Modeling structure and dynamics of protein complexes with SAXS profiles

Dina Schneidman-Duhovny*, Michal Hammel

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

31 Scopus citations

Abstract

Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. SAXS profiles can be utilized in a variety of molecular modeling applications, such as comparing solution and crystal structures, structural characterization of flexible proteins, assembly of multi-protein complexes, and modeling of missing regions in the high-resolution structure. Here, we describe protocols for modeling atomic structures based on SAXS profiles. The first protocol is for comparing solution and crystal structures including modeling of missing regions and determination of the oligomeric state. The second protocol performs multi-state modeling by finding a set of conformations and their weights that fit the SAXS profile starting from a single-input structure. The third protocol is for protein-protein docking based on the SAXS profile of the complex. We describe the underlying software, followed by demonstrating their application on interleukin 33 (IL33) with its primary receptor ST2 and DNA ligase IV-XRCC4 complex.

Original languageAmerican English
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages449-473
Number of pages25
DOIs
StatePublished - 2018

Publication series

NameMethods in Molecular Biology
Volume1764
ISSN (Print)1064-3745

Bibliographical note

Publisher Copyright:
© 2018, Springer Science+Business Media, LLC, part of Springer Nature.

Keywords

  • Conformational ensembles
  • Conformational heterogeneity
  • Multi-state models
  • Protein-protein docking
  • Small-angle X-ray scattering (SAXS)

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