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Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles
Dina Schneidman-Duhovny1, Michal Hammel2
1School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. dina@cs.huji.ac.il.
Methods in Molecular Biology (Clifton, N.J.)
|April 2, 2018
Summary
Small-angle X-ray scattering (SAXS) provides molecular structural insights. New protocols enable atomic modeling from SAXS profiles for comparing structures, analyzing flexibility, and protein complex assembly.
Area of Science:
- Biophysics
- Structural Biology
- Computational Biology
Background:
- Small-angle X-ray scattering (SAXS) is a powerful technique for characterizing molecule structures in solution.
- SAXS experiments yield a SAXS profile, representing scattering intensity versus spatial frequency.
- SAXS data is valuable for diverse molecular modeling tasks, including comparing solution and crystal structures, analyzing protein flexibility, and modeling multi-protein complexes.
Purpose of the Study:
- To present protocols for atomic structure modeling using SAXS profiles.
- To demonstrate the application of these protocols in various structural biology scenarios.
Main Methods:
- Development and description of three distinct protocols for SAXS-based atomic modeling.
- Protocol 1: Compares solution and crystal structures, models missing regions, and determines oligomeric state.
- Protocol 2: Performs multi-state modeling to identify conformations and weights fitting SAXS data.
- Protocol 3: Enables protein-protein docking based on SAXS profiles of complexes.
- Utilized specific software for implementing and demonstrating the protocols.
Main Results:
- Demonstrated successful application of the SAXS modeling protocols on specific protein systems.
- Successfully modeled atomic structures from SAXS data for interleukin 33 (IL33) with ST2 and the DNA ligase IV-XRCC4 complex.
- Validated the utility of the described protocols for structural characterization and modeling.
Conclusions:
- The presented protocols offer a robust framework for atomic structure modeling using SAXS data.
- These methods enhance the structural characterization of molecules in solution, including flexible proteins and complexes.
- The software and protocols facilitate advanced molecular modeling applications in structural biology.
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