Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram

被引:74
作者
Burdukiewicz, Michal [1 ]
Sidorczuk, Katarzyna [2 ]
Rafacz, Dominik [1 ]
Pietluch, Filip [2 ]
Chilimoniuk, Jaroslaw [2 ]
Roediger, Stefan [3 ,4 ]
Gagat, Przemyslaw [2 ]
机构
[1] Warsaw Univ Technol, Fac Math & Informat Sci, PL-00662 Warsaw, Poland
[2] Univ Wroclaw, Fac Biotechnol, Dept Bioinformat & Genom, PL-50383 Wroclaw, Poland
[3] Brandenburg Univ Technol Cottbus Senftenberg, Fac Nat Sci, D-01968 Senftenberg, Germany
[4] Joint Fac Brandenburg Univ Technol CottbusSenften, Fac Hlth Sci, D-01968 Senftenberg, Germany
关键词
AMP; antimicrobial peptides; host defense peptides; multidrug-resistant bacteria; prediction; proteomic screening; random forest; DATABASE; CLASSIFIER; RESISTANCE; MILK; TOOL;
D O I
10.3390/ijms21124310
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Antimicrobial peptides (AMPs) are molecules widespread in all branches of the tree of life that participate in host defense and/or microbial competition. Due to their positive charge, hydrophobicity and amphipathicity, they preferentially disrupt negatively charged bacterial membranes. AMPs are considered an important alternative to traditional antibiotics, especially at the time when multidrug-resistant bacteria being on the rise. Therefore, to reduce the costs of experimental research, robust computational tools for AMP prediction and identification of the best AMP candidates are essential. AmpGram is our novel tool for AMP prediction; it outperforms top-ranking AMP classifiers, including AMPScanner, CAMPR3R and iAMPpred. It is the first AMP prediction tool created for longer AMPs and for high-throughput proteomic screening. AmpGram prediction reliability was confirmed on the example of lactoferrin and thrombin. The former is a well known antimicrobial protein and the latter a cryptic one. Both proteins produce (after protease treatment) functional AMPs that have been experimentally validated at molecular level. The lactoferrin and thrombin AMPs were located in the antimicrobial regions clearly detected by AmpGram. Moreover, AmpGram also provides a list of shot 10 amino acid fragments in the antimicrobial regions, along with their probability predictions; these can be used for further studies and the rational design of new AMPs. AmpGram is available as a web-server, and an easy-to-use R package for proteomic analysis at CRAN repository.
引用
收藏
页码:1 / 13
页数:13
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