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PhaLP: A Database for the Study of Phage Lytic Proteins and Their Evolution

Phage lytic proteins are a clinically advanced class of novel enzyme-based antibiotics, so-called enzybiotics. A growing community of researchers develops phage lytic proteins with the perspective of their use as enzybiotics. A successful translation of enzybiotics to the market requires well-consid...

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Autores principales: Criel, Bjorn, Taelman, Steff, Van Criekinge, Wim, Stock, Michiel, Briers, Yves
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8310338/
https://www.ncbi.nlm.nih.gov/pubmed/34206969
http://dx.doi.org/10.3390/v13071240
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author Criel, Bjorn
Taelman, Steff
Van Criekinge, Wim
Stock, Michiel
Briers, Yves
author_facet Criel, Bjorn
Taelman, Steff
Van Criekinge, Wim
Stock, Michiel
Briers, Yves
author_sort Criel, Bjorn
collection PubMed
description Phage lytic proteins are a clinically advanced class of novel enzyme-based antibiotics, so-called enzybiotics. A growing community of researchers develops phage lytic proteins with the perspective of their use as enzybiotics. A successful translation of enzybiotics to the market requires well-considered selections of phage lytic proteins in early research stages. Here, we introduce PhaLP, a database of phage lytic proteins, which serves as an open portal to facilitate the development of phage lytic proteins. PhaLP is a comprehensive, easily accessible and automatically updated database (currently 16,095 entries). Capitalizing on the rich content of PhaLP, we have mapped the high diversity of natural phage lytic proteins and conducted analyses at three levels to gain insight in their host-specific evolution. First, we provide an overview of the modular diversity. Secondly, datamining and interpretable machine learning approaches were adopted to reveal host-specific design rules for domain architectures in endolysins. Lastly, the evolution of phage lytic proteins on the protein sequence level was explored, revealing host-specific clusters. In sum, PhaLP can act as a starting point for the broad community of enzybiotic researchers, while the steadily improving evolutionary insights will serve as a natural inspiration for protein engineers.
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spelling pubmed-83103382021-07-25 PhaLP: A Database for the Study of Phage Lytic Proteins and Their Evolution Criel, Bjorn Taelman, Steff Van Criekinge, Wim Stock, Michiel Briers, Yves Viruses Article Phage lytic proteins are a clinically advanced class of novel enzyme-based antibiotics, so-called enzybiotics. A growing community of researchers develops phage lytic proteins with the perspective of their use as enzybiotics. A successful translation of enzybiotics to the market requires well-considered selections of phage lytic proteins in early research stages. Here, we introduce PhaLP, a database of phage lytic proteins, which serves as an open portal to facilitate the development of phage lytic proteins. PhaLP is a comprehensive, easily accessible and automatically updated database (currently 16,095 entries). Capitalizing on the rich content of PhaLP, we have mapped the high diversity of natural phage lytic proteins and conducted analyses at three levels to gain insight in their host-specific evolution. First, we provide an overview of the modular diversity. Secondly, datamining and interpretable machine learning approaches were adopted to reveal host-specific design rules for domain architectures in endolysins. Lastly, the evolution of phage lytic proteins on the protein sequence level was explored, revealing host-specific clusters. In sum, PhaLP can act as a starting point for the broad community of enzybiotic researchers, while the steadily improving evolutionary insights will serve as a natural inspiration for protein engineers. MDPI 2021-06-26 /pmc/articles/PMC8310338/ /pubmed/34206969 http://dx.doi.org/10.3390/v13071240 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Criel, Bjorn
Taelman, Steff
Van Criekinge, Wim
Stock, Michiel
Briers, Yves
PhaLP: A Database for the Study of Phage Lytic Proteins and Their Evolution
title PhaLP: A Database for the Study of Phage Lytic Proteins and Their Evolution
title_full PhaLP: A Database for the Study of Phage Lytic Proteins and Their Evolution
title_fullStr PhaLP: A Database for the Study of Phage Lytic Proteins and Their Evolution
title_full_unstemmed PhaLP: A Database for the Study of Phage Lytic Proteins and Their Evolution
title_short PhaLP: A Database for the Study of Phage Lytic Proteins and Their Evolution
title_sort phalp: a database for the study of phage lytic proteins and their evolution
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8310338/
https://www.ncbi.nlm.nih.gov/pubmed/34206969
http://dx.doi.org/10.3390/v13071240
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