biostudies-literatureShimizu MInstitute for Integrated Radiation and Nuclear Science, Kyoto UniversityJapan Society for the Promotion of SciencThe Japan Science SocietyThe Ministry of Education,Culture,Sports,Science and Technology(MEXT)/Japan Society for the Promotion of Scienc9970https://www.ebi.ac.uk/biostudies/studies/S-EPMC9200744biostudies-literatureUnknown12(1)Solving structural ensembles of flexible biomolecules is a challenging research area. Here, we propose a method to obtain possible structural ensembles of a biomolecule based on small-angle X-ray scattering (SAXS) and molecular dynamics simulations. Our idea is to clip a time series that matches a SAXS profile from a simulation trajectory. To examine its practicability, we applied our idea to a multi-domain protein ER-60 and successfully extracted time series longer than 1 micro second from trajectories of coarse-grained molecular dynamics simulations. In the extracted time series, the domain conformation was distributed continuously and smoothly in a conformational space. Preferred domain conformations were also observed. Diversity among scattering curves calculated from each ER-60 structure was interpreted to reflect an open-close motion of the protein. Although our approach did not provide a unique solution for the structural ensemble of the biomolecule, each extracted time series can be an element of the real behavior of ER-60. Considering its low computational cost, our approach will play a key role to identify biomolecular dynamics by integrating SAXS, simulations, and other experiments.Scientific reportsExtracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations.PMC9200744JP17K07816JP20K22629JP21K15051JP19KK0071JP20K06579JP18H05229JP18H05534JP19K16088Shimizu MYunoki YInoue ROkuda ASato NUrade RMorishima KSugiyama MfalseExtracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations.Solving structural ensembles of flexible biomolecules is a challenging research area. Here, we propose a method to obtain possible structural ensembles of a biomolecule based on small-angle X-ray scattering (SAXS) and molecular dynamics simulations. Our idea is to clip a time series that matches a SAXS profile from a simulation trajectory. To examine its practicability, we applied our idea to a multi-domain protein ER-60 and successfully extracted time series longer than 1 micro second from trajectories of coarse-grained molecular dynamics simulations. In the extracted time series, the domain conformation was distributed continuously and smoothly in a conformational space. Preferred domain conformations were also observed. Diversity among scattering curves calculated from each ER-60 structure was interpreted to reflect an open-close motion of the protein. Although our approach did not provide a unique solution for the structural ensemble of the biomolecule, each extracted time series can be an element of the real behavior of ER-60. Considering its low computational cost, our approach will play a key role to identify biomolecular dynamics by integrating SAXS, simulations, and other experiments.2022-01-01T00:00:00Z2022 Jun2026-05-10T01:42:59.522Z2025-02-19T02:57:43.521ZS-EPMC92007443570564410.1038/s41598-022-13982-9