scholarly journals SAXS4COLL: an integrated software tool for analysing fibrous collagen-based tissues

2017 ◽  
Vol 50 (4) ◽  
pp. 1235-1240 ◽  
Author(s):  
Ahmed Abass ◽  
James S. Bell ◽  
Martin T. Spang ◽  
Sally Hayes ◽  
Keith M. Meek ◽  
...  
Keyword(s):  
Background Subtraction ◽  
Software Tool ◽  
Peak Detection ◽  
Saxs Data ◽  
X Ray ◽  
Cylindrically Symmetric ◽  
X Ray Scattering ◽  
Integrated Software ◽  
Scattering Systems

This article provides an overview of a new integrated software tool for reduction and analysis of small-angle X-ray scattering (SAXS) data from fibrous collagen tissues, with some wider applicability to other cylindrically symmetric scattering systems.SAXS4COLLcombines interactive features for data pre-processing, bespoke background subtraction, semi-automated peak detection and calibration. Both equatorial and meridional SAXS peak parameters can be measured, and the former can be deconstructed into cylinder and lattice contributions. Finally, the software combines functionality for determination of collagen spatial order parameters with a rudimentary orientation plot capability.

Determination of the Growth Rate of Hydrothermally Synthesised ZnO2 Crystallites

2017 ◽  
Vol 50 ◽  
pp. 41-47 ◽  
Author(s):  
Martin Egblewogbe ◽  
Garu Gebreyesus ◽  
Samuel A. Atarah
Keyword(s):  
Growth Rate ◽  
Zinc Acetate Dihydrate ◽  
Hydrothermal Process ◽  
Growth Rate Constant ◽  
Acetate Dihydrate ◽  
X Ray ◽  
X Ray Scattering ◽  
Transmission Electron ◽  
Zinc Peroxide

Powders consisting of nanoparticles of zinc peroxide were prepared via a simple hydrothermal process using zinc acetate dihydrate and hydrogen peroxide precursors. The size of the crystallites was determined using x-ray powder diffraction. Over a period of 5 hours the crystallite radius increased from 4 nm – 9 nm at a temperature of 68 °C ± 5 °C, with growth rate constant of 0.23 nm3 min−1 calculated using the Lifshitz, Slyozov, and Wagner model. The powders were further characterised with High Resolution Transmission Electron Microscopy, Energy Dispersive X-ray analysis, and Small Angle X-ray Scattering, showing well-crystallised ZnO2 nanoparticles.

Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule

2004 ◽  
Vol 37 (1) ◽  
pp. 103-109 ◽  
Author(s):  
Masaki Kojima ◽  
Alexander A. Timchenko ◽  
Junichi Higo ◽  
Kazuki Ito ◽  
Hiroshi Kihara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Small Angle ◽  
Protein Structures ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Saxs Curve ◽  
Restrained Molecular Dynamics ◽  
Ray Scattering

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.

scholarly journals Structural Analysis of the Partially Disordered Protein EspK from Mycobacterium tuberculosis

Crystals ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 18
Author(s):  
Abril Gijsbers ◽  
Nuria Sánchez-Puig ◽  
Ye Gao ◽  
Peter J. Peters ◽  
Raimond B. G. Ravelli ◽  
...  
Keyword(s):  
Host Response ◽  
Limited Proteolysis ◽  
Maximal Dimension ◽  
Globular Domain ◽  
Saxs Data ◽  
X Ray ◽  
Disordered Protein ◽  
X Ray Scattering ◽  
C Terminus ◽  
New Treatments

For centuries, tuberculosis has been a worldwide burden for human health, and gaps in our understanding of its pathogenesis have hampered the development of new treatments. ESX-1 is a complex machinery responsible for the secretion of virulence factors that manipulate the host response. Despite the importance of these secreted proteins for pathogenicity, only a few of them have been structurally and functionally characterised. Here, we describe a structural study of the ESX-secretion associated protein K (EspK), a 74 kDa protein known to be essential for the secretion of other substrates and the cytolytic effects of ESX-1. Small-Angle X-ray Scattering (SAXS) data show that EspK is a long molecule with a maximal dimension of 228 Å. It consists of two independent folded regions at each end of the protein connected by a flexible unstructured region driving the protein to coexist as an ensemble of conformations. Limited proteolysis identified a 26 kDa globular domain at the C-terminus of the protein consisting of a mixture of α-helices and β-strands, as shown by circular dichroism (CD) and SAXS. In contrast, the N-terminal portion is mainly helical with an elongated shape. Sequence conservation suggests that this architecture is preserved amongst the different mycobacteria species, proposing specific roles for the N- and C-terminal domains assisted by the middle flexible linker.

scholarly journals ASAXS study of CaF2nanoparticles embedded in a silicate glass matrix

2014 ◽  
Vol 47 (1) ◽  
pp. 60-66 ◽  
Author(s):  
Armin Hoell ◽  
Zoltan Varga ◽  
Vikram Singh Raghuwanshi ◽  
Michael Krumrey ◽  
Christian Bocker ◽  
...  
Keyword(s):  
Heat Treatment ◽  
Spatial Distribution ◽  
Glass Matrix ◽  
Structural Parameters ◽  
Pixel Detector ◽  
Oxyfluoride Glass ◽  
X Ray ◽  
X Ray Scattering ◽  
Silicate Glass Matrix

