scholarly journals Facilitating model reconstruction for single-particle scattering using small-angle X-ray scattering methods

2016 ◽  
Vol 49 (2) ◽  
pp. 665-671 ◽  
Author(s):  
Shufen Ma ◽  
Haiguang Liu

X-ray free-electron lasers generate intense femtosecond X-ray pulses, so that high-resolution structure determination becomes feasible from noncrystalline samples, such as single particles or single molecules. At the moment, the orientation of sample particles cannot be precisely controlled, and consequently the unknown orientation needs to be recovered using computational algorithms. This delays the model reconstruction until all the scattering patterns have been re-oriented, which often entails a long elapse of time and until the completion of the experiment. The scattering patterns from single particles or multiple particles can be summed to form a virtual powder diffraction pattern, and the low-resolution region, corresponding to the small-angle X-ray scattering (SAXS) regime, can be analysed using existing SAXS methods. This work presents a pipeline that converts single-particle data sets into SAXS data, from which real-time model reconstruction is achieved using the model retrieval approach implemented in the software package SASTBX [Liu, Hexemer & Zwart (2012). J. Appl. Cryst. 45, 587–593]. To illustrate the applications, two case studies are presented with real experimental data sets collected at the Linac Coherent Light Source.

2019 ◽  
Vol 85 (24) ◽  
Author(s):  
Sabine Rosenfeldt ◽  
Cornelius N. Riese ◽  
Frank Mickoleit ◽  
Dirk Schüler ◽  
Anna S. Schenk

ABSTRACT Magnetosomes are membrane-enveloped single-domain ferromagnetic nanoparticles enabling the navigation of magnetotactic bacteria along magnetic field lines. Strict control over each step of biomineralization generates particles of high crystallinity, strong magnetization, and remarkable uniformity in size and shape, which is particularly interesting for many biomedical and biotechnological applications. However, to understand the physicochemical processes involved in magnetite biomineralization, close and precise monitoring of particle production is required. Commonly used techniques, such as transmission electron microscopy (TEM) or Fe measurements, allow only for semiquantitative assessment of the magnetosome formation without routinely revealing quantitative structural information. In this study, lab-based small-angle X-ray scattering (SAXS) is explored as a means to monitor the different stages of magnetosome biogenesis in the model organism Magnetospirillum gryphiswaldense. SAXS is evaluated as a quantitative stand-alone technique to analyze the size, shape, and arrangement of magnetosomes in cells cultivated under different growth conditions. By applying a simple and robust fitting procedure based on spheres aligned in linear chains, it is demonstrated that the SAXS data sets contain information on both the diameter of the inorganic crystal and the protein-rich magnetosome membrane. The analyses corroborate a narrow particle size distribution with an overall magnetosome radius of 19 nm in Magnetospirillum gryphiswaldense. Furthermore, the averaged distance between individual magnetosomes is determined, revealing a chain-like particle arrangement with a center-to-center distance of 53 nm. Overall, these data demonstrate that SAXS can be used as a novel stand-alone technique allowing for the at-line monitoring of magnetosome biosynthesis, thereby providing accurate information on the particle nanostructure. IMPORTANCE This study explores lab-based small-angle X-ray scattering (SAXS) as a novel quantitative stand-alone technique to monitor the size, shape, and arrangement of magnetosomes during different stages of particle biogenesis in the model organism Magnetospirillum gryphiswaldense. The SAXS data sets contain volume-averaged, statistically accurate information on both the diameter of the inorganic nanocrystal and the enveloping protein-rich magnetosome membrane. As a robust and nondestructive in situ technique, SAXS can provide new insights into the physicochemical steps involved in the biosynthesis of magnetosome nanoparticles as well as their assembly into well-ordered chains. The proposed fit model can easily be adapted to account for different particle shapes and arrangements produced by other strains of magnetotactic bacteria, thus rendering SAXS a highly versatile method.


