A high-flux automated laboratory small-angle X-ray scattering instrument optimized for solution scattering

Lyngsø, Jeppe; Pedersen, Jan Skov

doi:10.1107/s1600576720016209

Cited by 35 publications

(16 citation statements)

References 47 publications

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“…HipBST S57A purified as specified in “Protein purification and structure determination” was used for the SAXS analysis. The SAXS measurements were performed on the optimized NanoSTAR instrument (Bruker AXS) at the iNANO center at Aarhus University (Lyngsø & Pedersen, 2021). It uses a high brilliance Ga metal-jet X-ray source (Excillum), special long optics, a two-pinhole collimation with a home-built ‘scatterless’ slit pinhole, and a VÅNTEC-2000 (Bruker AXS) microgap 2D gas proportional detector.…”

Section: Methodsmentioning

confidence: 99%

Structural basis for kinase inhibition in the tripartiteE. coliHipBST toxin-antitoxin system

Bærentsen

Nielsen

Lyngsø

et al. 2022

Preprint

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Many bacteria encode multiple toxin-antitoxin (TA) systems targeting separate, but closely related, cellular functions. The toxin of the E. coli hipBA system, HipA, is a kinase that inhibits inhibits translation via phosphorylation of glutamyl-tRNA synthetase. Enteropathogenic E. coli (EPEC) O127:H6 encodes an additional, tripartite TA module, hipBST, for which the HipT toxin was shown to specifically target tryptophanyl-tRNA synthetase, TrpS. Surprisingly, the function as antitoxin has been taken over by the third protein, HipS, but the molecular details of how activity of HipT is controlled remain poorly understood. Here, we show that HipBST is markedly different from HipBA and that the unique HipS protein, which is homologous to the N-terminal subdomain of HipA, has evolved to function as antitoxin by breaking the kinase active site. We also show how auto-phosphorylation at two conserved sites in the kinase toxin serve to dually regulate binding of HipS and kinase activity. Finally, we demonstrate that the HipBST complex is dynamic and present a cohesive model for the regulation and activation of this type of three-component system.

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Section: Methodsmentioning

confidence: 99%

Structural basis for kinase inhibition in the tripartiteE. coliHipBST toxin-antitoxin system

Bærentsen

Nielsen

Lyngsø

et al. 2022

Preprint

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“…The SAXS measurement was performed on the in-house SAXS instrument at Aarhus University [ 57 ], equipped with a rotating Cu anode source, side-by-side Montel multilayer mirrors to monochromatize and focus the beam, and a Vantec 500 (Bruker AXS, East Cheryl Parkway, Madison, WI, USA) detector upgrade. The collimation consists of two pinholes, where the one close to the sample is a scatterless pinhole with edges of Ge crystal [ 58 , 59 ]. The Me-S-H/PCE suspension was mounted in a glass capillary and measured.…”

Section: Methodsmentioning

confidence: 99%

An Atomistic Model Describing the Structure and Morphology of Cu-Doped C-S-H Hardening Accelerator Nanoparticles

Sasso

Dalconi

Ferrari³

et al. 2022

Nanomaterials

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Calcium silicate hydrate (C-S-H) is the main binding phase in Portland cement. The addition of C-S-H nanoparticles as nucleation seeds has successfully been used to accelerate the hydration process and the precipitation of binding phases either in conventional Portland cement or in alternative binders. Indeed, the modulation of the hydration kinetics during the early-stage dissolution-precipitation reactions, by acting on the nucleation and growth of binding phases, improves the early strength development. The fine-tuning of concrete properties in terms of compressive strength and durability by designed structural modifications can be achieved through the detailed description of the reaction products at the atomic scale. The nano-sized, chemically complex and structurally disordered nature of these phases hamper their thorough structural characterization. To this aim, we implement a novel multi-scale approach by combining forefront small-angle X-ray scattering (SAXS) and synchrotron wide-angle X-ray total scattering (WAXTS) analyses for the characterization of Cu-doped C-S-H nanoparticles dispersed in a colloidal suspension, used as hardening accelerator. SAXS and WAXTS data were analyzed under a unified modeling approach by developing suitable atomistic models for C-S-H nanoparticles to be used to simulate the experimental X-ray scattering pattern through the Debye scattering equation. The optimization of atomistic models against the experimental pattern, together with complementary information on the structural local order from 29Si solid-state nuclear magnetic resonance and X-ray absorption spectroscopy, provided a comprehensive description of the structure, size and morphology of C-S-H nanoparticles from the atomic to the nanometer scale. C-S-H nanoparticles were modeled as an assembly of layers composed of 7-fold coordinated Ca atoms and decorated by silicate dimers and chains. The structural layers are a few tens of nanometers in length and width, with a crystal structure resembling that of a defective tobermorite, but lacking any ordering between stacking layers.

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“…SAXS data were recorded at the HyperSAXS facility in Aarhus, Denmark. 18 The data were calibrated to an absolute scale and displayed as a function of the modulus of the scattering vector, q . The forward scattering data yield a mass of about 390 kDa corresponding to six spike proteins per scatterer.…”

Section: Methodsmentioning

confidence: 99%

Structure and Orientation of the SARS-Coronavirus-2 Spike Protein at Air–Water Interfaces

et al. 2022

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The SARS coronavirus 2 (SARS-CoV-2) spike protein is located at the outermost perimeter of the viral envelope and is the first component of the virus to make contact with surrounding interfaces. The stability of the spike protein when in contact with surfaces plays a deciding role for infection pathways and for the viability of the virus after surface contact. While cryo-EM structures of the spike protein have been solved with high resolution and structural studies in solution have provided information about the secondary and tertiary structures, only little is known about the folding when adsorbed to surfaces. We here report on the secondary structure and orientation of the S1 segment of the spike protein, which is often used as a model protein for in vitro studies of SARS-CoV-2, at the air–water interface using surface-sensitive vibrational sum-frequency generation (SFG) spectroscopy. The air–water interface plays an important role for SARS-CoV-2 when suspended in aerosol droplets, and it serves as a model system for hydrophobic surfaces in general. The SFG experiments show that the S1 segment of the spike protein remains folded at the air–water interface and predominantly binds in its monomeric state, while the combination of small-angle X-ray scattering and two-dimensional infrared spectroscopy measurements indicate that it forms hexamers with the same secondary structure in aqueous solution.

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A high-flux automated laboratory small-angle X-ray scattering instrument optimized for solution scattering

Cited by 35 publications

References 47 publications

Structural basis for kinase inhibition in the tripartiteE. coliHipBST toxin-antitoxin system

Structural basis for kinase inhibition in the tripartiteE. coliHipBST toxin-antitoxin system

An Atomistic Model Describing the Structure and Morphology of Cu-Doped C-S-H Hardening Accelerator Nanoparticles

Structure and Orientation of the SARS-Coronavirus-2 Spike Protein at Air–Water Interfaces

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