Skip to main content

Atomic Force Microscopy Study of the Interactions of Indolicidin with Model Membranes and DNA

  • Protocol
  • First Online:
Antimicrobial Peptides

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1548))

Abstract

The cell membrane is the first barrier and quite often the primary target that antimicrobial peptides (AMPs) have to destroy or penetrate to fulfill their mission. Upon penetrating through the membrane, the peptides can further attack intracellular targets, in particular DNA. Studying the interaction of an antimicrobial peptide with a cell membrane and DNA holds keys to understanding its killing mechanisms. Commonly, these interactions are studied by using optical or scanning electron microscopy and appropriately labeled peptides. However, labeling can significantly affect the hydrophobicity, conformation, and size of the peptide, hence altering the interaction significantly. Here, we describe the use of atomic force microscopy (AFM) for a label-free study of the interactions of peptides with model membranes under physiological conditions and DNA as a possible intracellular target.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 179.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Casuso I, Rico F, Scheuring S (2011) Biological AFM: where we come from–where we are–where we may go. J Mol Recognit 24:406–413

    Article  CAS  PubMed  Google Scholar 

  2. Lyubchenko YL (2013) AFM visualization of protein–DNA interactions. In: Oberhauser AF (ed) Single-molecule studies of proteins. Springer, New York, NY, pp 97–117

    Google Scholar 

  3. Yip CM, McLaurin J (2001) Amyloid-β peptide assembly: a critical step in fibrillogenesis and membrane disruption. Biophys J 80:1359–1371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Slade A, Luh J, Ho S, Yip CM (2002) Single molecule imaging of supported planar lipid bilayer—reconstituted human insulin receptors by in situ scanning probe microscopy. J Struct Biol 137:283–291

    Article  CAS  PubMed  Google Scholar 

  5. Epand RF, Martinou J-C, Montessuit S, Epand RM, Yip CM (2002) Direct evidence for membrane pore formation by the apoptotic protein Bax. Biochem Biophys Res Commun 298:744–749

    Article  CAS  PubMed  Google Scholar 

  6. Ha TH, Kim CH, Park JS, Kim K (2000) Interaction of indolicidin with model lipid bilayer: quartz crystal microbalance and atomic force microscopy study. Langmuir 16:871–875

    Article  CAS  Google Scholar 

  7. Zhao H, Mattila J-P, Holopainen JM, Kinnunen PK (2001) Comparison of the membrane association of two antimicrobial peptides, magainin 2 and indolicidin. Biophys J 81:2979–2991

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Falla TJ, Karunaratne DN, Hancock RE (1996) Mode of action of the antimicrobial peptide indolicidin. J Biol Chem 271:19298–19303

    Article  CAS  PubMed  Google Scholar 

  9. Askou HJ, Jakobsen RN, Fojan P (2008) An atomic force microscopy study of the interactions between indolicidin and supported planar bilayers. J Nanosci Nanotechnol 8:4360–4369

    Article  CAS  PubMed  Google Scholar 

  10. Shaw JE, Alattia J-R, Verity JE, Privé GG, Yip CM (2006) Mechanisms of antimicrobial peptide action: studies of indolicidin assembly at model membrane interfaces by in situ atomic force microscopy. J Struct Biol 154:42–58

    Article  CAS  PubMed  Google Scholar 

  11. Prim N, Iversen L, Diaz P, Bjørnholm T (2006) Atomic force microscope studies on the interactions of Candida rugosa lipase and supported lipidic bilayers. Colloids Surf B Biointerfaces 52:138–142

    Article  CAS  PubMed  Google Scholar 

  12. Subbalakshmi C, Sitaram N (1998) Mechanism of antimicrobial action of indolicidin. FEMS Microbiol Lett 160:91–96

    Article  CAS  PubMed  Google Scholar 

  13. Hsu C-H, Chen C, Jou M-L, Lee AY-L, Lin Y-C, Yu Y-P, Huang W-T, Wu S-H (2005) Structural and DNA-binding studies on the bovine antimicrobial peptide, indolicidin: evidence for multiple conformations involved in binding to membranes and DNA. Nucleic Acids Res 33:4053–4064

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Marchand C, Krajewski K, Lee H-F, Antony S, Johnson AA, Amin R, Roller P, Kvaratskhelia M, Pommier Y (2006) Covalent binding of the natural antimicrobial peptide indolicidin to DNA abasic sites. Nucleic Acids Res 34:5157–5165

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ghosh A, Kar RK, Jana J, Saha A, Jana B, Krishnamoorthy J, Kumar D, Ghosh S, Chatterjee S, Bhunia A (2014) Indolicidin targets duplex DNA: structural and mechanistic insight through a combination of spectroscopy and microscopy. ChemMedChem 9:2052–2058

    Article  CAS  PubMed  Google Scholar 

  16. Som A, Tew GN (2008) Influence of lipid composition on membrane activity of antimicrobial phenylene ethynylene oligomers. J Phys Chem B 112:3495–3502

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Horcas I, Fernández R, Gómez-Rodríguez JM, Colchero J, Gómez-Herrero J, Baro AM (2007) WSXM: a software for scanning probe microscopy and a tool for nanotechnology. Rev Sci Instrum 78:013705

    Article  CAS  PubMed  Google Scholar 

  18. Shlyakhtenko LS, Gall AA, Lyubchenko YL (2013) Mica functionalization for imaging of DNA and protein-DNA complexes with atomic force microscopy. In: Cell imaging techniques. Springer, New York, NY, pp 295–312

    Google Scholar 

  19. Shlyakhtenko LS, Gall AA, Filonov A, Cerovac Z, Lushnikov A, Lyubchenko YL (2003) Silatrane-based surface chemistry for immobilization of DNA, protein-DNA complexes and other biological materials. Ultramicroscopy 97:279–287

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was generously supported by grants from the Spar Nord Foundation and the Det Obelske Familiefond. The authors also acknowledge fruitful discussions with Patrick Markus.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Peter Fojan .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Fojan, P., Gurevich, L. (2017). Atomic Force Microscopy Study of the Interactions of Indolicidin with Model Membranes and DNA. In: Hansen, P. (eds) Antimicrobial Peptides. Methods in Molecular Biology, vol 1548. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6737-7_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6737-7_14

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6735-3

  • Online ISBN: 978-1-4939-6737-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics