Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

By Greg L. Hura, A. Menon, M. Hammel, R. Rambo, F. Poole, S. Tsutakawa, F. Jenney, S. Classen, K. Frankel, R. C. Hopkins and 5 more. Nature Methods, 2009

645 citations recorded by the source corpus.

We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e7f16c880ada856530ddc4c3f5bd3bbba55c33a9

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Citations in the corpus

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source (2013, methodology): “The basic beamline optics design (Table 1) is similar to the other MX superbend beamlines at the ALS (MacDowell et al., 2004; Trame et al., 2004).”
Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “SAXS is a common structural characterization technique that is performed with the protein sample in solution, and usually takes only a few seconds on a well-equipped synchrotron beamline (Hura et al., 2009).”
Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment (2016, methodology): “Information on the oligo-meric state is in principle derived using experimental methods such as gel filtration or small-angle X-ray scattering (SAXS), 22 and is usually communicated by the authors upon submission of the atomic coordinates to the PDB.”
Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “SAXS is a common structural characterization technique that is performed with the protein sample in solution, and usually takes only a few seconds on a well-equipped synchrotron beamline (Hura et al., 2009).”
New developments in the ATSAS program package for small-angle scattering data analysis (2012, neutral): “Modern SAS instrumentation, including high-flux dedicated synchrotron radiation and neutron beamlines and advanced laboratory X-ray sources, allows one to collect high-quality experimental data (Hura et al., 2009; Round et al., 2008; Teixeira et al., 2008; Toft et al., 2008).”
Modular repeat protein sculpting using rigid helical junctions (2020, positive): “The maximum value of Vr obtained for the design models of the four-junction crystal structures compared to the corresponding experimental SAXS spectra was 2.0, and among 15 previously determined crystal structures of DHRs that have similar size and aspect ratio as the junctions, the maximum value wa”
Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy (2018, background): “32 As all targets are known to form crystals and therefore to undergo “ ordered aggregation ” , multimerization is not unexpected.”
FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles (2016, methodology): “It usually takes only a few minutes on a well-equipped synchrotron beam line (1,2) and can be conducted for a range of conditions (3).”