggest that the B2 SINE ribozyme has a well-defined secondary and dynamic tertiary structure that depends on the integrity of the critical region, which confers ribozymatic activity and repressive extent by POL-II. Using an RNA engineering approach, we examine the effects of point mutations, deletions of the main cleavage site, and deletions of the cleavage domain on the structural ensemble of the RNA. Combining this approach with in vitro and in vivo functional perturbation methods highlights the relationships between structural ensembles and various biologically relevant functional outcomes.

RNA, Catalytic↗

PubMed2006

Structure of full-length bacterial chitinase containing two fibronectin type III domains revealed by small angle X-ray scattering.

Chitinase A1 (ChiA1) from Bacillus circulans WL-12 consists of an N-terminal catalytic domain, two fibronectin type III domains (FnIIIDs), and a C-terminal chitin-binding domain. The full-length structure of ChiA1 was studied by small angle X-ray scattering. The obtained low-resolution structure showed that ChiA1 is an elongated molecule with a length of approximately 145 A composed of a large globular head and a rod-like tail. Combination with known high-resolution structures of individual ChiA1 domains provided a model of the domain arrangement. In this model, two FnIIIDs connect to each other in an extended rod-like shape without large bending between the FnIIIDs, and contribute largely to the length of ChiA1.

Bacillus↗

PubMed2005

The liquidlike ordering of lipid A-diphosphate colloidal crystals: the influence of Ca2+, Mg2+, Na+, and K+ on the ordering of colloidal suspensions of lipid A-diphosphate in aqueous solutions.

A comprehensive study was performed on electrostatically stabilized aqueous dispersion of lipid A-diphosphate in the presence of bound Ca2+, Mg2+, K+, and Na+ ions at low ionic strength (0.10-10.0-mM NaCl, 25 degrees C) over a range of volume fraction of 1.0 x 10(-4)< or =phi< or =4.95 x 10(-4). These suspensions were characterized by light scattering (LS), quasielastic light scattering, small-angle x-ray scattering, transmission electron microscopy, scanning electron microscopy, conductivity measurements, and acid-base titrations. LS and electron microscopy yielded similar values for particle sizes, particle size distributions, and polydispersity. The measured static structure factor, S(Q), of lipid A-diphosphate was seen to be heavily dependent on the nature and concentration of the counterions, e.g., Ca2+ at 5.0 nM, Mg2+ at 15.0 microM, and K+ at 100.0 microM (25 degrees C). The magnitude and position of the S(Q) peaks depend not only on the divalent ion concentration (Ca2+ and Mg2+) but also on the order of addition of the counterions to the lipid A-diphosphate suspension in the presence of 0.1-microM NaCl. Significant changes in the rms radii of gyration (R2G) 1/2 of the lipid A-diphosphate particles were observed in the presence of Ca2+ (24.8+/-0.8 nm), Mg2+ (28.5+/-0.7 nm), and K+ (25.2+/-0.6 nm), whereas the Na+ salt (29.1+/-0.8 nm) has a value similar to the one found for the de-ionized lipid A-diphosphate suspensions (29.2+/-0.8 nm). Effective particle charges were determined by fits of the integral equation calculations of the polydisperse static structure factor, S(Q), to the light-scattering data and they were found to be in the range of Z*=700-750 for the lipid A-diphosphate salts under investigation. The light-scattering data indicated that only a small fraction of the ionizable surface sites (phosphate) of the lipid A-diphosphate was partly dissociated (approximately 30%). It was also discovered that a given amount of Ca2+ (1.0-5.0 nM) or K+ (100 microM) influenced the structure much more than Na+ (0.1-10.0-mM NaCl) or Mg2+ (50 microM). By comparing the heights and positions of the structure factor peaks S(Q) for lipid A-diphosphate-Na+ and lipid A-diphosphate-Ca2+, it was concluded that the structure factor does not depend simply on ionic strength but more importantly on the internal structural arrangements of the lipid A-diphosphate assembly in the presence of the bound cations. The liquidlike interactions revealed a considerable degree of ordering in solution accounting for the primary S(Q) peak and also the secondary minimum at large particle separation. The ordering of lipid A-diphosphate-Ca2+ colloidal crystals in suspension showed six to seven discrete diffraction peaks and revealed a face-centered-cubic (fcc) lattice type (a=56.3 nm) at a volume fraction of 3.2 x 10(-4)< or =phi< or =3.9 x 10(-4). The K+ salt also exhibited a fcc lattice (a=55.92 nm) at the same volume fractions, but reveals a different peak intensity distribution, as seen for the lipid A-diphosphate-Ca2+ salt. However, the Mg2+ and the Na+ salts of lipid A-diphosphate showed body-centered-cubic (bcc) lattices with a=45.50 nm and a=41.50 nm, respectively (3.2 x 10(-4)< or =phi< or =3.9 x 10(-4)), displaying the same intensity distribution with the exception of the (220) diffraction peaks, which differ in intensity for both salts of lipid A-diphosphate.