2015 ◽  
Vol 48 (4) ◽  
pp. 1102-1113 ◽  
Author(s):  
Andrew W. Malaby ◽  
Srinivas Chakravarthy ◽  
Thomas C. Irving ◽  
Sagar V. Kathuria ◽  
Osman Bilsel ◽  
...  

Size-exclusion chromatography in line with small-angle X-ray scattering (SEC–SAXS) has emerged as an important method for investigation of heterogeneous and self-associating systems, but presents specific challenges for data processing including buffer subtraction and analysis of overlapping peaks. This paper presents novel methods based on singular value decomposition (SVD) and Guinier-optimized linear combination (LC) to facilitate analysis of SEC–SAXS data sets and high-quality reconstruction of protein scattering directly from peak regions. It is shown that Guinier-optimized buffer subtraction can reduce common subtraction artifacts and that Guinier-optimized linear combination of significant SVD basis components improves signal-to-noise and allows reconstruction of protein scattering, even in the absence of matching buffer regions. In test cases with conventional SAXS data sets for cytochrome c and SEC–SAXS data sets for the small GTPase Arf6 and the Arf GTPase exchange factors Grp1 and cytohesin-1, SVD–LC consistently provided higher quality reconstruction of protein scattering than either direct or Guinier-optimized buffer subtraction. These methods have been implemented in the context of a Python-extensible Mac OS X application known asData Evaluation and Likelihood Analysis(DELA), which provides convenient tools for data-set selection, beam intensity normalization, SVD, and other relevant processing and analytical procedures, as well as automated Python scripts for common SAXS analyses and Guinier-optimized reconstruction of protein scattering.


2004 ◽  
Vol 37 (1) ◽  
pp. 103-109 ◽  
Author(s):  
Masaki Kojima ◽  
Alexander A. Timchenko ◽  
Junichi Higo ◽  
Kazuki Ito ◽  
Hiroshi Kihara ◽  
...  

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.


2022 ◽  
Vol 55 (1) ◽  
Author(s):  
Nie Zhao ◽  
Chunming Yang ◽  
Fenggang Bian ◽  
Daoyou Guo ◽  
Xiaoping Ouyang

In situ synchrotron small-angle X-ray scattering (SAXS) is a powerful tool for studying dynamic processes during material preparation and application. The processing and analysis of large data sets generated from in situ X-ray scattering experiments are often tedious and time consuming. However, data processing software for in situ experiments is relatively rare, especially for grazing-incidence small-angle X-ray scattering (GISAXS). This article presents an open-source software suite (SGTools) to perform data processing and analysis for SAXS and GISAXS experiments. The processing modules in this software include (i) raw data calibration and background correction; (ii) data reduction by multiple methods; (iii) animation generation and intensity mapping for in situ X-ray scattering experiments; and (iv) further data analysis for the sample with an order degree and interface correlation. This article provides the main features and framework of SGTools. The workflow of the software is also elucidated to allow users to develop new features. Three examples are demonstrated to illustrate the use of SGTools for dealing with SAXS and GISAXS data. Finally, the limitations and future features of the software are also discussed.


2010 ◽  
Vol 43 (2) ◽  
pp. 237-243 ◽  
Author(s):  
Shuji Akiyama

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.


2014 ◽  
Vol 67 (12) ◽  
pp. 1786 ◽  
Author(s):  
Lachlan W. Casey ◽  
Alan E. Mark ◽  
Bostjan Kobe

The role of small-angle X-ray scattering (SAXS) in structural biology is now well established, and its usefulness in combination with macromolecular crystallography is clear. However, the highly averaged SAXS data present a significant risk of over-interpretation to the unwary practitioner, and it can be challenging to frame SAXS results in a manner that maximises the reliability of the conclusions drawn. In this review, a series of recent examples are used to illustrate both the challenges for interpretation and approaches through which these can be overcome.


