Abstract
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 antioxidative 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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Zasloff M (2002) Antimicrobial peptides of multicellullar organisms. Nature 415:359–365
Lehrer RI (2007) Multispecific myeloid defensins. Curr Opin Hematol 14:16–21
Boman HG (2003) Antibacterial peptides: basic facts and emerging concepts. J Intern Med 254:197–215
Hancock RE, Sahl HG (2006) Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies. Nat Biotechnol 24:1551–1557
Lai Y, Gallo RL (2009) AMPed up immunity: how antimicrobial peptides have multiple roles in immune defense. Trends Immunol 30:131–141
Wang G (ed) (2010) Antimicrobial peptides: discovery, design and novel therapeutic strategies. CABI, Oxfordshire, UK
Steiner H, Hultmark D, Engström Å, Bennich H, Boman HG (1981) Sequence and specificity of two antibacterial proteins involved in insect immunity. Nature 292:246–248
Selsted ME, Harwig SS, Ganz T, Schilling JW, Lehrer RI (1985) Primary structures of three human neutrophil defensins. J Clin Invest 76:1436–1439
Zasloff M (1987) Magainins, a class of antimicrobial peptides from Xenopus skin: isolation, characterization of two active forms, and partial cDNA sequence of a precursor. Proc Natl Acad Sci U S A 84:5449–5453
Wang Z, Wang G (2004) APD: the antimicrobial peptide database. Nucleic Acids Res 32:D590–D592
Wang G, Li X, Wang Z (2009) The updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res 37:D933–D937
Tossi A, Sandri L (2002) Molecular diversity in gene-coded, cationic antimicrobial polypeptides. Curr Pharm Des 8:743–761
Brahmachary M, Krishnan SP, Koh JL, Khan AM, Seah SH, Tan TW, Brusic V, Bajic VB (2004) ANTIMIC: a database of antimicrobial sequences. Nucleic Acids Res 32:D586–D589
Seshadri Sundararajan V, Gabere MN, Pretorius A, Adam S, Christoffels A, Lehväslaiho M, Archer JA, Bajic VB (2012) DAMPD: a manually curated antimicrobial peptide database. Nucleic Acids Res 40:D1108–D1112
Gueguen Y, Garnier J, Robert L, Lefranc MP, Mougenot I, de Lorgeril J, Janech M, Gross PS, Warr GW, Cuthbertson B, Barracco MA, Bulet P, Aumelas A, Yang Y, Bo D, Xiang J, Tassanakajon A, Piquemal D, Bachère E (2006) PenBase, the shrimp antimicrobial peptide penaeidin database: sequence-based classification and recommended nomenclature. Dev Comp Immunol 30:283–288
Seebah S, Suresh A, Zhou S, Choong YH, Chua H, Chuon D, Beuerman R, Verma C (2007) Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides. Nucleic Acids Res 35:D265–D268
Hammami R, Zouhir A, Ben Hamida J, Fliss I (2007) BACTIBASE: a new web-accessible database for bacteriocin characterization. BMC Microbiol 7:89
Wang CK, Kaas Q, Chiche L, Craik DJ (2008) Cybase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering. Nucleic Acids Res 36:D206–D210
Hammami R, Ben Hamida J, Vergoten G, Fliss I (2009) PhytAMP: a database dedicated to antimicrobial plant peptides. Nucleic Acids Res 37:D963–D968
Li Y, Chen Z (2008) RAPD: a database of recombinantly-produced antimicrobial peptides. FEMS Microbiol Lett 289:126–129
de Jong A, van Heel AJ, Kok J, Kuipers OP (2010) BAGEL2: mining for bacteriocins in genomic data. Nucleic Acids Res 38:W647–W651
Novković M, Simunić J, Bojović V, Tossi A, Juretić D (2012) DADP: the database of anuran defense peptides. Bioinformatics 28:1406–1407
Li J, Qu X, He X, Duan L, Wu G, Bi D, Deng Z, Liu W, Ou HY (2012) ThioFinder: a web-based tool for the identification of thiopeptide gene clusters in DNA sequences. PLoS One 7:e45878
Fjell CD, Hancock RE, Cherkasov A (2007) AMPer: a database and an automated discovery tool for antimicrobial peptides. Bioinformatics 23:1148–1155
Wade D, Englund J (2002) Synthetic antibiotic peptides database. Protein Pept Lett 9:53–57
Whitmore L, Wallace BA (2004) The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols. Nucleic Acids Res 32:D593–D594
Wu H, Lu H, Huang J, Li G, Huang Q (2012) EnzyBase: a novel database for enzybiotic studies. BMC Microbiol 12:54
Theolier J, Fliss I, Jean J, Hammami R (2013) MilkAMP: a comprehensive database of antimicrobial peptides of dairy origin. Dairy Sci Technol 94:181–193
Thomas S, Karnik S, Barai RS, Jayaraman VK, Idicula-Thomas S (2010) CAMP: a useful resource for research on antimicrobial peptides. Nucleic Acids Res 38:D774–D780
Piotto SP, Sessa L, Concilio S, Iannelli P (2012) YADAMP: yet another database of antimicrobial peptides. Int J Antimicrob Agents 39:346–351
Zhao X, Wu H, Lu H, Li G, Huang Q (2013) LAMP: a database linking antimicrobial peptides. PLoS One 8:e66557
Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O’Donovan C, Redaschi N, Suzek B (2006) The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 34:D187–D191
