Advertisement

European Biophysics Journal

, Volume 48, Issue 8, pp 701–710 | Cite as

Insights into conformation and membrane interactions of the acyclic and dicarba-bridged brevinin-1BYa antimicrobial peptides

  • Patrick Brendan Timmons
  • Donal O’Flynn
  • J. Michael Conlon
  • Chandralal M. HewageEmail author
Original Article
  • 107 Downloads

Abstract

Brevinin-1BYa is a 24-amino acid residue host-defense peptide, first isolated from skin secretions of the foothill yellow-legged frog Rana boylii. The peptide is of interest, as it shows broad-spectrum antimicrobial activity, and is particularly effective against opportunistic yeast pathogens. Its potential for clinical use, however, is hindered by its latent haemolytic activity. The structures of two analogues, the less haemolytic [C18S,C24S]brevinin-1BYa and the more potent cis-dicarba-brevinin-1BYa, were investigated in various solution and membrane-mimicking environments by \({}^{1}\hbox {H-NMR}\) spectroscopy and molecular modelling techniques. Neither peptide possesses a secondary structure in aqueous solution. In both the membrane-mimicking sodium dodecyl sulphate micelles and 33% 2,2,2-trifluoroethanol (\(\hbox {TFE-d}_{3})\hbox {-H}_{2}\hbox {O}\) solvent mixture, the peptides’ structures are characterised by two \(\upalpha\)-helices connected by a flexible hinge located at the \(\hbox {Gly}^{13}/\hbox {Pro}^{14}\) residues. With the aid of molecular dynamics simulations and paramagnetic probes, it was determined that the peptides’ helical segments lie parallel to the micellar surface, with their hydrophobic residues facing towards the micelle core and the hydrophilic residues pointing outwards, suggesting that both peptides exert their biological activity by a non-pore-forming mechanism. Unlike that of the dicarba analogue, the C-terminus of the acyclic peptide is only weakly associated with the micellar surface and is in direct contact with the surrounding aqueous solvent.

Keywords

NMR Antimicrobial peptide Brevinin-1 Molecular modelling 

Notes

Acknowledgements

We are grateful to University College Dublin for Research Scholarship to PBT and DOF. Authors would like to acknowledge the funding from Science Foundation Ireland for the NMR spectrometer upgrade. The authors also wish to acknowledge the DJEI/DES/SFI/HEA Irish Centre for High-End Computing (ICHEC) for the provision of computational facilities and support. Structural coordinates and chemical shifts were deposited in the PDB at RCSB (codes in Table 1).

Supplementary material

249_2019_1395_MOESM1_ESM.pdf (107 kb)
Supplementary material 1 (pdf 106 KB)

