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Results for “Scattering, Small Angle”

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PubMed2005

SOMO (SOlution MOdeler) differences between X-Ray- and NMR-derived bead models suggest a role for side chain flexibility in protein hydrodynamics.

Reduced numbers of frictional/scattering centers are essential for tractable hydrodynamic and small-angle scattering data modeling. We present a method for generating medium-resolution models from the atomic coordinates of proteins, basically by using two nonoverlapping spheres of differing radii per residue. The computed rigid-body hydrodynamic parameters of BPTI, RNase A, and lysozyme models were compared with a large database of critically assessed experimental values. Overall, very good results were obtained, but significant discrepancies between X-ray- and NMR-derived models were found. Interestingly, they could be accounted for by properly considering the extent to which highly mobile surface side chains differently affect translational/rotational properties. Models of larger structures, such as fibrinogen fragment D and citrate synthase, also produced consistent results. Foremost among this method's potential applications is the overall conformation and dynamics of modular/multidomain proteins and of supramolecular complexes. The possibility of merging data from high- and low-resolution structures greatly expands its scope.

Algorithms↗

PubMed2004

Computational methods for generating models of denatured and partially folded proteins.

Partially folded and denatured proteins can give important insights into protein folding, misfolding, and aggregation. Such non-native states of proteins are however very difficult to characterise in detail as they are dynamic, heterogeneous systems comprising of ensembles of interconverting conformers. This article describes methods that produce models for non-native proteins in atomic detail. A variety of molecular dynamics based protocols are discussed together with some recent procedures that include restraints from experimental data. These models provide an important framework for interpreting experimental data from studies of non-native states using nuclear magnetic resonance spectroscopy, fluorescence, circular dichroism, and small angle scattering techniques.

Animals↗

PubMed1994

X-ray diffraction measurements of the extensibility of actin and myosin filaments in contracting muscle.

We have used a small angle scattering system assembled on the high flux multipole wiggler beam line at CHESS (Cornell) to make very accurate spacing measurements of certain meridional and layer-line reflections from contracting muscles. During isometric contraction, the actin 27.3 A reflection increases in spacing from its resting value by approximately 0.3%, and other actin reflections, including the 59 and 51 A off-meridional reflections, show corresponding changes in spacing. When tension is augmented or diminished by applying moderate speed length changes to a contracting muscle, changes in spacing in the range of 0.19-0.24% (when scaled to full isometric tension) can be seen. The larger difference between the resting and isometric spacings suggests either nonlinearity at low tension levels or the presence of a component related to activation itself. Myosin filaments also show similar increases in axial period during slow stretch, in addition to the well known larger change associated with activation. An actin spacing change of 0.25-0.3% can also be measured during a 2 ms time frame immediately after a quick release, showing that the elastic behavior is rapid. These observations of filament extensions totaling 2-3 nm per half-sarcomere may necessitate some significant revision of the interpretation of a number of mechanical experiments in muscle, in which it has usually been assumed that virtually all of the elasticity resides in the cross-bridges.

Actins↗

PubMed1998

Intensive extrusion and occlusion of water in ganglioside micelles with thermal reversibility.

By using a shell-modeling analysis for small-angle scattering data of ganglioside micellar dispersion, we recently reported that the elevation of temperature induces a significant shrinkage of the hydrophilic region of the ganglioside micelle, suggesting that the oligosaccharide chains with sialic acid residues of ganglioside molecules change the conformation, sensitively responding to a change in temperature (Hirai et al., 1996. Biophys. J. 70:1761-1768; J. Phys. Chem. 100:11675-11680). We have carried out further analyses of the temperature dependence of the structural parameters reported previously, and we have found clear evidence of reversible extrusion and occlusion of a large amount of water in the hydrophilic region of the ganglioside micelle in the physiological temperature range of 6-60 degrees C. The present results suggest a remarkable function of ganglioside molecules: they change the hydrophilicity of the cell surface locally as a response to variations in temperature. This phenomenon might be involved in various surface events, such as cell-cell interaction and cell surface-protein interaction.

