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Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides
Author(s) -
Ward Michael D.,
Nangia Shivangi,
May Eric R.
Publication year - 2017
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24694
Subject(s) - melittin , membrane , molecular dynamics , pace , chemistry , folding (dsp implementation) , lipid bilayer fusion , biophysics , physics , computational chemistry , biochemistry , engineering , biology , electrical engineering , astronomy
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.