Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering - PubMed
Review
doi: 10.1039/c1mb05275f. Epub 2011 Sep 22.
Affiliations
- PMID: 21947276
- DOI: 10.1039/c1mb05275f
Review
Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering
Pau Bernadó et al. Mol Biosyst. 2012 Jan.
Abstract
Small-angle scattering of X-rays (SAXS) is an established method to study the overall structure and structural transitions of biological macromolecules in solution. For folded proteins, the technique provides three-dimensional low resolution structures ab initio or it can be used to drive rigid-body modeling. SAXS is also a powerful tool for the quantitative analysis of flexible systems, including intrinsically disordered proteins (IDPs), and is highly complementary to the high resolution methods of X-ray crystallography and NMR. Here we present the basic principles of SAXS and review the main approaches to the characterization of IDPs and flexible multidomain proteins using SAXS. Together with the standard approaches based on the analysis of overall parameters, a recently developed Ensemble Optimization Method (EOM) is now available. The latter method allows for the co-existence of multiple protein conformations in solution compatible with the scattering data. Analysis of the selected ensembles provides quantitative information about flexibility and also offers insights into structural features. Examples of the use of SAXS and combined approaches with NMR, X-ray crystallography, and computational methods to characterize completely or partially disordered proteins are presented.
Similar articles
-
Kikhney AG, Svergun DI. Kikhney AG, et al. FEBS Lett. 2015 Sep 14;589(19 Pt A):2570-7. doi: 10.1016/j.febslet.2015.08.027. Epub 2015 Aug 29. FEBS Lett. 2015. PMID: 26320411 Review.
-
Structural characterization of proteins and complexes using small-angle X-ray solution scattering.
Mertens HD, Svergun DI. Mertens HD, et al. J Struct Biol. 2010 Oct;172(1):128-41. doi: 10.1016/j.jsb.2010.06.012. Epub 2010 Jun 15. J Struct Biol. 2010. PMID: 20558299 Review.
-
Application of SAXS for the Structural Characterization of IDPs.
Kachala M, Valentini E, Svergun DI. Kachala M, et al. Adv Exp Med Biol. 2015;870:261-89. doi: 10.1007/978-3-319-20164-1_8. Adv Exp Med Biol. 2015. PMID: 26387105 Review.
-
Tsutakawa SE, Hura GL, Frankel KA, Cooper PK, Tainer JA. Tsutakawa SE, et al. J Struct Biol. 2007 May;158(2):214-23. doi: 10.1016/j.jsb.2006.09.008. Epub 2006 Oct 27. J Struct Biol. 2007. PMID: 17182256
-
Sibille N, Bernadó P. Sibille N, et al. Biochem Soc Trans. 2012 Oct;40(5):955-62. doi: 10.1042/BST20120149. Biochem Soc Trans. 2012. PMID: 22988847 Review.
Cited by
-
Intrinsically disordered energy landscapes.
Chebaro Y, Ballard AJ, Chakraborty D, Wales DJ. Chebaro Y, et al. Sci Rep. 2015 May 22;5:10386. doi: 10.1038/srep10386. Sci Rep. 2015. PMID: 25999294 Free PMC article.
-
Databases for intrinsically disordered proteins.
Piovesan D, Monzon AM, Quaglia F, Tosatto SCE. Piovesan D, et al. Acta Crystallogr D Struct Biol. 2022 Feb 1;78(Pt 2):144-151. doi: 10.1107/S2059798321012109. Epub 2022 Jan 21. Acta Crystallogr D Struct Biol. 2022. PMID: 35102880 Free PMC article. Review.
-
Panigrahi R, Matsui T, Song AH, Caldo KMP, Young HS, Weselake RJ, Lemieux MJ. Panigrahi R, et al. Sci Rep. 2018 Nov 12;8(1):16665. doi: 10.1038/s41598-018-34339-1. Sci Rep. 2018. PMID: 30420764 Free PMC article.
-
Protein Dynamics to Define and Refine Disordered Protein Ensembles.
Naullage PM, Haghighatlari M, Namini A, Teixeira JMC, Li J, Zhang O, Gradinaru CC, Forman-Kay JD, Head-Gordon T. Naullage PM, et al. J Phys Chem B. 2022 Mar 10;126(9):1885-1894. doi: 10.1021/acs.jpcb.1c10925. Epub 2022 Feb 25. J Phys Chem B. 2022. PMID: 35213160 Free PMC article.
-
Koren G, Meir S, Holschuh L, Mertens HDT, Ehm T, Yahalom N, Golombek A, Schwartz T, Svergun DI, Saleh OA, Dzubiella J, Beck R. Koren G, et al. Proc Natl Acad Sci U S A. 2023 Jul 25;120(30):e2220180120. doi: 10.1073/pnas.2220180120. Epub 2023 Jul 17. Proc Natl Acad Sci U S A. 2023. PMID: 37459524 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources