scholarly journals Conservative interpretation of small-angle X-ray scattering data from biological macromolecules

2017 ◽  
Author(s):  
Lachlan Casey
Keyword(s):  
Small Angle ◽  
Scattering Data ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

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.

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.

scholarly journals Atomically detailed lipid bilayer models for the interpretation of small angle neutron and X-ray scattering data

2015 ◽  
Vol 1848 (2) ◽  
pp. 662-672 ◽  
Author(s):  
Joseph C. Fogarty ◽  
Mihir Arjunwadkar ◽  
Sagar A. Pandit ◽  
Jianjun Pan
Keyword(s):  
Lipid Bilayer ◽  
Small Angle ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

scholarly journals SAXSDom: Modeling multidomain protein structures using small‐angle X‐ray scattering data

2019 ◽  
Vol 88 (6) ◽  
pp. 775-787 ◽  
Author(s):  
Jie Hou ◽  
Badri Adhikari ◽  
John J. Tanner ◽  
Jianlin Cheng
Keyword(s):  
Small Angle ◽  
Protein Structures ◽  
Scattering Data ◽  
Multidomain Protein ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

scholarly journals Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data

2020 ◽  
Vol 124 (25) ◽  
pp. 5186-5200 ◽  
Author(s):  
Milka Doktorova ◽  
Norbert Kučerka ◽  
Jacob J. Kinnun ◽  
Jianjun Pan ◽  
Drew Marquardt ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Small Angle ◽  
Fluid Phase ◽  
Scattering Data ◽  
Joint Analysis ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Quality control of protein standards for molecular mass determinations by small-angle X-ray scattering

2010 ◽  
Vol 43 (2) ◽  
pp. 237-243 ◽  
Author(s):  
Shuji Akiyama
Keyword(s):  
Quality Control ◽  
Molecular Mass ◽  
Small Angle ◽  
Biological Macromolecules ◽  
Average Deviation ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Standard Quality ◽  
Ray Scattering

Small-angle X-ray scattering (SAXS) is a powerful technique with which to evaluate the size and shape of biological macromolecules in solution. Forward scattering intensity normalized relative to the particle concentration,I(0)/c, is useful as a good measure of molecular mass. A general method for deducing the molecular mass from SAXS data is to determine the ratio ofI(0)/cof a target protein to that of a standard protein with known molecular mass. The accuracy of this interprotein calibration is affected considerably by the monodispersity of the prepared standard, as well as by the precision in estimating its concentration. In the present study, chromatographic fractionation followed by hydrodynamic characterization is proposed as an effective procedure by which to prepare a series of monodispersed protein standards. The estimation of molecular mass within an average deviation of 8% is demonstrated using monodispersed bovine serum albumin as a standard. The present results demonstrate the importance of protein standard quality control in order to take full advantage of interprotein calibration.

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