Distinctive Low-Resolution Structural Features of Dimers of Antibody–Drug Conjugates and Parent Antibody Determined by Small-Angle X-ray Scattering

AbstractViral infections are responsible for numerous deaths worldwide. Flaviviruses, which contain RNA as their genetic material, are one of the most pathogenic families of viruses. There is an increasing amount of evidence suggesting that their 5’ and 3’ non-coding terminal regions are critical for their survival. In this study, the 5’ and 3’ terminal regions of Murray Valley Encephalitis and Powassan virus were examined using biophysical and computational modeling methods. First, the purity of in-vitro transcribed RNAs were investigated using size exclusion chromatography and analytical ultracentrifuge methods. Next, we employed small-angle X-ray scattering techniques to study solution conformation and low-resolution structures of these RNAs, which suggested that the 3’ terminal regions are highly extended, compared to the 5’ terminal regions for both viruses. Using computational modeling tools, we reconstructed 3-dimensional structures of each RNA fragment and compared them with derived small-angle X-ray scattering low-resolution structures. This approach allowed us to further reinforce that the 5’ terminal regions adopt more dynamic structures compared to the mainly double-stranded structures of the 3’ terminal regions.

Download Full-text

The inertia-equivalent ellipsoid: a link between atomic structure and low-resolution models of small globular proteins determined by small-angle X-ray scattering

Journal of Applied Crystallography ◽

10.1107/s0021889891011421 ◽

1992 ◽

Vol 25 (2) ◽

pp. 181-191 ◽

Cited By ~ 14

Author(s):

J. J. Müller ◽

H. Schrauber

Keyword(s):

Small Angle ◽

Computer Experiment ◽

Density Fluctuations ◽

Molecular Surface ◽

Triaxial Ellipsoid ◽

Correction Factors ◽

Low Resolution ◽

X Ray ◽

X Ray Scattering ◽

Ray Scattering

Low-resolution three-parameter models of the shape of a biopolymer in solution can be determined by a new indirect method from small-angle X-ray scattering without contrast-variation experiments. The basic low-resolution model employed is a triaxial ellipsoid – the inertia-equivalent ellipsoid (IEE). The IEE is related to the tensor of inertia of a body and the eigenvalues and eigenvectors of this tensor can be calculated directly from the atomic coordinates and from the homogeneous solvent-excluded body of a molecule. The IEE defines a mean molecular surface (like the sea level on earth) which models the molecular shape adequately if the IEE volume is not more than 30% larger than the dry volume of the molecule. Approximately 10 to 15% of the solvent-excluded volume is outside the ellipsoid; the radii of gyration of the IEE and of the homogeneous molecular body are identical. The largest diameter of the IEE is about 5 to 15% (~0.2–0.8 nm) smaller than the maximum dimension of globular molecules with molecular masses smaller than 65000 daltons. From the scattering curve of a molecule in solution the IEE can be determined by a calibration procedure. 29 proteins of known crystal structure have been used as a random sample. Systematic differences between the axes of the IEE, calculated directly from the structure, and the axes of the scattering-equivalent ellipsoids of revolution, estimated from the scattering curve of the molecule in solution, are used to derive correction factors for the axial dimensions. Distortions of model dimensions of 20 to 40% (up to 1 nm), caused by misinterpretation of scattering contributions from electron density fluctuations within the molecule, are reduced to a quarter by applying these correction factors to the axes of the scattering-equivalent ellipsoids of revolution. In a computer experiment the axes of the inertia-equivalent ellipsoids have been determined for a further nine proteins with the same accuracy. The automated estimation of the IEE from the scattering curve of a molecule in solution is realized by the Fortran77 program AUTOIEE.

Download Full-text

Characterizing nanoparticles with a laboratory diffractometer: from small-angle to total X-ray scattering

Powder Diffraction ◽

10.1017/s0885715614001043 ◽

2014 ◽

Vol 29 (S1) ◽

pp. S47-S53 ◽

Cited By ~ 7

Author(s):

Marco Sommariva ◽

Milen Gateshki ◽

Jan-André Gertenbach ◽

Joerg Bolze ◽

Uwe König ◽

...

Keyword(s):

Small Angle ◽

Structural Features ◽

Bragg Diffraction ◽

X Ray Diffraction ◽

X Ray ◽

X Ray Scattering ◽

Transmission Electron ◽

Pdf Analysis ◽

Comprehensive Picture ◽

Ray Scattering

X-ray diffraction and scattering on a single multipurpose X-ray platform have been used to probe the structure, composition, and thermal behavior of TiO2 nanoparticles ranging in size from 1 to 10 nm. Ambient and non-ambient Bragg diffraction, small-angle X-ray scattering (SAXS), as well as total scattering and pair-distribution function (PDF) analysis are combined to obtain a comprehensive picture of the samples. At these ultrasmall particle-size dimensions, SAXS and PDF prove powerful in distinguishing the salient features of the materials, in particular the size distribution of the primary particles (SAXS) and the identification of the TiO2 polymorphs (PDF). Structural features determined by X-ray scattering techniques are corroborated by high-resolution transmission electron microscopy. The elemental make-up of the materials has been measured using X-ray fluorescence spectrometry and energy-dispersive X-ray analysis.

