Literature DB >> 32696362

Determining Rg of IDPs from SAXS Data.

Ellen Rieloff1, Marie Skepö2.   

Abstract

There is a great interest within the research community to understand the structure-function relationship for intrinsically disordered proteins (IDPs); however, the heterogeneous distribution of conformations that IDPs can adopt limits the applicability of conventional structural biology methods. Here, scattering techniques, such as small-angle X-ray scattering, can contribute. In this chapter, we will describe how to make a model-free determination of the radius of gyration by using two different approaches, the Guinier analysis and the pair distance distribution function. The ATSAS package (Franke et al., J Appl Crystallogr 50:1212-1225, 2017) has been used for the evaluation, and throughout the chapter, different examples will be given to illustrate the discussed phenomena, as well as the pros and cons of using the different approaches.

Entities:  

Keywords:  ATSAS; Flexible proteins; GNOM; Guinier; Intrinsically disordered proteins; PRIMUS; Pair distance distribution function; Radius of gyration; Scattering

Mesh:

Substances:

Year:  2020        PMID: 32696362     DOI: 10.1007/978-1-0716-0524-0_13

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  16 in total

1.  Heat-induced unfolding of neocarzinostatin, a small all-beta protein investigated by small-angle X-ray scattering.

Authors:  J Pérez; P Vachette; D Russo; M Desmadril; D Durand
Journal:  J Mol Biol       Date:  2001-05-11       Impact factor: 5.469

2.  Net charge per residue modulates conformational ensembles of intrinsically disordered proteins.

Authors:  Albert H Mao; Scott L Crick; Andreas Vitalis; Caitlin L Chicoine; Rohit V Pappu
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-19       Impact factor: 11.205

Review 3.  A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins.

Authors:  Alexey G Kikhney; Dmitri I Svergun
Journal:  FEBS Lett       Date:  2015-08-29       Impact factor: 4.124

Review 4.  X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.

Authors:  Christopher D Putnam; Michal Hammel; Greg L Hura; John A Tainer
Journal:  Q Rev Biophys       Date:  2007-08       Impact factor: 5.318

5.  Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues.

Authors:  Rahul K Das; Rohit V Pappu
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-30       Impact factor: 11.205

6.  Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy.

Authors:  Hagen Hofmann; Andrea Soranno; Alessandro Borgia; Klaus Gast; Daniel Nettels; Benjamin Schuler
Journal:  Proc Natl Acad Sci U S A       Date:  2012-09-14       Impact factor: 11.205

7.  Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods.

Authors:  Alessandro Borgia; Wenwei Zheng; Karin Buholzer; Madeleine B Borgia; Anja Schüler; Hagen Hofmann; Andrea Soranno; Daniel Nettels; Klaus Gast; Alexander Grishaev; Robert B Best; Benjamin Schuler
Journal:  J Am Chem Soc       Date:  2016-09-01       Impact factor: 15.419

8.  Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy.

Authors:  Armin Hoffmann; Avinash Kane; Daniel Nettels; David E Hertzog; Peter Baumgärtel; Jan Lengefeld; Gerd Reichardt; David A Horsley; Robert Seckler; Olgica Bakajin; Benjamin Schuler
Journal:  Proc Natl Acad Sci U S A       Date:  2006-12-21       Impact factor: 11.205

Review 9.  How random are intrinsically disordered proteins? A small angle scattering perspective.

Authors:  Veronique Receveur-Brechot; Dominique Durand
Journal:  Curr Protein Pept Sci       Date:  2012-02       Impact factor: 3.272

10.  ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions.

Authors:  D Franke; M V Petoukhov; P V Konarev; A Panjkovich; A Tuukkanen; H D T Mertens; A G Kikhney; N R Hajizadeh; J M Franklin; C M Jeffries; D I Svergun
Journal:  J Appl Crystallogr       Date:  2017-06-26       Impact factor: 3.304

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