Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics.

29 November 2019, Version 2
This content is a preprint and has not undergone peer review at the time of posting.


SAXS experiments provide low-resolution but valuable information about the dynamics of biomolecular systems, which could be ideally integrated into 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 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 metainference with the aim to investigate the dynamical behavior of flexible biomolecules. The efficacy of the method is assessed on the K63-diubiquitin, showing that the inclusion of SAXS-restraints is effective in generating a reliable conformational ensemble, improving the agreement with independent experimental data.


conformational ensemble
protein dynamics
Molecular Dynamics

Supplementary materials

Paissoni et al-SI


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