ProGuide: a flexible framework for modeling global conformational rearrangements in proteins using DEER-derived distance restraints.

Conformational heterogeneity is integral to protein function - ranging from enzyme catalysis to signal transduction - and visualizing distinct conformational states requires experimental techniques capable of providing such structural information. One particularly powerful method, double electron-electron resonance (DEER) spectroscopy, can provide a high-resolution, long-range (~15-80 Å) probability distributions of distances between site-selected pairs of spin labels to resolve intra-protein distance parameters of unique protein conformations, as well as their respective likelihoods within a conformational ensemble. A current frontier in the field of DEER spectroscopy is utilizing this distance information in computational modeling to generate complete structural models of these multiple conformations. Although several methods have been developed for this purpose, modeling protein backbone structural rearrangements using multiple distance restraints remains challenging, due in part to the complexity provided by rotameric flexibility of the spin label side chain. Here, we overcome these challenges with ProGuide, a new framework for generating accurate structural models guided by DEER distance distribution information. Large conformational rearrangements are captured by performing iterative experimentally biased molecular dynamics simulations. In each iteration, spin-label rotameric heterogeneity is modeled using chiLife, and then