Low-Resolution Structure of the Full-Length Barley (Hordeum vulgare) SGT1 Protein in Solution, Obtained Using 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.

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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.

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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

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

Molecular Pharmaceutics ◽

10.1021/acs.molpharmaceut.9b00792 ◽

2019 ◽

Vol 16 (12) ◽

pp. 4902-4912

Author(s):

Didier Law-Hine ◽

Sergii Rudiuk ◽

Audrey Bonestebe ◽

Romain Ienco ◽

Sylvain Huille ◽

...

Keyword(s):

Small Angle ◽

Structural Features ◽

Low Resolution ◽

X Ray ◽

Antibody Drug Conjugates ◽

Drug Conjugates ◽

X Ray Scattering ◽

Antibody Drug ◽

Ray Scattering

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Low-resolution structure of immunoglobulins IgG1, IgM and rheumatoid factor IgM-RF from solution X-ray scattering data

Journal of Applied Crystallography ◽

10.1107/s0021889803005156 ◽

2003 ◽

Vol 36 (3) ◽

pp. 503-508 ◽

Cited By ~ 21

Author(s):

Vladimir V. Volkov ◽

Viktor A. Lapuk ◽

Renata L. Kayushina ◽

Eleonora V. Shtykova ◽

Elena Yu. Varlamova ◽

...

Keyword(s):

Rheumatoid Factor ◽

Scattering Data ◽

Low Resolution ◽

X Ray ◽

X Ray Scattering ◽

Resolution Structure ◽

Ray Scattering

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Domain Organization in Plant Blue-Light Receptor Phototropin2 of Arabidopsis thaliana Studied by Small-Angle X-ray Scattering

International Journal of Molecular Sciences ◽

10.3390/ijms21186638 ◽

2020 ◽

Vol 21 (18) ◽

pp. 6638

Author(s):

Masayoshi Nakasako ◽

Mao Oide ◽

Yuki Takayama ◽

Tomotaka Oroguchi ◽

Koji Okajima

Keyword(s):

Blue Light ◽

Small Angle ◽

Structural Changes ◽

Structural Parameters ◽

Kinase Domain ◽

Full Length ◽

Receptor Protein ◽

X Ray ◽

X Ray Scattering ◽

Ray Scattering

Phototropin2 (phot2) is a blue-light (BL) receptor protein that regulates the BL-dependent activities of plants for efficient photosynthesis. Phot2 is composed of two light-oxygen-voltage sensing domains (LOV1 and LOV2) to absorb BL, and a kinase domain. Photo-activated LOV domains, especially LOV2, play a major role in photo-dependent increase in the phosphorylation activity of the kinase domain. The atomic details of the overall structure of phot2 and the intramolecular mechanism to convert BL energy to a phosphorylation signal remain unknown. We performed structural studies on the LOV fragments LOV1, LOV2, LOV2-linker, and LOV2-kinase, and full-length phot2, using small-angle X-ray scattering (SAXS). The aim of the study was to understand structural changes under BL irradiation and discuss the molecular mechanism that enhance the phosphorylation activity under BL. SAXS is a suitable technique for visualizing molecular structures of proteins in solution at low resolution and is advantageous for monitoring their structural changes in the presence of external physical and/or chemical stimuli. Structural parameters and molecular models of the recombinant specimens were obtained from SAXS profiles in the dark, under BL irradiation, and after dark reversion. LOV1, LOV2, and LOV2-linker fragments displayed minimal structural changes. However, BL-induced rearrangements of functional domains were noted for LOV2-kinase and full-length phot2. Based on the molecular model together with the absorption measurements and biochemical assays, we discuss the intramolecular interactions and domain motions necessary for BL-enhanced phosphorylation activity of phot2.

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