scholarly journals DATASW, a tool for HPLC–SAXS data analysis

2015 ◽  
Vol 71 (6) ◽  
pp. 1347-1350 ◽  
Author(s):  
Alexander V. Shkumatov ◽  
Sergei V. Strelkov
Keyword(s):  
High Performance ◽  
Model Building ◽  
Sliding Window ◽  
Data Interpretation ◽  
Resolution Method ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Heterogeneous Samples ◽  
Folding State

Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement the high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The programDATASWperforms averaging of individual data frames from HPLC–SAXS experiments using a sliding window of a user-specified size, calculates overall parameters [I(0),Rg,Dmaxand molecular weight] and predicts the folding state (folded/unfolded) of the sample. Applications ofDATASWare illustrated for several proteins with various oligomerization behaviours recorded on different beamlines.DATASWbinaries for major operating systems can be downloaded from http://datasw.sourceforge.net/.

scholarly journals Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries

2021 ◽  
Author(s):  
Christian Prehal ◽  
Sara Drvarič Talian ◽  
Alen Vizintin ◽  
Heinz Amenitsch ◽  
Robert Dominko ◽  
...  
Keyword(s):  
High Performance ◽  
Surface Film ◽  
Rate Capability ◽  
Stochastic Modelling ◽  
Phase Evolution ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Chemical Phase

Abstract Insufficient understanding of the mechanism that reversibly converts sulphur into lithium sulphide (Li2S) via soluble polysulphides (PS) hampers the realization of high performance lithium-sulphur cells. Typically Li2S formation is explained by direct electroreduction of a PS to Li2S; however, this is not consistent with the size of the insulating Li2S deposits. Here, we use in situ small and wide angle X-ray scattering (SAXS/WAXS) to track the growth and dissolution of crystalline and amorphous deposits from atomic to sub-micron scales during charge and discharge. Stochastic modelling based on the SAXS data allows quantification of the chemical phase evolution during discharge and charge. We show that Li2S deposits predominantly via disproportionation of transient, solid Li2S2 to form primary Li2S crystallites and solid Li2S4 particles. We further demonstrate that this process happens in reverse during charge. These findings show that the discharge capacity and rate capability in Li-S battery cathodes are therefore limited by mass transport through the increasingly tortuous network of Li2S / Li2S4 / carbon pores rather than electron transport through a passivating surface film.

The Structural Characteristics Features of the Nanocomposite Systems of CdS Quantum Dots in the Gel Matrix Obtained by the Method of Small-Angle X-Ray Scattering

2014 ◽  
Vol 213 ◽  
pp. 216-221
Author(s):  
Anna N. Galkina ◽  
Alexander A. Sergeev
Keyword(s):  
Quantum Dots ◽  
Small Angle ◽  
Structural Characteristics ◽  
Data Interpretation ◽  
Cds Quantum Dots ◽  
Particle Structure ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

The strucrture of CdS quantum dots 0,3% (mass), stabilized by the solution of the mercaptosuccinic acid in the gel matrix 50% THEOS is investigated by small-angle X-ray scattering (SAXS). Application of modern methods of SAXS data interpretation, including procedure of ab initio modeling of particle structure, allowed us for the to reveal structural organization of both individual nanoparticles and of their clusters incorporated in the polymer matrix. As a result, the shape, size, and size distribution of the obtained nanoparticles and their clusters depended on the structure of the gel matrix used as a formation medium.

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.

Diffuse X-ray scattering from tiny sample volumes

2005 ◽  
Vol 220 (12) ◽  
Author(s):  
Gene E. Ice ◽  
Rozaliya I. Barabash ◽  
Wenjun Liu
Keyword(s):  
Local Structure ◽  
Diffuse Scattering ◽  
High Performance ◽  
Sensitive Area ◽  
X Ray ◽  
X Ray Scattering ◽  
Defect Content ◽  
Ray Scattering

AbstractThe emergence of intense synchrotron X-ray sources, efficient focusing optics and high-performance X-ray sensitive area detectors allows for measurements of diffuse scattering from cubic micron-scale sample vol umes. Here we present an experiment that illustrates methods for studying the local structure and defect content of tiny sample volumes. In the experiment, an X-ray microbeam illuminating about ∼5 μm

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 Plasmodium falciparum Kelch13 and its artemisinin-resistant mutants assemble as hexamers in solution: a SAXS data driven shape restoration study

2021 ◽  
Author(s):  
Nainy Goel ◽  
Kanika Dhiman ◽  
Nidhi Kalidas ◽  
Anwesha Mukhopadhyay ◽  
Ashish ◽  
...  
Keyword(s):  
Artemisinin Resistance ◽  
Resistant Mutant ◽  
Data Driven ◽  
Wild Type ◽  
Saxs Data ◽  
Mutant Proteins ◽  
X Ray ◽  
X Ray Scattering ◽  
Shape Restoration ◽  
Spatial Positioning