Animals↗

PubMed2000

Computational studies on carbohydrates: solvation studies on maltose and cyclomaltooligosaccharides (cyclodextrins) using a DFT/ab initio-derived empirical force field, AMB99C.

An empirical force field, denoted AMB99C, has been used to study molecular properties of alpha-(1-->4)-linked carbohydrates in solution. AMB99C was parameterized using structural and energetic parameters from density functional ab initio methodology. In this work we examine the solution behavior of the beta anomer of maltose and cyclohexa-, cyclohepta-, and cyclooctaamyloses (alpha-, beta-, and gamma-cyclodextrins or alpha-, beta-, and gamma-CDs, respectively), as well as of two larger (DP 10, epsilon-CD; DP 21) cyclomaltooligosaccharides, CA10 and CA21. Experimental data used for comparison purposes include X-ray structures, small-angle scattering radius of gyration values, NMR nuclear Overhauser enhancements (NOEs), and proton coupling constants. Molecular dynamics simulations were carried out using explicit water molecules (TIP3P) to establish equilibrium populations of conformations in solution, and these results are compared with other calculated values and a variety of experimental parameters, such as average H-1-H-4' distances between the rings in beta-maltose, and the primary hydroxyl groups' conformational populations. Medium-to-large cyclomaltooligosaccharide molecules were studied to test for glucose ring puckering and stability of kinked and 'flipped' conformations. The results of the solvation studies are in excellent agreement with experimental structural parameters.

Carbohydrate Conformation↗

PubMed2003

The active conformation of glutamate synthase and its binding to ferredoxin.

Glutamate synthases (GltS) are crucial enzymes in ammonia assimilation in plants and bacteria, where they catalyze the formation of two molecules of L-glutamate from L-glutamine and 2-oxoglutarate. The plant-type ferredoxin-dependent GltS and the functionally homologous alpha subunit of the bacterial NADPH-dependent GltS are complex four-domain monomeric enzymes of 140-165 kDa belonging to the NH(2)-terminal nucleophile family of amidotransferases. The enzymes function through the channeling of ammonia from the N-terminal amidotransferase domain to the FMN-binding domain. Here, we report the X-ray structure of the Synechocystis ferredoxin-dependent GltS with the substrate 2-oxoglutarate and the covalent inhibitor 5-oxo-L-norleucine bound in their physically distinct active sites solved using a new crystal form. The covalent Cys1-5-oxo-L-norleucine adduct mimics the glutamyl-thioester intermediate formed during L-glutamine hydrolysis. Moreover, we determined a high resolution structure of the GltS:2-oxoglutarate complex. These structures represent the enzyme in the active conformation. By comparing these structures with that of GltS alpha subunit and of related enzymes we propose a mechanism for enzyme self-regulation and ammonia channeling between the active sites. X-ray small-angle scattering experiments were performed on solutions containing GltS and its physiological electron donor ferredoxin (Fd). Using the structure of GltS and the newly determined crystal structure of Synechocystis Fd, the scattering experiments clearly showed that GltS forms an equimolar (1:1) complex with Fd. A fundamental consequence of this result is that two Fd molecules bind consecutively to Fd-GltS to yield the reduced FMN cofactor during catalysis.

Crystallography, X-Ray↗

PubMed2000

Tissue structure study through ultrasonic forward scattering.

A procedure is demonstrated for characterization of biological tissues at small scattering angles. The power spectra of ultrasonic pulses transmitted through excised tissue samples were measured and compared to the spectra of signals transmitted through a water path. The specimens were examined in two spatial-frequency bands by acquiring data at scattering angles of 10 degrees and 20 degrees using 2.25 MHz transducers. Peaks in the measured power spectra are interpreted using two signal models. The medium is modelled either as a periodic structure producing a single spectral peak, or by two discrete targets producing a periodic modulation of the spectrum. The periodic structure model appears to be the more promising method for interpretation of forward-scattered signals. Data acquired from hyperplastic spleen and atheromatous aorta specimens both exhibited increases in pulse-tissue interaction at low spatial frequencies compared to normal specimens of those tissues. This observation is tentatively linked to increases in the size or separation of distributed scattering structures resulting from those pathologies.

