Dataset Information

Structural and Functional Enrichment Analyses for Antimicrobial Peptides.

ABSTRACT: 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.

SUBMITTER: Lo SC

PROVIDER: S-EPMC7699717 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Structural and Functional Enrichment Analyses for Antimicrobial Peptides.

Lo Sheng C SC Xie Zhong-Ru ZR Chang Kuan Y KY

International journal of molecular sciences 20201120 22

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 wi ...[more]

PMID: 33233636

Similar Datasets

Project description:Antimicrobial activity of many AMPs can be improved by lysine-to-arginine substitution due to a more favourable interaction of arginine guanidinium moiety with bacterial membranes. In a previous work, the structural and functional characterization of an amphipathic antimicrobial peptide named RiLK1, including lysine and arginine as the positively charged amino acids in its sequence, was reported. Specifically, RiLK1 retained its β-sheet structure under a wide range of environmental conditions (temperature, pH, and ionic strength), and exhibited bactericidal activity against Gram-positive and Gram-negative bacteria and fungal pathogens with no evidence of toxicity on mammalian cells. To further elucidate the influence of a lysine-to-arginine replacement on RiLK1 conformational properties, antimicrobial activity and peptide-liposome interaction, a new RiLK1-derivative, named RiLK3, in which the lysine is replaced with an arginine residue, was projected and characterised in comparison with its parental compound. The results evidenced that lysine-to-arginine mutation not only did not assure an improvement in the antimicrobial potency of RiLK1 in terms of bactericidal, virucidal and fungicidal activities, but rather it was completely abolished against the hepatitis A virus. Therefore, RiLK1 exhibited a wide range of antimicrobial activity like other cationic peptides, although the exact mechanisms of action are not completely understood. Moreover, tryptophan fluorescence measurements confirmed that RiLK3 bound to negatively charged lipid vesicles with an affinity lower than that of RiLK1, although no substantial differences from the structural and self-assembled point of view were evidenced. Therefore, our findings imply that antimicrobial efficacy and selectivity are affected by several complex and interrelated factors related to substitution of lysine with arginine, such as their relative proportion and position. In this context, this study could provide a better rationalisation for the optimization of antimicrobial peptide sequences, paving the way for the development of novel AMPs with broad applications.

Project description:Effects of antimicrobial peptides (AMP) added to diets on aquatic animal health and body function are influenced by multiple factors such as animal species, initial body weight, the dosage of AMP and feeding duration. However, there is limited knowledge on the relationship between these factors and the body function of aquatic animals. Here, we aimed to perform multiple meta-analyses to investigate the effects of dietary AMP on growth performance (feed conversion ratio [FCR], specific growth rate [SGR]), enzyme activity (superoxide dismutase activity [SOD], lysozyme activity [LSA]), disease resistance (cumulative survival rate [CSR], the expression of immune-related genes [GENE]) and the abundance of gut microbiota (MICRO) from a pool of empirical studies. Additionally, the dose-effect model was applied to determine the optimal AMP dose, initial body weight and feeding duration to maximize body function. To conduct the meta-analyses, we included 34 publications that estimated 705 effect sizes across 21 fish, 2 shrimp and 2 shellfish species. The results confirmed that the inclusion of AMP in the diet can significantly improve SGR, SOD, LSA, CSR and GENE and decrease FCR for aquatic animals. Interestingly, our findings implied a slight positive effect of AMP on MICRO albeit with a limited number of studies available on fish gut microbial communities. Although no significant linear or quadratic relationship was predicted by meta-regression, the dose-effect indicated that the optimal AMP doses for FCR, SGR, SOD and LSA were 707.5, 750.0, 1,050.0 and 937.5 mg/kg, respectively. Taken together, fish with an initial body weight of 30 g could be fed with a dose of 600 to 800 mg/kg for 2 mo when AMP-supplemented diets were applied in aquaculture, which can effectively improve body function and health while lowering aquafeed costs. In addition, more studies should address fish gut microbiota to delimitate the influence of dietary AMP on MICRO in the future.

Dataset Information

Structural and Functional Enrichment Analyses for Antimicrobial Peptides.

Publications

Structural and Functional Enrichment Analyses for Antimicrobial Peptides.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets