ENSEMBLE 375 Application of Ensemble Models to Study Biomolecular Dynamics by SAXS 376

IDPs 376 Multidomain Proteins 381

Concerted Motions in Multidomain Proteins 383 Highly Flexible Multidomain Proteins 385

Ensemble Methods in Nucleic Acids 387 Biomolecular Complexes 390

Dynamics in Biomolecular Complexes 390 Transient Biomolecular Complexes 393

Systems with Complex Dynamics 395 Final Remarks 396 Acknowledgments 397 References 397

In this chapter, we present modern computational approaches to use smallangle x-ray scattering (SAXS) in the analysis of exible proteins. SAXS is a powerful method for analyzing the structure and structural changes of biological macromolecules in solution (Svergun et al. 2013). e method is most often used for puried solutions of globular proteins and complexes where all particles can be considered identical and the experimental scattering can be related to the structure of a single particle (although the scattering is typically isotropic due to the average over particle orientations). In this case, SAXS provides information about the overall shape and can construct three-dimensional (3-D) low-resolution models, either ab initio or using rigid body analysis in terms of known high resolution structures of domains or subunits.