2-Dimensional HP Foldings of Dermaseptin-J2

Shaomin Yan, Guang Wu

State Key Laboratory of Non-Food Biomass Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, Nanning, China.

DOI: 10.4236/eng.2013.510B016                

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.

Keywords

Dermaseptin; Folding Configuration; HP Model; Hydrophobicity Index; Minimal Energy; Native State

Conflicts of Interest

The authors declare no conflicts of interest.

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