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Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles

  • Dina Schneidman-Duhovny
  • Michal Hammel
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1764)

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.

Key words

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

Notes

Acknowledgments

We thank Drs. Andrej Sali, John Tainer, Ben Webb, David Agard, Friedrich Foerster, Seung Jong Kim, Hiro Tsuruta, Tsutomu Matsui, Lester Carter, Greg Hura, Riccardo Pellarin, Barak Raveh, Patrick Weinkam, and many others who contributed to our SAXS-based modeling efforts over the years. SAXS at the Advanced Light Source SIBYLS beamline in supported by National Institutes of Health (NIH) grants CA92584, DOE BER Integrated Diffraction Analysis Technologies (IDAT) program and NIGMS grant P30 GM124169-01, ALS-ENABLE.

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Authors and Affiliations

  1. 1.School of Computer Science and Engineering, Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
  2. 2.Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyUSA

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