Molecular dynamics simulations of an apoliprotein A–I derived peptide in explicit water

Molecular dynamics simulations have been performed for the 104–117 α-helical fragment of apoliprotein A–I using the CHARMM22 force field and the Namd simulation engine. Simulation (50 ns in explicit water) resulted in significant appearance of π-helix conformation, which was totally diminished when the CMAP correction of the CHARMM force field was applied. This is consistent with other similar studies which suggest that the observation of π-helix in peptide conformation was force field biased rather actually existed. This study suggests that the 104–117 fragment of apoliprotein A–I has a stable α-helical conformation in water.