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PubMed1984

Neutron small-angle scattering studies of ribonuclease in mixed aqueous solutions and determination of the preferentially bound water.

Neutron small-angle measurements of ribonuclease A in mixed solutions of ethanol-water and glycerol-water have been used to estimate the region near the molecule that only contains water. When glycerol is used as probe, the region corresponds to an interaction parameter xi of 0.23 +/- 0.05 g of water/g of protein. For ethanol xi is -0.07 +/- 0.05, corresponding to the macromolecule being equally accessible to ethanol and water. The observations of the radius of gyration in the mixed solutions are used to show that the volume excluding glycerol is found on the exterior of the protein.

Ethanol↗

PubMed2004

A study of carbon black Corax N330 with small-angle scattering of neutrons and X-rays.

Carbon black Corax N330 (hereinafter called CB) is used as a filler in elastomers. The properties of the surface are important for the binding of the elastomer to the carbon black particles. Porod's law requires the intensity to satisfy I(q) approximately q(-alpha) with alpha = 4 for large q. Rieker et al. observed alpha = 3.7 +/- 0.1 for small-angle X-ray scattering (SAXS) data and concluded that the particle surface is fractally rough. Ruland critized this and suggested that the observed deviation is due to fluctuations of the spacing of the graphitic layer planes ("graphenes") which contribute a component I(q)fluc = 1Cflucq(-2) to the intensity component satisfying Porod's law. We studied CB by nitrogen adsorption, high-resolution transmission electron microscopy, synchroton SAXS, and small-angle neutron scattering (SANS). Our SAXS experiments with samples of high transmission (Tr = 0.96) confirmed the form of the scattering curves published by Rieker et al., but the correction for I(q)fluc restored Porod's law. SANS experiments were performed with a sample of low transmission in order to analyze the high q-range for scattering from voids and isolated graphenes. We found I(q) approximately q(-beta) with beta approximately 2 at q > 2.5 nm(-1) and will show that this intensity component requires graphenes consisting of about 12 benzene rings. The contrast matching technique revealed the presence of inaccessible voids. The SANS data for a sample with Tr = 0.363 satisfy Porods law, in contrast to the SAXS data for the high transmission samples. The latter discrepancy is likely due to the lower resolution of the SANS measurements because of wavelength smearing and multiple scattering. A SANS sample with Tr = 0.97 shows a minor deviation from Porod's law only (alpha = 3.9). The original SANS data and the SAXS data corrected for the fluctuation component indicate that the CB surface is essentially smooth.

Journal Article↗

PubMed1990

Small-angle scattering studies show distinct conformations of calmodulin in its complexes with two peptides based on the regulatory domain of the catalytic subunit of phosphorylase kinase.

Small-angle X-ray and neutron scattering have been used to study the solution structures of calmodulin complexed with synthetic peptides corresponding to residues 342-366 and 301-326, designated PhK5 and PhK13, respectively, in the regulatory domain of the catalytic subunit of skeletal muscle phosphorylase kinase. The scattering data show that binding of PhK5 to calmodulin induces a dramatic contraction of calmodulin, similar to that previously observed when calmodulin is complexed with the calmodulin-binding domain peptide from rabbit skeletal muscle myosin light chain kinase. In contrast, calmodulin remains extended upon binding PhK13. In the presence of both peptides, calmodulin also remains extended. Apparently, the presence of PhK13 inhibits calmodulin from undergoing the PhK5-induced contraction. These data indicate that there is a fundamentally different type of calmodulin-target enzyme interaction in the case of the catalytic subunit of phosphorylase kinase compared with that for myosin light chain kinase.

Amino Acid Sequence↗

PubMed1980

The conformation of a large RNA fragment from the E.coli ribosomal 16S-RNA. An X-ray and neutron small-angle scattering study.

A large 12S RNA fragment which constitutes the 5' two-thirds of 16S-RNA from the E. coli 30S subunit has been investigated by small-angle X-ray and neutron scattering. The results indicate that in reconstitution buffer the 12S-RNA fragment has a molecular weight of 270,000 +/- 20,000 and a radius of gyration of 7.1 nm. The scattering data are compatible with the RNA being folded into two major domains with the shapes of two adjacent, quite similar cylinders.

Escherichia coli↗

PubMed2000

Calmodulin remains extended upon binding to smooth muscle caldesmon: a combined small-angle scattering and fourier transform infrared spectroscopy study.

