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Bioinformatics Advance Access published online on February 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth027
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received August 5, 2003
Revised November 2, 2003
Accepted November 10, 2003

Article

Sequence analysis and membrane partitioning energies of {alpha}-helical antimicrobial peptides

Xing Han 1* Wenjun Kang 2

1 DuPont Haskell Laboratory for Health and Environmental Sciences, P.O. Box 50, Newark, DE 19714
2 University of Minnesota School of Dentistry, 515 Delaware ST. SE, RM 6-30, Minneapolis, MN 55455

* To whom correspondence should be addressed. E-mail: xing.han{at}usa.dupont.com.


  Abstract

Sequences of 221 {alpha}-helical antimicrobial peptides ({alpha}AMPs) 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 {alpha}AMPs. The weighed mean membrane partitioning energies at positions from 1 to 25 of {alpha}AMPs were calculated. Profile of the partitioning energies suggests oblique membrane insertion and an amphipathic {alpha}-helical structure of the N-terminus of {alpha}AMP (residues from 1 to 13), a bend structure at positions 13 and 14, and a less structured C-terminus that parallels to 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 (Han et al., Nat. Struct. Biol. 2001, 8, 715-720.). We hypothesize that this (N-terminal oblique {alpha}-helix) - central bend - (C-terminus) could be a common structural motif of membrane-disruptive peptides.


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