Abstract
Antimicrobial peptides (AMPs) are indivisible part of the innate immune system in invertebrates. AMPs have been proven to have crucial role with a wide range of biological activities, mainly with immunomodulatory and broad spectrum of antimicrobial activity against various pathogens. The unique and salient features of the AMPs show its exceptional nature of therapeutic activity and serves as an alternative agent for conventional antibiotics. The search for potential AMPs persist, as the emergence of multiple drug resistant bacterial strains has been spreading in higher number. Here, the putative antimicrobial peptide sequences were identified from 19,915 sequences of prawn transcriptome and analyzed with various in silico tools such as EXPASY, AMPA, and helical wheel projection and so on. The characteristic antimicrobial properties have been determined for 660 putative AMPs with above mentioned tools. We have demonstrated an efficient bioinformatics approach to derive and analyze the AMPs from the transcriptome data of Macrobrachium rosenbergii. Even though, 660 peptide regions were identified among those five peptide sequences were demonstrated comprehensively with each characteristic property contributes the antimicrobial activity. In this study, we have proposed a rapid and successful protocol that would help to predict AMP in sequential procedure using various in silico methods. Also, we have shown a distinctive method to shortlist the AMPs based on their various physico-chemical properties. Until now, no sequential protocol has been developed to identify and characterize the AMPs from protein database.
References
Arockiaraj J, Kumaresan V, Bhatt P, Palanisamy R, Gnanam AJ, Pasupuleti M, Kasi M, Chaurasia MK (2014) A novel single-domain peptide, anti-LPS factor from prawn: synthesis of peptide, antimicrobial properties and complete molecular characterization. Peptides 53:79–88
Arockiaraj J, Chaurasia MK, Kumaresan V, Palanisamy R, Harikrishnan R, Pasupuleti M, Kasi M (2015) Macrobrachium rosenbergii mannose binding lectin: synthesis of MrMBL-N20 and MrMBL-C16 peptides and their antimicrobial characterization, bioinformatics and relative gene expression analysis. Fish Shellfish Immunol 43(2):364–374
Bahar AA, Ren D (2013) Antimicrobial peptides. Pharmaceuticals 6(12):1543–1575
Cameselle JC, Ribeiro JM, Sillero A (1986) Derivation and use of a formula to calculate the net charge of acid-base compounds: its application to amino acids, proteins and nucleotides. Biochem Educ 14(3):131–136
Chan DI, Prenner EJ, Vogel HJ (2006) Tryptophan-and arginine-rich antimicrobial peptides: structures and mechanisms of action. Biochim Biophys Acta 1758(9):1184–1202
Chaurasia MK, Palanisamy R, Bhatt P, Kumaresan V, Gnanam AJ, Pasupuleti M, Kasi M, Harikrishnan R, Arockiaraj J (2015) A prawn core histone 4: derivation of N-and C-terminal peptides and their antimicrobial properties, molecular characterization and mRNA transcription. Microbiol Res 170:78–86
Chaurasia MK, Nizam F, Ravichandran G, Arasu MV, Al-Dhabi NA, Arshad A, Elumalai P, Arockiaraj J (2016) Molecular importance of prawn large heat shock proteins 60, 70 and 90. Fish Shellfish Immunol 48:228–238
Chen Y, Guarnieri MT, Vasil AI, Vasil ML, Mant CT, Hodges RS (2007) Role of peptide hydrophobicity in the mechanism of action of α-helical antimicrobial peptides. Antimicrob Agents Chemother 51(4):1398–1406
Destoumieux D, Bulet P, Loew D, Van Dorsselaer A, Rodriguez J, Bachère E (1997) Penaeidins, a new family of antimicrobial peptides isolated from the shrimp Penaeus vannamei (decapoda). J Biol Chem 272(45):28398–28406
Farook M, Raj NS, Madan N, Vimal S, Majeed SA, Taju G, Rajkumar T, Santhoshkumar S, Sivakumar S, Hameed AS (2014) Immunomodulatory effect of recombinant Macrobrachium rosenbergii nodavirus capsid protein (r-MCP) against white tail disease of giant freshwater prawn, Macrobrachium rosenbergii (de man, 1879). Aquaculture 433:395–403
Fernandez DI, Lee TH, Sani MA, Aguilar MI, Separovic F (2013) Proline facilitates membrane insertion of the antimicrobial peptide maculatin 1.1 via surface indentation and subsequent lipid disordering. Biophys J 104(7):1495–1507
