On the analysis of SAXS data from oriented 2D cylindrical mesostructures measured in symmetric reflection

2006 ◽  
Vol 246 (1) ◽  
pp. 249-253 ◽  
Author(s):  
B. Smarsly ◽  
H. Kaper ◽  
W. Ruland
Keyword(s):  
Saxs Data ◽  
Symmetric Reflection

Pushing the Envelope

2018 ◽  
Author(s):  
Eaton E. Lattman ◽  
Thomas D. Grant ◽  
Edward H. Snell
Keyword(s):  
High Resolution ◽  
Electron Density ◽  
Structural Information ◽  
Hydration Shell ◽  
Three Dimensional ◽  
Scattering Data ◽  
Saxs Data ◽  
Electron Density Function ◽  
Angle Scattering ◽  
Iterative Structure

Direct electron density determination from SAXS data opens up new opportunities. The ability to model density at high resolution and the implicit direct estimation of solvent terms such as the hydration shell may enable high-resolution wide angle scattering data to be used to calculate density when combined with additional structural information. Other diffraction methods that do not measure three-dimensional intensities, such as fiber diffraction, may also be able to take advantage of iterative structure factor retrieval. While the ability to reconstruct electron density ab initio is a major breakthrough in the field of solution scattering, the potential of the technique has yet to be fully uncovered. Additional structural information from techniques such as crystallography, NMR, and electron microscopy and density modification procedures can now be integrated to perform advanced modeling of the electron density function at high resolution, pushing the boundaries of solution scattering further than ever before.

scholarly journals Effect of Posttranslational Modifications on the Structure and Activity of FTO Demethylase

2021 ◽  
Vol 22 (9) ◽  
pp. 4512
Author(s):  
Michał Marcinkowski ◽  
Tomaš Pilžys ◽  
Damian Garbicz ◽  
Jan Piwowarski ◽  
Damian Mielecki ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Size Exclusion Chromatography ◽  
Posttranslational Modifications ◽  
Size Exclusion ◽  
Saxs Data ◽  
Wide Range ◽  
Exclusion Chromatography ◽  
Demethylase Activity ◽  
Structure And Activity

The FTO protein is involved in a wide range of physiological processes, including adipogenesis and osteogenesis. This two-domain protein belongs to the AlkB family of 2-oxoglutarate (2-OG)- and Fe(II)-dependent dioxygenases, displaying N6-methyladenosine (N6-meA) demethylase activity. The aim of the study was to characterize the relationships between the structure and activity of FTO. The effect of cofactors (Fe2+/Mn2+ and 2-OG), Ca2+ that do not bind at the catalytic site, and protein concentration on FTO properties expressed in either E. coli (ECFTO) or baculovirus (BESFTO) system were determined using biophysical methods (DSF, MST, SAXS) and biochemical techniques (size-exclusion chromatography, enzymatic assay). We found that BESFTO carries three phosphoserines (S184, S256, S260), while there were no such modifications in ECFTO. The S256D mutation mimicking the S256 phosphorylation moderately decreased FTO catalytic activity. In the presence of Ca2+, a slight stabilization of the FTO structure was observed, accompanied by a decrease in catalytic activity. Size exclusion chromatography and MST data confirmed the ability of FTO from both expression systems to form homodimers. The MST-determined dissociation constant of the FTO homodimer was consistent with their in vivo formation in human cells. Finally, a low-resolution structure of the FTO homodimer was built based on SAXS data.

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 Molecular insights on CALX-CBD12 inter-domain dynamics from MD simulations, RDCs and SAXS

2020 ◽  
Author(s):  
Maximilia F. de Souza Degenhardt ◽  
Phelipe A. M. Vitale ◽  
Layara A. Abiko ◽  
Martin Zacharias ◽  
Michael Sattler ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Md Simulations ◽  
Bound State ◽  
Conformational Ensemble ◽  
Regulation Mechanism ◽  
Multiple Sources ◽  
Intracellular Loop ◽  
Saxs Data ◽  
Structure Information ◽  
Apo State