Animals↗

PubMed1997

Structural studies of the glycine decarboxylase complex from pea leaf mitochondria.

The glycine decarboxylase complex consists of four different component enzymes (P-, H-, T- and L-proteins). The 14-kDa lipoamide-containing H-protein plays a pivotal role in the complete sequence of reactions since its prosthetic group (lipoic acid) interacts successively with the three other components of the complex and undergoes a cycle of reductive methylamination, methylamine transfer and electron transfer. The X-ray crystal structure of different forms of the H-protein has shown a unique conformation of the protein. This leads to the hypothesis of a three-dimensional recognition of the H-protein by the other components of the system and also by the ligase which lipoylates the H-protein. Striking structural similarities are observed between the H-protein and other lipoate domains of 2-oxo acid dehydrogenases and with the biotin carrier protein of acetyl-CoA carboxylase. In the H-protein, the lipoamide arm is free to move in the solvent when oxidized but is pivoted and tightly bound into a cleft at the protein surface when methylamine-loaded. This implies that the H-protein and the T-component form a stable complex during the catalytic transfer of the methylene unit to the tetrahydrofolate cofactor of the T-protein. This complex has been detected by small angle scattering experiments. In conclusion, in the glycine decarboxylase system, the lipoamide arm does not swing freely from one catalytic site to another as was proposed in other systems.

Amino Acid Oxidoreductases↗

PubMed1997

Quartz balance DNA sensor.

Single-strand DNA-containing thin films were deposited onto quartz oscillators by the Langmuir-Blodgett technique towards the realization of a device capable of sensing the presence of the complementary DNA sequences which hybridize with the immobilized ones. DNA, once complexed with aliphatic amines, appears as a monolayer in a single-stranded form by X-ray small angle scattering. A quartz nanobalance is then utilized to monitor mass increment related to specific hybridization with a complementary DNA probe. The crystal quartz nanobalance, capable of high sensitivity, indeed appears capable of obtaining a prototype of a device capable of sensing the occurrence of particular genes or sequences in the sample under investigation. The validity of the nanogravimetric assay was confirmed by independent fluorescence measurements utilizing DAPI and a CCD camera.

Biosensing Techniques↗

PubMed2001

Structural Insights into the A1 ATPase from the archaeon, Methanosarcina mazei Gö1.

The low-resolution structure and overall dimensions of the A(3)B(3)CDF complex of the A(1) ATPase from Methanosarcina mazei Gö1 in solution is analyzed by synchrotron X-ray small-angle scattering. The radius of gyration and the maximum size of the complex are 5.03 +/- 0.1 and 18.0 +/- 0.1 nm, respectively. The low-resolution shape of the protein determined by two independent ab initio approaches has a knob-and-stalk-like feature. Its headpiece is approximately 9.4 nm long and 9.2 nm wide. The stalk, which is known to connect the headpiece to its membrane-bound A(O) part, is approximately 8.4 nm long. Limited tryptic digestion of the A(3)B(3)CDF complex was used to probe the topology of the smaller subunits (C-F). Trypsin was found to cleave subunit C most rapidly at three sites, Lys(20), Lys(21), and Arg(209), followed by subunit F. In the A(3)B(3)CDF complex, subunit D remained protected from proteolysis.

Adenosine Triphosphatases↗

PubMed2005

SAS solution structures of the apo and Mg2+/BeF3(-)-bound receiver domain of DctD from Sinorhizobium meliloti.

