Accurate assessment of mass, models and resolution by small-angle scattering

By R. Rambo, John A. Tainer. Nature, 2013

723 citations recorded by the source corpus.

Modern small-angle scattering (SAS) experiments with X-rays or neutrons provide a comprehensive, resolution-limited observation of the thermodynamic state. However, methods for evaluating mass and validating SAS-based models and resolution have been inadequate. Here we define the volume of correlation, Vc, a SAS invariant derived from the scattered intensities that is specific to the structural state of the particle, but independent of concentration and the requirements of a compact, folded particle. We show that Vc defines a ratio, QR, that determines the molecular mass of proteins or RNA ranging from 10 to 1,000 kilodaltons. Furthermore, we propose a statistically robust method for assessing model-data agreements (χ2free) akin to cross-validation. Our approach prevents over-fitting of the SAS data and can be used with a newly defined metric, RSAS, for quantitative evaluation of resolution. Together, these metrics (Vc, QR, χ2free and RSAS) provide analytical tools for unbiased and accurate macromolecular structural characterizations in solution.

Subfields: Condensed Matter Physics, Materials Chemistry, Radiation

View Paper: https://www.semanticscholar.org/paper/c08a3b344ea16d866a063056c2c3e458a04b3c0a

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Citations in the corpus

Structural and biophysical properties of FopA, a major outer membrane protein of Francisella tularensis (2022, methodology): “Molecular weight (MW) was estimated using two methods: Porod volume (MWPorod) [44] and Volume of Correlation (MWVcorr) [45] by GNOM in ATSAS using the DATPOROD and DATVC tools [59].”
Generation of ordered protein assemblies using rigid three-body fusion (2020, neutral): “…(37 – 41), 3) SAXS sample preparation and analytical tools for data collected at the Structurally Integrated Biology for Life Sciences (SIBYLS) Beamline (42 – 44), 4) negative-stain EM procedures and tools (32, 33, 45, 46), and 5) cryo-EM sample preparation and processing schemes (32, 33, 46 – 57).”
ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions (2017, methodology): “DATMOW and DATVC are implementations of the SAXS MoW MW estimation as originally described by Fischer et al. (2010) and the volume of correlation (Vc) MW estimate by Rambo & Tainer (2013), respectively.”
BioXTAS RAW: improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis (2017, methodology): “…et al., 2000; Mylonas & Svergun, 2007), (iii) the adjusted Porod volume method (Fischer et al., 2010) and (iv) the volume of correlation method (Rambo & Tainer, 2013). xS1 in the supporting information describes the validation of the implementations of methods (iii) and (iv) [for additional…”
Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy (2018, background): “33 When the MassSAXS is greater than the theoretical mass of the protein sequence, multimerization is indicated.”
FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles (2016, background): “6, which is within the experimental noise (35).”