Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram
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 cons...
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| Format: | Article |
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MDPI AG
2020-06-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/12/4310 |
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| author | Michał Burdukiewicz Katarzyna Sidorczuk Dominik Rafacz Filip Pietluch Jarosław Chilimoniuk Stefan Rödiger Przemysław Gagat |
| author_facet | Michał Burdukiewicz Katarzyna Sidorczuk Dominik Rafacz Filip Pietluch Jarosław Chilimoniuk Stefan Rödiger Przemysław Gagat |
| author_sort | Michał Burdukiewicz |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T19:07:12Z |
| format | Article |
| id | doaj.art-83b78edafcb644488ceb6481dc686aa3 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T19:07:12Z |
| publishDate | 2020-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-83b78edafcb644488ceb6481dc686aa32023-11-20T04:05:04ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-06-012112431010.3390/ijms21124310Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGramMichał Burdukiewicz0Katarzyna Sidorczuk1Dominik Rafacz2Filip Pietluch3Jarosław Chilimoniuk4Stefan Rödiger5Przemysław Gagat6Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, PolandDepartment of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, PolandFaculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, PolandDepartment of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, PolandDepartment of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, PolandFaculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, 01968 Senftenberg, GermanyDepartment of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, PolandAntimicrobial 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.https://www.mdpi.com/1422-0067/21/12/4310AMPantimicrobial peptideshost defense peptidesmultidrug-resistant bacteriapredictionproteomic screening |
| spellingShingle | Michał Burdukiewicz Katarzyna Sidorczuk Dominik Rafacz Filip Pietluch Jarosław Chilimoniuk Stefan Rödiger Przemysław Gagat Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram International Journal of Molecular Sciences AMP antimicrobial peptides host defense peptides multidrug-resistant bacteria prediction proteomic screening |
| title | Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram |
| title_full | Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram |
| title_fullStr | Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram |
| title_full_unstemmed | Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram |
| title_short | Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram |
| title_sort | proteomic screening for prediction and design of antimicrobial peptides with ampgram |
| topic | AMP antimicrobial peptides host defense peptides multidrug-resistant bacteria prediction proteomic screening |
| url | https://www.mdpi.com/1422-0067/21/12/4310 |
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