SEARCH · PubMed Health

Results for “Scattering, Small Angle”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,279 records · Page 71Linked to original sources

PubMed1999

Formation of the myosin.ADP.gallium fluoride complex and its solution structure by small-angle synchrotron X-ray scattering.

In the presence of MgADP, a novel phosphate analogue of gallium fluoride (GaFn) forms a ternary complex with the myosin subfragment-1 (S-1), in the same way that has been previously reported with aluminum fluoride (AlF4-), beryllium fluoride (BeFn), scandium fluoride (ScFn), and vanadate (Vi), and this complex formation may mimic different states along the ATPase kinetic pathway. This novel complex has been characterized and compared with other complexes to ascertain whether it forms a transition-state analogue of myosin ATPase. The complex formed quickly, although several times slower than the BeFn complex. The half-life of the myosin.ADP.GaFn complex was about 50 h at 4 degreesC. The formation of the myosin.ADP.GaFn complex was accompanied by an increase in tryptophane fluorescence, similar to that observed upon the addition of ATP, but slightly lower than that of the M**.ADP.Pi complex. Upon addition of GaFn to acto-myosin.ADP, acto-myosin did not dissociate, and the S-1.ADP.GaFn complex was scarcely decomposed by actin, like the AlF4- and ScFn complexes but unlike the BeFn and Vi complexes. The conformations at the localized region of SH1, SH2, and RLR, which are very accessible to the binding of ATP, were studied by fluorescent labeling and chemical modification, and the results suggested that these conformations are very similar to that of the M**.ADP.Pi state. Small-angle X-ray solution scattering showed that the radius of gyration value decreases by about 3 A when S-1 forms an S-1.ADP.GaFn complex, suggesting that the shape of the complex becomes compact or rounded in shape, similar to that in the presence of ATP or complexes with other phosphate analogues, and thus mimics the myosin**.ADP.Pi state closely. The overall results may indicate that the complex mimics a somewhat different transient state from that of other complexes but has a similar global conformation along the ATPase kinetic pathway.

Actins↗

PubMed1988

Time-resolved solution X-ray scattering of tobacco mosaic virus coat protein: kinetics and structure of intermediates.

The kinetics of assembly and disassembly of tobacco mosaic virus coat protein (TMVP) following temperature jumps have been studied by small-angle X-ray scattering and turbidimetry. The structures of the principal aggregates of TMVP oligomers (A protein), intermediate size (helix I) and large size helical rods (helix II), have been characterized by their average radii of gyration of thickness, cross section, and shape obtained from the corresponding regimes of the small-angle scattering pattern. This structural information was obtained within seconds after the temperature-induced initiation of either polymerization or depolymerization and allowed us to detect transient intermediates. This methodology made it possible to observe and characterize the structure of a principal intermediate. Taken together with other kinetic information, these data suggest that polymerization of TMVP under virus self-assembly conditions may proceed via a single-layered helical nucleus that contains about 20 subunits. Previous studies have shown that overshoot polymerization of TMVP can occur and results in metastable long helical viruslike rods which subsequently depolymerize and then form short helical rods, depending on the conditions of the final equilibrium state. The longer rods (helix II) are overshoot polymers which form within seconds and contain 17 1/3 subunits per turn (helix IIB), in contrast to the subunit packing arrangement of 16 1/3 subunits per turn found in the shorter helical rods (helix IA). The latter packing arrangement is the one found in TMV. An overall polymerization scheme is proposed for the formation of these two helical forms of TMVP.

Capsid Proteins↗

PubMed1990

Structural change of troponin C molecule and its domains upon Ca2+ binding in the presence of Mg2+ ions measured by a solution X-ray scattering technique.

A small-angle X-ray scattering study on troponin C showed that two domains of the molecule move closer to each other and the molecule shrinks along its long axis upon Ca2+ binding in the absence of Mg2+ ions (Fujisawa, T., Ueki, T., & Iida S. (1988) J. Biochem. 105, 377-383). When Mg2+ ions bind to troponin-C, the radius of gyration changes from 27.8 to 24.3 A and the average radius of gyration of the two domains is estimated to be 15.1 A. These radii indicate that the distance between the centers of the two domains is 38.1 A. Such a change is analogous to the previous result for troponin C with two Ca2+ ions bound at the high-affinity sites. Thus, the structural behavior of troponin C molecule is essentially the same when Ca2+/Mg2+ ions bind to its high-affinity sites. On the other hand, the effect of Ca2+ binding to the low-affinity sites in the presence of Mg2+ ions is quite different from the previous result. The binding of Ca2+ ions causes a dimerization of troponin C molecules with an apparent constant of 511 M-1. Such a characteristic behavior, implying the occurrence of a surface property change, may be related to the physiological role of troponin C molecule in the muscle. The scattering experiments on the tryptic fragments of troponin C also had interesting and important results: the C-domain shrinks, with the radius of gyration changing from 17.0 to 14.9 A while the N-domain swells from 13.9 to 15.0 A upon Ca2+ binding. Such an opposite change is consistent with the results of circular dichroism and spectroscopic studies of the domains.