We show that calmodulin (CaM) has an extended conformation in its complexes with sequences from the smooth muscle thin filament protein caldesmon (CaD) by using small-angle X-ray and neutron scattering with contrast variation. The CaD sequences used in these experiments were a C-terminal fragment, 22kCaD, and a smaller peptide sequence within this fragment, MG56C. Each of these sequences contains the CaM-binding sites A and B previously shown to interact with the C- and N-terminal lobes of CaM, respectively [Wang et al. (1997) Biochemistry 36, 15026]. By modeling the scattering data, we show that the majority of the MG56C sequence binds to the N-terminal domain of CaM. FTIR data on CaM complexed with 22kCaD or with MG56C peptide show the 22kCaD sequence contains unordered, helix, and extended structures, and that the extended structures reside primarily in the MG56C portion of the sequence. There are small changes in secondary structure, involving approximately 12 residues, induced by CaM binding to CaD. These changes involve a net decrease in extended structures accompanied by an increase in alpha-helix, and they occur within the CaM and/or in the MG56C sequence.

Animals↗

PubMed1989

Large intramolecular movement in human complement protein C3 induced by methylamine. A small-angle scattering study using monoclonal antibodies as markers.

The reaction of methylamine with complement protein C3, which involves cleavage of a labile thiol ester bond, yields a large intramolecular rearrangement. This is shown by small-angle neutron and X-ray scattering using a Fab antibody as a marker. For the C3(Fab) 1:1 complex, the methylamine reaction yields an increase in the radius of gyration, R, from 4.6 nm to 6.0 nm. In the absence of Fab the corresponding R values increase from 4.4 nm to 5.1 nm. It is estimated that the methylamine-induced increase in R may correspond to a movement of the epitope to a position 5 nm away from the centre of gravity of the C3 molecule. In agreement with this finding, the maximum distance within the C3(Fab) complex increases from 16 nm to 22 nm as a result of the methylamine reaction. In order to explain this conformational change, it is tentatively suggested that the methylamine-induced cleavage of the C3 thiol ester bond leads to a domain rotation within the C3 molecule. In agreement with this idea, the data is consistent with a model which enables a globular domain within the molecule to rotate without redistributing the molecular mass more than that corresponding to the radii of gyration observed.

Antibodies, Monoclonal↗

PubMed2004

Conformations of variably linked chimeric proteins evaluated by synchrotron X-ray small-angle scattering.

We constructed chimeric proteins that consist of two green fluorescent protein variants, EBFP and EGFP, connected by flexible linkers, (GGGGS)n (n = 3 approximately 4), and helical linkers, (EAAAK)n (n = 2 approximately 5). The conformations of the chimeric proteins with the various linkers were evaluated using small-angle X-ray scattering (SAXS). The SAXS experiments showed that introducing the short helical linkers (n = 2 approximately 3) causes multimerization, while the longer linkers (n = 4 approximately 5) solvate monomeric chimeric proteins. With the moderate-length linkers (n = 4), the observed radius of gyration (R(g)) and maximum dimension (D(max)) were 38.8 A and 120 A with the flexible linker, and 40.2 A and 130 A with the helical linker, respectively. The chimeric protein with the helical linker assumed a more elongated conformation as compared to that with the flexible linker. When the length of the helical linker increased (n = 5), R(g) and D(max) increased to 43.2 A and 140 A, respectively. These results suggest that the longer helix effectively separates the two domains of the chimeric protein. Considering the connectivity of the backbone peptide of the protein, the helical linker seems to connect the two domains diagonally. Surprisingly, the chimeric proteins with the flexible linker exhibited an elongated conformation, rather than the most compact side-by-side conformation expected from the fluorescence resonance energy transfer (FRET) analysis. Furthermore, the SAXS analyses suggest that destabilization of the short helical linker causes multimerization of the chimeric proteins. Information about the global conformation of the chimeric protein is thus be necessary for optimization of the linker design.

Fluorescence Resonance Energy Transfer↗

PubMed2003

Structural characterization of T-protein of the Escherichia coli glycine cleavage system by X-ray small angle scattering.

