scholarly journals Intermediate-resolution crystal structure of the human adenovirus B serotype 3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2

2019 ◽  
Vol 75 (12) ◽  
pp. 750-757 ◽  
Author(s):  
Emilie Vassal-Stermann ◽  
Stephanie Hutin ◽  
Pascal Fender ◽  
Wim P. Burmeister
Keyword(s):  
Crystal Structure ◽  
Calcium Ions ◽  
Distal Part ◽  
Human Adenovirus ◽  
Anomalous Scattering ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Cryo Electron Microscopy ◽  
Concentrated Solution

The cryo-electron microscopy (cryo-EM) structure of the complex between the trimeric human adenovirus B serotype 3 fibre knob and human desmoglein 2 fragments containing cadherin domains EC2 and EC3 has been published, showing 3:1 and 3:2 complexes. Here, the crystal structure determined at 4.5 Å resolution is presented with one EC2-EC3 desmoglein fragment bound per fibre knob monomer in the asymmetric unit, leading to an apparent 3:3 stoichiometry. However, in concentrated solution the 3:2 complex is predominant, as shown by small-angle X-ray scattering (SAXS), while cryo-EM at lower concentrations showed a majority of the 3:1 complex. Substitution of the calcium ions bound to the desmoglein domains by terbium ions allowed confirmation of the X-ray model using their anomalous scattering and shows that at least one binding site per cluster of calcium ions is intact and exchangeable and, combined with SAXS data, that the cadherin domains are folded even in the distal part that is invisible in the cryo-EM reconstruction.

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 Heat induces end to end repetitive association in P. furiosus l-asparaginase which enables its thermophilic property

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Pankaj Sharma ◽  
Rachana Tomar ◽  
Shivpratap Singh Yadav ◽  
Maulik D. Badmalia ◽  
Samir Kumar Nath ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Self Assembly ◽  
Elevated Temperatures ◽  
Contact Point ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Crystallographic Structures ◽  
End To End ◽  
Enhanced Stability

AbstractIt remains undeciphered how thermophilic enzymes display enhanced stability at elevated temperatures. Taking l-asparaginase from P. furiosus (PfA) as an example, we combined scattering shapes deduced from small-angle X-ray scattering (SAXS) data at increased temperatures with symmetry mates from crystallographic structures to find that heating caused end-to-end association. The small contact point of self-binding appeared to be enabled by a terminal short β-strand in N-terminal domain, Leu179-Val-Val-Asn182 (LVVN). Interestingly, deletion of this strand led to a defunct enzyme, whereas suplementation of the peptide LVVN to the defunct enzyme restored structural frameworkwith mesophile-type functionality. Crystal structure of the peptide-bound defunct enzyme showed that one peptide ispresent in the same coordinates as in original enzyme, explaining gain-of lost function. A second peptide was seen bound to the protein at a different location suggesting its possible role in substrate-free molecular-association. Overall, we show that the heating induced self-assembly of native shapes of PfA led to an apparent super-stable assembly.

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 Vibrational anisotropy of <i>δ</i>-(Al,Fe)OOH single crystals as probed by nuclear resonant inelastic X-ray scattering

2021 ◽  
Vol 33 (4) ◽  
pp. 485-502
Author(s):  
Johannes Buchen ◽  
Wolfgang Sturhahn ◽  
Takayuki Ishii ◽  
Jennifer M. Jackson
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Single Crystals ◽  
Vibrational Properties ◽  
Phonon Density ◽  
Phonon Density Of States ◽  
X Ray ◽  
X Ray Scattering ◽  
The Mean ◽  
Vibrational Anisotropy

Abstract. The formation of high-pressure oxyhydroxide phases spanned by the components AlOOH–FeOOH–MgSiO2(OH)2 in experiments suggests their capability to retain hydrogen in Earth's lower mantle. Understanding the vibrational properties of high-pressure phases provides the basis for assessing their thermal properties, which are required to compute phase diagrams and physical properties. Vibrational properties can be highly anisotropic, in particular for materials with crystal structures of low symmetry that contain directed structural groups or components. We used nuclear resonant inelastic X-ray scattering (NRIXS) to probe lattice vibrations that involve motions of 57Fe atoms in δ-(Al0.87Fe0.13)OOH single crystals. From the recorded single-crystal NRIXS spectra, we calculated projections of the partial phonon density of states along different crystallographic directions. To describe the anisotropy of central vibrational properties, we define and derive tensors for the partial phonon density of states, the Lamb–Mössbauer factor, the mean kinetic energy per vibrational mode, and the mean force constant of 57Fe atoms. We further show how the anisotropy of the Lamb–Mössbauer factor can be translated into anisotropic displacement parameters for 57Fe atoms and relate our findings on vibrational anisotropy to the crystal structure of δ-(Al,Fe)OOH. As a potential application of single-crystal NRIXS at high pressures, we discuss the evaluation of anisotropic thermal stresses in the context of elastic geobarometry for mineral inclusions. Our results on single crystals of δ-(Al,Fe)OOH demonstrate the sensitivity of NRIXS to vibrational anisotropy and provide an in-depth description of the vibrational behavior of Fe3+ cations in a crystal structure that may motivate future applications of NRIXS to study anisotropic vibrational properties of minerals.

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.

An instrument for time-resolved and anomalous simultaneous small- and wide-angle X-ray scattering (SWAXS) at NSRRC

2006 ◽  
Vol 39 (6) ◽  
pp. 871-877 ◽  
Author(s):  
Ying-Huang Lai ◽  
Ya-Sen Sun ◽  
U-Ser Jeng ◽  
Jhih-Min Lin ◽  
Tsang-Lang Lin ◽  
...  
Keyword(s):  
Lipid Membrane ◽  
Quantum Wires ◽  
Grazing Incidence ◽  
Anomalous Scattering ◽  
Wide Angle ◽  
Scanning Calorimetry ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

A SWAXS (small- and wide-angle X-ray scattering) instrument was recently installed at the wiggler beamline BL17B3 of the National Synchrotron Radiation Research Center (NSRRC), Taiwan. The instrument, which is designed for studies of static and dynamic nanostructures and correlations between the nano (ormeso) structure (SAXS) and crystalline structure (WAXS), provides a flux of 1010–1011photon s−1at the sample at energies between 5 and 14 keV. With a SAXS area detector and a WAXS linear detector connected to two data acquisition systems operated in master–slave mode, the instrument allows one to perform time-resolved as well as anomalous scattering measurements. Data reduction algorithms have been developed for rapid processing of the large SWAXS data sets collected during time-resolved measurements. The performance of the instrument is illustrated by examples taken from different classes of ongoing projects: (i) time-resolved SAXS/WAXS/differential scanning calorimetry (DSC) with a time resolution of 10 s on a semicrystalline poly(hexamethylene terephthalate) sample, (ii) anomalous SAXS/WAXS measurements on a nanoparticulate PtRu catalyst, and (iii) grazing-incidence SAXS of a monolayer of oriented semiconductor quantum wires, and humidity-controlled ordering of Alamethicin peptides embedded in an oriented lipid membrane.

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