Characterization of a large glycoprotein proteoglycan by size-exclusion chromatography combined with light and X-ray scattering methods

2013 ◽  
Vol 1303 ◽  
pp. 100-104 ◽  
Author(s):  
Yasushi Watanabe ◽  
Yoji Inoko
2018 ◽  
Vol 51 (6) ◽  
pp. 1623-1632 ◽  
Author(s):  
Saskia Bucciarelli ◽  
Søren Roi Midtgaard ◽  
Martin Nors Pedersen ◽  
Søren Skou ◽  
Lise Arleth ◽  
...  

Coupling of size-exclusion chromatography with biological solution small-angle X-ray scattering (SEC-SAXS) on dedicated synchrotron beamlines enables structural analysis of challenging samples such as labile proteins and low-affinity complexes. For this reason, the approach has gained increased popularity during the past decade. Transportation of perishable samples to synchrotrons might, however, compromise the experiments, and the limited availability of synchrotron beamtime renders iterative sample optimization tedious and lengthy. Here, the successful setup of laboratory-based SEC-SAXS is described in a proof-of-concept study. It is demonstrated that sufficient quality data can be obtained on a laboratory instrument with small sample consumption, comparable to typical synchrotron SEC-SAXS demands. UV/vis measurements directly on the SAXS exposure cell ensure accurate concentration determination, crucial for direct molecular weight determination from the scattering data. The absence of radiation damage implies that the sample can be fractionated and subjected to complementary analysis available at the home institution after SEC-SAXS. Laboratory-based SEC-SAXS opens the field for analysis of biological samples at the home institution, thus increasing productivity of biostructural research. It may further ensure that synchrotron beamtime is used primarily for the most suitable and optimized samples.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rintaro Inoue ◽  
Tatsuo Nakagawa ◽  
Ken Morishima ◽  
Nobuhiro Sato ◽  
Aya Okuda ◽  
...  

2015 ◽  
Vol 11 (1) ◽  
pp. 190-196 ◽  
Author(s):  
Cyril C. Curtain ◽  
Nigel M. Kirby ◽  
Haydyn D. T. Mertens ◽  
Kevin J. Barnham ◽  
Robert B. Knott ◽  
...  

Size exclusion chromatography with small angle X-ray scattering and ensemble optimisation modelling reveals conformers in random pool of α-synuclein.


Polymers ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1237
Author(s):  
Jia Yang ◽  
Takahiro Sato

Size exclusion chromatography equipped with a multi-angle, light-scattering online detector (SEC-MALS) measurements were carried out on a hydrophobically modified pullulan (PUL-OSA) with degrees of substitution (DS) of 0.14, 0.2, and 0.3 in 0.01 M aqueous NaCl to obtain the degree of polymerization (N0) dependence of the radius of gyration (⟨S2⟩1/2) for PUL-OSA in the aqueous NaCl. The result was consistent with the loose flower necklace model proposed in a previous study, and the increase in the chain size with introducing OSA groups was explained by the backbone stiffness of the loose flower necklace formed by PUL-OSA. For PUL-OSA samples with DS = 0.2 and 0.3, ⟨S2⟩1/2 obtained by SEC-MALS in a high N0 region deviated downward from ⟨S2⟩1/2 expected by the loose flower necklace model. This deviation came from a tiny amount of the aggregating component of PUL-OSA, taking a branched architecture composed of loose flower necklaces. Although the aggregating component of PUL-OSA was also detected by previous small angle X-ray scattering measurements, its conformation was revealed in this study by SEC-MALS.


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.


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