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

Chemical Physics Letters 461 (2008) 294–299 Contents lists available at ScienceDirect Chemical Physics Letters journal homepage: www.else /locate/cplett Molecular dynamics simulations of an apoliprotein A–I derived peptide in explicit water Athanassios Stavrakoudis * Department of Economics, University of Ioannina, 45110 Ioannina, Greece a r t i c l e i n f o a b s t r a c t Article history: Molecular dynamics simulations have been performed for the 104–117 a-helical fragment of apoliprotein Received 31 March 2008 A–I using the CHARMM22 force field and the NAMD simulation engine. Simulation (50 ns in explicit water) In final form 1 July 2008 resulted in significant appearance of p-helix conformation, which was totally diminished when the CMAP Available online 8 July 2008 correction of the CHARMM force field was applied. This is consistent with other similar studies which suggest that the observation of p-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 a-helical confor- mation in water. 2008 Elsevier B.V. All rights reserved. 1. Introduction ApoA–I is a member of lipoprotein