References

  1. Bax A, Davis DG (1969) MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy. J Magn Reson (1985) 65:355–360.  https://doi.org/10.1016/0022-2364(85)90018-6 CrossRefGoogle Scholar
  2. Benetti S, Timmons PB, Hewage CM (2019) NMR model structure of the antimicrobial peptide maximin 3. Eur Biophys J 48:203–212.  https://doi.org/10.1007/s00249-019-01346-7 CrossRefPubMedGoogle Scholar
  3. Beyaz A, Oh WS, Reddy V (2004) Ionic liquids as modulators of the critical micelle concentration of sodium dodecyl sulfate. Colloids Surf B Biointerfaces 35:119–124.  https://doi.org/10.1016/J.COLSURFB.2004.02.014 CrossRefPubMedGoogle Scholar
  4. Biller JR, Elajaili H, Meyer V, Rosen GM, Eaton SS, Eaton GR (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802.  https://doi.org/10.1016/j.jmr.2013.08.006 CrossRefGoogle Scholar
  5. Chen Y, Guarnieri MT, Vasil AI, Vasil ML, Mant CT, Hodges RS (2007) Role of peptide hydrophobicity in the mechanism of action of alpha-helical antimicrobial peptides. Antimicrob Agents Chemother 51:1398–406.  https://doi.org/10.1128/AAC.00925-06 CrossRefPubMedGoogle Scholar
  6. Conlon JM, Kolodziejek J, Nowotny N (2004) Antimicrobial peptides from ranid frogs: taxonomic and phylogenetic markers and a potential source of new therapeutic agents. Biochimica et Biophysica Acta Proteins Proteom 1696:1–14.  https://doi.org/10.1016/j.bbapap.2003.09.004 CrossRefGoogle Scholar
  7. Conlon JM, Sonnevend A, Patel M, Davidson C, Nielsen PF, Pál T, Rollins-Smith LA (2003) Isolation of peptides of the brevinin-1 family with potent candidacidal activity from the skin secretions of the frog Rana boylii. J Pept Res 62:207–13CrossRefGoogle Scholar
  8. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092.  https://doi.org/10.1063/1.464397 CrossRefGoogle Scholar
  9. Feller SE, Zhang Y, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys 103:4613–4621.  https://doi.org/10.1063/1.470648 CrossRefGoogle Scholar
  10. Guilhelmelli F, Vilela N, Albuquerque P, Derengowski LdS, Silva-Pereira I, Kyaw CM (2013) Antibiotic development challenges: the various mechanisms of action of antimicrobial peptides and of bacterial resistance. Front Microbiol 4:353.  https://doi.org/10.3389/fmicb.2013.00353 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Güntert P, Braun W, Wüthrich K (1991) Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J Mol Biol 217:517–530.  https://doi.org/10.1016/0022-2836(91)90754-T CrossRefPubMedGoogle Scholar
  12. Güntert P, Mumenthaler C, Wüthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program Dyana. J Mol Biol 273:283–298.  https://doi.org/10.1006/JMBI.1997.1284 CrossRefPubMedGoogle Scholar
  13. Hossain MA, Guilhaudis L, Sonnevend A, Attoub S, van Lierop BJ, Robinson AJ, Wade JD, Conlon JM (2011) Synthesis, conformational analysis and biological properties of a dicarba derivative of the antimicrobial peptide, brevinin-1BYa. Eur Biophys J 40:555–564.  https://doi.org/10.1007/s00249-011-0679-2 CrossRefPubMedGoogle Scholar
  14. Hultmark D (2003) Drosophila immunity: paths and patterns. Current Opin Immunol 15:12–19.  https://doi.org/10.1016/S0952-7915(02)00005-5 CrossRefGoogle Scholar
  15. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Gr 14:33–38.  https://doi.org/10.1016/0263-7855(96)00018-5 CrossRefGoogle Scholar
  16. Jakobtorweihen S, Ingram T, Smirnova I (2013) Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane-water partition coefficients. J Comput Chem 34:1332–1340.  https://doi.org/10.1002/jcc.23262 CrossRefPubMedGoogle Scholar
  17. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935.  https://doi.org/10.1063/1.445869 CrossRefGoogle Scholar
  18. Kumar A, Ernst R, Wüthrich K (1980) A two-dimensional nuclear overhauser enhancement (2D NOE) experiment for the elucidation of complete proton–proton cross-relaxation networks in biological macromolecules. Biochem Biophys Res Commun 95:1–6.  https://doi.org/10.1016/0006-291X(80)90695-6 CrossRefPubMedGoogle Scholar
  19. Kwon MY, Hong SY, Lee KH (1998) Structure-activity analysis of brevinin 1E amide, an antimicrobial peptide from Rana esculenta. Biochimica et Biophysica Acta (BBA) Protein Struct Mol Enzymol 1387:239–248.  https://doi.org/10.1016/S0167-4838(98)00123-X CrossRefGoogle Scholar
  20. Lee W, Tonelli M, Markley JL (2015) NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31:1325–1327.  https://doi.org/10.1093/bioinformatics/btu830 CrossRefPubMedGoogle Scholar
  21. Lindberg M, Gräslund A (2001) The position of the cell penetrating peptide penetratin in SDS micelles determined by NMR. FEBS Lett 497:39–44.  https://doi.org/10.1016/S0014-5793(01)02433-4 CrossRefPubMedGoogle Scholar
