Poster Presentation 2014 International Biophysics Congress

Molecular dynamics simulations of GPCR: The effect of different protein-lipid force field parameters (#461)

MD. Iqbal Mahmood 1 , Nozomu Kamiya , Hideaki Fujitani , Takefumi Yamashita
  1. The University of Tokyo, Chiba, Japan

Molecular dynamics (MD) simulations can serve as a tool to provide information about the dynamics of biological macromolecules at the atomic level, while X-ray crystallography becomes a powerful tool to clarify the static structures. To predict physical properties accurately based on MD simulations, good force field parameters are necessary for all the molecules in a system. In the present work, we examine the different force fields for the structural behavior of GPCR, β2 adrenergic receptor (β2AR). We perform the 1 µs MD simulations of β2AR embedded in palmitoyal-oleoyl-phosphatidyl-choline (POPC) bilayer membrane with FUJI+Slipids, FUJI+GAFFlipid, CHARMM27 and CHARMM36 force fields and thendiscuss to what extent the choice of force field affects the GPCR structures. In the FUJI+GAFFlipid force field model case, β2AR forms a stable salt bridge (ionic lock) between Arg131 of helix 3 and Glu268 of helix 6 during the MD simulations whereas the ionic lock is broken in FUJI+Slipids model. In the CHARMM27 and CHARMM36 force field models, the ionic lock forms only transiently. Furthermore, the distance between the side chains of Lys267 and Asp331 of β2AR in FUJI+GAFFlipid model is shorter than that of other force field models. These data suggest that the choice of force field models influences the structural changes significantly. The results lead us to develop a more accurate force field for protein-lipid MD simulations.