AbstractArtemisinin-resistant mutations in PfKelch13 identified worldwide are mostly confined to its BTB/POZ and KRP domains. To date, only two crystal structures of the BTB/POZ-KRP domains as tight dimers are available, which limits structure-based interpretations of its functionality. Our solution Small-Angle X-ray Scattering (SAXS) data driven shape restoration of larger length of protein brought forth that: i) PfKelch13 forms a stable hexamer in P6 symmetry, ii) interactions of the N-termini drive the hexameric assembly, and iii) the six KRP domains project independently in space, forming a cauldron-like architecture. While artemisinin-sensitive mutant A578S packed like the wild-type, hexameric assemblies of dominant artemisinin-resistant mutant proteins R539T and C580Y displayed detectable differences in spatial positioning of their BTB/POZ-KRP domains. Lastly, mapping of mutations known to enable artemisinin resistance explained that most mutations exist mainly in these domains because they are non-detrimental to assembly of mutant PfKelch13 and yet can alter the flux of downstream events essential for susceptibility to artemisinin.

Quality control of protein standards for molecular mass determinations by small-angle X-ray scattering

2010 ◽  
Vol 43 (2) ◽  
pp. 237-243 ◽  
Author(s):  
Shuji Akiyama
Keyword(s):  
Quality Control ◽  
Molecular Mass ◽  
Small Angle ◽  
Biological Macromolecules ◽  
Average Deviation ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Standard Quality ◽  
Ray Scattering

Small-angle X-ray scattering (SAXS) is a powerful technique with which to evaluate the size and shape of biological macromolecules in solution. Forward scattering intensity normalized relative to the particle concentration,I(0)/c, is useful as a good measure of molecular mass. A general method for deducing the molecular mass from SAXS data is to determine the ratio ofI(0)/cof a target protein to that of a standard protein with known molecular mass. The accuracy of this interprotein calibration is affected considerably by the monodispersity of the prepared standard, as well as by the precision in estimating its concentration. In the present study, chromatographic fractionation followed by hydrodynamic characterization is proposed as an effective procedure by which to prepare a series of monodispersed protein standards. The estimation of molecular mass within an average deviation of 8% is demonstrated using monodispersed bovine serum albumin as a standard. The present results demonstrate the importance of protein standard quality control in order to take full advantage of interprotein calibration.

scholarly journals Structural Study of the Photo-Mediated Growth of Silver Nanoprisms

Molecules ◽  
2020 ◽  
Vol 25 (22) ◽  
pp. 5413
Author(s):  
Matti Knaapila ◽  
Ulla Vainio ◽  
Sophie E. Canton ◽  
Gunnel Karlsson
Keyword(s):  
Particle Size ◽  
Small Angle ◽  
Volume Ratio ◽  
Direct Methods ◽  
Saxs Data ◽  
Aqueous Dispersions ◽  
X Ray ◽  
Silver Nanoprisms ◽  
X Ray Scattering ◽  
Ag Particles

We present a small-angle X-ray scattering (SAXS) study of the anisotropic photoinduced growth of silver (Ag) nanoprisms in aqueous dispersions. The growth of nearly spherical (<10 nm) Ag particles into large (>40 nm) and thin (<10 nm) triangular nanoprisms induced by 550 nm laser is followed in terms of particle size using indirect and direct methods for irradiation times up to 150 min. During the process, the surface-to-volume ratio of the particles decreased. The SAXS data of the initial solution fit well to the model of polydisperse spheres with pronounced average diameters around 7.4 nm and 10 nm. The data after 45 min irradiation fit well to the model containing approximately the same amount of the initial particles and the end product, the nanoprisms.

When dendrimers are not better – rational design of nanolayers for high-performance organic electronic devices

Nanoscale ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 4463-4470 ◽  
Author(s):  
Maxim A. Shcherbina ◽  
Oleg V. Borshchev ◽  
Alexandra P. Pleshkova ◽  
Sergei A. Ponomarenko ◽  
Sergei N. Chvalun
Keyword(s):  
High Performance ◽  
Rational Design ◽  
Electronic Devices ◽  
Carbosilane Dendrimers ◽  
Scanning Calorimetry ◽  
Organic Electronic Devices ◽  
X Ray ◽  
Force Microscopy ◽  
X Ray Scattering ◽  
Atomic Force

Several generations of carbosilane dendrimers with quaterthiophene end groups were studied by X-ray scattering, differential scanning calorimetry, polarizing optical and atomic force microscopy and molecular modelling.

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