August Issue of Biopolymers is a special issue dedicated to SAXS.

Unstructured proteins, RNA or DNA components provide functionally important flexibility that is key to many macromolecular assemblies throughout cell biology. As objective, quantitative experimental measures of flexibility and disorder in solution are limited, small angle scattering (SAS), and in particular small angle X-ray scattering (SAXS), provides a critical technology to assess macromolecular flexibility as well as shape and assembly. In a recent paper published in Biopolymers, Rob Rambo and John Tainer consider the Porod-Debye law as a powerful tool for detecting biopolymer flexibility in SAS experiments. They show that the Porod-Debye region fundamentally describes the nature of the scattering intensity decay, which captures information needed for distinguishing between folded and flexible particles. Particularly for comparative SAS experiments, application of the law, as described in their manuscript, can distinguish between discrete conformational changes and localized flexibility relevant to molecular recognition and interaction networks. This approach aids insightful analyses of fully and partly flexible macromolecules that is more robust and conclusive than traditional Kratky analyses. Furthermore, they demonstrate for prototypic SAXS data that the ability to calculate particle density by the Porod-Debye criteria provides an objective quality assurance parameter that may prove of general use for SAXS modeling and validation.

New SAS analysis software is available called SASTBX. SASTBX provides a novel parameterization of shape using Zernicke polynomials. A databases of prior shapes parameterized using the Zernicke coefficients can be quickly searched with experimental SAXS data within seconds to provide an initial shape estimate. Further refinement of the shape can be achieved. SASTBX is also developing a refinement procedure using a starting atomistic model.

The last decade has seen a dramatic increase in the use of small-angle scattering for the study of biological macromolecules in solution. The drive for more complete structural characterization of proteins and their interactions, coupled with the increasing availability of instrumentation and easy-to-use software for data analysis and interpretation, is expanding the utility of the technique beyond the domain of the biophysicist and into the realm of the protein scientist. However, the absence of publication standards and the ease with which 3D models can be calculated against the inherently 1D scattering data means that an understanding of sample quality, data quality, and modeling assumptions is essential to have confidence in the results. This review is intended to provide a road map through the small-angle scattering experiment, while also providing a set of guidelines for the critical evaluation of scattering data. Examples of current best practice are given that also demonstrate the power of the technique to advance our understanding of protein structure and function.

A comprehensive review on macromolecular SAXS has been published in Current Opinion in Structural Biology by Rambo, R.P. and Tainer, J.A.

Small-angle X-ray scattering (SAXS) is changing how we perceive biological structures, because it reveals dynamic macromolecular conformations and assemblies in solution. SAXS information captures thermodynamic ensembles, enhances static structures detailed by high-resolution methods, uncovers commonalities among diverse macromolecules, and helps define biological mechanisms. SAXS-based experiments on RNA riboswitches and ribozymes and on DNA–protein complexes including DNA–PK and p53 discover flexibilities that better define structure–function relationships. Furthermore, SAXS results suggest conformational variation is a general functional feature of macromolecules. Thus, accurate structural analyses will require a comprehensive approach that assesses both flexibility, as seen by SAXS, and detail, as determined by X-ray crystallography and NMR. Here, we review recent SAXS computational tools, technologies, and applications to nucleic acids and related structures.