Proteins and protein complexes with high conformational flexibility participate in a wide range of biological processes. These processes include genome maintenance, gene expression, signal transduction, cell cycle regulation, and many others. Gaining a structural understanding of conformationally flexible proteins and protein complexes is arguably the greatest problem facing structural biologists today. Over the last decade, some progress has been made toward understanding the conformational flexibility of such systems using hybrid approaches. One particularly fruitful strategy has been the combination of small-angle X-ray scattering (SAXS) and molecular simulations. In this article, we provide a brief overview of SAXS and molecular simulations and then discuss two general approaches for combining SAXS data and molecular simulations: minimal ensemble approaches and full ensemble approaches. In minimal ensemble approaches, one selects a minimal ensemble of structures from the simulations that best fit the SAXS data. In full ensemble approaches, one validates a full ensemble of structures from the simulations using SAXS data. We argue that full ensemble models are more realistic than minimal ensemble searches models and that full ensemble approaches should be used wherever possible.
Keywords: BD, Brownian dynamics; CG, coarse-grained; Cryo-EM, cryo-electron microscopy; DNA polymerase; DNA replication; Dmax, maximal distance; LD, Langevin dynamics; MD, molecular dynamics; Minimal ensemble search; NMR, nuclear magnetic resonance; PCNA, proliferating cell nuclear antigen; Pol η, DNA polymerase eta; Protein structure; RPA, replication protein A; Rg, radius of gyration; SANS; SANS, small-angle neutron scattering; SAXS; SAXS, small-angle X-ray scattering; SEC, size exclusion chromatography; SUMO, small ubiquitin-like modifie.