title: Sequence analysis and membrane partitioning energies of alpha-helical antimicrobial peptides.
abstract: Sequences of 221 alpha-helical antimicrobial peptides (alphaAMPs) were compared and 63-166 of them were selected and analyzed using Perl programs. The results showed that aliphatic amino acids Gly, Leu, Ala, Ile and two positively charged amino acids Lys and Arg were composed of more than 63% of the first 20 residues of alphaAMPs. The weighed mean membrane partitioning energies at positions from 1 to 25 of alphaAMPs were calculated. Profile of the partitioning energies suggests oblique membrane insertion and an amphipathic alpha-helical structure of the N-terminus of alphaAMP (residues from 1 to 13), a bend structure at positions 13 and 14, and a less structured C-terminus that parallels the surface of the membrane. These structural features are in good agreement with the experimentally determined membrane structure of hemagglutinin fusion peptide from influenza virus. We hypothesize that this (N-terminal oblique alpha-helix)-central bend-(C-terminus) could be a common structural motif of membrane-disruptive peptides.
authors.affiliation: DuPont Haskell Laboratory for Health and Environmental Sciences, PO Box 50, Newark, DE 19714, USA. xing.han@usa.dupont.com
authors.forename: Xing
authors.initials: X
authors.lastname: Han
authors.forename: Wenjun
authors.initials: W
authors.lastname: Kang
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D023181:Antimicrobial Cationic Peptides / Q000737:chemistry*; D002462:Cell Membrane / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship
chemical_list: D000596:Amino Acids; D023181:Antimicrobial Cationic Peptides