2015 ◽  
Vol 48 (6) ◽  
pp. 1935-1942 ◽  
Author(s):  
Wenjia Wang ◽  
Eleonora V. Shtykova ◽  
Vladimir V. Volkov ◽  
Guangcai Chang ◽  
Lianhui Zhang ◽  
...  

Pink beams are now widely used for small-angle X-ray scattering (SAXS) data collection owing to their high intensity. However, the wavelength spread of a pink beam is a factor of 100 higher than that of a monochromatic beam, thus causing the experimental data to be smeared. To reveal the influence of polychromaticity on shape reconstruction, four geometric bodies (sphere, cube, helix and long cylinder) were used for SAXS data analysis. The results reveal that the influence of polychromaticity on the process of shape reconstruction is significantly more dependent on the geometry of the body than on its size. Scattering objects with smoothed scattering curves can tolerate a higher wavelength spread than those with tortuous curves. It is further demonstrated that the structural parameters calculated from the smeared data sets have little deviation from the ideal ones, which indicates the possibility of using a light source with a greater wavelength spread than a conventional pink beam for special time-resolved SAXS experiments. Finally, it is concluded that SAXS data collected in pink-beam mode can be used directly for structural calculations and model reconstructions without a desmearing procedure.


1990 ◽  
Vol 23 (5) ◽  
pp. 430-432 ◽  
Author(s):  
P. R. Jemian ◽  
G. G. Long

A photodiode X-ray detector was built to measure small-angle X-ray scattering (SAXS) at a synchrotron-radiation source in conjunction with a double-crystal diffractometer SAXS camera at photon energies between 5 and 11 keV. The photodiode detector response in this energy range is linear at photon counting rates up to 1012 photons s−1 and thus it was not necessary to attenuate the monochromatic X-ray beam with calibrated foils. SAXS data taken with a scintillation counter and the photodiode detector are compared, demonstrating marked improvement in counting statistics, rate of data acquisition and signal-to-noise ratio.


2016 ◽  
Vol 49 (5) ◽  
pp. 1412-1419 ◽  
Author(s):  
Christopher D. Putnam

The Guinier region in small-angle X-ray scattering (SAXS) defines the radius of gyration,Rg, and the forward scattering intensity,I(0). In Guinier peak analysis (GPA), the plot ofqI(q)versus q2transforms the Guinier region into a characteristic peak for visual and automated inspection of data. Deviations of the peak position from the theoretical position in dimensionless GPA plots can suggest parameter errors, problematic low-resolution data, some kinds of intermolecular interactions or elongated scatters. To facilitate automated analysis by GPA, the elongation ratio (ER), which is the ratio of the areas in the pair-distribution functionP(r) after and before theP(r) maximum, was characterized; symmetric samples have ER values around 1, and samples with ER values greater than 5 tend to be outliers in GPA analysis. Use of GPA+ER can be a helpful addition to SAXS data analysis pipelines.


1970 ◽  
Vol 23 ◽  
pp. 74-81
Author(s):  
Lok Kumar Shrestha

Structure of nonionic surfactant diglycerol monomyristate (C14G2) micelles in cyclohexane has been investigated by small-angle X-ray scattering (SAXS) technique. Structural modulation of reverse micelle (RM) has been systematically studied by changing composition, temperature change and added-water. The SAXS data were evaluated by the generalized indirect Fourier transformation (GIFT) method, which gives pair-distance distribution function (PDDF). Unlike conventional poly(oxyethylene) type nonionic surfactants, C14G2 forms RM in cyclohexane without water addition at normal room temperature. A clear indication of one dimensional (1-D) micellar growth was found with increasing C14G2 concentrations. On the other hand, temperature induced cylinder-to-sphere type transition in the RM structure. The maximum dimension and the cross-sectional diameter of the RM increased upon addition of trace water indicating the formation of water pool in the reverse micellar core.Keywords: Diglycerol monomyristate, small-angle X-ray scattering, reverse micelles.DOI: 10.3126/jncs.v23i0.2099J. Nepal Chem. Soc., Vol. 23, 2008/2009Page: 74-81


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