BMB Reports

Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
권호 표지
DOI QR코드

DOI QR Code

NMR Spectroscopic Assessment of the Structure and Dynamic Properties of an Amphibian Antimicrobial Peptide (Gaegurin 4) Bound to SDS Micelles

  • Park, Sang-Ho (Department of Chemistry and Biochemistry, University of California) ;
  • Son, Woo-Sung (Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University) ;
  • Kim, Yong-Jin (Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University) ;
  • Kwon, Ae-Ran (Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University) ;
  • Lee, Bong-Jin (Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University)
  • Published : 2007.03.31
Download PDF
⟨ Previous Next ⟩

Abstract

The structure and dynamics of a 37-residue antimicrobial peptide gaegurin 4 (GGN4) isolated from the skin of the native Korean frog, Rana rugosa, was determined in SDS micelles by NMR spectroscopy. The solution structure of the peptide in SDS micelles was determined from 352 NOE-derived distance constraints and 22 backbone torsion angle constraints. Dynamic properties for the amide backbone were characterized by $^1H-^{15}N $heteronuclear NOE experiments. The structural study revealed two amphipathic helices spanning residues 2-10 and 16-32 and that the helices were connected by a flexible loop. An intraresidue disulfide bridge was formed between residues Cys31 and Cys37 near the C-terminus. The loop region (11-15) connecting the two helices are were slightly more flexible than these helices themselves. From the fact that since there is no contact NOEs between two helices, it is implied that the GGN4 peptide shows an independent motion of both helices which has an angle of about $ 60^{\circ}-120^{\circ}$ from each other.

