Progress in small-angle scattering from biological solutions at high-brilliance synchrotrons

Abstract

Small-angle X-ray scattering (SAXS) is an established technique that provides low-resolution structural information on macromolecular solutions. Recent decades have witnessed significant progress in both experimental facilities and in novel data-analysis approaches, making SAXS a mainstream method for structural biology. The technique is routinely applied to directly reconstruct lowresolution shapes of proteins and to generate atomistic models of macromolecular assemblies using hybrid approaches. Very importantly, SAXS is capable of yielding structural information on systems with size and conformational polydispersity, including highly flexible objects. In addition, utilizing high-flux synchrotron facilities, time-resolved SAXS allows analysis of kinetic processes over time ranges from microseconds to hours. Dedicated bioSAXS beamlines now offer fully automated data-collection and analysis pipelines, where analysis and modelling is conducted on the fly. This enables SAXS to be employed as a high-throughput method to rapidly screen various sample conditions and additives. The growing SAXS user community is supported by developments in data and model archiving and quality criteria. This review illustrates the latest developments in SAXS, in particular highlighting timeresolved applications aimed at flexible and evolving systems.

Recording and Analyzing Nucleic Acid Distance Distributions with X‐Ray Scattering Interferometry (XSI)

“…Be aware that important details of the scattering profile can be lost in the low S -range for X-ray energies chosen too low or depleted by low signal-to-noise at X-ray energies set too high. For general protocols on SAXS sample preparation, data collection, and data analysis see Unit 7.14, Unit 17.18 and (Doniach & Lipfert, 2012; Dyer et al, 2014; Greg L. Hura et al, 2013; Jeffries et al, 2016; Lipfert & Doniach, 2007; Tuukkanen et al, 2017). …”

Chemically Denatured Structures of Porcine Pepsin using Small-Angle X-ray Scattering

“…It provides information regarding the sizes and shapes of proteins and complexes over a broad range of molecular sizes ranging from several kDa to GDa [32][33][34]. In particular, SAXS can comprehensively characterize dynamic processes in systems where macromolecular structures are evolving under varying experimental conditions (e.g., time, pH, pressure, or different reagents) [35][36][37][38]. In general, a highly purified monodisperse ideal sample without intermolecular interactions is essential for the reconstruction of 3D models from SAXS data.…”

Neighborhood Preference of Amino Acids in Protein Structures and its Applications in Protein Structure Assessment

“…In many cases, it is difficult to determine a high-quality structure based solely on experimental information. Hybrid methods that integrate structure prediction results and experimental data are promising for exploiting information from both experimental data and computational modeling or predictions [16][17][18] . For a structure prediction method to be successful, it must have two components: (1) an algorithm to generate a structure ensemble that includes good models, i.e., at least some models in the ensemble are similar to the correct structure (or the native structure); and (2) a scoring function that can rank the generated structures, so that the good models can be identified.…”