Membrane-bound ARF1 peptide: Interpretation of neutron diffraction data by molecular dynamics simulation methods

K. Balali-Mood, T. A. Harroun, J. P. Bradshaw

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Adenosine diphosphate ribosylation factor-1 (ARF1) is activated by cell membrane binding of a self-folding N-terminal domain. We have previously presented four possible conformations of the membrane bound, human ARF1 N-terminal peptide in planar lipid bilayers of DOPC and DOPG (7:3 molar ratio), determined from lamellar neutron diffraction and circular dichroism data. In this paper we analyse the four possible conformations by molecular dynamics simulations. The aim of these simulations was to use MD to distinguish which of the four possible membrane bound structures was the most likely. The most likely conformation was determined according to the following criteria: (a) location of label positions on the peptide in relation to the bilayer, (b) lowest mean square displacement from the initial structure, (c) lowest system energy, (d) most peptide-lipid headgroup hydrogen bonding, (e) analysis of phi/psi angles of the peptide. These findings demonstrate the application of molecular dynamics simulations to explore neutron diffraction data.

Original languageEnglish
Pages (from-to)379-388
Number of pages10
JournalMolecular Membrane Biology
Volume22
Issue number5
DOIs
Publication statusPublished - 1 Sep 2005

Keywords

  • Adenosine diphosphate ribosylation factor
  • Molecular dynamics simulation
  • Neutron diffraction
  • Phospholipid bilayers

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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