scholarly journals Structural comparisons of the native and reactive-centre-cleaved forms of α1-antitrypsin by neutron- and X-ray-scattering in solution

1990 ◽  
Vol 267 (1) ◽  
pp. 203-212 ◽  
Author(s):  
K F Smith ◽  
R A Harrison ◽  
S J Perkins
Keyword(s):  
Conformational Changes ◽  
Potassium Phosphate ◽  
Radius Of Gyration ◽  
Neutron Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Alpha 1 Antitrypsin ◽  
Internal Inhomogeneity ◽  
Good Agreement ◽  
Ray Scattering

alpha 1-Antitrypsin is the best-characterized member of the serpin (serine-proteinase inhibitor) superfamily. Its solution structure was studied by high-flux neutron-scattering and synchrotron X-ray-scattering. Neutron data show that its absorption coefficient A1% 280,1cm is 5.4. The neutron radius of gyration RG at infinite contrast for native alpha 1-antitrypsin is 2.61 nm, characteristic of a moderately elongated structure, and its cross-sectional RG is 1.34 nm. The internal inhomogeneity of scattering densities within alpha 1-antitrypsin is high at 29 x 10(-5). The X-ray RG is 2.91 nm, in good agreement with the neutron RG of 2.82 nm in 1H2O. This RG is unchanged in reactive-centre-cleaved alpha 1-antitrypsin. These parameters are also unchanged at pH 8 in sodium/potassium phosphate buffers up to 0.6 M. The neutron and X-ray curves for native alpha 1-antitrypsin were compared with Debye simulation based on the crystal structure of reactive-centre-cleaved (papain) alpha 1-antitrypsin. After allowance for residues not visible in the crystallographic electron-density map, and rejoining the proteolysed site between Met-358 and Ser-359 by means of a relatively minor conformational re-arrangement, good agreement to a structural resolution of 4 nm is obtained with the neutron data in two contrasts and with the X-ray data. The structures of the native and cleaved forms of alpha 1-antitrypsin are thus similar within the resolution of solution scattering. This places an upper limit on the magnitude of the presumed conformational changes that occur in alpha 1-antitrypsin on reactive-centre cleavage, as indicated in earlier spectroscopic investigations of the Met-358-Ser-359 peptide-bond cleavage. Methods for scattering-curve simulations from crystal structures are critically assessed. The RG data lead to dimensions of 7.8 nm x 4.9 nm x 2.2 nm for native alpha 1-antitrypsin. The high internal inhomogeneity and the asymmetric shorter semi-axes of 4.9 nm and 2.2 nm suggest that the three oligosaccharide chains of alpha 1-antitrypsin are essentially freely extended into solvent in physiological conditions. This conclusion is also supported by the Debye simulations, and by modelling based on hydrodynamic parameters.

Evidence of a single-q incommensurate phase in quartz by synchrotron X-ray diffraction

1988 ◽  
Vol 21 (1) ◽  
pp. 72-74 ◽  
Author(s):  
A. Zarka ◽  
B. Capelle ◽  
M. Petit ◽  
G. Dolino ◽  
P. Bastie ◽  
...  
Keyword(s):  
Neutron Scattering ◽  
Uniaxial Stress ◽  
Incommensurate Phase ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Scattering ◽  
Good Agreement ◽  
Ray Scattering

X-ray scattering is used to demonstrate the existence in quartz of an incommensurate phase with a single modulation when a uniaxial stress is applied in the X Y plane. Good agreement with earlier neutron scattering experiments is found.

Calcium-induced increase in the radius of gyration and maximum dimension of calmodulin measured by small-angle x-ray scattering

Biochemistry ◽  
1985 ◽  
Vol 24 (24) ◽  
pp. 6740-6743 ◽  
Author(s):  
B. A. Seaton ◽  
J. F. Head ◽  
D. M. Engelman ◽  
F. M. Richards
Keyword(s):  
Small Angle ◽  
Radius Of Gyration ◽  
Maximum Dimension ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

ULTRA SMALL-ANGLE X-RAY SCATTERING STUDY OF FLOCCULATION IN SILICA-FILLED RUBBER

2014 ◽  
Vol 87 (2) ◽  
pp. 348-359 ◽  
Author(s):  
Satoshi Mihara ◽  
Rabin N. Datta ◽  
Wilma K. Dierkes ◽  
Jacques W. M. Noordermeer ◽  
Naoya Amino ◽  
...  
Keyword(s):  
Fractal Dimension ◽  
Small Angle ◽  
Radius Of Gyration ◽  
X Ray ◽  
X Ray Scattering ◽  
Mass Fractal ◽  
Mass Fractal Dimension ◽  
Lower Mobility ◽  
Low Mass ◽  
Ray Scattering

