CAMP: Collection of sequences and structures of antimicrobial peptides

Waghu, Faiza Hanif; Gopi, Lijin; Barai, Ram Shankar; Ramteke, Pranay; Nizami, Bilal; Idicula‐Thomas, Susan

doi:10.1093/nar/gkt1157

Cited by 238 publications

(168 citation statements)

References 29 publications

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“…The major classes of peptides are (i) anionic, (ii) cationic, (iii) cationic and amphipathic, and (iv) ␣-helical (4,5). More than 5,000 AMPs have been identified from a wide range of organisms, including bacteria, plants, invertebrates, and vertebrates, through biochemical characterization of purified peptides or through in silico analyses of peptides based on gene sequence or on structural and/or physicochemical similarities to known AMPs (6)(7)(8)(9)(10)(11). Rational combinatorial peptide design, coupled with high-throughput screening, has also been employed to design novel synthetic AMPs (12).…”

Section: Importancementioning

confidence: 99%

Comparative Analysis of the Antimicrobial Activities of Plant Defensin-Like and Ultrashort Peptides against Food-Spoiling Bacteria

Kraszewska

Beckett

James

et al. 2016

Appl Environ Microbiol

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Antimicrobial peptides offer potential as novel therapeutics to combat food spoilage and poisoning caused by pathogenic and nonpathogenic bacteria. Our previous studies identified the peptide human beta-defensin 3 (HBD3) as a potent antimicrobial agent against a wide range of beer-spoiling bacteria. Thus, HBD3 is an excellent candidate for development as an additive to prevent food and beverage spoilage. To expand the repertoire of peptides with antimicrobial activity against bacteria associated with food spoilage and/or food poisoning, we carried out an in silico discovery pipeline to identify peptides with structure and activity similar to those of HBD3, focusing on peptides of plant origin. Using a standardized assay, we compared the antimicrobial activities of nine defensin-like plant peptides to the activity of HBD3. Only two of the peptides, fabatin-2 and Cp-thionin-2, displayed antimicrobial activity; however, the peptides differed from HBD3 in being sensitive to salt and were thermostable. We also compared the activities of several ultrashort peptides to that of HBD3. One of the peptides, the synthetic tetrapeptide O3TR, displayed biphasic antimicrobial activity but had a narrower host range than HBD3. Finally, to determine if the peptides might act in concert to improve antimicrobial activity, we compared the activities of the peptides in pairwise combinations. The plant defensin-like peptides fabatin-2 and Cp-thionin-2 displayed a synergistic effect with HBD3, while O3TR was antagonistic. Thus, some plant defensin-like peptides are effective antimicrobials and may act in concert with HBD3 to control bacteria associated with food spoilage and food poisoning. IMPORTANCEFood spoilage and food poisoning caused by bacteria can have major health and economic implications for human society. With the rise in resistance to conventional antibiotics, there is a need to identify new antimicrobials to combat these outbreaks in our food supply. Here we screened plant peptide databases to identify peptides that share structural similarity with the human defensin peptide HBD3, which has known antimicrobial activity against food-spoiling bacteria. We show that two of the plant peptides display antimicrobial activity against bacteria associated with food spoilage. When combined with HBD3, the peptides are highly effective. We also analyzed the activity of an easily made ultrashort synthetic peptide, O3TR. We show that this small peptide also displays antimicrobial activity against food-spoiling bacteria but is not as effective as HBD3 or the plant peptides. The plant peptides identified are good candidates for development as natural additives to prevent food spoilage.A ntimicrobial peptides (AMPs) are short oligopeptides ranging from 4 to 100 amino acids that display antimicrobial activity against a broad range of pathogens, including Gram-positive and -negative bacteria, fungi, viruses, protists, parasites, and even insects (1). AMPs form part of the innate immune response, acting as a first line of defense and...

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Section: Importancementioning

confidence: 99%

Comparative Analysis of the Antimicrobial Activities of Plant Defensin-Like and Ultrashort Peptides against Food-Spoiling Bacteria

Kraszewska

Beckett

James

et al. 2016

Appl Environ Microbiol

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“…Amino acid sequences of histone H2A were submitted to CAMP server [18] and each fragmented into 20 amino acid segments. All fragments were predicted with 4 algorithm provided by the server.…”

Section: Antimicrobial Peptides Predictionmentioning

confidence: 99%

“…Prediction of fragment peptides that have potential as antimicrobial peptides (AMPs) was conducted by submitting the histone H2A amino acid sequence to collection of antimicrobial peptides release 2 (CAMP R2) server [18]. A total 130 amino acids were used as a template and resulted in 111 fragment peptides with 20 amino acids each.…”

Section: Prediction Of Potent Antimicrobial Peptides Derived From Hismentioning

confidence: 99%

Analysis and Prediction of some Histone-derived Antimicrobial Peptides from Toads Duttaphrynus melanostictus and Phyrinoidis asper

Dailami

Artika

Kusrini

2016

J. Pure App. Chem. Res.

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Antimicrobial peptides in skin secretions of toads are promising methods to combat a wide spectrum of bacteria. Histone H2A is a type of DNA-binding protein that acts as a precursor for several antimicrobial peptides. In toads (family Bufonidae) buforin I and buforin II are examples of antimicrobial peptides that derived from histone H2A. This study investigated the genetic diversity and phylogenetic analysis and in silico prediction of antimicrobial peptides derived from histone H2A of Duttaphrynus melanostictus and Phyrinoidis asper, which were collected from Bogor Agricultural University's campus area. A new set of primers (Buf_fwd and Buf_rev) were designed by using PrimerBLAST, to amplify 393 nucleotides of the histone H2A gene that codes 131 amino acids. Haplotype diversity of both species are very low. Phylogenetic analysis shows the sample D. melanostictus and P. asper are separated to each other in two different clades. Several short predicted peptides from histone H2A show a potential as an antimicrobial peptides based on in silico prediction. Psychochemical characteristics and 3D structure of potent antimicrobial peptides are described.

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“…Then, the peptides were tested in silico for antimicrobial activity at the CAMP database (http://www.camp.bicnirrh.res.in/). The antimicrobial prediction tools available at the CAMP database were used to determine the antimicrobial potential of the peptides [24]. For prediction, four multivariate methods were used such as Support Vector Machines (SVM), Random Forest (RF), Artificial Neural Network (ANN) and Discriminant Analysis (DA) [24].…”

Section: Identification Of Potential Antimicrobial Peptidesmentioning

confidence: 99%

MB1533 is a Defensin-Like Antimicrobial Peptide from the Intracellular Meristem Endophyte of Scots Pine Methylobacterium extorquens DSM13060

MV¹,

Andersen²

2015

J Microb Biochem Technol

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CAMP: Collection of sequences and structures of antimicrobial peptides

Cited by 238 publications

References 29 publications

Comparative Analysis of the Antimicrobial Activities of Plant Defensin-Like and Ultrashort Peptides against Food-Spoiling Bacteria

Comparative Analysis of the Antimicrobial Activities of Plant Defensin-Like and Ultrashort Peptides against Food-Spoiling Bacteria

Analysis and Prediction of some Histone-derived Antimicrobial Peptides from Toads Duttaphrynus melanostictus and Phyrinoidis asper

MB1533 is a Defensin-Like Antimicrobial Peptide from the Intracellular Meristem Endophyte of Scots Pine Methylobacterium extorquens DSM13060

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