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.

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.

Small-angle x-ray scattering studies of early-stage colloid formation by thermohydrolytic polymerization of aqueous zirconyl salt solutions

1999 ◽  
Vol 14 (1) ◽  
pp. 103-113 ◽  
Author(s):  
Michael Z-C. Hu ◽  
Jason T. Zielke ◽  
J-S. Lin ◽  
Charles H. Byers
Keyword(s):  
Small Angle ◽  
Elevated Temperatures ◽  
Early Stage ◽  
Radius Of Gyration ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Primary Particles ◽  
Colloid Formation ◽  
Ray Scattering

Early-stage processes involving the polymerization of zirconium species in aqueous solutions at elevated temperatures (∼100 °C) as well as colloid formation were studied. Small-angle x-ray scattering (SAXS) data were analyzed via Guinier, “longrods,” and Porod plots to determine particle growth kinetics and morphology. Our SAXS data suggest that zirconium tetramers and octamers polymerize into larger clusters and elongated-rod-(or needle)-shaped primary particles, which have a length of a few nanometers and a radius of gyration of cross section between 4 and 5 Å. Cube-shaped particles are aggregates of the needlelike primary particles. The transition from zirconium tetramer to a colloidal sol particle follows a mass-fractal growth (1 < fractal dimension, D <3)

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.

In situ Time-Resolved Small-Angle X-ray Scattering Reveals the Formation Kinetics of Polyelectrolyte Complex Micelles

2019 ◽  
Author(s):  
Hao Wu ◽  
Jeffrey Ting ◽  
Siqi Meng ◽  
Matthew Tirrell
Keyword(s):  
Small Angle ◽  
Self Assembly ◽  
Electrostatic Interactions ◽  
Polyelectrolyte Complex ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Kinetics Of ◽  
Ray Scattering

We have directly observed the <i>in situ</i> self-assembly kinetics of polyelectrolyte complex (PEC) micelles by synchrotron time-resolved small-angle X-ray scattering, equipped with a stopped-flow device that provides millisecond temporal resolution. This work has elucidated one general kinetic pathway for the process of PEC micelle formation, which provides useful physical insights for increasing our fundamental understanding of complexation and self-assembly dynamics driven by electrostatic interactions that occur on ultrafast timescales.

scholarly journals Alpha helical surfactant-like peptides self-assemble into pH-dependent nanostructures

Soft Matter ◽  
2021 ◽  
Vol 17 (11) ◽  
pp. 3096-3104
Author(s):  
Valeria Castelletto ◽  
Jani Seitsonen ◽  
Janne Ruokolainen ◽  
Ian W. Hamley
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Small Angle ◽  
Self Assembly ◽  
X Ray ◽  
Cryogenic Transmission Electron Microscopy ◽  
X Ray Scattering ◽  
Transmission Electron ◽  
Ph Dependent ◽  
Ray Scattering

A designed surfactant-like peptide is shown, using a combination of cryogenic-transmission electron microscopy and small-angle X-ray scattering, to have remarkable pH-dependent self-assembly properties.

scholarly journals Controlling water evaporation through self-assembly

2016 ◽  
Vol 113 (37) ◽  
pp. 10275-10280 ◽  
Author(s):  
Kevin Roger ◽  
Marianne Liebi ◽  
Jimmy Heimdal ◽  
Quoc Dat Pham ◽  
Emma Sparr
Keyword(s):  
Self Assembly ◽  
Feedback Loop ◽  
Ambient Air ◽  
Underlying Mechanism ◽  
Water Evaporation ◽  
Air Humidity ◽  
X Ray ◽  
X Ray Scattering ◽  
Composition And Structure ◽  
Living Organisms

Water evaporation concerns all land-living organisms, as ambient air is dryer than their corresponding equilibrium humidity. Contrarily to plants, mammals are covered with a skin that not only hinders evaporation but also maintains its rate at a nearly constant value, independently of air humidity. Here, we show that simple amphiphiles/water systems reproduce this behavior, which suggests a common underlying mechanism originating from responding self-assembly structures. The composition and structure gradients arising from the evaporation process were characterized using optical microscopy, infrared microscopy, and small-angle X-ray scattering. We observed a thin and dry outer phase that responds to changes in air humidity by increasing its thickness as the air becomes dryer, which decreases its permeability to water, thus counterbalancing the increase in the evaporation driving force. This thin and dry outer phase therefore shields the systems from humidity variations. Such a feedback loop achieves a homeostatic regulation of water evaporation.

scholarly journals Exploring the in meso crystallization mechanism by characterizing the lipid mesophase microenvironment during the growth of single transmembrane α-helical peptide crystals

2016 ◽  
Vol 374 (2072) ◽  
pp. 20150125 ◽  
Author(s):  
Leonie van 't Hag ◽  
Konstantin Knoblich ◽  
Shane A. Seabrook ◽  
Nigel M. Kirby ◽  
Stephen T. Mudie ◽  
...  
Keyword(s):  
Crystal Growth ◽  
Self Assembly ◽  
Lamellar Phase ◽  
Cubic Phase ◽  
Supporting Evidence ◽  
X Ray ◽  
X Ray Scattering ◽  
Standard Procedures ◽  
Helical Peptide ◽  
Saxs Analysis

The proposed mechanism for in meso crystallization of transmembrane proteins suggests that a protein or peptide is initially uniformly dispersed in the lipid self-assembly cubic phase but that crystals grow from a local lamellar phase, which acts as a conduit between the crystal and the bulk cubic phase. However, there is very limited experimental evidence for this theory. We have developed protocols to investigate the lipid mesophase microenvironment during crystal growth using standard procedures readily available in crystallography laboratories. This technique was used to characterize the microenvironment during crystal growth of the DAP12-TM peptide using synchrotron small angle X-ray scattering (SAXS) with a micro-sized X-ray beam. Crystal growth was found to occur from the gyroid cubic mesophase. For one in four crystals, a highly oriented local lamellar phase was observed, providing supporting evidence for the proposed mechanism for in meso crystallization. A new observation of this study was that we can differentiate diffraction peaks from crystals grown in meso , from peaks originating from the surrounding lipid matrix, potentially opening up the possibility of high-throughput SAXS analysis of in meso grown crystals. This article is part of the themed issue ‘Soft interfacial materials: from fundamentals to formulation’.

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.

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