Calcium↗

PubMed2006

X-ray interference studies of crossbridge action in muscle contraction: evidence from quick releases.

We have used a high-resolution small angle X-ray scattering system, together with a high-performance CCD camera, on the BioCAT beamline at the APS synchrotron radiation facility at the Argonne National Laboratory, to study X-ray interference effects in the meridional reflections generated by the arrays of myosin crossbridges in contracting muscle. These give information about axial movements of the myosin heads during contraction with sub-nanometer resolution. Using whole intact muscle preparations (frog sartorius) we have been able to record the detailed behavior of M3 (the first order meridional reflection from the myosin crossbridges, at 14.56 nm) at each of a number of quick releases of increasing magnitude, on the same specimen, and at the same time make similar measurements on higher order myosin meridional reflections, particularly M6. The latter provides information about the dispersion of lever arm angles of the actin-attached myosin heads. The observations show that in isometric contraction the lever arm angles are dispersed through +/- 20-25 degrees on either side of a mean orientation that is about 60 degrees away from their orientation at the end of the working stroke: and that they move towards that orientation in synchronized fashion, with constant dispersion, during quick releases. The relationship between the shift in the interference fringes (which measures the shift of the myosin heads scattering mass towards the center of the sarcomere, and the changes in the total intensity of the reflections, which measures the changes in the axial profile of the heads, is consistent with the tilting lever arm mechanism of muscle contraction. Significant fixed contributions to the meridional reflections come from unattached myosin heads and from backbone components of the myosin filaments, and the interaction of these with the contributions from actin-attached myosin heads determines the behavior of these reflections.

Animals↗

PubMed2006

Morphological characterization of self-assembled peptide nucleic acid amphiphiles.

Peptide nucleic acid amphiphiles (PNAA) are a promising set of materials for sequence-specific separation of nucleic acids from complex mixtures. To implement PNAA in micellar separations, the morphology and size of PNAA micelles in the presence and absence of a sodium dodecyl sulfate (SDS) cosurfactant have been studied by small-angle X-ray scattering and dynamic light scattering. We find that a 6-mer PNAA with a 12-carbon n-alkane tail forms ellipsoidal micelles (a = 5.15 nm; b = 3.20 nm) above its critical micelle concentration (CMC) of 110.9 microM. On addition of a stoichiometric amount of complementary DNA, PNAA hybridizes to DNA, suppressing the formation of PNAA micelles. At a ratio of 19:1 SDS/PNAA (total concentration = 20 mM), spherical micelles are formed with outer radius Rs = 2.67 nm, slightly larger than spherical micelles of pure SDS. Capillary electrophoresis studies show that PNAA/DNA duplexes do not comicellize with SDS micelles. No such effects are observed using noncomplementary DNA. The shape and size of the PNAA micelles is also verified by dynamic light scattering (DLS) studies. These results provide an interesting case study with competing electrostatic, hydrophobic, and hydrogen-bonding interactions in micellar systems and make possible the use of PNAA in micellar separations of DNA oligomers.