Two-component signal transduction is the predominant information processing mechanism in prokaryotes and is also present in single-cell eukaryotes and higher plants. A phosphorylation-based switch is commonly used to activate as many as 40 different types of output domains in more than 6000 two-component response regulators that can be identified in the sequence databases. Previous biochemical and crystallographic studies showed that phosphorylation of the two-component receiver domain of DctD causes a switch between alternative dimeric forms, but it was unclear from the crystal lattice of the activated protein precisely which of four possible dimeric configurations is the biologically relevant one [Park, S., et al. (2002) FASEB J. 16, 1964-1966]. Here we report solution structures of the apo and activated DctD receiver domain derived from small angle scattering data. The apo dimer closely resembles that seen in the crystal structure, and the solution data for the activated protein eliminate two of the possible four dimeric conformations seen in the crystal lattice and strongly implicate one as the biologically relevant structure. These results corroborate the previously proposed model for how receiver domains regulate their downstream AAA+ ATPase domains.

Beryllium↗

PubMedDate not supplied

Aggregation during coniferyl alcohol polymerization in pectin solution: a biomimetic approach of the first steps of lignification.

Coniferyl alcohol was polymerized in pectin solution in order to mimic the lignification that is the final step of biosynthesis of plant cell wall. Dehydrogenated polymers (DHP = coniferyl alcohol polymers = synthetic lignin) interact with pectin to form hydrophobic clusters as monitored by pyrene fluorescence spectroscopy. The structure of these clusters was studied during the polymerization of synthetic lignin by static and quasielastic light scattering and small angle neutron scattering experiments. We show that synthetic lignin and pectin contribute to the same clusters, but the inner structure of these clusters is very heterogeneous and displays three phases. One observes a segregation between well separated pectin and lignin rich phases at length scales below approximately 30 nm. As a corollary of this segregation, clusters embody a large amount of solvent. On average, the density of the polymer rich phase (lignin plus pectin) inside clusters increases while its specific surface area decreases throughout the polymerization process. These results are discussed with respect to in vivo lignification of the plant cell wall.

Biomimetic Materials↗

PubMed2006

Transition of nanostructure in DNA-cationic surfactant complexes with the added salt.

Nanostructures of complexes of DNA with single-chain surfactant of octadecyltrimethylammonium (OTA) and double-chain surfactant of didodecyldimethylammonium (DDA) in aqueous NaCl solution at concentration, Cs, from 0 to 500 mM were studied using small-angle-scattering techniques (SAXS). SAXS profiles of the DNA-OTA complex show two SAXS peaks with a spacing ratio of 1:3(1/2) in the solution at Cs below 150 mM and three peaks with a spacing ratio of 1:3(1/2):4(1/2) at Cs above 250 mM. Contents of Na+ and Cl- ions in the complexes evaluated from the atomic absorbance for Na+ and the potentiometry for Cl- revealed charge molar ratios of OTA/DNA = 1 and DDA/DNA = 1.25. Contents of Na+ and Cl- ions per ionic unit of DNA molecule in the DNA-OTA complex equilibrating with the solution at Cs below 100 mM were much less than 0.1, while they increased with NaCl concentration at Cs above 200 mM. The DNA-OTA complex in the solution at Cs above 260 mM exhibited an endothermic peak in the DSC measurements, and the others did not. On the basis of the experimental results, the salt concentration dependent nanostructures are discussed.

Cations↗

PubMed2002

The formation of polymer vesicles or "peptosomes" by polybutadiene-block-poly(L-glutamate)s in dilute aqueous solution.

Polybutadiene-block-poly(L-glutamate) copolymers were made by anionic polymerization and subsequent ring-opening polymerization of N-carboxyanhydrides and were characterized by NMR, IR, SEC, and circular dichroism. These polymers, when appropriately designed, form so-called "polymersomes" or "peptosomes", vesicles composed of modified protein units. The size and structure of the vesicles are determined by dynamic light scattering, small-angle neutron scattering, and freeze-fracture electron microscopy. It is also shown that the size of the peptosomes does not depend on the pH; that is, the solvating peptide units can perform a helix-coil transition without serious changes of the vesicle morphology.

Butadienes↗

PubMed2005

Chemically tuned amphiphilic diblock copolymers dispersed in water: from colloids to soluble macromolecules.