ABSTRACT The flocculation of silica during vulcanization is monitored using the ultra small-angle X-ray scattering technique for two different types of silica: a highly dispersible silica (HD) and a conventional silica (CV), mixed into a blend of S-SBR and BR rubbers. The cutoff length of the silica aggregate Rss and the mass fractal dimension Dm, which indicate the degree of flocculation of aggregates, are estimated according to the modified unified equation. The aggregate radius Ra is estimated to be related to the lower cutoff length Rss, indicating the radius of gyration of the mass-fractal structure. For both silicas, Ra increases during vulcanization. For the CV silica, an increase of Dm is observed, whereas no significant increase of Dm can be seen for the HD silica. The Ra of CV is relatively high compared with that of HD. On the other hand, the CV silica shows a relatively lower Dm compared with that of HD. These results indicate that CV has a larger size of aggregates and lower degree of agglomeration of its aggregates. The presence of di(tri-ethoxy-silyl-propyl)tetrasulfide (TESPT) as coupling agent between the silica and rubber decreases the aggregate radius of silica. However, in the absence of TESPT, a low mass-fractal dimension, which means a low degree of agglomeration of aggregates, is observed. This results from a lower mobility of silica aggregates, depending on the size of the aggregates. The silica loading also has an influence on the flocculation process. The aggregate radius increases as the silica loading is increased. At the same time, a higher mass-fractal dimension, and therefore also a higher degree of agglomeration, can be seen at higher silica loading.

Investigation of Ribulose-1,5-bisphosphate Carboxylase-Oxygenase from Tobacco by Small Angle X-Ray Scattering: A Structural Model for the Enzyme in Solution

1988 ◽  
Vol 43 (5-6) ◽  
pp. 373-376 ◽  
Author(s):  
P. M. Abuja ◽  
I. Pilz
Keyword(s):  
Small Angle ◽  
Quaternary Structure ◽  
Higher Plants ◽  
Maximum Diameter ◽  
Radius Of Gyration ◽  
Bisphosphate Carboxylase ◽  
X Ray ◽  
X Ray Scattering ◽  
Inactive Form ◽  
Ray Scattering

The quaternary structure of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco (Nicotiana tabacum) was investigated in solution by means of small angle X-ray scattering. The most important molecular parameters as the radius of gyration (Rg) and the maximum diameter (Dmax) were determined. Both the active and the inactive form of the enzyme were measured at 5 °C and at 20 °C. A more distinct difference in size could be detected between the inactive forms at these two temperatures (Rg = 4.80 nm (5 °C) and 4.68 nm (20 °C)) than between the active forms (Rg = 4.73 nm and 4.69 nm). The maximum diameters were determined to be 13.1 nm for the inactive form at 5 °C and 12.8 nm for the other forms. A model is proposed consisting of eight large and eight small subunits arranged in the way that seems to be typical for this enzyme in higher plants.

Structural Insights of the Nucleotide-Dependent Conformational Changes of Thermotoga maritima MutL Using Small-Angle X-ray Scattering Analysis

2008 ◽  
Vol 145 (2) ◽  
pp. 199-206 ◽  
Author(s):  
Tae Gyun Kim ◽  
Hyung Jin Cha ◽  
Hyung Ju Lee ◽  
Seong-Dal Heo ◽  
Kwan Yong Choi ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Small Angle ◽  
Thermotoga Maritima ◽  
X Ray ◽  
X Ray Scattering ◽  
Structural Insights ◽  
Ray Scattering

scholarly journals Small-Angle X-Ray Scattering Study for Conformational Changes of Unusual Transcription Factor at the Operator

2014 ◽  
Vol 106 (2) ◽  
pp. 497a
Author(s):  
Walid Al-Zyoud ◽  
Rob Hynson ◽  
Anthony Duff ◽  
Thomas Sobey ◽  
Lawrence Lee ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Conformational Changes ◽  
Small Angle ◽  
X Ray ◽  
X Ray Scattering ◽  
Scattering Study ◽  
Ray Scattering

Ostwald ripening of cobalt precipitates in silica aerogels? An ultra-small-angle X-ray scattering study

2005 ◽  
Vol 38 (1) ◽  
pp. 132-138 ◽  
Author(s):  
Artur Braun ◽  
Jan Ilavsky ◽  
Brian C. Dunn ◽  
Pete R. Jemian ◽  
Frank E. Huggins ◽  
...  
Keyword(s):  
Size Distribution ◽  
Small Angle ◽  
Ostwald Ripening ◽  
Supercritical Drying ◽  
Silica Aerogels ◽  
Radial Symmetry ◽  
Radius Of Gyration ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Monolithic silica aerogels with radial symmetry were synthesized by supercritical drying, doped to 2% and 10% with cobalt, and reduced with hydrogen. All samples were investigated with ultra-small-angle X-ray scattering. The non-doped aerogels have three populations of scatterers with radii of gyration of about 10, 40 and 60–70 Å. The doped aerogels show an additional structure with a radius of gyration ranging from 1050 to 3000 Å. This structure causes intensity oscillations, thus revealing a relatively narrow size distribution. Scattering curves of the 10%-doped aerogels fitted well to a Lifshitz–Slyozov–Wagner particle size distribution, thus revealing that Ostwald ripening might have occurred during aerogel preparation. The same range also shows differences depending on whether the samples were reduced, or in their as-prepared condition. Scattering curves obtained from the cylinder-axis region were different from the scattering curves obtained from the sample boundary, indicating a process-dependent skin effect.