Binding Sites↗

PubMed1994

The hydration of Ras p21 in solution during GTP hydrolysis based on solution X-ray scattering profile.

The small-angle X-ray scattering technique was used to characterize the structure in solution of wild type ras p21 as well as the oncogenic proteins mutated at residue 12, 59, or 61. In the presence of GDP, the radius of gyration, Rg, determined for wild type ras p21 was 16.89 +/- 0.01 A, while the wild type ras p21 bound to the GTP analogue GDPNHP (5'-guanyl imido diphosphate beta-gamma-imidoguanosine 5'-triphosphate) showed an Rg value of 17.46 +/- 0.01 A, which is 3.3% larger. The result shows that ras p21 expands upon GTP binding. The Rgs of mutated proteins were 17.04 +/- 0.01, 16.98 +/- 0.01, and 17.03 +/- 0.01 A for the Gly-12 to Val, Ala-59 to Thr, and Gln-61 to Leu mutants, respectively. The scattering profiles were analyzed by simulation of hydrated ras p21, based on the crystal atomic coordinates, and it was concluded that the ras p21 molecule incorporates 20% more bulk water upon GTP binding. The increase of bulk water is especially conspicuous around the interface between switch I (residues 32-40) and switch II (residues 60-66) regions. This suggests that hydration plays an important role in the interaction with GAP.

Computer Simulation↗

PubMedDate not supplied

The solution structures of calmodulin and its complexes with synthetic peptides based on target enzyme binding domains.

Small-angle X-ray and neutron scattering experiments have given important information on the solution structures of calmodulin and its complexes with synthetic peptides used to model target enzyme interactions. In combination with crystallographic data, site directed mutagenesis and various spectroscopic studies, these experiments have contributed to our understanding of the solution structure of calmodulin in different functional states. We have gained important insights into the conformational flexibility in calmodulin that appears to be crucial to its regulatory functions. Specifically, flexibility in the interconnecting helix region of calmodulin has been shown to play a critical role in facilitating calmodulin's binding to a wide variety of target enzymes whose activities are thus regulated. This review will focus mainly on the contributions small-angle scattering has made to our understanding of the solution structure of calmodulin in the context of other studies, with particular regard to circular dichroism and Fourier transform infrared studies that complement the small-angle scattering data.

Binding Sites↗

PubMed1982

The structure of the cell wall of Staphylococcus aureus studied with neutron scattering and magnetic birefringence.

The cell wall complex was extracted from Staphylococcus aureus and characterized in suspension by means of small-angle neutron scattering and magnetically induced birefringence. The neutron scattering measurements show that the complex has a thickness of approximately 420 A, a mass per unit area of 93 +/- 11 daltons/A2 and is approximately 75% water by volume. The neutron scattering density is higher near the surface than in the interior in accordance with a trilamellar structure. The magnetically induced birefringence measurements demonstrate that a high degree of magnetic orientation is possible due to the anisotropic nature of the wall complex structure.

Cell Wall↗

PubMed2005

The Pyrococcus exosome complex: structural and functional characterization.

The exosome is a conserved eukaryotic enzymatic complex that plays an essential role in many pathways of RNA processing and degradation. Here, we describe the structural characterization of the predicted archaeal exosome in solution using small angle x-ray scattering. The structure model calculated from the small angle x-ray scattering pattern provides an indication of the existence of a disk-shaped structure, corresponding to the "RNases PH ring" complex formed by the proteins aRrp41 and aRrp42. The RNases PH ring complex corresponds to the core of the exosome, binds RNA, and has phosphorolytic and polymerization activities. Three additional molecules of the RNA-binding protein aRrp4 are attached to the core as extended and flexible arms that may direct the substrates to the active sites of the exosome. In the presence of aRrp4, the activity of the core complex is enhanced, suggesting a regulatory role for this protein. The results shown here also indicate the participation of the exosome in RNA metabolism in Archaea, as was established in Eukarya.