We investigate by small-angle scattering the structural behavior in water of a family of asymmetric poly(styrene-stat-(acrylic acid))-block-poly(acrylic acid), i.e., P(S-stat-AA)-b-PAA, diblock copolymers. These diblocks are of constant block ratio and increasing molar fraction, phi(AA), ranging from 0 to 1, of acrylic acid in the first P(S-stat-AA) statistical block. We identify three types of structural behavior in water: (i) for phi(AA) </= 0.25, the structures found in water are out-of-equilibrium micelle-like objects, reminiscent of the macrophase separation in the solid state, with no reorganization upon dispersion; (ii) for phi(AA) >/= 0.50, the diblocks dispersions in water are at equilibrium. For high phi(AA), the diblocks are soluble in water, demonstrating that a transition from colloid-like objects to soluble macromolecules is achieved. Close to the transition, (phi(AA) approximately 0.50), the diblocks form objects interpreted as comprising a water-swollen core formed by the P(S-stat-AA) block, surrounded by a swollen brush composed of the majority PAA block, above a apparent critical micelle concentration. However, these diblocks do not behave as macrosurfactants, and their self-association behavior is rather interpreted as a microphase separation which can arise from the incompatibility between two polymer blocks P(S-stat-AA) and PAA placed in a common solvent water.

Journal Article↗

PubMed2005

Nonspherical assemblies generated from polystyrene-b-poly(L-lysine) polyelectrolyte block copolymers.

This report describes the aqueous solution self-assembly of a series of polystyrene(m)-b-poly(L-lysine)n block copolymers (m = 8-10; n = 10-70). The polymers are prepared by ring-opening polymerization of epsilon-benzyloxycarbonyl-L-lysine N-carboxyanhydride using amine terminated polystyrene macroinitiators, followed by removal of the benzyloxycarbonyl side chain protecting groups. The critical micelle concentration of the block copolymers determined using the pyrene probe technique shows a parabolic dependence on peptide block length exhibiting a maximum at n = approximately 20 (m = 8) or n = approximately 60 (m = 10). The shape and size of the aggregates has been studied by dynamic and static light scattering, small-angle neutron scattering (SANS), and analytical ultracentrifugation (AUC). Surprisingly, Holtzer and Kratky analysis of the static light scattering results indicates the presence of nonspherical, presumably cylindrical objects independent of the poly(L-lysine)n block length. This is supported by SANS data, which can be fitted well by assuming cylindrical scattering objects. AUC analysis allows the molecular weight of the aggregates to be estimated as several million g/mol, corresponding to aggregation numbers of several 10s to 100s. These aggregation numbers agree with those that can be estimated from the length and diameter of the cylinders obtained from the scattering results.

Journal Article↗

PubMed2005

Large-scale structure in gels of attractive block copolymer micelles.

We have used ultra-small-angle scattering (USANS) and fluorescence microscopy to demonstrate the existence of a nonfractal large-scale structure in attractive micellar gels of poly(styrene)-poly(acrylic acid) block copolymers, which have some characteristics of attractive colloidal glasses. The nature of the large-scale structure appears to depend systematically on the strength of attraction. Our systems display scattering that follows I approximately q(x) in the low q regime, with x varying from approximately -3 to -4 as the strength of attraction is decreased. This scattering behavior appears to be the result of surface scattering from large, highly polydisperse aggregates with rough interfaces.

Journal Article↗

PubMed2005

Structure factors of dispersible units of carbon black filler in rubbers.

We report the structures of dispersible units, a most fundamental but minimal dispersible structural unit of a carbon black (CB) filler that is formed in two kinds of rubber (polyisoprene and styrene-butadiene random copolymer) matrices under a given processing condition. The results obtained from various small-angle scattering techniques showed that the CB aggregates, as observed after the sonification of a CB/toluene solution, were a spherical shape composed of approximately nine primary CB particles fused together. In the rubber matrices, the aggregates clustered into higher order structures defined in this work as the dispersible units, which are the fundamental structural elements (or the "lower cutoff structures") that build up a higher order mass-fractal structure. Furthermore, we found that the morphology of the dispersible units strongly depended on the rubber matrix, although the mass-fractal dimensions remained unchanged.

Journal Article↗