Biosensing Techniques↗

PubMed2005

Multicomponent cationic lipid-DNA complex formation: role of lipid mixing.

Multicomponent cationic lipid-DNA complexes (lipoplexes) were prepared by adding linear DNA to mixed lipid dispersions containing two populations of binary cationic liposomes and characterized by means of small angle X-ray scattering (SAXS). Four kinds of cationic liposomes were used. The first binary lipid mixture was made of the cationic lipid (3'[N-(N',N'-dimethylaminoethane)-carbamoyl]cholesterol (DC-Chol) and the neutral helper lipid dioleoylphosphocholine (DOPC) (DC-Chol/DOPC liposomes), the second one of the cationic 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) and the neutral dioleoylphosphatidylethanolamine (DOPE) (DOTAP/DOPE liposomes), the third one of DC-Chol and DOPE (DC-Chol/DOPE liposomes), and the fourth one of DOTAP and DOPC (DOTAP/DOPC liposomes). Upon DNA-induced fusion of liposomes, large lipid mixing at the molecular level occurs. As a result, highly organized mixed lipoplexes spontaneously form with membrane properties intermediate between those of starting liposomes. By varying the composition of lipid dispersions, different DNA packing density regimes can also be achieved. Furthermore, occurring lipid mixing was found to induce hexagonal to lamellar phase transition in DOTAP/DOPE membranes. Molecular mechanisms underlying experimental findings are discussed.

Cations↗

PubMed2005

Structure modifications of AOT reverse micelles due to protein incorporation.

Structural modifications of AOT/water/isooctane reverse micelles due to incorporation of proteins were studied at various water contents and protein concentrations, using small-angle X-ray scattering (SAXS) experiments under static conditions, rheometry analysis, and SR-SAXS experiments under induced shear flow. Two proteins, lysozyme (pI 11.1, Mw 14,300 Da) and BSA (pI 4.3, Mw 66,700 Da), were chosen as models. SAXS analysis of protein-containing reverse micelles at low water content detected minima in the average micelle size versus protein concentration curve, for both proteins, below and above their isoelectric point. This minimum was attributed to changes in the size distribution of the reverse micelles. SAXS measurements of reverse micelles at high water content have shown them to have a cylindrical form. Incorporation of lysozyme at pH 7 into the cylindrical micelles induced a shape transition to spherical micelles, which was associated with a decreased viscosity. SR-SAXS measurements under induced shear flow and dynamic conditions revealed alignment of the cylindrical micelles in the flow direction. The anisotropy parameter, a measure of the degree of the spatial order, was found to increase with increasing shear rate and to decrease with increasing lysozyme concentration.

Micelles↗

PubMed2006

Electric and structural studies of hormone interaction with chloroplast envelope membranes isolated from vegetative and generative rape.

The electric and structural properties of envelope membranes of chloroplasts obtained from vegetative and generative plants of rape and the effect of hormone (IAA, GA(3) and zearalenone) treatment were determined by zeta potential and small-angle X-ray scattering (SAXS) methods. Chloroplasts were isolated from leaves cut off from the vegetative (before cooling) and generative apical parts of plants. The lipid composition of chloroplast envelope membranes were analyzed by chromatographic techniques. Envelopes from generative plants contained higher levels of digalactosyldiacylglycerol (DGDG) and smaller amounts of phospholipids (PLs) in comparison to those obtained from vegetative ones. Moreover, envelopes of generative plants were characterized by higher fractions of unsaturated fatty acids. The zeta potential changes caused by hormone treatment were higher for chloroplasts isolated from vegetative plants in comparison to chloroplasts isolated from generative ones. An especially strong effect was observed for chloroplasts treated with IAA. The thickness of bilayers of untreated chloroplasts from vegetative plants were larger by 0.4 nm when comparing to the thickness of layers obtained from generative ones. The effect of hormones (GA(3) and zearalenone) was detected only for vegetative chloroplasts. Both applied methods indicated differences in the properties of untreated and hormone-treated chloroplasts obtained from vegetative and generative plants.