  22. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616.  https://doi.org/10.1021/jp973084f CrossRefPubMedGoogle Scholar
  23. MacKerell AD, Feig M, Brooks CL (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulation. J Comput Chem 25:1400–1415.  https://doi.org/10.1002/jcc.20065 CrossRefPubMedGoogle Scholar
  24. MacRaild CA, Illesinghe J, Van Lierop BJ, Townsend AL, Chebib M, Livett BG, Robinson AJ, Norton RS (2009) Structure and activity of (2,8)-dicarba-(3,12)-cystino \(\alpha\)-ImI, an a-conotoxin containing a nonreducible cystine analogue. J Med Chem 52:755–762.  https://doi.org/10.1021/jm8011504 CrossRefPubMedGoogle Scholar
  25. Martyna GJ, Tobias DJ, Klein ML (1994) Constant pressure molecular dynamics algorithms. J Chem Phys 101:4177–4189.  https://doi.org/10.1063/1.467468 CrossRefGoogle Scholar
  26. Mechkarska M, Ojo OO, Meetani MA, Coquet L, Jouenne T, Abdel-Wahab YH, Flatt PR, King JD, Conlon JM (2011) Peptidomic analysis of skin secretions from the bullfrog Lithobates catesbeianus (Ranidae) identifies multiple peptides with potent insulin-releasing activity. Peptides 32:203–208.  https://doi.org/10.1016/J.PEPTIDES.2010.11.002 CrossRefPubMedGoogle Scholar
  27. Pál T, Abraham B, Sonnevend A, Jumaa P, Conlon JM (2006) Brevinin-1BYa: a naturally occurring peptide from frog skin with broad-spectrum antibacterial and antifungal properties. Int J Antimicrob Agents 27:525–9.  https://doi.org/10.1016/j.ijantimicag.2006.01.010 CrossRefPubMedGoogle Scholar
  28. Park SH, Kim HE, Kim CM, Yun HJ, Choi EC, Lee BJ (2002) Role of proline, cysteine and a disulphide bridge in the structure and activity of the anti-microbial peptide gaegurin 5. Biochem J 368:171–82.  https://doi.org/10.1042/BJ20020385 CrossRefPubMedPubMedCentralGoogle Scholar
  29. Park SH, Kim YK, Park JW, Lee B, Lee BJ (2000) Solution structure of the antimicrobial peptide gaegurin 4 by H and 15N nuclear magnetic resonance spectroscopy. Eur J Biochem 267:2695–2704CrossRefGoogle Scholar
  30. Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:321–341CrossRefGoogle Scholar
  31. Sani MA, Separovic F (2016) How membrane-active peptides get into lipid membranes. Acc Chem Res 49:1130–1138.  https://doi.org/10.1021/acs.accounts.6b00074 CrossRefPubMedGoogle Scholar
  32. Sani MA, Whitwell TC, Gehman JD, Robins-Browne RM, Pantarat N, Attard TJ, Reynolds EC, O’Brien-Simpson NM, Separovic F (2013) Maculatin 1.1 disrupts Staphylococcus aureus lipid membranes via a pore mechanism. Antimicrob Agents Chemother 57:3593–600.  https://doi.org/10.1128/AAC.00195-13 CrossRefPubMedPubMedCentralGoogle Scholar
  33. Subasinghage AP, O’Flynn D, Conlon JM, Hewage CM (2011) Conformational and membrane interaction studies of the antimicrobial peptide alyteserin-1c and its analogue [E4K]alyteserin-1c. Biochimica et Biophysica Acta (BBA) Biomemb 1808:1975–1984.  https://doi.org/10.1016/j.bbamem.2011.04.012 CrossRefGoogle Scholar
  34. Suh JY, Lee KH, Chi SW, Hong SY, Choi BW, Moon HM, Choi BS (1996) Unusually stable helical kink in the antimicrobial peptide—a derivative of gaegurin. FEBS Lett 392:309–312.  https://doi.org/10.1016/0014-5793(96)00840-X CrossRefPubMedGoogle Scholar
  35. Timmons PB, O’Flynn D, Conlon JM, Hewage CM (2019) Structural and positional studies of the antimicrobial peptide brevinin-1BYa in membrane-mimetic environments. J Pept Sci.  https://doi.org/10.1002/psc.3208 (in press)CrossRefGoogle Scholar
  36. Wüthrich K (1986) NMR of proteins and nucleic acids. Wiley Interscience. https://www.wiley.com/en-ie/NMR+of+Proteins+and+Nucleic+Acids-p-9780471828938
  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 CrossRefPubMedGoogle Scholar
  38. Zhang S, Hughes RA, Bathgate RA, Shabanpoor F, Hossain MA, Lin F, Van Lierop B, Robinson AJ, Wade JD (2010) Role of the intra-A-chain disulfide bond of insulin-like peptide 3 in binding and activation of its receptor, RXFP2. Peptides 31:1730–1736.  https://doi.org/10.1016/j.peptides.2010.05.021 CrossRefPubMedGoogle Scholar

Copyright information

© European Biophysical Societies' Association 2019

Authors and Affiliations

  1. 1.UCD School of Biomolecular and Biomedical Science, UCD Centre for Synthesis and Chemical Biology, UCD Conway InstituteUniversity College DublinDublin 4Ireland
  2. 2.ProVerum Medical Limited, Trinity Translational Medicine Institute, Trinity Centre for Health SciencesSt James’s HospitalDublin 8Ireland
  3. 3.Diabetes Research Group, School of Biomedical SciencesUlster UniversityColeraineNorthern Ireland

Personalised recommendations