title: Structure and orientation of antibiotic peptide alamethicin in phospholipid bilayers as revealed by chemical shift oscillation analysis of solid state nuclear magnetic resonance and molecular dynamics simulation.
abstract: The structure, topology and orientation of membrane-bound antibiotic alamethicin were studied using solid state nuclear magnetic resonance (NMR) spectroscopy. (13)C chemical shift interaction was observed in [1-(13)C]-labeled alamethicin. The isotropic chemical shift values indicated that alamethicin forms a helical structure in the entire region. The chemical shift anisotropy of the carbonyl carbon of isotopically labeled alamethicin was also analyzed with the assumption that alamethicin molecules rotate rapidly about the bilayer normal of the phospholipid bilayers. It is considered that the adjacent peptide planes form an angle of 100° or 120° when it forms α-helix or 310-helix, respectively. These properties lead to an oscillation of the chemical shift anisotropy with respect to the phase angle of the peptide plane. Anisotropic data were acquired for the 4 and 7 sites of the N- and C-termini, respectively. The results indicated that the helical axes for the N- and C-termini were tilted 17° and 32° to the bilayer normal, respectively. The chemical shift oscillation curves indicate that the N- and C-termini form the α-helix and 310-helix, respectively. The C-terminal 310-helix of alamethicin in the bilayer was experimentally observed and the unique bending structure of alamethicin was further confirmed by measuring the internuclear distances of [1-(13)C] and [(15)N] doubly-labeled alamethicin. Molecular dynamics simulation of alamethicin embedded into dimyristoyl phophatidylcholine (DMPC) bilayers indicates that the helical axes for α-helical N- and 310-helical C-termini are tilted 12° and 32° to the bilayer normal, respectively, which is in good agreement with the solid state NMR results.
authors.affiliation: Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Nagao
authors.affiliation: Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Mishima
authors.affiliation: Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan; Center for Nanoscience and Nanotechnology, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia.
authors.forename: Namsrai
authors.initials: N
authors.lastname: Javkhlantugs
authors.affiliation: Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Ishioka
authors.affiliation: Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan.
authors.forename: Kiyonobu
authors.initials: K
authors.lastname: Yokota
authors.affiliation: Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan.
authors.forename: Kazushi
authors.initials: K
authors.lastname: Norisada
authors.affiliation: Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan.
authors.forename: Izuru
authors.initials: I
authors.lastname: Kawamura
authors.affiliation: Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan.
authors.forename: Kazuyoshi
authors.initials: K
authors.lastname: Ueda
authors.affiliation: Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan. Electronic address: naito@ynu.ac.jp.
authors.forename: Akira
authors.initials: A
authors.lastname: Naito
mesh_terms: D000408:Alamethicin / Q000737:chemistry* / Q000378:metabolism; D000595:Amino Acid Sequence; D016880:Anisotropy; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism; D002247:Carbon Isotopes; D004134:Dimyristoylphosphatidylcholine / Q000737:chemistry / Q000378:metabolism; D008051:Lipid Bilayers / Q000737:chemistry* / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009587:Nitrogen Isotopes; D010743:Phospholipids / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary
chemical_list: D000900:Anti-Bacterial Agents; D002247:Carbon Isotopes; D008051:Lipid Bilayers; D009587:Nitrogen Isotopes; D010743:Phospholipids; D000408:Alamethicin; D004134:Dimyristoylphosphatidylcholine
keywords: Antibiotic peptide; Chemical shift oscillation; Ion-channel; Molecular dynamics simulation; Phospholipid bilayer; Solid state NMR