T-protein, one of the components of the glycine cleavage complex, catalyses the formation of ammonia and methylene-tetrahydrofolate from H-protein-bound intermediate. Native T-protein of the glycine cleavage system from E. coli was efficiently purified using a combination of hydrophobic interaction, gel permeation and ion exchange chromatography. Synchrotron radiation small angle X-ray solution scattering indicates that T-protein has an extended structure in solution. A low resolution model of the protein was constructed ab initio and tentative models of the tertiary structure were built using prediction methods constrained by the scattering data.

Aminomethyltransferase↗

PubMed2006

Carbide-derived carbons: a comparative study of porosity based on small-angle scattering and adsorption isotherms.

Porous carbons have received much attention recently for potential applications in energy generation and storage, molecular sieving, and environmental remediation. Property optimization for specific applications rests largely on controlling the volume, size, and shape of the pores at the synthetic level. Direct atom-scale experiments which might accurately and reliably measure these quantities are problematic, so indirect methods such as gas sorption are generally employed. Here we apply a second indirect method, small-angle X-ray scattering (SAXS), to study porosity in carbide-derived carbons (CDC). The results qualitatively confirm and reinforce model-dependent conclusions drawn from gas sorption isotherms. In particular, both techniques indicate the onset of broad polydispersity under the same processing conditions for particular porous carbon materials.

Journal Article↗

PubMed2004

Pressure-induced formation of diblock copolymer "micelles" in supercritical fluids. A combined study by small angle scattering experiments and mean-field theory. II. Kinetics of the unimer-aggregate transition.

We developed a simple time-dependent mean-field theory to describe the phase separation kinetics of either homopolymers or AB-diblock copolymers in supercritical (SC) fluids. The model, previously used to describe the phase behavior of AB-block copolymers under the assumption of strong solvent selectivity for just one copolymer chain, has been extended to study the kinetics of the phase separation process. Time resolved small angle x-ray scattering (TR-SAXS) measurements have been performed on different AB-diblock copolymers containing a perfluorinated chain and dissolved in SC-CO2. The data obtained over a wide range of pressure and temperature confirm our theoretical predictions. Particularly interesting is the presence of two relaxation frequencies for the homogeneous solution --> spherical aggregate transition, where the two relaxation processes depend on the depth of the pressure jump and on temperature. The whole phenomenon could be explained as an initial SC solvent/polymer phase separation followed by a slow reorientation process to form spherical aggregates driven by the copolymer solvophilic moiety.

Journal Article↗

PubMed1995

Scanning transmission electron microscopy and small-angle scattering provide evidence that native Escherichia coli ClpP is a tetradecamer with an axial pore.

The Escherichia coli ATP-dependent caseinolytic protease (Clp) is composed of two distinct subunits; protease, ClpP, and ATPase, ClpA. Active ClpP has been overexpressed to approximately 50% of soluble protein in E. coli, and purified to homogeneity. Direct mass determination of individual particles using scanning transmission electron microscopy (STEM) yields a mean native molecular mass of 305 +/- 9 kDa for the ClpP oligomer, suggesting that it has a tetradecameric structure. Small-angle X-ray scattering (SAXS) curves were determined for ClpP in solution at concentrations of 1-10 mg/mL. A combination of STEM and SAXS data was used to derive a model for ClpP, comprising a cylindrical oligomer about 100 A in diameter and about 75 A in height with an axial pore about 32-36 A in diameter. The volume of the pore is estimated to be approximately 70,000 A3, similar in size to those found in chaperone proteins, and is large enough to accommodate unfolded polypeptide chains, although most globular folded proteins would be excluded.

Adenosine Triphosphatases↗

PubMed1986

Connective tissue polarity. Optical second-harmonic microscopy, crossed-beam summation, and small-angle scattering in rat-tail tendon.