Brassica napus↗

PubMed2002

Thermotropic behavior of poly(oxyethylene) cholesterol ethers.

The thermotropic behavior of poly(oxyethylene) cholesterol ether surfactants was studied by differential scanning calorimetry and small-angle X-ray scattering. Contrary to what is usually observed in conventional poly(oxyethylene)-type surfactant systems, poly(oxyethylene) cholesterol ether surfactants show a change of the fusion mechanism as the chain length is varied. For long chain lengths (n > or = 15) the usual solid-liquid transition is found, but for short chain lengths (n < or = 10) the transition goes through a birefringent lamellar phase. The appearance of this liquid crystal (LC) phase seems to be related with the predominance of the cholesterol part in the short chain polyoxyethylene surfactants. On the contrary, for long polyexyethylene chains the polymer gains in importance and only a solid crystalline structure is observed at low temperatures. An antiparallel packing structure with totally overlapped chains is found for both, the solid and the LC phase. The chains seem to be in a zigzag configuration, and only for the longest surfactant here studied (n = 30) a change of the chain configuration to a much shorter meander configuration is observed.

Calorimetry, Differential Scanning↗

PubMed2006

Phase behavior of a DNA-based surfactant mixed with water and n-alcohols.

The self-assembly behavior of a cationic surfactant (dodecyltrimethylammonium, DTA) with DNA as counterion in mixtures of water and n-alcohols (decanol, octanol, hexanol, butanol, and ethanol) was investigated. The phase diagrams were established and the different regions of the phase diagram characterized with respect to microstructure by (2)H NMR, small-angle X-ray scattering (SAXS), and other techniques. The DNA-DTA surfactant is soluble in all of the studied alcohols, showing increased solubility from decanol down to ethanol. All of the phase diagrams are analogous with respect to the occurrence of liquid crystalline (LC) regions, but the area of the LC region increases as one goes from decanol to ethanol. In all phase diagrams, hexagonal phases (of the reversed type) for the alcohol-rich side and lamellar phases for the other side were detected. For balanced proportions of the components, there is a coexistence of the lamellar and the hexagonal phase, here detected with a double quadrupole splitting in the (2)H NMR spectra. The correctness of the phase diagrams is confirmed by the fact that along the tie-lines the splitting magnitude remains nearly constant. All of the alcohols except for ethanol act as cosurfactants penetrating the DNA-DTA film. Adding salt to the ternary mixtures causes an increase in the unit cell dimension of the lamellar and the hexagonal phases. The phase diagram becomes more complicated when butanol is used for the alcohol phase. Here, there is the occurrence of a new isotropic phase with some properties analogous to those of the disordered sponge (L3) phase obtained for simple surfactant systems.

Alcohols↗

PubMed2006

Quantitative SAXS analysis of the P123/water/ethanol ternary phase diagram.

The ternary phase diagram of the amphiphilic triblock copolymer PEO-PPO-PEO ((EO)(20)(PO)(70)(EO)(20) commercialized under the generic name P123), water, and ethanol has been investigated at constant temperature (T = 23 degrees C) by small-angle X-ray scattering (SAXS). The microstructure resulting from the self-assembly of the PEO-PPO-PEO block copolymer varies from micelles in solution to various types of liquid crystalline phases such as cubic, 3D hexagonal close packed spheres (HCPS), 2D hexagonal, and lamellar when the concentration of the polymer is increased. In the isotropic liquid phase, the micellar structural parameters are obtained as a function of the water-ethanol ratio and block copolymer concentration by fitting the scattering data to a model involving core-shell form factor and a hard sphere structure factor of interaction. The micellar core, the aggregation number, and the hard sphere interaction radius decrease when increasing the ethanol/water ratio in the mixed solvent. We show that the fraction of ethanol present in the core is responsible for the swelling of the PPO blocks. In the different liquid crystalline phases, structural parameters such as lattice spacing, interfacial area of PEO block, and aggregation number are also evaluated. In addition to classical phases such as lamellar, 2D hexagonal, and liquid isotropic phases, we have observed a two-phase region in which cubic Fm3m and P6(3)mmc (hexagonally close packing of spheres (HCPS)) phases coexist. This appears at 30% (w/w) of P123 in pure water and with 5% (w/w) of ethanol. At 10% (w/w) ethanol, only the HCPS phase remains present.