Archaeal Proteins↗

PubMed2004

Effect of cholesterol on the bilayer thickness in unilamellar extruded DLPC and DOPC liposomes: SANS contrast variation study.

Small-angle neutron scattering on extruded unilamellar vesicles in water was used to study bilayer thickness when cholesterol (CHOL) was added to dilauroylphosphatidylcholine (DLPC) and dioleoylphosphatidylcholine (DOPC) bilayers in molar fraction 0.44. Using the H2O/2H2O contrast variation and the small-angle form of Kratky-Porod approximation, the bilayer gyration radius at infinite contrast R(g,infinity) and the bilayer thickness parameter d(g,infinity) = 12(0.5)R(g,infinity) were obtained at 25 degrees C. Addition of CHOL to DLPC increased the d(g,infinity) from 4.058 +/- 0.028 nm to 4.62 +/- 0.114 nm, while in case of DOPC the d(g,infinity) values were the same in the absence (4.618 +/- 0.148 nm) and in the presence (4.577 +/- 0.144 nm) of CHOL within experimental errors. The role of CHOL-induced changes of bilayer thickness in the protein insertion, orientation and function in membranes is discussed.

Cholesterol↗

PubMed1998

The FE-lspd model for electron beam dosimetry.

The FE-lspd model is a two-component electron beam model that distinguishes between electrons that can be described by small-angle transport theory and electrons that are too widely scattered for small-angle transport theory to be applicable. The two components are called the primary beam and the laterally scattered primary distribution (lspd). The primary beam component incorporates a simple version of the Fermi-Eyges model and dominates dose calculations at therapeutic depths. The lspd component corrects erros in the lateral spreading of the primary beam component, thereby improving the accuracy by which the FE-lspd model calculates dose distribution in blocked fields. Comparisons were made between dose profiles and central-axis depth dose distributions in small fields calculated by the FE-lspd, Fermi-Eyges and EGS4 Monte Carlo models for a 10 MeV beam in a homogeneous water phantom. The maximum difference between the dose calculated using the FE-lspd model and EGS4 Monte Carlo is about 6% at a field diameter of about 1 cm, and less than 2% for field sizes greater than 3 cm diameter. The maximum difference between the Fermi-Eyges and Monte Carlo calculations is about 18% at a field diameter of about 2.5 cm. A comparison was made with the central-axis depth dose distribution measured in water for a 3 cm diameter field in a 10 MeV clinical electron beam. The errors in the dose distribution were found to be less than 2% using the FE-lspd model but almost 18% using the Fermi-Eyges model. A comparison was also made with pencil beam profiles calculated using the second-order Fermi-Eyges transport model.

Calibration↗

PubMed2006

Structural studies of the phase, aggregation and surface behaviour of 1-alkyl-3-methylimidazolium halide + water mixtures.

The surface, phase and aggregation behaviour of mixtures of 1-alkyl-3-methylimidazolium halide, [C(n)mim]X, where n is the alkyl chain length, with water has been explored using a variety of methods. Critical micelle concentrations (cmc) and micelle structures have been determined for aqueous [C(n)mim]Br solutions for n=2, 4, 6, 8, and 10. Small-angle neutron scattering (SANS) measurements reveal that for the n=8 and 10 systems, at concentrations just above the cmc, small near-spherical aggregates exist, which, after initial growth, possess core radii (aggregation numbers) at intermediate concentrations of 10.5+/-0.5 Angstrom (22+/-2) and 13.2+/-0.5 Angstrom (40+/-3), respectively, for n=8 and n=10. Towards higher concentrations, the aggregates appear to grow, with the aggregates in the [C(10)mim]Br system becoming increasingly elongated (prolate) with increasing concentration. No evident aggregates are formed in the systems with n=2 and 4. In the n=6 system, it appears that oblate aggregates with radius approximately 9 Angstrom form at the cmc and that the radius increases with increasing concentration. For longer alkyl chain lengths, at high concentrations lyotropic mesophases form in some systems. The mesophase region for the [C(8)mim]Cl system has been explored across the composition range using X-ray diffraction and (2)H NMR spectroscopy. Both techniques suggest that a major hexagonal phase with lattice parameter of 29.5+/-0.5 Angstrom coexists with a minor lamellar phase (23.5+/-0.3 Angstrom) or possibly a second hexagonal phase (27.1+/-0.4 Angstrom). The area per adsorbed molecule at the surface of [C(8)mim]Br solutions has been measured as a function of concentration using neutron reflectometry. A minimum in the area per molecule behaviour is coincident with a minimum identified in the surface tension isotherm occurring close to the cmc. The data suggest depletion of [C(8)mim]Br from the surface region occurs at concentrations immediately above the cmc.

