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Structural and Functional Enrichment Analyses for Antimicrobial Peptides

Whether there is any inclination between structures and functions of antimicrobial peptides (AMPs) is a mystery yet to be unraveled. AMPs have various structures associated with many different antimicrobial functions, including antibacterial, anticancer, antifungal, antiparasitic and antiviral activ...

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Autores principales: Lo, Sheng C., Xie, Zhong-Ru, Chang, Kuan Y.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7699717/
https://www.ncbi.nlm.nih.gov/pubmed/33233636
http://dx.doi.org/10.3390/ijms21228783
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author Lo, Sheng C.
Xie, Zhong-Ru
Chang, Kuan Y.
author_facet Lo, Sheng C.
Xie, Zhong-Ru
Chang, Kuan Y.
author_sort Lo, Sheng C.
collection PubMed
description Whether there is any inclination between structures and functions of antimicrobial peptides (AMPs) is a mystery yet to be unraveled. AMPs have various structures associated with many different antimicrobial functions, including antibacterial, anticancer, antifungal, antiparasitic and antiviral activities. However, none has yet reported any antimicrobial functional tendency within a specific category of protein/peptide structures nor any structural tendency of a specific antimicrobial function with respect to AMPs. Here, we examine the relationships between structures categorized by three structural classification methods (CATH, SCOP, and TM) and seven antimicrobial functions with respect to AMPs using an enrichment analysis. The results show that antifungal activities of AMPs were tightly related to the two-layer sandwich structure of CATH, the knottin fold of SCOP, and the first structural cluster of TM. The associations with knottin and TM Cluster 1 even sustained through the AMPs with a low sequence identity. Moreover, another significant mutual enrichment was observed between the third cluster of TM and anti-Gram-positive-bacterial/anti-Gram-negative-bacterial activities. The findings of the structure–function inclination further our understanding of AMPs and could help us design or discover new therapeutic potential AMPs.
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spelling pubmed-76997172020-11-29 Structural and Functional Enrichment Analyses for Antimicrobial Peptides Lo, Sheng C. Xie, Zhong-Ru Chang, Kuan Y. Int J Mol Sci Article Whether there is any inclination between structures and functions of antimicrobial peptides (AMPs) is a mystery yet to be unraveled. AMPs have various structures associated with many different antimicrobial functions, including antibacterial, anticancer, antifungal, antiparasitic and antiviral activities. However, none has yet reported any antimicrobial functional tendency within a specific category of protein/peptide structures nor any structural tendency of a specific antimicrobial function with respect to AMPs. Here, we examine the relationships between structures categorized by three structural classification methods (CATH, SCOP, and TM) and seven antimicrobial functions with respect to AMPs using an enrichment analysis. The results show that antifungal activities of AMPs were tightly related to the two-layer sandwich structure of CATH, the knottin fold of SCOP, and the first structural cluster of TM. The associations with knottin and TM Cluster 1 even sustained through the AMPs with a low sequence identity. Moreover, another significant mutual enrichment was observed between the third cluster of TM and anti-Gram-positive-bacterial/anti-Gram-negative-bacterial activities. The findings of the structure–function inclination further our understanding of AMPs and could help us design or discover new therapeutic potential AMPs. MDPI 2020-11-20 /pmc/articles/PMC7699717/ /pubmed/33233636 http://dx.doi.org/10.3390/ijms21228783 Text en © 2020 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Lo, Sheng C.
Xie, Zhong-Ru
Chang, Kuan Y.
Structural and Functional Enrichment Analyses for Antimicrobial Peptides
title Structural and Functional Enrichment Analyses for Antimicrobial Peptides
title_full Structural and Functional Enrichment Analyses for Antimicrobial Peptides
title_fullStr Structural and Functional Enrichment Analyses for Antimicrobial Peptides
title_full_unstemmed Structural and Functional Enrichment Analyses for Antimicrobial Peptides
title_short Structural and Functional Enrichment Analyses for Antimicrobial Peptides
title_sort structural and functional enrichment analyses for antimicrobial peptides
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7699717/
https://www.ncbi.nlm.nih.gov/pubmed/33233636
http://dx.doi.org/10.3390/ijms21228783
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