title: Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides.
abstract: The PACE force field presents an attractive model for conducting molecular dynamics simulations of membrane-protein systems. PACE is a hybrid model, in which lipids and solvents are coarse-grained consistent with the MARTINI mapping, while proteins are described by a united atom model. However, given PACE is linked to MARTINI, which is widely used to study membranes, the behavior of proteins interacting with membranes has only been limitedly examined in PACE. In this study, PACE is used to examine the behavior of several peptides in membrane environments, namely WALP peptides, melittin and influenza hemagglutinin fusion peptide (HAfp). Overall, we find PACE provides an improvement over MARTINI for modeling helical peptides, based on the membrane insertion energetics for WALP16 and more realistic melittin pore dynamics. Our studies on HAfp, which forms a helical hairpin structure, do not show the hairpin structure to be stable, which may point toward a deficiency in the model. © 2017 Wiley Periodicals, Inc.
authors.affiliation: Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, 06269.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Ward
authors.affiliation: Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, 06269.
authors.forename: Shivangi
authors.initials: S
authors.lastname: Nangia
authors.affiliation: Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, 06269.
authors.forename: Eric R
authors.initials: ER
authors.lastname: May
mesh_terms: D008051:Lipid Bilayers / Q000737:chemistry*; D008563:Membrane Lipids / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D016062:Porosity; D011487:Protein Conformation; D017510:Protein Folding; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D008051:Lipid Bilayers; D008563:Membrane Lipids; D010455:Peptides; D012997:Solvents
keywords: WALP; coarse-grained models; hybrid resolution models; influenza hemagglutinin fusion peptide; melittin; membranes