Journal Article↗

PubMed1979

The shape of the fibrinogen molecule: sausage or banana?

The experimental results and the interpretation of small angle X-ray scattering measurements by the author and Hammel (1975) and of small angle neutron scattering measurements by Marguerie and Stuhrmann (1976) on dilute solutions of bovine fibrinogen are compared. The potential of both methods to discern straight and bent cylindrical structures is demonstrated. The study arrives at the conclusion that the question whether the fibrinogen molecule resembles more a banana or a straight sausage cannot be safely decided by the available data. This justifies the previous suggestion of the author to imagine the fibrinogen molecule as a swollen sausage 450 A long and 90 A thick with conceivable flexibility, a molecular model of sufficient universality to include the banana-shaped model of Marguerie and Stuhrmann (1976) as a special case.

Fibrinogen↗

PubMed2005

Physicochemical characterization of the reassembled dimer of an integral membrane protein OmpF porin.

The in vitro reassembled species of OmpF porin, which was renatured from its denatured monomer using n-octyl-beta-D-glucopyranoside, was characterized by low-angle laser light scattering photometry, circular dichroism spectroscopy and synchrotron radiation small-angle X-ray scattering measurements. The light scattering measurement reconfirmed that the reassembled species was the dimer of the protein. Circular dichroism spectra of the reassembled dimer showed a native-like beta-structure. A small-angle X-ray scattering measurement indicated that the size of the reassembled dimer was nearly equal to that of the native trimer under the present experimental conditions. In a thermal denaturation experiment followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the reassembled dimer was less stable than the native trimer.

Dimerization↗

PubMed2005

Co-translational myristoylation alters the quaternary structure of HIV-1 Nef in solution.

We have studied the solution properties of Nef, a 24-kDa cotranslationally myristoylated protein produced by HIV-1 and other primate lentiviruses. Nef is found in the cytosol and also in association with cytoplasmic membranes, the latter, mediated in part by the myristoyl group attached to the N-terminal glycine. Recombinant Nef was coexpressed in Escherichia coli in tandem with N-myristoyl-transferase and is fully myristoylated. Analysis by circular dichroism showed the myristoylated form to contain a greater alpha-helical content than the nonmyristoylated form. Analysis of modified and unmodified Nef in solution using small angle X-ray scattering, dynamic laser light scattering and analytical ultracentrifugation consistently showed differences in the oligomeric states of the two forms of Nef. Myristoylated Nef is predominantly monomeric and small oligomers which are also present, can be converted to the monomeric form under reducing conditions. By contrast, the nonmyristoylated form exists as a stable hexadecamer in solution which disassociates into tetramers upon addition of reducing agents. Shape reconstructions from small angle scattering curves of nonmyristoylated Nef are compatible with a large disc-like structure in the hexadecameric oligomer consisting of four Nef tetramers. From these findings, we hypothesize that Nef undergoes a substantial conformational change from an "open" into a "closed" form whereby the myristate group is sequestered in a hydrophobic pocket. The myristoylated protein can switch to the open conformation by association of the N-terminal region of molecule with membranes. These changes would allow Nef to carry out various functions depending on the conformational and oligomeric states.

Base Sequence↗

PubMed1983

Neutron scattering study of the binding of tRNAPhe to Escherichia coli phenylalanyl-tRNA synthetase.

Escherichia coli phenylalanyl-tRNA synthetase has been characterized by small-angle neutron scattering. In solution (20 mM imidazole hydrochloride, pH 7.6, 10 mM 2-mercaptoethanol, and 0.1 mM ethylenediaminetetraacetic acid), this enzyme has a molecular weight of 227K +/- 20K with a radius of gyration of 48.3 +/- 0.6 A, independent of the presence of MgCl2 up to 50 mM. The change of the scattering upon adding tRNAPhe to the enzyme has been followed with 10 mM MgCl2 present in the buffer. One enzyme molecule is capable of binding two tRNAPhe molecules with affinity constants larger than 10(6) M-1. Parallel titration experiments in 73% 2H2O, close to the matching point of tRNA, show that the RG of the enzyme is not changed by the binding of one or two tRNAPhe molecules. These results are compared with quasi-electric light scattering studies [Holler, E., Wang, C. C., & Ford, N.C., Jr. (1981) Biochemistry 20, 861-867] where the addition of either MgCl2 or tRNAPhe was shown to cause dramatic changes of the apparent translational diffusion constant of phenylalanyl-tRNA synthetase.

