Han Xing, Kang Wenjun
DuPont Haskell Laboratory for Health and Environmental Sciences, PO Box 50, Newark, DE 19714, USA.
Bioinformatics. 2004 Apr 12;20(6):970-3. doi: 10.1093/bioinformatics/bth027. Epub 2004 Feb 5.
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.
对221种α-螺旋抗菌肽（αAMPs）的序列进行了比较，并使用Perl程序从中选择了63 - 166种进行分析。结果表明，脂肪族氨基酸甘氨酸（Gly）、亮氨酸（Leu）、丙氨酸（Ala）、异亮氨酸（Ile）以及两个带正电荷的氨基酸赖氨酸（Lys）和精氨酸（Arg）占αAMPs前20个残基的63%以上。计算了αAMPs第1至25位的加权平均膜分配能。分配能图谱表明，αAMP（第1至13位残基）的N端呈倾斜膜插入和两亲性α-螺旋结构，第13和14位有一个弯曲结构，C端结构较少，与膜表面平行。这些结构特征与流感病毒血凝素融合肽的实验测定膜结构高度一致。我们推测，这种（N端倾斜α-螺旋）-中心弯曲-（C端）可能是膜破坏肽的一种常见结构基序。
