title: Efficiency of antimicrobial defense: molecular flexibility of natural defensin and artificial bis-quaternary ammonium compound.
abstract: BACKGROUND
  Human α-defensins (such as HD5 and HD6) are typical bactericidal peptides. We examined the molecular features of HD5 and HD6 by molecular dynamics (MD) analysis.
  
  
  METHODS
  Molecular features of natural defensins and artificial bis-quaternary ammonium compounds (e.g. 1,6-polymethylenedithio)bis(1-octylpyridinium iodide: 4DTBP-m,8) were analyzed using molecular simulation techniques.
  
  
  RESULTS
  HD5 and HD6 had different electrostatic potential profiles, which indicated the region-dependent hydrophobicity. 4DTBP-m,8 derivatives were significantly flexible, and many conformers existed.
  
  
  CONCLUSIONS
  HD5 and HD6 indicated antimicrobial activity by restricted conformation.
authors.affiliation: Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki-cho, Suzuka, Mie 513-8670, Japan. kohkura@sag.bekkoame.ne.jp
authors.forename: Kazuto
authors.initials: K
authors.lastname: Ohkura
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Shinohara
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Hori
mesh_terms: D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D003553:Cystine / Q000032:analysis; D006801:Humans; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009536:Niacinamide / Q000031:analogs & derivatives / Q000737:chemistry; D019879:Paneth Cells / Q000378:metabolism; D018583:Pliability; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011726:Pyridinium Compounds / Q000737:chemistry; D055672:Static Electricity; D013329:Structure-Activity Relationship; D013501:Surface-Active Agents / Q000737:chemistry; D023084:alpha-Defensins / Q000737:chemistry* / Q000502:physiology
chemical_list: C562083:4,4'-(1,6-hexamethylenedithio)bis(1-octylpyridinium); C500225:DEFA5 protein, human; C517765:DEFA6 protein, human; D011726:Pyridinium Compounds; D013501:Surface-Active Agents; D023084:alpha-Defensins; D009536:Niacinamide; D003553:Cystine