Amino Acyl-tRNA Synthetases↗

PubMed1999

Power-law fluctuations in phase-separated lipid membranes.

The spatial structure of three binary lipid mixtures, prepared as multilamellar vesicles, was studied by small-angle neutron scattering. In the fluid-gel coexistence region, large-scale concentration fluctuations appear which scatter like surface fractals for small acyl-chain mismatch and like mass fractals for large mismatch over about one decade of length. The transition is highly discontinuous: The fractal dimension of the boundary between the gel and fluid drops from 2.7 to 1.7, the gel fraction in the fluctuations drops from about 0.5 to 0.07, and the gel domains interlamellar correlation drops from strong to weak. We interpret the fluctuations as long-lived descendants of the incipient two-phase equilibrium state and the transition as due to changes in the gel rigidity and phase diagram.

Deuterium↗

PubMed1998

The assembly of immunoglobulin-like modules in titin: implications for muscle elasticity.

Titin, a giant muscle protein, forms filaments that span half of the sarcomere and cover, along their length, quite diversified functions. The region of titin located in the sarcomere I-band is believed to play a major rôle in extensibility and passive elasticity of muscle. In the I-band, the titin sequence contains tandem immunoglobulin-like (Ig) modules intercalated by a potentially non-globular region. By a combined approach making use of small angle X-ray scattering and nuclear magnetic resonance techniques, we have addressed the questions of what are the average mutual orientation of poly-Igs and the degree of flexibility around the domain interfaces. Various recombinant fragments containing one, two and four titin I-band tandem domains were analysed. The small-angle scattering data provide a picture of the domains in a mostly extended configuration with their long axes aligned head-to-tail. There is a small degree of bending and twisting of the modules with respect to each other that results in an overall shortening in their maximum linear dimension compared with that expected for the fully extended, linear configurations. This shortening is greatest for the four module construct ( approximately 15%). 15N NMR relaxation studies of one and two-domain constructs show that the motions around the interdomain connecting regions are restricted, suggesting that titin behaves as a row of beads connected by rigid hinges. The length of the residues in the interface seems to be the major determinant of the degree of flexibility. Possible implications of our results for the structure and function of titin in muscles are discussed.

Connectin↗

PubMed2005

How does surface modification aid in the dispersion of carbon nanofibers?

Small-angle light scattering is used to assess the dispersion behavior of vapor-grown carbon nanofibers suspended in water. These data provide the first insights into the mechanism by which surface treatment promotes dispersion. Both acid-treated and untreated nanofibers exhibit hierarchical morphology consisting of small-scale aggregates (small bundles) that agglomerate to form fractal clusters that eventually precipitate. Although the morphology of the aggregates and agglomerates is nearly independent of surface treatment, their time evolution is quite different. The time evolution of the small-scale bundles is studied by extracting the size distribution from the angle-dependence of the scattered intensity, using the maximum entropy method in conjunction with a simplified tube form factor. The bundles consist of multiple tubes possibly aggregated side-by-side. Acid oxidation has little effect on this bundle morphology. Rather acid treatment inhibits agglomeration of the bundles. The time evolution of agglomeration is followed by fitting the scattering data to a generalized fractal model. Agglomerates appear immediately after cessation of sonication for untreated fibers but only after hours for treated fibers. Eventually, however, both systems precipitate.

Journal Article↗

PubMed2000

Long-range density fluctuations in orthoterphenyl as studied by means of ultrasmall-angle x-ray scattering.

The structure factor of a fragile glass-forming liquid orthoterphenyl was measured in the previously inaccessible intermediate q range between the conventional light scattering (LS) and small-angle x-ray scattering (SAXS) q ranges using the low-angle scattering beam line at the European Synchrotron Radiation Facility. At low q the structure factor exhibits an excess scattering and matches well the LS data. This excess scattering is due to long-range density fluctuations also observed in the isotropic component of scattered light. At high q the structure factor decays to a plateau corresponding to the isothermal compressibility in agreement with the conventional SAXS data. In the intermediate q range, the structure factor exhibits a power law q dependence which indicates that the excess scattering is due to fractal aggregates of denser domains.

Journal Article↗