Small-angle X-ray scattering (SAXS) experiments provide low-resolution but valuable information about the dynamics of biomolecular systems, which could be ideally integrated into molecular dynamics (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.
Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics / C. Paissoni, A. Jussupow, C. Camilloni. - In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. - ISSN 1549-9618. - 16:4(2020 Apr 14), pp. 2825-2834.
|Titolo:||Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics|
PAISSONI, CRISTINA (Primo) (Corresponding)
CAMILLONI, CARLO (Ultimo) (Corresponding)
|Settore Scientifico Disciplinare:||Settore FIS/07 - Fisica Applicata(Beni Culturali, Ambientali, Biol.e Medicin)|
Settore BIO/10 - Biochimica
|Data di pubblicazione:||14-apr-2020|
|Data ahead of print / Data di stampa:||11-mar-2020|
|Digital Object Identifier (DOI):||http://dx.doi.org/10.1021/acs.jctc.9b01181|
|Appare nelle tipologie:||01 - Articolo su periodico|