Insilico Alpha-Helical Structural Recognition of Temporin Antimicrobial Peptides and Its Interactions with Middle East Respiratory Syndrome-Coronavirus
Tóm tắt
Many antimicrobial peptides (AMPs) have multiple antimicrobial immunity effects. One such class of peptides is temporins. Temporins are the smallest (AMPs) found in nature and are highly active against gram-positive bacteria. Nowadays, there was a rapid increase in the availability of the 3D structure of proteins in PDB (protein data bank). The conserved residues and 3D structural conformations of temporins (AMPs) were still unknown. The present study explores the sequence analysis, alpha-helical structural conformations of temporins. The sequence of temporins was deracinated from APD3 database, the three-dimensional structure was constructed by homology modeling studies. The sequence analysis results show that the conserved residues among the peptide sequences, the maximum of the sequences are 70% alike to each other. The secondary structure prediction results revealed that 99% of temporin (AMPs) exhibited in alpha-helical form. The 3D structure speculated using RAMPAGE exposes the alpha-helical conformation in all temporins (AMPs). The phylogenetic analysis reveals the evolutionary relationships of temporins (AMPs), which are branched into seven clusters. As a result, we identified a list of potential temporin AMPs which docked to the antiviral protein (MERS-CoV), it shows good protein-peptide binding. This computational approach may serve as a good model for the rationale design of temporin based antibiotics.
Tài liệu tham khảo
Ahmed A, Siman-Tov G, Hall G et al (2019) Human antimicrobial peptides as therapeutics for viral infections. Viruses 11:704. https://doi.org/10.3390/v11080704
Babicki S, Arndt D, Marcu A et al (2016) Heatmapper: web-enabled heat mapping for all. Nucleic Acids Res 44:W147–W153. https://doi.org/10.1093/nar/gkw419
Bahar AA, Ren D (2013) Antimicrobial peptides. Pharmaceuticals (Basel) 6:1543–1575. https://doi.org/10.3390/ph6121543
Batoni G, Maisetta G, Brancatisano FL et al (2011) Use of antimicrobial peptides against microbial biofilms: advantages and limits. Curr Med Chem 18:256–279
Cho A (2012) Constructing phylogenetic trees using maximum likelihood. Scripps Sr Theses
Crooks GE, Hon G, Chandonia J-M, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14:1188–1190. https://doi.org/10.1101/gr.849004
Du L, Yang Y, Zhou Y et al (2017) MERS-CoV spike protein: a key target for antivirals. Expert Opin Ther Targets 21:131–143. https://doi.org/10.1080/14728222.2017.1271415
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340
Fiser A, Do RKG, Šali A (2000) Modeling of loops in protein structures. Protein Sci 9:1753–1773. https://doi.org/10.1110/ps.9.9.1753
Hancock RE, Chapple DS (1999) Peptide antibiotics. Antimicrob Agents Chemother 43:1317–1323
Hancock REW, Brown KL, Mookherjee N (2006) Host defence peptides from invertebrates—emerging antimicrobial strategies. Immunobiology 211:315–322. https://doi.org/10.1016/j.imbio.2005.10.017
Hof van t W, Veerman ECI, Helmerhorst EJ, Amerongen AVN (2001) Antimicrobial peptides: properties and applicability. Biol Chem 382:597–619. https://doi.org/10.1515/BC.2001.072
Huang Y, Huang J, Chen Y (2010a) Alpha-helical cationic antimicrobial peptides: relationships of structure and function. Protein Cell 1:143–152. https://doi.org/10.1007/s13238-010-0004-3
Huang Y, Niu B, Gao Y et al (2010b) CD-HIT suite: a web server for clustering and comparing biological sequences. Bioinformatics 26:680–682. https://doi.org/10.1093/bioinformatics/btq003
Kozakov D, Beglov D, Bohnuud T et al (2013) How good is automated protein docking? Proteins Struct Funct Bioinforma 81:2159–2166. https://doi.org/10.1002/prot.24403
Kozakov D, Hall DR, Xia B et al (2017) The ClusPro web server for protein–protein docking. Nat Protoc 12:255–278. https://doi.org/10.1038/nprot.2016.169
Kustanovich I, Shalev DE, Mikhlin M et al (2002) Structural requirements for potent versus selective cytotoxicity for antimicrobial dermaseptin S4 derivatives. J Biol Chem 277:16941–16951. https://doi.org/10.1074/jbc.M111071200
Lee DG, Kim HN, Park Y et al (2002) Design of novel analogue peptides with potent antibiotic activity based on the antimicrobial peptide, HP (2–20), derived from N-terminus of Helicobacter pylori ribosomal protein L1. Biochim Biophys Acta 1598:185–194
Letunic I, Bork P (2016) Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 44:W242–W245. https://doi.org/10.1093/nar/gkw290
Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659. https://doi.org/10.1093/bioinformatics/btl158
Lovell SC, Davis IW, Arendall WB et al (2003) Structure validation by Cα geometry: ϕ, ψ and Cβ deviation. Proteins Struct Funct Bioinforma 50:437–450. https://doi.org/10.1002/prot.10286
Malanovic N, Lohner K (2016) Antimicrobial peptides targeting Gram-positive bacteria. Pharmaceuticals 9:59. https://doi.org/10.3390/ph9030059
Marcocci ME, Amatore D, Villa S et al (2018) The amphibian antimicrobial peptide temporin b inhibits in vitro herpes simplex virus 1 infection. Antimicrob Agents Chemother 62:e02367. https://doi.org/10.1128/AAC.02367-17
Martí-Renom MA, Stuart AC, Fiser A et al (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291–325. https://doi.org/10.1146/annurev.biophys.29.1.291
Matsuzaki K (1999) Why and how are peptide-lipid interactions utilized for self-defense? Magainins and tachyplesins as archetypes. Biochim Biophys Acta 1462:1–10
Melo MN, Ferre R, Castanho MARB (2009) Antimicrobial peptides: linking partition, activity and high membrane-bound concentrations. Nat Rev Microbiol 7:245–250. https://doi.org/10.1038/nrmicro2095
Milne-Price S, Miazgowicz KL, Munster VJ (2014) The emergence of the middle east respiratory syndrome coronavirus. Pathog Dis 71:121–136. https://doi.org/10.1111/2049-632X.12166
Mustafa S, Balkhy H, Gabere M (2019) Peptide-protein interaction studies of antimicrobial peptides targeting middle east respiratory syndrome coronavirus spike protein: an in silico approach. Adv Bioinform 2019:1–16. https://doi.org/10.1155/2019/6815105
Roy M, Lebeau L, Chessa C et al (2019) Comparison of anti-viral activity of frog skin anti-microbial peptides temporin-sha and [K3]SHa to LL-37 and temporin-Tb against herpes simplex virus type 1. Viruses 11:77. https://doi.org/10.3390/v11010077
Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779–815. https://doi.org/10.1006/jmbi.1993.1626
Sharma A, Singla D, Rashid M, Raghava GP (2014) Designing of peptides with desired half-life in intestine-like environment. BMC bioinform 15(1):282. https://doi.org/10.1186/1471-2105-15-282
Sharma A, Gupta P, Kumar R, Bhardwaj A (2016) dPABBs: a novel in silico approach for predicting and designing anti-biofilm peptides. Sci Rep 6:21839. https://doi.org/10.1038/srep21839
Shen Y, Maupetit J, Derreumaux P, Tufféry P (2014) Improved PEP-FOLD approach for peptide and miniprotein structure prediction. J Chem Theory Comput 10:4745–4758. https://doi.org/10.1021/ct500592m
Skalickova S, Heger Z, Krejcova L et al (2015) Perspective of use of antiviral peptides against influenza virus. Viruses 7:5428–5442
Steinegger M, Söding J (2017) MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. https://doi.org/10.1038/nbt.3988
Steiner H, Andreu D, Merrifield RB (1988) Binding and action of cecropin and cecropin analogues: antibacterial peptides from insects. Biochim Biophys Acta 939:260–266
Tamura K, Stecher G, Peterson D et al (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. https://doi.org/10.1093/molbev/mst197
Thevenet P, Shen Y, Maupetit J et al (2012) PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Res 40:W288–W293. https://doi.org/10.1093/nar/gks419
Vajda S, Yueh C, Beglov D et al (2017) New additions to the ClusPro server motivated by CAPRI. Proteins Struct Funct Bioinform 85:435–444. https://doi.org/10.1002/prot.25219
Wang Z, Wang G (2004) APD: the antimicrobial peptide database. Nucleic Acids Res 32:590D–592. https://doi.org/10.1093/nar/gkh025
Wang G, Li X, Wang Z (2009) APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res 37:D933–D937. https://doi.org/10.1093/nar/gkn823
Wang G, Li X, Wang Z (2016) APD3: the antimicrobial peptide database as a tool for research and education. Nucleic Acids Res 44:D1087–D1093. https://doi.org/10.1093/nar/gkv1278
Webb B, Sali A (2016) Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci 86:2.9.1–2.9.37
Yeaman MR, Yount NY (2003) Mechanisms of antimicrobial peptide action and resistance. Pharmacol Rev 55:27–55. https://doi.org/10.1124/pr.55.1.2
Zasloff M (2002) Antimicrobial peptides of multicellular organisms. Nature 415:389–395. https://doi.org/10.1038/415389a
Zelezetsky I, Tossi A (2006) Alpha-helical antimicrobial peptides—using a sequence template to guide structure—activity relationship studies. Biochim Biophys Acta 1758:1436–1449. https://doi.org/10.1016/j.bbamem.2006.03.021
Zimmermann L, Stephens A, Nam S-Z et al (2018) A completely reimplemented MPI bioinformatics toolkit with a new hhpred server at its core. J Mol Biol 430:2237–2243. https://doi.org/10.1016/J.JMB.2017.12.007