Keywords

References

  1. Almeida, F. C. and Opella, S. J. (1997) Fd coat protein structure in membrane environments: structural dynamics of the loop between the hydrophobic trans-membrane helix and the amphipathic in-plane helix. J. Mol. Biol. 270, 481-495. https://doi.org/10.1006/jmbi.1997.1114
  2. Bechinger, B., Zasloff, M. and Opella, S. J. (1993) Structure and orientation of the antibiotic peptide magainin in membranes by solid-state nuclear magnetic resonance spectroscopy. Protein Sci. 2, 2077-2084. https://doi.org/10.1002/pro.5560021208
  3. Boman, H. G. (1995) Peptide antibiotics and their role in innate immunity. Annu. Rev. Immunol. 13, 61-92. https://doi.org/10.1146/annurev.iy.13.040195.000425
  4. Brunger, A. T. (1992) X-PLOR, Version 3.1: a system for X-ray crystallography and NMR. Yale University Press, New Haven, USA.
  5. Christensen, B., Fink, J., Merrifield, R. B. and Mauzerall, D. (1988) Channel-forming properties of cecropins and related model compounds incorporated into planar lipid membranes. Proc. Natl. Acad. Sci. USA 85, 5072-5076. https://doi.org/10.1073/pnas.85.14.5072
  6. Clark, D. P., Durell, S., Maloy, W. L. and Zasloff, M. (1994) Ranalexin. A novel antimicrobial peptide from bullfrog (Rana catesbeiana) skin, structurally related to the bacterial antibiotic, polymyxin. J. Biol. Chem. 269, 10849-10855.
  7. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J. and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293.
  8. Farrow, N. A., Muhandiram, R., Singer, A. U., Pascal, S. M., Kay, C. M., Gish, G., Shoelson, S. E., Pawson, T., Forman-Kay, J. D. and Kay, L. E. (1994) Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry 33, 5984-6003. https://doi.org/10.1021/bi00185a040
  9. Gabay, J. E. (1994) Ubiquitous natural antibiotics. Science 264, 373-374. https://doi.org/10.1126/science.8153623
  10. Gesell, J., Zasloff, M. and Opella, S. J. (1997) Two-dimensional 1H NMR experiments show that the 23-residue magainin antibiotic peptide is an alpha-helix in dodecylphosphocholine micelles, sodium dodecylsulfate micelles, and trifluoroethanol/water solution. J. Biomol. NMR 9, 127-135. https://doi.org/10.1023/A:1018698002314
  11. Gibson, B. W., Tang, D. Z., Mandrell, R., Kelly, M. and Spindel, E. R. (1991) Bombinin-like peptides with antimicrobial activity from skin secretions of the Asian toad, Bombina orientalis. J. Biol. Chem. 266, 23103-23111.
  12. Holak, T. A., Engstrom, A., Kraulis, P. J., Lindeberg, G., Bennich, H., Jones, T. A., Gronenborn, A. M. and Clore, G. M. (1988) The solution conformation of the antibacterial peptide cecropin A: a nuclear magnetic resonance and dynamical simulated annealing study. Biochemistry 27, 7620-7629. https://doi.org/10.1021/bi00420a008
  13. Karplus, M. and McCammon, J. A. (1986) The dynamics of proteins. Sci. Am. 254, 42-51.
  14. Kay, L. E. and Bax, A. (1990) New methods for the measurement of NH-CaH coupling constants in 15N-labeled proteins. J. Magn. Reson. 86, 110-126.
  15. Kim, H. J., Han, S. K., Park, J. B., Baek, H. J., Lee, B. J. and Ryu, P. D. (1999) Gaegurin 4, a peptide antibiotic of frog skin, forms voltage-dependent channels in planar lipid bilayers. J. Pept. Res. 53, 1-7. https://doi.org/10.1111/j.1399-3011.1999.tb01611.x
  16. Leetachewa, S., Katzenmeier, G. and Angsuthanasombat, C. (2006) Novel preparation and characterization of the alpha4-loopalpha5 membrane-perturbing peptide from the Bacillus thuringiensis Cry4Ba delta-endotoxin. J. Biochem. Mol. Biol. 39, 270-277. https://doi.org/10.5483/BMBRep.2006.39.3.270
  17. Ludtke, S. J., He, K., Heller, W. T., Harroun, T. A., Yang, L. and Huang, H. W. (1996) Membrane pores induced by magainin. Biochemistry 35, 13723-13728. https://doi.org/10.1021/bi9620621
  18. Maeda, Y., Nakagawa, T. and Kuroda, Y. (2003) Oligopeptidemediated helix stabilization of model peptides in aqueous solution. J. Pept. Sci. 9, 106-113. https://doi.org/10.1002/psc.435
  19. Mor, A., Nguyen, V. H., Delfour, A., Migliore-Samour, D. and Nicolas, P. (1991) Isolation, amino acid sequence, and synthesis of dermaseptin, a novel antimicrobial peptide of amphibian skin. Biochemistry 30, 8824-8830. https://doi.org/10.1021/bi00100a014
  20. Morikawa, N., Hagiwara, K. and Nakajima, T. (1992) Brevinin-1 and -2, unique antimicrobial peptides from the skin of the frog, Rana brevipoda porsa. Biochem. Biophys. Res. Commun. 189, 184-190. https://doi.org/10.1016/0006-291X(92)91542-X
  21. Nelson, J. W. and Kallenbach, N. R. (1986) Stabilization of the ribonuclease S-peptide alpha-helix by trifluoroethanol. Proteins 1, 211-217. https://doi.org/10.1002/prot.340010303
  22. Nicolas, P. and Mor, A. (1995) Peptides as weapons against microorganisms in the chemical defense system of vertebrates. Annu. Rev. Microbiol. 49, 277-304. https://doi.org/10.1146/annurev.mi.49.100195.001425
  23. Nilges, M., Gronenborn, A. M., Brunger, A. T. and Clore, G. M. (1988) Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng. 2, 27-38. https://doi.org/10.1093/protein/2.1.27
  24. Oren, Z. and Shai, Y. (1998) Mode of action of linear amphipathic alpha-helical antimicrobial peptides. Biopolymers 47, 451-463. https://doi.org/10.1002/(SICI)1097-0282(1998)47:6<451::AID-BIP4>3.0.CO;2-F
  25. Papavoine, C. H., Remerowski, M. L., Horstink, L. M., Konings, R. N., Hilbers, C. W. and van de Ven, F. J. (1997) Backbone dynamics of the major coat protein of bacteriophage M13 in detergent micelles by 15N nuclear magnetic resonance relaxation measurements using the model-free approach and reduced spectral density mapping. Biochemistry 36, 4015-4026. https://doi.org/10.1021/bi962650e
  26. Park, J. M., Jung, J. E. and Lee, B. J. (1994) Antimicrobial peptides from the skin of a Korean frog, Rana rugosa. Biochem. Biophys. Res. Commun. 205, 948-954. https://doi.org/10.1006/bbrc.1994.2757
  27. Park, S. H., Kim, H. E., Kim, C. M., Yun, H. J., Choi, E. C. and Lee, B. J. (2002) Role of proline, cysteine and a disulphide bridge in the structure and activity of the anti-microbial peptide gaegurin 5. Biochem. J. 368, 171-182. https://doi.org/10.1042/BJ20020385
  28. Park, S. H., Kim, Y. K., Park, J. W., Lee, B. and Lee, B. J. (2000) Solution structure of the antimicrobial peptide gaegurin 4 by H and 15N nuclear magnetic resonance spectroscopy. Eur. J. Biochem. 267, 2695-2704. https://doi.org/10.1046/j.1432-1327.2000.01287.x
  29. Park, S. J., Kim, J. S., Son, W. S., Ahn, H. C. and Lee, B. J. (2003) Backbone 1H, 15N, and 13C resonance assignments of the Helicobacter pylori acyl carrier protein. J. Biochem. Mol. Biol. 36, 505-507. https://doi.org/10.5483/BMBRep.2003.36.5.505
  30. Roccatano, D., Colombo, G., Fioroni, M. and Mark, A. E. (2002) Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: a molecular dynamics study. Proc. Natl. Acad. Sci. USA 99, 12179-12184. https://doi.org/10.1073/pnas.182199699
  31. Shon, K. J., Kim, Y., Colnago, L. A. and Opella, S. J. (1991) NMR studies of the structure and dynamics of membranebound bacteriophage Pf1 coat protein. Science 252, 1303-1305. https://doi.org/10.1126/science.1925542
  32. Simmaco, M., Barra, D., Chiarini, F., Noviello, L., Melchiorri, P., Kreil, G. and Richter, K. (1991) A family of bombinin-related peptides from the skin of Bombina variegata. Eur. J. Biochem. 199, 217-222. https://doi.org/10.1111/j.1432-1033.1991.tb16112.x
  33. Simmaco, M., Mignogna, G., Barra, D. and Bossa, F. (1993) Novel antimicrobial peptides from skin secretion of the European frog Rana esculenta. FEBS Lett. 324, 159-161. https://doi.org/10.1016/0014-5793(93)81384-C
  34. Vignal, E., Chavanieu, A., Roch, P., Chiche, L., Grassy, G., Calas, B. and Aumelas, A. (1998) Solution structure of the antimicrobial peptide ranalexin and a study of its interaction with perdeuterated dodecylphosphocholine micelles. Eur. J. Biochem. 253, 221-228. https://doi.org/10.1046/j.1432-1327.1998.2530221.x
  35. Wishart, D. S., Sykes, B. D. and Richards, F. M. (1992) The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31, 1647-1651. https://doi.org/10.1021/bi00121a010
  36. Won, H. S., Park, S. H., Kim, H. E., Hyun, B., Kim, M., Lee, B. J. and Lee, B. J. (2002) Effects of a tryptophanyl substitution on the structure and antimicrobial activity of C-terminally truncated gaegurin 4. Eur. J. Biochem. 269, 4367-4374. https://doi.org/10.1046/j.1432-1033.2002.03139.x
  37. Wuthrich, K. (1986) NMR of proteins and nucleic acids. Wiley, New York, USA.
  38. Wuthrich, K., Billeter, M. and Braun, W. (1983) Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular protonproton distance constraints with nuclear magnetic resonance. J. Mol. Biol. 169, 949-961. https://doi.org/10.1016/S0022-2836(83)80144-2
  39. 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. USA 84, 5449-5453. https://doi.org/10.1073/pnas.84.15.5449

