Using Confocal Microscopy and Computational Modeling to Investigate the Cell-Penetrating Properties of Antimicrobial Peptides

  • Gabriel Del Rio
  • Edda Klipp
  • Andreas Herrmann
Part of the Methods in Molecular Biology book series (MIMB, volume 1548)


Antimicrobial peptides (AMPs) may display the ability to penetrate cells, which may be relevant for their antibiotic activity. To investigate the relevance of the penetrating activity for the antibiotic activity of AMPs, here we describe a method based on the combined use of confocal microscopy and computational modeling coupled with cell death kinetics.

Key words

Antimicrobial peptides Cell-penetrating peptides Mathematical modeling Confocal microscopy Multifunctional peptides Cell death kinetics 



We would like to thank Dr. Maria Teresa Lara Ortiz for her technical assistance in the writing of this work. Grants from the Alexander von Humboldt Foundation (FKZ: 3.4-IP-DEU/113263) and PAPIIT (IN205911) to GDR supported this work.


  1. 1.
    Wang G, Li X, Wang Z (2009) APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res 37:D933–D937CrossRefPubMedGoogle Scholar
  2. 2.
    Seo MD, Won HS, Kim JH, Mishig-Ochir T, Lee BJ (2012) Antimicrobial peptides for therapeutic applications: a review. Molecules 17:12276–12286CrossRefPubMedGoogle Scholar
  3. 3.
    Splith K, Neundorf I (2011) Antimicrobial peptides with cell-penetrating peptide properties and vice versa. Eur Biophys J 40:387–397CrossRefPubMedGoogle Scholar
  4. 4.
    Falco A, Ortega-Villaizan M, Chico V, Brocal I, Perez L, Coll JM, Estepa A (2009) Antimicrobial peptides as model molecules for the development of novel antiviral agents in aquaculture. Mini Rev Med Chem 9:1159–1164CrossRefPubMedGoogle Scholar
  5. 5.
    Haney EF, Hancock RE (2013) Peptide design for antimicrobial and immunomodulatory applications. Biopolymers 100:572–583CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Henriques ST, Melo MN, Castanho MA (2006) Cell-penetrating peptides and antimicrobial peptides: how different are they? Biochem J 399:1–7CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Palm C, Netzereab S, Hällbrink M (2006) Quantitatively determined uptake of cell-penetrating peptides in non-mammalian cells with an evaluation of degradation and antimicrobial effects. Peptides 27:1710–1716CrossRefPubMedGoogle Scholar
  8. 8.
    Matsuzaki K, Murase O, Fujii N, Miyajima K (1995) Translocation of a channel-forming antimicrobial peptide, magainin 2, across lipid bilayers by forming a pore. Biochemistry 34:6521–6526CrossRefPubMedGoogle Scholar
  9. 9.
    Otvos L, Cudic M (2007) Broth microdilution antibacterial assay of peptides. Methods Mol Biol 386:309–320PubMedGoogle Scholar
  10. 10.
    Jorgensen JH, Ferraro MJ (2009) Antimicrobial susceptibility testing: a review of general principles and contemporary practices. Clin Infect Dis 49:1749–1755CrossRefPubMedGoogle Scholar
  11. 11.
    Gee ML, Burton M, Grevis-James A, Hossain MA, McArthur S, Palombo EA, Wade JD, Clayton AH (2013) Imaging the action of antimicrobial peptides on living bacterial cells. Sci Rep 3:1557CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Marchand C, Krajewski K, Lee HF, 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 34:5157–5165CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Shai Y (2002) Mode of action of membrane active antimicrobial peptides. Biopolymers 66:236–248CrossRefPubMedGoogle Scholar
  14. 14.
    Bechara C, Sagan S (2013) Cell-penetrating peptides: 20 years later, where do we stand? FEBS Lett 587:1693–1702CrossRefPubMedGoogle Scholar
  15. 15.
    Rodriguez Plaza JG, Morales-Nava R, Diener C, Schreiber G, Gonzalez ZD, Lara Ortiz MT, Ortega Blake I, Pantoja O, Volkmer R, Klipp E, Herrmann A, Del Rio G (2014) Cell penetrating peptides and cationic antibacterial peptides: two sides of the same coin. J Biol Chem 289:14448–14457CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Rodríguez Plaza JG, Villalón Rojas A, Herrera S, Garza-Ramos G, Torres Larios A, Amero C, Zarraga Granados G, Gutiérrez Aguilar M, Lara Ortiz MT, Polanco Gonzalez C, Uribe Carvajal S, Coria R, Peña Díaz A, Bredesen DE, Castro-Obregon S, del Rio G (2012) Moonlighting peptides with emerging function. PLoS One 7:e40125CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Gabriel Del Rio
    • 1
  • Edda Klipp
    • 2
  • Andreas Herrmann
    • 2
  1. 1.Biochemistry and Structural Biology DepartmentInstituto de Fisiología Celular, Universidad Nacional Autónoma de MéxicoMéxico D.F.Mexico
  2. 2.Theoretische und Molekulare BiophysikHumboldt-Universität zu BerlinBerlinGermany

Personalised recommendations