Crystallization↗

PubMed2006

Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae.

Riboswitches are complex folded RNA domains found in noncoding regions of mRNA that regulate gene expression upon small molecule binding. Recently, Breaker and coworkers reported a tandem aptamer riboswitch (VCI-II) that binds glycine cooperatively. Here, we use hydroxyl radical footprinting and small-angle X-ray scattering (SAXS) to study the conformations of this tandem aptamer as a function of Mg(2+) and glycine concentration. We fit a simple three-state thermodynamic model that describes the energetic coupling between magnesium-induced folding and glycine binding. Furthermore, we characterize the structural conformations of each of the three states: In low salt with no magnesium present, the VCI-II construct has an extended overall conformation, presumably representing unfolded structures. Addition of millimolar concentrations of Mg(2+) in the absence of glycine leads to a significant compaction and partial folding as judged by hydroxyl radical protections. In the presence of millimolar Mg(2+) concentrations, the tandem aptamer binds glycine cooperatively. The glycine binding transition involves a further compaction, additional tertiary packing interactions and further uptake of magnesium ions relative to the state in high Mg(2+) but no glycine. Employing density reconstruction algorithms, we obtain low resolution 3-D structures for all three states from the SAXS measurements. These data provide a first glimpse into the structural conformations of the VCI-II aptamer, establish rigorous constraints for further modeling, and provide a framework for future mechanistic studies.

Aptamers, Nucleotide↗

PubMed2004

Small angle x-ray scattering from lipid-bound myelin basic protein in solution.

The structure of myelin basic protein (MBP), purified from the myelin sheath in both lipid-free (LF-MBP) and lipid-bound (LB-MBP) forms, was investigated in solution by small angle x-ray scattering. The water-soluble LF-MBP, extracted at pH < 3.0 from defatted brain, is the classical preparation of MBP, commonly regarded as an intrinsically unfolded protein. LB-MBP is a lipoprotein-detergent complex extracted from myelin with its native lipidic environment at pH > 7.0. Under all conditions, the scattering from the two protein forms was different, indicating different molecular shapes. For the LB-MBP, well-defined scattering curves were obtained, suggesting that the protein had a unique, compact (but not globular) structure. Furthermore, these data were compatible with earlier results from molecular modeling calculations on the MBP structure which have been refined by us. In contrast, the LF-MBP data were in accordance with the expected open-coil conformation. The results represent the first direct structural information from x-ray scattering measurements on MBP in its native lipidic environment in solution.

Computer Simulation↗

PubMed2000

GroES co-chaperonin small-angle X-ray scattering study shows ring orifice increase in solution.

GroES consists of seven identical 10 kDa subunits and is involved in assisting protein folding as the partner of another oligomeric protein, the GroEL chaperonin. Here we studied the GroES structure in solution using small-angle X-ray scattering (SAXS). The SAXS pattern, calculated for the GroES crystal structure, was found to be different from the experimental one measured in solution. The synchronic shift in the radial direction and some turning of the protein subunits eliminate the difference and result in the increase of the hole diameter in the GroES ring-like structure from 8 A in the crystal to 21 A in solution.

Chaperonin 10↗

PubMed2005

Thermal-induced phase transitions in self-assembled mesostructured films studied by small-angle X-ray scattering.