ABSTRACTNa+/Ca2+ exchangers (NCX) are secondary active transporters that couple the translocation of Na+ with the transport of Ca2+ in the opposite direction. The exchanger is an essential Ca2+ extrusion mechanism in excitable cells. It consists of a transmembrane domain and a large intracellular loop that contains two Ca2+-binding domains, CBD1 and CBD2. The two CBDs are adjacent to each other and form a two-domain Ca2+-sensor called CBD12. Binding of intracellular Ca2+ to CBD12 activates the NCX but inhibits the Na+/Ca2+ exchanger of Drosophila, CALX. NMR spectroscopy and SAXS studies showed that CALX and NCX CBD12 constructs display significant inter-domain flexibility in the Apo state, but assume rigid inter-domain arrangements in the Ca2+-bound state. However, detailed structure information on CBD12 in the Apo state is missing. Structural characterization of proteins formed by two or more domains connected by flexible linkers is notoriously challenging and requires the combination of orthogonal information from multiple sources. As an attempt to characterize the conformational ensemble of CALX-CBD12 in the Apo state, we applied molecular dynamics (MD) simulations, NMR (1H-15N RDCs) and Small-Angle X-Ray Scattering (SAXS) data in a combined modelling strategy that generated atomistic information on the most representative conformations. This joint approach demonstrated that CALX-CBD12 preferentially samples closed conformations, while the wide-open inter-domain arrangement characteristic of the Ca2+-bound state is less frequently sampled. These results are consistent with the view that Ca2+ binding shifts the CBD12 conformational ensemble towards extended conformers, which could be a key step in the Na+/Ca2+ exchangers’ allosteric regulation mechanism. The present strategy, combining MD with NMR and SAXS, provides a powerful approach to select representative structures from ensembles of conformations, which could be applied to other flexible multi-domain systems.SIGNIFICANCEThe conformational ensemble of CALX-CBD12, the main Ca2+-sensor of Drosophila’s Na+/Ca2+ exchanger, was characterized by a combination of MD simulations with SAXS and NMR data using the EOM approach. This analysis showed that this two-domain construct experiences opening-closing motions, providing molecular information about CALX-CBD12 in the Apo state. Ca2+-binding shifts the conformational ensemble towards extended conformers. These findings are consistent with a model according to which Ca2+ modulation of CBD12 plasticity is a key step in the Ca2+-regulation mechanism of the full-length exchanger.

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 Order and disorder—An integrative structure of the full-length human growth hormone receptor

2021 ◽  
Vol 7 (27) ◽  
pp. eabh3805
Author(s):  
Noah Kassem ◽  
Raul Araya-Secchi ◽  
Katrine Bugge ◽  
Abigail Barclay ◽  
Helena Steinocher ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Human Growth Hormone ◽  
Hormone Receptor ◽  
Growth Hormone Receptor ◽  
Lipid Membrane ◽  
Human Growth ◽  
Full Length ◽  
Saxs Data ◽  
X Ray ◽  
Human Growth Hormone Receptor

Because of its small size (70 kilodalton) and large content of structural disorder (>50%), the human growth hormone receptor (hGHR) falls between the cracks of conventional high-resolution structural biology methods. Here, we study the structure of the full-length hGHR in nanodiscs with small-angle x-ray scattering (SAXS) as the foundation. We develop an approach that combines SAXS, x-ray diffraction, and NMR spectroscopy data obtained on individual domains and integrate these through molecular dynamics simulations to interpret SAXS data on the full-length hGHR in nanodiscs. The hGHR domains reorient freely, resulting in a broad structural ensemble, emphasizing the need to take an ensemble view on signaling of relevance to disease states. The structure provides the first experimental model of any full-length cytokine receptor in a lipid membrane and exemplifies how integrating experimental data from several techniques computationally may access structures of membrane proteins with long, disordered regions, a widespread phenomenon in biology.

scholarly journals Printable Alginate Hydrogels with Embedded Network of Halloysite Nanotubes: Effect of Polymer Cross-Linking on Rheological Properties and Microstructure

Polymers ◽  
2021 ◽  
Vol 13 (23) ◽  
pp. 4130
Author(s):  
Svetlana A. Glukhova ◽  
Vyacheslav S. Molchanov ◽  
Boris V. Lokshin ◽  
Andrei V. Rogachev ◽  
Alexey A. Tsarenko ◽  
...  
Keyword(s):  
3D Printing ◽  
Rheological Properties ◽  
Shear Thinning ◽  
Halloysite Nanotubes ◽  
Polymer Chains ◽  
Cross Linking ◽  
Saxs Data ◽  
Nanocomposite Hydrogels ◽  
Embedded Network ◽  
The Cross

Rapidly growing 3D printing of hydrogels requires network materials which combine enhanced mechanical properties and printability. One of the most promising approaches to strengthen the hydrogels consists of the incorporation of inorganic fillers. In this paper, the rheological properties important for 3D printability were studied for nanocomposite hydrogels based on a rigid network of percolating halloysite nanotubes embedded in a soft alginate network cross-linked by calcium ions. Particular attention was paid to the effect of polymer cross-linking on these properties. It was revealed that the system possessed a pronounced shear-thinning behavior accompanied by a viscosity drop of 4–5 orders of magnitude. The polymer cross-links enhanced the shear-thinning properties and accelerated the viscosity recovery at rest so that the system could regain 96% of viscosity in only 18 s. Increasing the cross-linking of the soft network also enhanced the storage modulus of the nanocomposite system by up to 2 kPa. Through SAXS data, it was shown that at cross-linking, the junction zones consisting of fragments of two laterally aligned polymer chains were formed, which should have provided additional strength to the hydrogel. At the same time, the cross-linking of the soft network only slightly affected the yield stress, which seemed to be mainly determined by the rigid percolation network of nanotubes and reached 327 Pa. These properties make the alginate/halloysite hydrogels very promising for 3D printing, in particular, for biomedical purposes taking into account the natural origin, low toxicity, and good biocompatibility of both components.

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