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

preprint
revised on 22.11.2019 and posted on 29.11.2019 by Cristina Paissoni, Alexander Jussupow, Carlo Camilloni

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.

History

Email Address of Submitting Author

carlo.camilloni@unimi.it

Institution

University of Milano

Country

Italy

ORCID For Submitting Author

0000-0002-9923-8590

Declaration of Conflict of Interest

no conflict of interest

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