Two examples of phase transition in self-assembled mesostructured hybrid thin films are reported. The materials have been synthesized using tetraethoxysilane as the silica source hydrolyzed with or without the addition of methyltriethoxysilane. The combined use of transmission electron microscopy, small-angle X-ray scattering and computer simulation has been introduced to achieve a clear identification of the organized phases. A structural study of the self-assembled mesophases as a function of thermal treatment has allowed the overall phase transition to be followed. The initial symmetries of mesophases in as-deposited films have been linked to those observed in samples after thermal treatment. The monodimensional shrinkage of silica films during calcination has induced a phase transition from face-centered orthorhombic to body-centered cubic. In hybrid films, instead, the phase transition has not involved a change in the unit cell but a contraction of the cell parameter normal to the substrate.

Journal Article↗

PubMed1981

A small-angle X-ray scattering study of the complex formation between elongation factor Tu . GTP and valyl-tRNA Val I from Escherichia coli.

The complex formation between elongation factor Tu (EF-Tu) . GTP and valyl-tRNA Val 1 has been investigated using the small-angle X-ray scattering titration technique. The main species observed is a 1:1 complex with a stability constant log K greater than or equal to 6. The corresponding interaction between EF-Tu . GTP and non-aminoacylated tRNA appears to be much weaker with an estimated log K approximately equal to 4. The radius of gyration determined for the EF-Tu . GTP -- valyl-tRNA Val 1 complex is larger (R = 3.6 nm) than that of EF-Tu . GTP (R = 2.5 nm). Likewise, the maximum distance within this complex is larger (Dmax = 12.5 nm) than the one within EF-Tu . GTP (Dmax = 8.5 nm). These data as well as the p(r) curve are consistent with a multiellipsoid model for the complex. From this model it is indicated that the acceptor stem of tRNA is attached to EF-Tu and that the anticodon stem and loop protrude into the solution.

Bacterial Proteins↗

PubMed2006

The molecular basis of self-assembly of dendron-rod-coils into one-dimensional nanostructures.

We describe here a comprehensive study of solution and solid-state properties of self-assembling triblock molecules composed of a hydrophilic dendron covalently linked to an aromatic rigid rod segment, which is in turn connected to a hydrophobic flexible coil. These dendron-rod-coil (DRC) molecules form well-defined supramolecular structures that possess a ribbonlike morphology as revealed by transmission-electron and atomic-force microscopy. In a large variety of aprotic solvents, the DRC ribbons create stable networks that form gels at concentrations as low as 0.2% by weight DRC. The gels are thermally irreversible and do not melt at elevated temperatures, indicating high stability as a result of strong noncovalent interactions among DRC molecules. NMR experiments show that the strong interactions leading to aggregation involve mainly the dendron and rodlike blocks, whereas oligoisoprene coil segments remain solvated after gelation. Small-angle X-ray scattering (SAXS) profiles of different DRC molecules demonstrate an excellent correlation between the degree-of-order in the solid-state and the stability of gels. Studies on two series of analogous molecules suggest that self-assembly is very sensitive to subtle structural changes and requires the presence of at least four hydroxyl groups in the dendron, two biphenyl units in the rod, and a coil segment with a size comparable to that of the rodlike block. A detailed analysis of crystal structures of model compounds revealed the formation of stable one-dimensional structures that involve two types of noncovalent interactions, aromatic pi-pi stacking and hydrogen bonding. Most importantly, the crystal structure of the rod-dendron compound shows that hydrogen bonding not only drives the formation of head-to-head cyclic structures, but also generates multiple linkages between them along the stacking direction. The cyclic structures are tetrameric in nature and stack into ribbonlike objects. We believe that DRC molecules utilize the same arrangement of hydrogen bonds and stacking of aromatic blocks observed in the crystals, explaining the exceptional stability of the nanostructures in extremely dilute solutions as well the thermal stability of the gels they form. This study provides mechanistic insights on self-assembly of triblock molecules, and unveils general strategies to create well-defined one-dimensional supramolecular objects.

Anthracenes↗