Characterization and Identification of Natural Antimicrobial Peptides on Different Organisms.

Chia-Ru Chung,Yu Wan,Jorng-Tzong Horng,Siyu Chen,Jhih-Hua Jhong,Zhuo Wang,Tzong-Yi Lee

doi:10.3390/ijms21030986

Abstract

Because of the rapid development of multidrug resistance, conventional antibiotics cannot kill pathogenic bacteria efficiently. New antibiotic treatments such as antimicrobial peptides (AMPs) can provide a possible solution to the antibiotic-resistance crisis. However, the identification of AMPs using experimental methods is expensive and time-consuming. Meanwhile, few studies use amino acid compositions (AACs) and physicochemical properties with different sequence lengths against different organisms to predict AMPs. Therefore, the major purpose of this study is to identify AMPs on seven categories of organisms, including amphibians, humans, fish, insects, plants, bacteria, and mammals. According to the one-rule attribute evaluation, the selected features were used to construct the predictive models based on the random forest algorithm. Compared to the accuracies of iAMP-2L (a web-server for identifying AMPs and their functional types), ADAM (a database of AMP), and MLAMP (a multi-label AMP classifier), the proposed method yielded higher than 92% in predicting AMPs on each category. Additionally, the sensitivities of the proposed models in the prediction of AMPs of seven organisms were higher than that of all other tools. Furthermore, several physicochemical properties (charge, hydrophobicity, polarity, polarizability, secondary structure, normalized van der Waals volume, and solvent accessibility) of AMPs were investigated according to their sequence lengths. As a result, the proposed method is a practical means to complement the existing tools in the characterization and identification of AMPs in different organisms.

Highlights

Antimicrobial peptides (AMPs), naturally encoded by genes and usually containing 12–100 amino acids, are the essential components of the innate immune system and can protect the host from viruses and various pathogenic bacteria [1,2]
The composition of “G” of AMPs was higher than the one for non-AMPs. This observation is consistent with that of a previous study, which indicated that the glycine-rich proteins (GRPs) are a group of proteins that occurs in a wide variety of organisms [23]
Computational identification can efficiently and effectively discover candidate peptides as antimicrobial peptides for subsequent experimental assessment, which helps shorten the process of drug discovery [32,33]

Summary

Introduction

Antimicrobial peptides (AMPs), naturally encoded by genes and usually containing 12–100 amino acids, are the essential components of the innate immune system and can protect the host from viruses and various pathogenic bacteria [1,2]. They are produced by various organisms, including protozoa, bacteria, and animals, and can cause the cell death of microbes by disrupting either their cell membrane or intracellular functions [3]. Cysteine is a major residue in AMPs from plants, probably because of the advantage of disulfide-bonded and defensive-like molecules [17]. The net charge, isoelectric point, composition, and tendency for secondary structure are related to the activities of AMPs, such as antibacterial, antifungal, and antiviral activities [6,12,18]

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Conclusion