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Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations

Shimizu, Masahiro Okuda, Aya Morishima, Ken Inoue, Rintaro Sato, Nobuhiro Yunoki, Yasuhiro Urade, Reiko Sugiyama, Masaaki 京都大学 DOI:10.1038/s41598-022-13982-9

2022

概要

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.

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Acknowledgements

This work was supported by MEXT/JSPS KAKENHI Grant Numbers (JP20K22629 to M. Shimizu; JP19K16088

and 21K15051 to K. M.; JP19KK0071, and JP20K06579 to R. I.; JP17K07816 to N. S.; JP18H05229 and

JP18H05534 to M. Sugiyama), and the Sasakawa Scientific Research Grant from The Japan Science Society

assigned to A. O. The study was also partially supported by a project for the construction of the basis for advanced

materials science and analytical study by the innovative use of quantum beams and nuclear sciences at the

Institute for Integrated Radiation and Nuclear Science, Kyoto University (KURNS) and a grants for research

promotion in KURNS to M. Shimizu and Y. Y. The study was partially supported by the Platform Project for

Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and

Life Science Research (BINDS)) from AMED (JP22ama121001j0001) to M. Sugiyama.

Author contributions

M.Sh. and M.Su. designed the modeling method. M.Sh. performed MD simulations and analysed the simulation

data. All authors wrote the paper.

Competing interests The authors declare no competing interests.

Additional information

Supplementary Information The online version contains supplementary material available at https://​doi.​org/​

10.​1038/​s41598-​022-​13982-9.

Correspondence and requests for materials should be addressed to M.S. or M.S.

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