The formation and growth of nanosized CaF2crystallites by heat treatment of an oxyfluoride glass of composition 7.65Na2O–7.69K2O–10.58CaO–12.5CaF2–5.77Al2O3–55.8SiO2(wt%) was investigated using anomalous small-angle X-ray scattering (ASAXS). A recently developed vacuum version of the hybrid pixel detector Pilatus 1M was used for the ASAXS measurements below the CaK-edge of 4038 eV down to 3800 eV. ASAXS investigation allows the determination of structural parameters such as size and size distribution of nanoparticles and characterizes the spatial distribution of the resonant element, Ca. The method reveals quantitatively that the growing CaF2crystallites are surrounded by a shell of lower electron density. This depletion shell of growing thickness hinders and finally limits the growth of CaF2crystallites. Moreover, in samples that were annealed for 10 h and more, additional very small heterogeneities (1.6 nm diameter) were found.

scholarly journals Operando SAXS Study of a Pt/C Fuel Cell Catalyst with an X-ray Laboratory Source

2021 ◽  
Author(s):  
Johanna Schröder ◽  
Jonathan Quinson ◽  
Jacob J. K. Kirkensgaard ◽  
Matthias Arenz
Keyword(s):  
Fuel Cell ◽  
Background Subtraction ◽  
Stress Test ◽  
High Surface ◽  
High Surface Area ◽  
Carbon Support ◽  
Grazing Incidence ◽  
Saxs Data ◽  
X Ray ◽  
Fuel Cell Catalysts

Small angle X-ray scattering (SAXS) is a powerful technique to investigate the degradation of catalyst materials. Ideally such investigations are performed <i>operando</i>, i.e., during a catalytic reaction. An example of <i>operando </i>measurements is to observe the degradation of fuel cell catalysts during an accelerated stress test (AST). Fuel cell catalysts consist of Pt or Pt alloy nanoparticles (NPs) supported on a high surface area carbon. A key challenge of operando SAXS measurements is a proper background subtraction of the carbon support to extract the information of the size distribution of the Pt NPs as a function of the AST treatment. Typically, such operando studies require the use of synchrotron facilities. The background measurement can then be performed by anomalous SAXS (aSAXS) or in a grazing incidence con-figuration. In this work we present a proof-of-concept study demonstrating the use of a laboratory X-ray diffractometer for <i>operando </i>SAXS. Data acquisition of <i>operando </i>SAXS with a laboratory X-ray diffractometer is desirable due to the general challenging and limited accessibility of synchrotron facilities. They become even more crucial under the ongoing and foreseen restrictions related to the COVID-19 pandemic. Although, it is not the aim to completely replace synchrotron-based studies, it is shown that the background subtraction can be achieved by a simple experimental consideration in the setup that can ultimately facilitate <i>operando </i>SAXS measurements at a synchrotron facility. <br>

scholarly journals Universal nature of collapsibility in the context of protein folding and evolution

2018 ◽  
Author(s):  
D. Thirumalai ◽  
Himadri S. Samanta ◽  
Hiranmay Maity ◽  
Govardhan Reddy
Keyword(s):  
Single Molecule ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Saxs Data ◽  
X Ray ◽  
Model Free ◽  
X Ray Scattering ◽  
Theoretical Predictions ◽  
Helical Proteins ◽  
Universal Nature

AbstractTheory and simulations predicted sometime ago that the sizes of unfolded states of globular proteins should decrease continuously as the denaturant concentration is shifted from a high to a low value. However, small angle X-ray scattering (SAXS) data were used to assert the opposite, while interpretation of single molecule Forster resonance energy transfer experiments (FRET) supported the theoretical predictions. The disagreement between the two experiments is the SAXS-FRET controversy. By harnessing recent advances in SAXS and FRET experiments and setting these findings in the context of a general theory and simulations, we establish that compaction of unfolded states is universal. The theory also predicts that proteins rich in β-sheets are more collapsible than α-helical proteins. Because the extent of compaction is small, experiments have to be accurate and their interpretations should be as model free as possible. Theory also suggests that collapsibility itself could be a physical restriction on the evolution of foldable sequences, and provides a physical basis for the origin of multi-domain proteins.

scholarly journals Size and Concentration Determination of Colloidal Nanocrystals by Small-Angle X-Ray Scattering

2018 ◽  
Author(s):  
Jorick Maes ◽  
Nicolo Castro ◽  
Kim De Nolf ◽  
Willem Walravens ◽  
Benjamin Abécassis ◽  
...  
Keyword(s):  
Band Gap ◽  
Small Angle ◽  
Accurate Determination ◽  
Band Gap Energy ◽  
Colloidal Nanocrystals ◽  
X Ray ◽  
Absolute Scale ◽  
X Ray Scattering ◽  
Ray Scattering

<div> <div> <div> <p>The accurate determination of the dimensions of a nano-object is paramount to the de- velopment of nanoscience and technology. Here, we provide procedures for sizing quasi- spherical colloidal nanocrystals (NCs) by means of small-angle x-ray scattering (SAXS). Using PbS NCs as a model system, the protocols outline the extraction of the net NC SAXS pattern by background correction and address the calibration of scattered x-ray intensity to an absolute scale. Different data analysis methods are compared, and we show that they yield nearly identical estimates of the NC diameter in the case of a NC ensemble with a monodisperse and monomodal size distribution. Extending the analysis to PbSe, CdSe </p> </div> </div> <div> <div> <p>and CdS NCs, we provide SAXS calibrated sizing curves, which relate the NC diameter and the NC band-gap energy as determined using absorbance spectroscopy. In compari- son with sizing curves calibrated by means of transmission electron microscopy (TEM), we systematically find that SAXS calibration assigns a larger diameter than TEM calibration to NCs with a given band gap. We attribute this difference to the difficulty of accurately sizing small objects in TEM images. To close, we demonstrate that NC concentrations can be directly extracted from SAXS patterns normalized to an absolute scale, and we show that SAXS-based concentrations agree with concentration estimates based on absorption spectroscopy.</p></div></div></div>

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