{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Shimizu M"],"funding":["Institute for Integrated Radiation and Nuclear Science, Kyoto University","Japan Society for the Promotion of Scienc","The Japan Science Society","The Ministry of Education,Culture,Sports,Science and Technology(MEXT)/Japan Society for the Promotion of Scienc"],"pagination":["9970"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9200744"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["12(1)"],"pubmed_abstract":["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."],"journal":["Scientific reports"],"pubmed_title":["Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations."],"pmcid":["PMC9200744"],"funding_grant_id":["JP17K07816","JP20K22629","JP21K15051","JP19KK0071","JP20K06579","JP18H05229","JP18H05534","JP19K16088"],"pubmed_authors":["Shimizu M","Yunoki Y","Inoue R","Okuda A","Sato N","Urade R","Morishima K","Sugiyama M"],"additional_accession":[]},"is_claimable":false,"name":"Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations.","description":"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.","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Jun","modification":"2026-05-10T01:42:59.522Z","creation":"2025-02-19T02:57:43.521Z"},"accession":"S-EPMC9200744","cross_references":{"pubmed":["35705644"],"doi":["10.1038/s41598-022-13982-9"]}}