scholarly journals Deciphering conformational transitions of proteins by small angle X-ray scattering and normal mode analysis

2016 ◽  
Vol 18 (8) ◽  
pp. 5707-5719 ◽  
Author(s):  
Alejandro Panjkovich ◽  
Dmitri I. Svergun
Keyword(s):  
Normal Mode ◽  
Small Angle ◽  
Normal Mode Analysis ◽  
Conformational Transitions ◽  
Scattering Data ◽  
Mode Analysis ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Scattering ◽  
Insight Into

SREFLEX employs normal mode analysis for the flexible refinement of atomic models of biological macromolecules against solution scattering data, providing insight into conformational transitions.

Recent developments in small-angle X-ray scattering and hybrid method approaches for biomacromolecular solutions

2018 ◽  
Vol 2 (1) ◽  
pp. 69-79 ◽  
Author(s):  
Martin A. Schroer ◽  
Dmitri I. Svergun
Keyword(s):  
Small Angle ◽  
Scattering Data ◽  
Quality Data ◽  
Biological Macromolecules ◽  
Ambient Conditions ◽  
X Ray ◽  
X Ray Scattering ◽  
Analysis Methods ◽  
Recent Developments ◽  
Ray Scattering

Small-angle X-ray scattering (SAXS) has become a streamline method to characterize biological macromolecules, from small peptides to supramolecular complexes, in near-native solutions. Modern SAXS requires limited amounts of purified material, without the need for labelling, crystallization, or freezing. Dedicated beamlines at modern synchrotron sources yield high-quality data within or below several milliseconds of exposure time and are highly automated, allowing for rapid structural screening under different solutions and ambient conditions but also for time-resolved studies of biological processes. The advanced data analysis methods allow one to meaningfully interpret the scattering data from monodisperse systems, from transient complexes as well as flexible and heterogeneous systems in terms of structural models. Especially powerful are hybrid approaches utilizing SAXS with high-resolution structural techniques, but also with biochemical, biophysical, and computational methods. Here, we review the recent developments in the experimental SAXS practice and in analysis methods with a specific focus on the joint use of SAXS with complementary methods.

Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis

2017 ◽  
Vol 85 (10) ◽  
pp. 1931-1943
Author(s):  
Agnes Thiane Pereira Machado ◽  
Emanuella Maria Barreto Fonseca ◽  
Marcelo Augusto dos Reis ◽  
Antonio Marcos Saraiva ◽  
Clelton Aparecido dos Santos ◽  
...  
Keyword(s):  
Stationary Phase ◽  
Small Angle ◽  
Xylella Fastidiosa ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
X Ray ◽  
Conformational Variability ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Stationary Phase Survival

scholarly journals Global Small-Angle X-ray Scattering Data Analysis of Triacylglycerols in the Molten State (Part I)

2018 ◽  
Vol 122 (45) ◽  
pp. 10320-10329 ◽  
Author(s):  
Amin Sadeghpour ◽  
Marjorie Ladd Parada ◽  
Josélio Vieira ◽  
Megan Povey ◽  
Michael Rappolt
Keyword(s):  
Data Analysis ◽  
Small Angle ◽  
Scattering Data ◽  
Molten State ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

scholarly journals REGALS: a general method to deconvolve X-ray scattering data from evolving mixtures

2020 ◽  
Author(s):  
Steve P. Meisburger ◽  
Da Xu ◽  
Nozomi Ando
Keyword(s):  
A Priori ◽  
Scattering Data ◽  
Biological Macromolecules ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Open Source Software Package ◽  
Saxs Analysis ◽  
Structural Methods ◽  
Ray Scattering

AbstractMixtures of biological macromolecules are inherently difficult to study using structural methods, as increasing complexity presents new challenges for data analysis. Recently, there has been growing interest in studying evolving mixtures using small-angle X-ray scattering (SAXS) in conjunction with time-resolved, high-throughput, or chromatography-coupled setups. Deconvolution and interpretation of the resulting datasets, however, are nontrivial when neither the scattering components nor the way in which they evolve are known a priori. To address this issue, we introduce the REGALS method (REGularized Alternating Least Squares), which incorporates simple expectations about the data as prior knowledge and utilizes parameterization and regularization to provide robust deconvolution solutions. The restraints used by REGALS are general properties such as smoothness of profiles and maximum dimensions of species, which makes it well-suited for exploring datasets with unknown species. Here we apply REGALS to analyze experimental data from four types of SAXS experiment: anion-exchange (AEX) coupled SAXS, ligand titration, time-resolved mixing, and time-resolved temperature jump. Based on its performance with these challenging datasets, we anticipate that REGALS will be a valuable addition to the SAXS analysis toolkit and enable new experiments. The software is implemented in both MATLAB and python and is available freely as an open-source software package.

scholarly journals The new NCPSS BL19U2 beamline at the SSRF for small-angle X-ray scattering from biological macromolecules in solution

2016 ◽  
Vol 49 (5) ◽  
pp. 1428-1432 ◽  
Author(s):  
Na Li ◽  
Xiuhong Li ◽  
Yuzhu Wang ◽  
Guangfeng Liu ◽  
Ping Zhou ◽  
...  
Keyword(s):  
Data Processing ◽  
Small Angle ◽  
Dynamic Range ◽  
Silicon Crystal ◽  
High Dynamic Range ◽  
Biological Macromolecules ◽  
Shanghai Synchrotron Radiation Facility ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

The beamline BL19U2 is located in the Shanghai Synchrotron Radiation Facility (SSRF) and is its first beamline dedicated to biological material small-angle X-ray scattering (BioSAXS). The electrons come from an undulator which can provide high brilliance for the BL19U2 end stations. A double flat silicon crystal (111) monochromator is used in BL19U2, with a tunable monochromatic photon energy ranging from 7 to 15 keV. To meet the rapidly growing demands of crystallographers, biochemists and structural biologists, the BioSAXS beamline allows manual and automatic sample loading/unloading. A Pilatus 1M detector (Dectris) is employed for data collection, characterized by a high dynamic range and a short readout time. The highly automated data processing pipeline SASFLOW was integrated into BL19U2, with help from the BioSAXS group of the European Molecular Biology Laboratory (EMBL, Hamburg), which provides a user-friendly interface for data processing. The BL19U2 beamline was officially opened to users in March 2015. To date, feedback from users has been positive and the number of experimental proposals at BL19U2 is increasing. A description of the new BioSAXS beamline and the setup characteristics is given, together with examples of data obtained.

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