Literature DB >> 33708400

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

Steve P Meisburger1, Da Xu1, Nozomi Ando1.   

Abstract

Mixtures 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, the REGALS method (regularized alternating least squares) is introduced, 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, making it well suited for exploring datasets with unknown species. Here, REGALS is applied to the analysis of 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, it is anticipated 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. © Meisburger, Xu and Ando 2021.

Entities:  

Keywords:  AEX-SAXS; deconvolution; high-throughput SAXS; ligand titration; multivariate curve resolution; pair-distance distribution function; regularized alternating least squares; singular value decomposition; small-angle X-ray scattering; time-resolved SAXS

Year:  2021        PMID: 33708400      PMCID: PMC7924237          DOI: 10.1107/S2052252521000555

Source DB:  PubMed          Journal:  IUCrJ        ISSN: 2052-2525            Impact factor:   4.769


  22 in total

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2.  Low-resolution structures of transient protein-protein complexes using small-angle X-ray scattering.

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3.  Protein denaturation: a small-angle X-ray scattering study of the ensemble of unfolded states of cytochrome c.

Authors:  D J Segel; A L Fink; K O Hodgson; S Doniach
Journal:  Biochemistry       Date:  1998-09-08       Impact factor: 3.162

4.  Kinetics of lysozyme refolding: structural characterization of a non-specifically collapsed state using time-resolved X-ray scattering.

Authors:  L Chen; G Wildegger; T Kiefhaber; K O Hodgson; S Doniach
Journal:  J Mol Biol       Date:  1998-02-13       Impact factor: 5.469

5.  A lysozyme folding intermediate revealed by solution X-ray scattering.

Authors:  L Chen; K O Hodgson; S Doniach
Journal:  J Mol Biol       Date:  1996-09-06       Impact factor: 5.469

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Authors:  Nigel M Kirby; Nathan P Cowieson
Journal:  Curr Opin Struct Biol       Date:  2014-08-09       Impact factor: 6.809

Review 7.  Deconvolutions based on singular value decomposition and the pseudoinverse: a guide for beginners.

Authors:  R W Hendler; R I Shrager
Journal:  J Biochem Biophys Methods       Date:  1994-01

Review 8.  Investigating increasingly complex macromolecular systems with small-angle X-ray scattering.

Authors:  Bente Vestergaard; Zehra Sayers
Journal:  IUCrJ       Date:  2014-10-21       Impact factor: 4.769

9.  BioXTAS RAW: improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis.

Authors:  Jesse Bennett Hopkins; Richard E Gillilan; Soren Skou
Journal:  J Appl Crystallogr       Date:  2017-09-05       Impact factor: 3.304

10.  An endogenous dAMP ligand in Bacillus subtilis class Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP.

Authors:  Mackenzie J Parker; Ailiena O Maggiolo; William C Thomas; Albert Kim; Steve P Meisburger; Nozomi Ando; Amie K Boal; JoAnne Stubbe
Journal:  Proc Natl Acad Sci U S A       Date:  2018-04-30       Impact factor: 11.205

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  2 in total

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Authors:  Petr V Konarev; Melissa A Graewert; Cy M Jeffries; Masakazu Fukuda; Taisiia A Cheremnykh; Vladimir V Volkov; Dmitri I Svergun
Journal:  Protein Sci       Date:  2021-11-22       Impact factor: 6.725

2.  Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade.

Authors:  Audrey A Burnim; Matthew A Spence; Da Xu; Colin J Jackson; Nozomi Ando
Journal:  Elife       Date:  2022-09-01       Impact factor: 8.713

  2 in total

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