May 2013 Archives

SIBYLS scientists have recently published and made available tools for generating SAXS structural comparison maps. Details of the methods have been published in Nature Methods.

Biological macromolecular functions require distinct conformational states that are challenging to examine comprehensively. Current methods to quantify conformational similarities and distinguish different assembly states are underdeveloped. Recent developments in small-angle X-ray scattering (SAXS) have shown that SAXS can provide the resolution to resolve conformational states, characterize flexible macromolecules and screen in high throughput under most solution conditions. However, robust tools for comprehensively characterizing and visualizing the different conformational states identified by SAXS have been lacking. Here we present the SAXS structural comparison map (SCM) and volatility of ratio (VR) difference metric, which together provide quantitative and superposition-independent evaluation of solution-state conformations.

read more in the full article…

Hura GL, Budworth H, Dyer KN, Rambo RP, Hammel M, McMurray CT, Tainer JA. “Comprehensive macromolecular conformations mapped by quantitative SAXS analyses.“Nat Methods.(28 April 2013)

Rob and John have a new review on SAXS and its application to systems biology published in the Annual Review of Biophysics. See if you can spot the musical theme.

Small-angle X-ray scattering (SAXS) is a robust technique for the comprehensive structural characterizations of biological macromolecular complexes in solution. Here, we present a coherent synthesis of SAXS theory and experiment with a focus on analytical tools for accurate, objective, and high-throughput investigations. Perceived SAXS limitations are considered in light of its origins, and we present current methods that extend SAXS data analysis to the super-resolution regime. In particular, we discuss hybrid structural methods, illustrating the role of SAXS in structure refinement with NMR and ensemble refinement with single-molecule FRET. High-throughput genomics and proteomics are far outpacing macromolecular structure determinations, creating information gaps between the plethora of newly identified genes, known structures, and the structure-function relationship in the underlying biological networks. SAXS can bridge these information gaps by providing a reliable, high-throughput structural characterization of macromolecular complexes under physiological conditions.

QRB_rambo_fig1.png

Rambo, R.P., Tainer, J.A. “Super-Resolution in Solution X-Ray Scattering and Its Applications to Structural Systems Biology” Annual Review of Biophysics 42, 415-441 (May 2013)

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