Impact of Cl- and Na+ ions on simulated structure and dynamics of βARK1 PH domain

Stefania Pfeiffer, David Fushman, David Cowburn

Research output: Contribution to journalArticlepeer-review

25 Scopus citations


A nonzero net charge of proteins at pH 7 is usually compensated by the addition of charge-balancing counter ions during molecular dynamics simulation, which reduces electrostatic interactions. For highly charged proteins, like the βARK1 PH domain used here, it seems reasonable to also add explicit salt ions. To assess the impact of explicit salt ions, two molecular dynamics simulations of solvated βARK1 PH domain have been carried out with different numbers of Cl- and Na+ ions, based on the Cornell et al. force field and the Ewald summation, which was used in the treatment of long- range electrostatic interactions. Initial positions of ions were obtained from the AMBER CION program. Increasing the number of ions alters the average structure in loop regions, as well as the fluctuation amplitudes of dihedral angles. We found unnaturally strong interactions between side chains in the absence of salt ions. The presence of salt ions reduces these electrostatic interactions. The time needed for the equilibration of the ionic environment around the protein, after initial placement of ions close to oppositely charged side chains, is in the nanosecond time range, which can be shortened by using a higher ionic strength. Our results also suggest selecting those methods that do not place the ions initially close to the protein surface.

Original languageEnglish
Pages (from-to)206-217
Number of pages12
JournalProteins: Structure, Function and Bioinformatics
Issue number2
StatePublished - 1 May 1999
Externally publishedYes


  • Counter ions
  • Electrostatic interaction
  • Equilibration
  • GRK2 PH domain
  • Hydrogen bonds
  • Ionic solvent
  • Ionic strength
  • Molecular dynamics simulation
  • Proteins


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