TITLE:
2-Dimensional HP Foldings of Dermaseptin-J2
AUTHORS:
Shaomin Yan, Guang Wu
KEYWORDS:
Dermaseptin; Folding Configuration; HP Model; Hydrophobicity Index; Minimal Energy; Native State
JOURNAL NAME:
Engineering,
Vol.5 No.10B,
October
25,
2013
ABSTRACT: Although the hydrophobic-polar (HP) model is a simple
model to study protein folding, it is an approximation to the real-life case.
Dermaseptin is a subfamily of frog skin active peptide family, which has
various antimicrobial activities, and dermaseptin-J2 is a newly found peptide
composed of 26 amino acids. In this study, the 2-dimensional HP model was used
to analyze the foldings of dermaseptin-J2 and its nine mutants, which were
converted to different HP sequences according to the normalized amino acid
hydrophobicity index with respect to pH levels and the conversion of glycine as
hydrophobic or polar, and each has 847,288,609,443 possible foldings. The
results show that the foldings with minimal energy have different native
states, which are chiral and can be numerically distinguished and ranked according
to the normalized amino acid hydrophobicity index. The nine mutants of
dermaseptin-J2 do not affect the minimal energy but affect their native states at
pH 7. The results demonstrate that two pH levels and conversion of glycine as
hydrophobic or polar affect the native state and minimal energy, suggesting
these are two ways to modify dermaseptin-J2.