scholarly journals Guinier peak analysis for visual and automated inspection of small-angle X-ray scattering data

2016 ◽  
Vol 49 (5) ◽  
pp. 1412-1419 ◽  
Author(s):  
Christopher D. Putnam
Keyword(s):  
Small Angle ◽  
Peak Position ◽  
Scattering Data ◽  
Radius Of Gyration ◽  
Automated Inspection ◽  
Elongation Ratio ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

The Guinier region in small-angle X-ray scattering (SAXS) defines the radius of gyration,Rg, and the forward scattering intensity,I(0). In Guinier peak analysis (GPA), the plot ofqI(q)versus q2transforms the Guinier region into a characteristic peak for visual and automated inspection of data. Deviations of the peak position from the theoretical position in dimensionless GPA plots can suggest parameter errors, problematic low-resolution data, some kinds of intermolecular interactions or elongated scatters. To facilitate automated analysis by GPA, the elongation ratio (ER), which is the ratio of the areas in the pair-distribution functionP(r) after and before theP(r) maximum, was characterized; symmetric samples have ER values around 1, and samples with ER values greater than 5 tend to be outliers in GPA analysis. Use of GPA+ER can be a helpful addition to SAXS data analysis pipelines.

In Situ X-Ray Scattering of Monolayers Adsorbed at Electrochemical Interfaces.

1988 ◽  
Vol 143 ◽  
Author(s):  
Michael F. Toney ◽  
Owen. R Melroy
Keyword(s):  
Near Neighbor ◽  
X Ray ◽  
X Ray Scattering ◽  
Electrochemical Interfaces ◽  
Ag Substrate ◽  
Near Neighbor Distance ◽  
Surface Diffraction ◽  
Good Agreement ◽  
Ray Scattering

AbstractSurface x-ray scattering has been used to study in-situ the structure of Pb monolayers electrochemically adsorbed on Ag (111) electrodes. Pb forms an incommensurate, hexagonal two-dimensional (2D) solid, which is rotated approximately 4.5° from the substrate symmetry directions and compressed relative to bulk Pb. Between monolayer formation and bulk deposition, the Pb-Pb near neighbor distance decreases linearly with applied potential. Due to the chemical equilibrium between the Pb monolayer and the Pb in solution, the isothermal compressibility of the monolayer can be measured and is in good agreement with that calculated for a 2D non-interacting free electron gas model of the monolayer. It is observed that the intensity of surface diffraction from the Ag substrate (the Ag crystal truncation rod) decreases when the Pb monolayer is adsorbed, although the cause of this is not known.

scholarly journals Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme

2018 ◽  
Author(s):  
Michael C. Thompson ◽  
Benjamin A. Barad ◽  
Alexander M. Wolff ◽  
Hyun Sun Cho ◽  
Friedrich Schotte ◽  
...  
Keyword(s):  
Protein Dynamics ◽  
Conformational Changes ◽  
Thermal Excitation ◽  
Relaxation Processes ◽  
Spectroscopic Techniques ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Solvent Molecules ◽  
Ray Scattering

AbstractCorrelated motions of proteins and their bound solvent molecules are critical to function, but these features are difficult to resolve using traditional structure determination techniques. Time-resolved methods hold promise for addressing this challenge but have relied on the exploitation of exotic protein photoactivity, and are therefore not generalizable. Temperature-jumps (T-jumps), through thermal excitation of the solvent, have been implemented to study protein dynamics using spectroscopic techniques, but their implementation in X-ray scattering experiments has been limited. Here, we perform T-jump small- and wide-angle X-ray scattering (SAXS/WAXS) measurements on a dynamic enzyme, cyclophilin A (CypA), demonstrating that these experiments are able to capture functional intramolecular protein dynamics. We show that CypA displays rich dynamics following a T-jump, and use the resulting time-resolved signal to assess the kinetics of conformational changes in the enzyme. Two relaxation processes are resolved, which can be characterized by Arrhenius behavior. We also used mutations that have distinct functional effects to disentangle the relationship of the observed relaxation processes. A fast process is related to surface loop motions important for substrate specificity, whereas a slower process is related to motions in the core of the protein that are critical for catalytic turnover. These results demonstrate the power of time-resolved X-ray scattering experiments for characterizing protein and solvent dynamics on the μs-ms timescale. We expect the T-jump methodology presented here will be useful for understanding kinetic correlations between local conformational changes of proteins and their bound solvent molecules, which are poorly explained by the results of traditional, static measurements of molecular structure.

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