Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations

Tomotaka Oroguchi, Mitsunori Ikeguchia

研究成果: Article査読

22 被引用数 (Scopus)

抄録

The combination of small-angle X-ray solution scattering (SAXS) experiments and molecular dynamics (MD) simulations is now becoming a powerful tool to study protein conformations in solution at an atomic resolution. In this study, we investigated effects of ionic strength on SAXS data theoretically by using MD simulations of hen egg white lysozyme at various NaCl concentrations from 0 to 1 M. The calculated SAXS excess intensities showed a significant dependence on ion concentration, which originates from the different solvent density distributions in the presence and absence of ions. The addition of ions induced a slow convergence of the SAXS data, and a ∼20 ns simulation is required to obtain convergence of the SAXS data with the presence of ions whereas only a 0.2 ns simulation is sufficient in the absence of ions. To circumvent the problem of the slow convergence in the presence of ions, we developed a novel method that reproduces the SAXS excess intensities with the presence of ions from short MD trajectories in pure water. By applying this method to SAXS data for the open and closed forms of transferrin at 1 M ion concentration, the correct form could be identified by simply using short MD simulations of the protein in pure water for 0.2 ns.

本文言語English
論文番号025102
ジャーナルJournal of Chemical Physics
134
2
DOI
出版ステータスPublished - 2011 1 14
外部発表はい

ASJC Scopus subject areas

  • 物理学および天文学(全般)
  • 物理化学および理論化学

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