Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics.
SAXS experiments provide low-resolution but valuable information about the dynamics of biomolecular systems, which could be ideally integrated in MD simulations to accurately determine conformational ensembles of flexible proteins. The applicability of this strategy is hampered by the high computational cost required to calculate scattering intensities from three-dimensional structures. We previously presented a metainference-based hybrid resolution method that makes atomistic SAXS-restrained MD simulation feasible by adopting a coarse-grained approach to efficiently back-calculate scattering intensities; here, we extend this technique, applying it in the framework of multiple-replica simulations with the aim to investigate the dynamical behavior of flexible biomolecules. The efficacy of the method is assessed on the K63-diubiquitin multi-domain protein, showing that inclusion of SAXS-restraints is effective in generating reliable and heterogenous conformational ensemble, also improving the agreement with independent experimental data.