Cited by

  1. Predicting the Minimal Inhibitory Concentration for Antimicrobial Peptides with Rana-Box Domain vol.55, pp.10, 2015, https://doi.org/10.1021/acs.jcim.5b00161
  2. Conformational Analysis of the Host-Defense Peptides Pseudhymenochirin-1Pb and -2Pa and Design of Analogues with Insulin-Releasing Activities and Reduced Toxicities vol.78, pp.12, 2015, https://doi.org/10.1021/acs.jnatprod.5b00843
  3. Mechanisms of Selective Antimicrobial Activity of Gaegurin 4 vol.13, pp.1, 2009, https://doi.org/10.4196/kjpp.2009.13.1.39
  4. Micelle bound structure and DNA interaction of brevinin-2-related peptide, an antimicrobial peptide derived from frog skin vol.20, pp.10, 2014, https://doi.org/10.1002/psc.2673
  5. Solution NMR studies of amphibian antimicrobial peptides: Linking structure to function? vol.1788, pp.8, 2009, https://doi.org/10.1016/j.bbamem.2009.01.002
  6. Solution structures and model membrane interactions of Ctriporin, an anti-methicillin-resistantStaphylococcus aureusPeptide from Scorpion Venom vol.101, pp.12, 2014, https://doi.org/10.1002/bip.22519
  7. Action mechanism and structural requirements of the antimicrobial peptides, gaegurins vol.1788, pp.8, 2009, https://doi.org/10.1016/j.bbamem.2008.10.021
  8. Influence of specific amino acid side-chains on the antimicrobial activity and structure of bovine lactoferrampin11This article is part of Special Issue entitled Lactoferrin and has undergone the Journal’s usual peer review process. vol.90, pp.3, 2012, https://doi.org/10.1139/o11-057