AMPA: an automated web server for prediction of protein antimicrobial regions

Torrent, M. C.; Tommaso, Paolo Di; Pulido, David; Nogués, M. Victòria; Notredame, Cédric; Boix, Ester; Andreu, David

doi:10.1093/bioinformatics/btr604

Cited by 137 publications

(116 citation statements)

References 13 publications

Supporting

Mentioning

114

Contrasting

Order By: Relevance

“…These properties facilitate their binding to negatively charged microbial cell membranes and result in bacterial cell death by a so-called carpet mechanism (Yeaman and Yount 2003). Continuous stretches of residues in each AMP candidate showing antimicrobial activity were predicted using AMPA (Torrent et al 2012).…”

Section: Screening Based On Physicochemical Propertiesmentioning

confidence: 99%

Antimicrobial peptides in the centipede Scolopendra subspinipes mutilans

Yoo

Lee

Shin

et al. 2014

Funct Integr Genomics

View full text Add to dashboard Cite

The centipede Scolopendra subspinipes mutilans is an environmentally beneficial and medically important arthropod species. Although this species is increasingly applied as a reliable source of new antimicrobial peptides, the transcriptome of this species is a prerequisite for more rational selection of antimicrobial peptides. In this report, we isolated total RNA from the whole body of adult centipedes, S. subspinipes mutilans, that were nonimmunized and immunized against Escherichia coli, and we generated a total of 77,063 pooled contigs and singletons using high-throughput sequencing. To screen putative antimicrobial peptides, in silico analyses of the S. subspinipes mutilans transcriptome were performed based on the physicochemical evidence of length, charge, isoelectric point, and in vitro and in vivo aggregation scores together with the existence of continuous antimicrobial peptide stretches. Moreover, we excluded some transcripts that showed similarity with both previously known antimicrobial peptides and the human proteome, had a proteolytic cleavage site, and had downregulated expression compared with the nonimmunized sample. As a result, we selected 17 transcripts and tested their antimicrobial activity with a radial diffusion assay. Among them, ten synthetic peptides experimentally showed antimicrobial activity against microbes and no toxicity to mouse erythrocytes. Our results provide not only a useful set of antimicrobial peptide candidates and an efficient strategy for novel antimicrobial peptide development but also the transcriptome data of a big centipede as a valuable resource.

show abstract

Section: Screening Based On Physicochemical Propertiesmentioning

confidence: 99%

Antimicrobial peptides in the centipede Scolopendra subspinipes mutilans

Yoo

Lee

Shin

et al. 2014

Funct Integr Genomics

View full text Add to dashboard Cite

show abstract

“…This has resulted in the creation of a structure-selectivity database (AMPad) of frog-derived, helical AMPs. The AMPA web application (http://tcoffee.crg.cat/apps/ampa) (Torrent et al 2011) was constructed for assessing the antimicrobial domains of proteins, based on an antimicrobial propensity scale for each amino acid (related to the IC 50 values for all amino acid replacements in the AMP bactenecin 2A) and identifying the regions (412 amino acids in length) located below the threshold, which are considered putative antimicrobial domains. There is also a search method (Fernandes et al 2009) for sequence similarity and physico-chemical properties followed by a fuzzy inference system in order to find AMPs that are more appropriate for certain target domains.…”

Section: Discovery and Classification Of Ampsmentioning

confidence: 99%

New trends in peptide-based anti-biofilm strategies: a review of recent achievements and bioinformatic approaches

2012

View full text Add to dashboard Cite

Antimicrobial peptides (AMPs) have a broad spectrum of activity and unspecific mechanisms of action. Therefore, they are seen as valid alternatives to overcome clinically relevant biofilms and reduce the chance of acquired resistance. This paper reviews AMPs and anti-biofilm AMP-based strategies and discusses ongoing and future work. Recent studies report successful AMP-based prophylactic and therapeutic strategies, several databases catalogue AMP information and analysis tools, and novel bioinformatics tools are supporting AMP discovery and design. However, most AMP studies are performed with planktonic cultures, and most studies on sessile cells test AMPs on growing rather than mature biofilms. Promising preliminary synergistic studies have to be consubstantiated and the study of functionalized coatings with AMPs must be further explored. Standardized operating protocols, to enforce the repeatability and reproducibility of AMP anti-biofilm tests, and automated means of screening and processing the ever-expanding literature are still missing.

show abstract

“…Exposure of a hydrophobic patch at the protein's N terminus induces the formation of amyloid-like protein aggregates (29) that can drive the cell agglutination process (27). The essential sequence requirements defining the protein's key active region were then outlined by a structure-based algorithm to identify new AMPs (30).…”

mentioning

confidence: 99%

A Novel RNase 3/ECP Peptide for Pseudomonas aeruginosa Biofilm Eradication That Combines Antimicrobial, Lipopolysaccharide Binding, and Cell-Agglutinating Activities

Pulido

Prats-Ejarque

Villalba

et al. 2016

Antimicrob Agents Chemother

Self Cite

View full text Add to dashboard Cite

bEradication of established biofilm communities of pathogenic Gram-negative species is one of the pending challenges for the development of new antimicrobial agents. In particular, Pseudomonas aeruginosa is one of the main dreaded nosocomial species, with a tendency to form organized microbial communities that offer an enhanced resistance to conventional antibiotics. We describe here an engineered antimicrobial peptide (AMP) which combines bactericidal activity with a high bacterial cell agglutination and lipopolysaccharide (LPS) affinity. The RN3(5-17P22-36) peptide is a 30-mer derived from the eosinophil cationic protein (ECP), a host defense RNase secreted by eosinophils upon infection, with a wide spectrum of antipathogen activity. The protein displays high biofilm eradication activity that is not dependent on its RNase catalytic activity, as evaluated by using an active site-defective mutant. On the other hand, the peptide encompasses both the LPS-binding and aggregation-prone regions from the parental protein, which provide the appropriate structural features for the peptide's attachment to the bacterial exopolysaccharide layer and further improved removal of established biofilms. Moreover, the peptide's high cationicity and amphipathicity promote the cell membrane destabilization action. The results are also compared side by side with other reported AMPs effective against either planktonic and/or biofilm forms of Pseudomonas aeruginosa strain PAO1. The ECP and its derived peptide are unique in combining high bactericidal potency and cell agglutination activity, achieving effective biofilm eradication at a low micromolar range. We conclude that the designed RN3(5-17P22-36) peptide is a promising lead candidate against Gram-negative biofilms.

show abstract

AMPA: an automated web server for prediction of protein antimicrobial regions

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 137 publications

References 13 publications

Antimicrobial peptides in the centipede Scolopendra subspinipes mutilans

Antimicrobial peptides in the centipede Scolopendra subspinipes mutilans

New trends in peptide-based anti-biofilm strategies: a review of recent achievements and bioinformatic approaches

A Novel RNase 3/ECP Peptide for Pseudomonas aeruginosa Biofilm Eradication That Combines Antimicrobial, Lipopolysaccharide Binding, and Cell-Agglutinating Activities

Contact Info

Product

Resources

About