Connective tissue polarity has remained an intractable enigma for over two decades. We present new data on optical second harmonic generation in native, wet, rat-tail tendon. Scanning second-harmonic microscopy has revealed, for the first time, the existence of a discrete network of fine, polar, filamentous or columnar, structures, and, also, the presence of strongly polar surface, or near-surface patches. The thickness of these features was probed via crossed-beam optical frequency summation and the polar material is estimated to occupy a few percent of the tendon volume. The three-dimensional spatial distribution of filaments was studied with the aid of small-angle second-harmonic scattering, and the filaments were found to permeate the tendon cross-section in an apparently random fashion. These latter measurements also revealed that essentially all polar filaments had the same directionality. Concomitant studies of the polar collagen fibrils that comprise the bulk of tendon were in full accord with prior electron microscope results that had demonstrated that the directionality of these fibrils varies up/down in a purely random fashion, and thus cannot yield a net macroscopic polarity. Quantitative analysis of the second-harmonic data yields the conclusion that the observed polar structures cannot be simply local regions containing some accidental net excess of similarly oriented fibrils. The analytical expressions used in the analysis of the data obtained for this complex tissue were supported by extensive, realistic computer simulations. The discovery that the polarity of rat-tail tendon, and possibly other forms of connective tissue, resides in discrete structures, some of which are located near the tendon surface, should permit the ready isolation of polar-rich material for further study by a variety of techniques.

Animals↗

PubMed2007

Microstructure of beta-lactoglobulin/pectin coacervates studied by small-angle neutron scattering.

Small-angle neutron scattering (SANS) has been used to investigate the microstructure of beta-lactoglobulin/pectin coacervates prepared by different initial protein/polysaccharide weight ratio (r), sodium chloride concentration (C(NaCl)), and pectin charge density. The higher r and higher pectin charge density lead to higher scattering intensity at small q range (0.007 Angstrom(-1) < q < 0.02 Angstrom(-1)), suggesting that the charges of pectin chains are screened significantly by the binding of oppositely charged protein molecules, leading to a tighter aggregation of pectin chains. On the other hand, the appearance of a shoulder peak at intermediate q range (0.04 Angstrom(-1) < q < 0.2 Angstrom(-1)) is used to interpret the formation of protein domains in beta-lactoglobulin/pectin coacervates. At C(NaCl) = 0.1 M, the coacervate of beta-lactoglobulin and pectin A does not show a shoulder peak at intermediate q range at r = 10:1, suggesting that protein molecules are separately bound on pectin chains. However, a shoulder peak appears at intermediate q range at r = 20:1 and 30:1, and the average protein domain size estimated from the shoulder peak position is 7.2 and 8.5 nm, respectively, for these two coacervates. When C(NaCl) increases from 0.05 to 0.2 M, the shoulder peak shifts toward smaller q and becomes broader, indicating that the addition of a higher amount of salt leads to a more heterogeneous coacervate structure. Pectin B with a lower linear charge density favors the formation of larger protein domains. The formation of protein domains in beta-lactoglobulin/pectin coacervates is partially ascribed to the self-aggregation of beta-lactoglobulin molecules. Two kinds of microstructures of beta-lactoglobulin/pectin coacervates with and without observable protein domains have been proposed.

Algorithms↗

PubMed2004

Pressure-induced formation of diblock copolymer "micelles" in supercritical fluids. A combined study by small angle scattering experiments and mean-field theory. I. The critical micellization density concept.

We developed a simple mean-field theory to describe polymer and AB diblock copolymer phase separation in supercritical (SC) fluids. The highly compressible SC fluid has been described by using a phenomenological hole theory, properly extended to consider the solvent/polymer/vacancy pseudoternary mixture. The model has been applied to describe the phase behavior of AB-diblock copolymers under the assumption of a strong solvent selectivity for just one copolymer chain. In our model the solvent selectivity is a strong function of the external pressure because in compressible fluids vacancies reduce the number of favorable solvent-polymer contacts. The combined effect of the pressure on the average solvent quality and selectivity for a single polymer chain makes the phase behavior of a diblock copolymer in SC fluids quite complex. Small angle neutron and x-ray scattering (SANS and SAXS) measurements have been performed on SC-CO2 solutions of different AB-diblock copolymers containing a perfluorinated chain. The data obtained over a wide range of pressure and temperature confirm our theoretical predictions.

Journal Article↗

PubMed2005

Structure and interaction in protein solutions as studied by small-angle neutron scattering.

Small-angle neutron scattering (SANS) measurements have been performed to compare the effect of the salts KF, KCl, and KBr on crystallization in aqueous solution of lysozyme protein. It is found that the propensity of the salt to crystallize protein follows the Hoffmeister series (KF<KCl<KBr) with marked differences in the effect of these salts. In pure protein solution, lysozyme macromolecules are prolate ellipsoidal with semimajor and semiminor axes as 22 and 13.5 A, respectively. SANS also gives that the effective (structural+counterion) charge(Z) on the protein as obtained by taking into account screened Coulomb interaction between the protein macromolecules is found to be much smaller than the structural charge. There is decrease in Z suggesting the higher counterion condensation on protein with the increase in the concentration. The counterion condensation seems to be responsible for the differences in the effect of different salts. It is also found that with the addition of salts, lysozyme macromolecules convert to dimers, and for the same salt concentration the comparative effect of different salts follows the Hoffmeister series. Time evolved measurements prior to and after the crystallization show that the protein solution mostly consists of monomers and dimers. Interestingly, higher-mers are not observed in these measurements as perhaps they are formed in very small numbers towards the process that leads to the crystallization. The time dependent data have been used to obtain the fraction of crystallization as a function of time.

Computer Simulation↗

PubMed2004

Shear-induced alignment of self-associated hemoglobin in human erythrocytes: small angle neutron scattering studies.

Small angle neutron scattering (SANS) was performed on suspensions of actively metabolising human erythrocytes in the constant shear field induced by a Couette cell. The SANS pattern recorded on a two-dimensional detector was a function of the shear rate; at zero shear, the SANS pattern had radial symmetry around the direction of the beam. The radial average of the SANS pattern consisted of a broad intensity maximum superimposed on a decay. The intensity maximum at q = 0.1 A(-1) was attributed to isotropically oriented self-associated complexes of the tetrameric oxygen transport protein hemoglobin inside the erythrocytes. A flow curve of the cell suspension was used to identify at what shear rate a suspension of uniaxially oriented ellipsoidal cells is produced. The radial symmetry of the SANS patterns persisted until the shear rate was sufficient to produce a suspension of uniaxially oriented ellipsoidal cells. Again, an intensity maximum was present in directions parallel and orthogonal to the shear axis, but this intensity maximum was superimposed upon quite different intensity decays in each direction from that of the primary neutron beam. The angular range of the SANS instrument was limited, however the results from shear-induced structural changes is consistent with a model that involves hemoglobin complexes that are aligned with respect to the plasma membranes of the elongated cells.

Cells, Cultured↗

PubMed1986

Low-resolution structure of the complex of human blood platelet factor 4 with heparin determined by small-angle neutron scattering.

Small-angle neutron scattering was used to confirm that human platelet factor 4 was a compact tetrameric globular protein of radius of gyration 1.74 nm and indistinguishable from a sphere. The same technique, when applied to the 1:1 mol/mol complex of platelet factor and heparin of Mr 14000, revealed that the radius of gyration of the particle varied, depending on the relative proportion of 2H2O to H2O in the solvent. Analysis of this variation by the method of Ibel and Stuhrmann (Ibel, K. and Stuhrmann, H.B. (1975) J. Mol. Biol. 93, 255-266) revealed that in the complex the material of greatest neutron-scattering length (the highly sulphated polysaccharide heparin) was furthest from the centre of the particle. This confirms the postulate of Luscombe and Holbrook (Luscombe, M. and Holbrook, J.J. (1983) in Glycoconjugates (Chester, A.M., Heinegård, D., Lundblad, A. and Svensson, S., eds.), pp. 818-819, Secretariat, Lund) that the exact 1:1 mole ratio of heparin (Mr greater than 10 000) to platelet factor in this stable complex arises from the heparin winding around the outside of a globular protein core.

Heparin↗

PubMed2004

Mixed spherical and wormlike micelles: a contrast-matching study by small-angle neutron scattering.

Small-angle neutron scattering studies were used to investigate the effect of adding an alcohol ethoxylate nonionic surfactant (d-C12E20) to aqueous solutions of a cationic surfactant, erucyl bis(hydroxyethyl) methylammonium chloride (EHAC), with and without salt (KCl). The systematic use of contrast-matching, by alternately highlighting or hiding one of the surfactants, confirms that mixed micelles are formed. In salt-free solutions, mixed spherical micelles are formed and a core-shell model combined with a Hayter-Penfold potential was used to describe the data. The core radius is dominated by the EHAC tails and the outer radius determined by the ethoxylate headgroups of the nonionic surfactant. Addition of KCl promotes micellar growth; however, results of varying the solvent contrast revealed that when the nonionic surfactant is incorporated into the wormlike structure micellar breaking is promoted. Thus, mixed wormlike micelles with shorter contour lengths compared to the pure EHAC worms are formed.

Journal Article↗