Grimsley GR, Scholtz JM, Pace CN (2009) A summary of the measured pK values of the ionizable groups in folded proteins. Protein Sci 18(1):247–251
Hancock RE (1997) Peptide antibiotics. Lancet 349(9049):418–422
Hancock RE, Lehrer R (1998) Cationic peptides: a new source of antibiotics. Trends Biotechnol 16(2):82–88
Jiang Z, Kullberg BJ, Van Der Lee H, Vasil AI, Hale JD, Mant CT, Hancock RE, Vasil ML, Netea MG, Hodges RS (2008a) Effects of hydrophobicity on the antifungal activity of α-helical antimicrobial peptides. Chem Biol Drug Des 72(6):483–495
Jiang Z, Vasil AI, Hale JD, Hancock RE, Vasil ML, Hodges RS (2008b) Effects of net charge and the number of positively charged residues on the biological activity of amphipathic α-helical cationic antimicrobial peptides. Pept Sci 90(3):369–383
Kastritis PL, Bonvin AM (2013) On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface 10(79):20120835
Malmsten M, Kasetty G, Pasupuleti M, Alenfall J, Schmidtchen A (2011) Highly selective end-tagged antimicrobial peptides derived from PRELP. PLoS One 6(1):16400
Park SC, Park Y, Hahm KS (2011) The role of antimicrobial peptides in preventing multidrug-resistant bacterial infections and biofilm formation. Int J Mol Sci 12(9):5971–5992
Pushpanathan M, Gunasekaran P, Rajendhran J (2013) Antimicrobial peptides: versatile biological properties. Int J Pept 2013:675391
Radek K, Gallo R (2007) Antimicrobial peptides: natural effectors of the innate immune system. Semin Immunopathol 29(1):27–43
Sato H, Feix JB (2006) Peptide–membrane interactions and mechanisms of membrane destruction by amphipathic α-helical antimicrobial peptides. Biochim Biophys Acta 1758(9):1245–1256
Schmidt NW, Wong GC (2013) Antimicrobial peptides and induced membrane curvature: geometry, coordination chemistry, and molecular engineering. Curr Opin Solid State Mater Sci 17(4):151–163
Schnapp D, Kemp GD, Smith VJ (1996) Purification and characterization of a proline-rich antibacterial peptide, with sequence similarity to bactenecin-7, from the haemocytes of the shore crab, Carcinus maenas. Eur J Biochem 240(3):532–539
Smith VJ, Fernandes JM, Kemp GD, Hauton C (2008) Crustins: enigmatic WAP domain-containing antibacterial proteins from crustaceans. Dev Comp Immunol 32(7):758–772
Sperstad SV, Haug T, Paulsen V, Rode TM, Strandskog G, Solem ST, Styrvold OB, Stensvåg K (2009) Characterization of crustins from the hemocytes of the spider crab, Hyas araneus, and the red king crab, Paralithodes camtschaticus. Dev Comp Immunol 33(4):583–591
Torrent M, Nogués VM, Boix E (2009) A theoretical approach to spot active regions in antimicrobial proteins. BMC Bioinform 10(1):1
Wang G (2010) Database-aided prediction and design of novel antimicrobial peptides. Antimicrobial peptides: discovery, design and novel therapeutic strategies. Eppley Institute, University of Nebraska Medical Center, Omaha, pp 72–81
Yin LM, Edwards MA, Li J, Yip CM, Deber CM (2012) Roles of hydrophobicity and charge distribution of cationic antimicrobial peptides in peptide–membrane interactions. J Biol Chem 287(10):7738–7745
Zasloff M (2002) Antimicrobial peptides of multicellular organisms. Nature 415(6870):389–395
Zasloff M, Martin B, Chen HC (1988) Antimicrobial activity of synthetic magainin peptides and several analogues. Proc Nat Acad Sci 85(3):910–913
Acknowledgments
The authors extend their sincere appreciation to the Deanship of Scientific Research at King Saud University for its funding through the Prolific Research Group (PRG-1437-28).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
Gayathri Ravichandran, Venkatesh Kumaresan, Prasanth Bhatt, Mariadhas Valan Arasu, Naif Abdullah Al-Dhabi and Jesu Arockiaraj declare that they have no conflict of interest.
Human and Animal Rights
This article does not contain any studies with human participants or animals performed by any of the authors.
Rights and permissions
About this article
Cite this article
Ravichandran, G., Kumaresan, V., Bhatt, P. et al. A Cumulative Strategy to Predict and Characterize Antimicrobial Peptides (AMPs) from Protein Database. Int J Pept Res Ther 23, 281–290 (2017). https://doi.org/10.1007/s10989-016-9559-z
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10989-016-9559-z