DAMPD: a manually curated antimicrobial peptide database

Sundararajan, Vijayaraghava Seshadri; Gabere, Musa Nur; Pretorius, Ashley; Adam, Saleem; Christoffels, Alan; Lehvaslaiho, Minna; Archer, John; Bajic, Vladimir B.

doi:10.1093/nar/gkr1063

Cited by 98 publications

(63 citation statements)

References 53 publications

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“…Our preference for arginine over lysine for incorporation into eCAPs was based on various studies indicating stronger membrane interaction and perturbation properties of Argcompared to Lys-enriched peptide sequences (Tencza et al, 1995;Mitchell et al, 2000;Phadke et al, 2002;Kalia et al, 2003;Phadke et al, 2003;Phadke et al, 2005;Su et al, 2009). However, a survey of natural AMP sequences reveals a predominance of lysine content in diverse AMP sequences, with minimal incorporation of arginine (Tossi et al, 2000;Wang & Wang, 2004;Wang et al, 2009;Seshadri Sundararajan et al, 2012). This apparent discrepancy led us to compare directly the antimicrobial activity of a parallel series of eCAPs containing only tryptophan and either arginine or lysine as the cationic component.…”

Section: Introductionmentioning

confidence: 99%

Comparative functional properties of engineered cationic antimicrobial peptides consisting exclusively of tryptophan and either lysine or arginine

Deslouches

Hasek

Craigo

et al. 2016

Journal of Medical Microbiology

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We previously reported a series of de novo engineered cationic antibiotic peptides (eCAPs) consisting exclusively of arginine and tryptophan (WR) that display potent activity against diverse multidrug-resistant (MDR) bacterial strains. In this study, we sought to examine the influence of arginine compared to lysine on antibacterial properties by direct comparison of the WR peptides (8-18 residues) with a parallel series of engineered peptides containing only lysine and tryptophan. WR and WK series were compared for antibacterial activity by bacterial killing and growth inhibition assays and for mechanism of peptide-bacteria interactions by surface plasmon resonance and flow cytometry. Mammalian cytotoxicity was also assessed by flow cytometry, haemolytic and tetrazolium-based assays. The shortest arginine-containing peptides (8 and 10 mers) displayed a statistically significant increase in activity compared to the analogous lysinecontaining peptides. The WR and WK peptides achieved maximum antibacterial activity at the 12-mer peptide (WK12 or WR12). Further examination of antibacterial mechanisms of the optimally active 12-mer peptides using surface plasmon resonance and flow cytometry demonstrates stronger interactions with Pseudomonas aeruginosa, greater membrane permeabilizing activity, and lower inhibitory effects of divalent cations on activity and membrane permeabilization properties of WR12 compared to WK12 (P < 0.05). Importantly, WK12 and WR12 displayed similar negligible haemolytic and cytotoxic effects at peptide concentrations up to ten times the MIC or 20 times the minimum bactericidal concentration. Thus, arginine, compared to lysine, can indeed yield enhanced antibacterial activity to minimize the required length to achieve functional antimicrobial peptides.

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Section: Introductionmentioning

confidence: 99%

Comparative functional properties of engineered cationic antimicrobial peptides consisting exclusively of tryptophan and either lysine or arginine

Deslouches

Hasek

Craigo

et al. 2016

Journal of Medical Microbiology

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“…To meet the need of better databases with a broad scope, two general databases were published side by side in 2004. ANTIMIC reported more than 1700 entries [13], while a new version of ANTIMIC called DAMPD [14] contains 1232 entries. In 2004, the first version of the APD [10] reported 525 peptide entries.…”

Section: Introductionmentioning

confidence: 99%

Improved Methods for Classification, Prediction, and Design of Antimicrobial Peptides

Wang

2014

Methods in Molecular Biology

149

133

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Peptides with diverse amino acid sequences, structures and functions are essential players in biological systems. The construction of well-annotated databases not only facilitates effective information management, search and mining, but also lays the foundation for developing and testing new peptide algorithms and machines. The antimicrobial peptide database (APD) is an original construction in terms of both database design and peptide entries. The host defense antimicrobial peptides (AMPs) registered in the APD cover the five kingdoms (bacteria, protists, fungi, plants, and animals) or three domains of life (bacteria, archaea, and eukaryota). This comprehensive database (http://aps.unmc.edu/AP) provides useful information on peptide discovery timeline, nomenclature, classification, glossary, calculation tools, and statistics. The APD enables effective search, prediction, and design of peptides with antibacterial, antiviral, antifungal, antiparasitic, insecticidal, spermicidal, anticancer activities, chemotactic, immune modulation, or anti-oxidative properties. A universal classification scheme is proposed herein to unify innate immunity peptides from a variety of biological sources. As an improvement, the upgraded APD makes predictions based on the database-defined parameter space and provides a list of the sequences most similar to natural AMPs. In addition, the powerful pipeline design of the database search engine laid a solid basis for designing novel antimicrobials to combat resistant superbugs, viruses, fungi or parasites. This comprehensive AMP database is a useful tool for both research and education.

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“…AMPs are not only another class of bactericidal or bacteriostatic molecules secreted by the innate immune system, but they are also major players in host defense systems (Brown and Hancock, 2006). Thus far, well over a thousand AMPs have been identified (Seshadri Sundararajan et al, 2012). Most AMPs are capable of selectively causing disruptions in the bacterial membrane integrity (Haney et al, 2010), however, the list of possible mechanisms is growing and a peptide may have multiple molecular targets to achieve its antimicrobial activities (Nicolas, 2009; Nguyen et al, 2011a).…”

Section: Introductionmentioning

confidence: 99%

Structural perspectives on antimicrobial chemokines

Nguyen

Vogel

2012

Front. Immun.

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Chemokines are best known as signaling proteins in the immune system. Recently however, a large number of human chemokines have been shown to exert direct antimicrobial activity. This moonlighting activity appears to be related to the net high positive charge of these immune signaling proteins. Chemokines can be divided into distinct structural elements and some of these have been studied as isolated peptide fragments that can have their own antimicrobial activity. Such peptides often encompass the α-helical region found at the C-terminal end of the parent chemokines, which, similar to other antimicrobial peptides, adopt a well-defined membrane-bound amphipathic structure. Because of their relatively small size, intact chemokines can be studied effectively by NMR spectroscopy to examine their structures in solution. In addition, NMR relaxation experiments of intact chemokines can provide detailed information about the intrinsic dynamic behavior; such analyses have helped for example to understand the activity of TC-1, an antimicrobial variant of CXCL7/NAP-2. With chemokine dimerization and oligomerization influencing their functional properties, the use of NMR diffusion experiments can provide information about monomer-dimer equilibria in solution. Furthermore, NMR chemical shift perturbation experiments can be used to map out the interface between self-associating subunits. Moreover, the unusual case of XCL1/lymphotactin presents a chemokine that can interconvert between two distinct folds in solution, both of which have been elucidated. Finally, recent advances have allowed for the determination of the structures of chemokines in complex with glycosaminoglycans, a process that could interfere with their antimicrobial activity. Taken together, these studies highlight several different structural facets that contribute to the way in which chemokines exert their direct microbicidal actions.

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DAMPD: a manually curated antimicrobial peptide database

Cited by 98 publications

References 53 publications

Comparative functional properties of engineered cationic antimicrobial peptides consisting exclusively of tryptophan and either lysine or arginine

Comparative functional properties of engineered cationic antimicrobial peptides consisting exclusively of tryptophan and either lysine or arginine

Improved Methods for Classification, Prediction, and Design of Antimicrobial Peptides

Structural perspectives on antimicrobial chemokines

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