title: Indolicidin binding induces thinning of a lipid bilayer.
abstract: We use all-atom molecular dynamics simulations on a massive scale to compute the standard binding free energy of the 13-residue antimicrobial peptide indolicidin to a lipid bilayer. The analysis of statistical convergence reveals systematic sampling errors that correlate with reorganization of the bilayer on the microsecond timescale and persist throughout a total of 1.4 ms of sampling. Consistent with experimental observations, indolicidin induces membrane thinning, although the simulations significantly overestimate the lipophilicity of the peptide.
authors.affiliation: Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Chris
authors.initials: C
authors.lastname: Neale
authors.affiliation: Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Jenny C Y
authors.initials: JC
authors.lastname: Hsu
authors.affiliation: Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Yip
authors.affiliation: Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada. Electronic address: pomes@sickkids.ca.
authors.forename: Régis
authors.initials: R
authors.lastname: Pomès
mesh_terms: D000595:Amino Acid Sequence; D023181:Antimicrobial Cationic Peptides / Q000737:chemistry / Q000378:metabolism*; D008051:Lipid Bilayers / Q000378:metabolism*; D008969:Molecular Sequence Data; D010713:Phosphatidylcholines / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding
chemical_list: D023181:Antimicrobial Cationic Peptides; D008051:Lipid Bilayers; D010713:Phosphatidylcholines; C073143:indolicidin; C028694:1-palmitoyl-2-oleoylphosphatidylcholine
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