Rose PW, Bi C, Bluhm WF, Christie CH, Dimitropoulos D, Dutta S, Green RK, Goodsell DS, Prlic A, Quesada M, Quinn GB, Ramos AG, Westbrook JD, Young J, Zardecki C, Berman HM, Bourne PE (2013) The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res 41:D475–D482
Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA (2002) Database resources of the National Center for Biotechnology Information: 2002 update. Nucleic Acids Res 30:13–16
Whittaker RH (1969) New concepts of kingdoms of organisms. Science 163:150–160
Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74:5088–5090
Wang G (2012) Chemical modifications of natural antimicrobial peptides and strategies for peptide engineering. Curr Biotechnol 1:72–79
Epand RM, Vogel HJ (1999) Diversity of antimicrobial peptides and their mechanisms of action. Biochim Biophys Acta 1462:11–28
Klaenhammer TR (1993) Genetics of bacteriocins produced by lactic acid bacteria. FEMS Microbiol Rev 12:39–85
Duquesne S, Destoumieux-Garzón D, Peduzzi J, Rebuffat S (2007) Microcins, gene-encoded antibacterial peptides from enterobacteria. Nat Prod Rep 24:708–734
Egorov TA, Odintsova TI, Pukhalsky VA, Grishin EV (2005) Diversity of wheat anti-microbial peptides. Peptides 26:2064–2073
Bulet P, Stocklin R (2005) Insect antimicrobial peptides: structures, properties and gene regulation. Protein Pept Lett 12:3–11
Conlon JM (2008) Reflections on a systematic nomenclature for antimicrobial peptides from the skins of frogs of the family Ranidae. Peptides 29:1815–1819
Lata S, Sharma BK, Raghava GP (2007) Analysis and prediction of antibacterial peptides. BMC Bioinformatics 8:263
Xiao X, Wang P, Lin WZ, Jia JH, Chou KC (2013) iAMP-2L: a two-level multi-label classifier for identifying antimicrobial peptides and their functional types. Anal Biochem 436:168–177
Wang G (2013) Database-guided discovery of potent peptides to combat HIV-1 or superbugs. Pharmaceuticals 6:728–758
O’Shea EF, O’Connor PM, O’Sullivan O, Cotter PD, Ross RP, Hill C (2013) Bactofencin a, a new type of cationic bacteriocin with unusual immunity. MBio 4:e00498–13
Menousek J, Mishra B, Hanke ML, Heim CE, Kielian T, Wang G (2012) Database screening and in vivo efficacy of antimicrobial peptides against methicillin-resistant Staphylococcus aureus USA300. Int J Antimicrob Agents 39:402–406
Wang G, Watson KM, Peterkofsky A, Buckheit RW Jr (2010) Identification of novel human immunodeficiency virus type 1 inhibitory peptides based on the antimicrobial peptide database. Antimicrob Agents Chemother 54:1343–1346
Loose C, Jensen K, Rigoutsos I, Stephanopoulos G (2006) A linguistic model for the rational design of antimicrobial peptides. Nature 443:867–869
Lam KS, Salmon SE, Hersh EM, Hruby VJ, Kazmierski WM, Knapp RJ (1991) A new type of synthetic peptide library for identifying ligand-binding activity. Nature 354:82–84
Cherkasov A, Hilpert K, Jenssen H, Fjell CD, Waldbrook M, Mullaly SC, Volkmer R, Hancock RE (2008) Use of artificial intelligence in the design of small peptide antibiotics effective against a broad spectrum of highly antibiotic-resistant superbugs. ACS Chem Biol 4:65–74
Mishra B, Wang G (2012) The importance of amino acid composition in natural AMPs: an evolutional, structural, and functional perspective. Front Immunol 3:221
Mishra B, Wang G (2012) Ab initio design of potent anti-MRSA peptides based on database filtering technology. J Am Chem Soc 134:12426–12429
Wang G (2008) Structures of human host defense cathelicidin LL-37 and its smallest antimicrobial peptide KR-12 in lipid micelles. J Biol Chem 283:32637–32643
Saether O, Craik DJ, Campbell ID, Sletten K, Juul J, Norman DG (1995) Elucidation of the primary and three-dimensional structure of the uterotonic polypeptide kalata B1. Biochemistry 34:4147–4158
Bauer F, Schweimer K, Klüver E, Conejo-Garcia JR, Forssmann WG, Rösch P, Adermann K, Sticht H (2001) Structure determination of human and murine beta-defensins reveals structural conservation in the absence of significant sequence similarity. Protein Sci 10:2470–2479
Rozek A, Friedrich CL, Hancock RE (2000) Structure of the bovine antimicrobial peptide indolicidin bound to dodecylphosphocholine and sodium dodecyl sulfate micelles. Biochemistry 39:15765–15774
Acknowledgements
This study was supported by grants from the NIH (1R01AI105147-01A1, 1R56AI105147-01) and the State of Nebraska. The author thanks Zhe Wang for programming the original database and Biswajit Mishra for conducting the ab initio design of novel antimicrobials.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Wang, G. (2015). Improved Methods for Classification, Prediction, and Design of Antimicrobial Peptides. In: Zhou, P., Huang, J. (eds) Computational Peptidology. Methods in Molecular Biology, vol 1268. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2285-7_3
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2285-7_3
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2284-0
Online ISBN: 978-1-4939-2285-7
eBook Packages: Springer Protocols