Download Full-text

On the nanostructure of radiation-amorphized zircon and pyrochlores: a small-angle x-ray scattering study

Zeitschrift für Kristallographie - Crystalline Materials ◽

10.1524/zkri.220.8.748.67082 ◽

2005 ◽

Vol 220 (8) ◽

Author(s):

Susana Ríos ◽

Christopher M. Martin ◽

Karl R. Whittle

Keyword(s):

Small Angle ◽

Annealing Temperature ◽

Characteristic Length ◽

Structural Features ◽

Density Fluctuations ◽

X Ray ◽

X Ray Scattering ◽

Scattering Study ◽

Electron Density Fluctuations ◽

Ray Scattering

AbstractNanoscale structural features of amorphous zircon and pyrochlore produced by self-irradiation induced amorphization have been characterized by small-angle X-ray scattering (SAXS). Electron density fluctuations were observed in the untreated samples and studied as a function of annealing temperature (up to 1300 °C). In untreated zircon, density fluctuations were found to have a characteristic length-scale of approximately 1 nanometer diameter. A clear scattering maximum develops at ∼3 nm

Download Full-text

Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling

Journal of Applied Crystallography ◽

10.1107/s0021889807001707 ◽

2007 ◽

Vol 40 (s1) ◽

pp. s229-s234 ◽

Cited By ~ 29

Author(s):

Jan Lipfert ◽

Vincent B. Chu ◽

Yu Bai ◽

Daniel Herschlag ◽

Sebastian Doniach

Keyword(s):

Nucleic Acids ◽

Small Angle ◽

Low Resolution ◽

X Ray ◽

X Ray Scattering ◽

Electrostatic Modeling ◽

Ray Scattering

Download Full-text

Low-Resolution Structure of the Full-Length Barley (Hordeum vulgare) SGT1 Protein in Solution, Obtained Using Small-Angle X-Ray Scattering

PLoS ONE ◽

10.1371/journal.pone.0093313 ◽

2014 ◽

Vol 9 (4) ◽

pp. e93313 ◽

Cited By ~ 4

Author(s):

Michał Taube ◽

Joanna R. Pieńkowska ◽

Artur Jarmołowski ◽

Maciej Kozak

Keyword(s):

Hordeum Vulgare ◽

Small Angle ◽

Full Length ◽

Low Resolution ◽

X Ray ◽

X Ray Scattering ◽

Resolution Structure ◽

Ray Scattering

Download Full-text

Low‐resolution structure of HIV‐1 genomic RNA regions obtained by small angle x‐ray scattering analysis

The FASEB Journal ◽

10.1096/fasebj.26.1_supplement.lb99 ◽

2012 ◽

Vol 26 (S1) ◽

Author(s):

Erik David Olson ◽

Christopher P Jones ◽

Karin Musier-Forsyth

Keyword(s):

Small Angle ◽

Genomic Rna ◽

Low Resolution ◽

X Ray ◽

X Ray Scattering ◽

Hiv 1 ◽

Resolution Structure ◽

Ray Scattering

Download Full-text

Small-angle X-ray scattering (SAXS) studies of the low-resolution structure of the ribosomal GTPase EFL1, the SBDS protein and their complex

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273316097308 ◽

2016 ◽

Vol 72 (a1) ◽

pp. s180-s181 ◽

Cited By ~ 1

Author(s):

Dritan Siliqi ◽

Davide Altamura ◽

Abril Gijsbers ◽

Eugenio de la Mora ◽

Cinzia Giannini ◽

...

Keyword(s):

Small Angle ◽

Low Resolution ◽

X Ray ◽

X Ray Scattering ◽

Resolution Structure ◽

Ray Scattering

Download Full-text

Nanocomposites of Au/Disentangled UHMWPE: A Combined Optical and Structural Study

Molecules ◽

10.3390/molecules25143225 ◽

2020 ◽

Vol 25 (14) ◽

pp. 3225

Author(s):

Stavros X. Drakopoulos ◽

Oreste Tarallo ◽

Linlin Guan ◽

Ignacio Martin-Fabiani ◽

Sara Ronca

Keyword(s):

Gold Nanoparticles ◽

Small Angle ◽

Near Infrared ◽

Polarized Light ◽

Structural Features ◽

X Ray ◽

Optical Absorbance ◽

Entanglement Density ◽

X Ray Scattering ◽

Ray Scattering

The term disentangled refers to polymers with fewer entanglements in the amorphous regions, a metastable condition that can significantly affect the material’s properties and processing behavior. The lower entanglement density in ultra-high molecular weight polyethylene (dis-UHMWPE) facilitates the solid-state processability into uniaxially-oriented specimens reaching very high draw ratios and crystallinities. In this study, Au/dis-UHMWPE nanocomposites were formulated and processed at variable draw ratios. Polarized light microscopy suggests gold nanoparticles are oriented in arrays following the drawing of polymer chains. The structural features, upon orientation, are studied by means of Raman spectroscopy, wide- and small-angle X-ray scattering, and near-infrared spectrophotometry. Crystallinity is found to increase by 15%, as calculated by wide-angle X-ray scattering. The change in optical absorbance in the visible spectrum indicates that, with orientation, the average size of gold aggregates increases, supported quantitatively by small-angle X-ray scattering. Since the gold nanoparticles are expected to be found within amorphous chain segments, the aforementioned findings are attributed to the increase of crystallinity and thus the decrease of available (amorphous) space.

Download Full-text