Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments

Toru Ekimoto, Yuichi Kokabu, Tomotaka Oroguchi, Mitsunori Ikeguchi

研究成果: Article査読

2 被引用数 (Scopus)

抄録

The combination of molecular dynamics (MD) simulations and small-angle X-ray scattering (SAXS), called the MD-SAXS method, is efficient for investigating protein dynamics. To overcome the time-scale limitation of all-atom MD simulations, coarse-grained (CG) representa-tions are often utilized for biomolecular simulations. In this study, we propose a method to combine CG MD simulations with SAXS, termed the CG-MD-SAXS method. In the CG-MD-SAXS method, the scattering factors of CG particles for proteins and nucleic acids are evaluated using high-resolution structural data in the Protein Data Bank, and the excluded volume and the hydration shell are modeled using two adjustable parameters to incorporate solvent effects. To avoid overfitting, only the two parameters are adjusted for an entire structure ensemble. To verify the developed method, theoretical SAXS profiles for various proteins, DNA/RNA, and a protein-RNA complex are compared with both experimental profiles and theoretical profiles obtained by the all-atom representation. In the present study, we applied the CG-MD-SAXS method to the Swi5-Sfr1 complex and three types of nucleosomes to obtain reliable ensemble models consistent with the experimental SAXS data.

本文言語English
ページ(範囲)377-390
ページ数14
ジャーナルBiophysics and physicobiology
16
DOI
出版ステータスPublished - 2019

ASJC Scopus subject areas

  • 生物理学
  • 生化学
  • 分子生物学
  • 生理学
  • 生化学、遺伝学、分子生物学(その他)

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