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

Tomotaka Oroguchi, Mitsunori Ikeguchia

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number025102
JournalJournal of Chemical Physics
Volume134
Issue number2
DOIs
Publication statusPublished - 2011 Jan 14
Externally publishedYes

Fingerprint

Molecular Dynamics Simulation
Ionic strength
Osmolar Concentration
Molecular dynamics
X-Rays
Scattering
Ions
molecular dynamics
proteins
X rays
Computer simulation
scattering
Proteins
x rays
simulation
ions
ion concentration
eggs
lysozyme
Egg White

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry
  • Medicine(all)

Cite this

Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations. / Oroguchi, Tomotaka; Ikeguchia, Mitsunori.

In: Journal of Chemical Physics, Vol. 134, No. 2, 025102, 14.01.2011.

Research output: Contribution to journalArticle

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