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Computational Insights into Membrane Disruption by Cell-Penetrating Peptides.

Eric Catalina-Hernandez1,2, Marcel Aguilella-Arzo3, Alex Peralvarez-Marin1,2

  • 1Unit of Biophysics, Department of Biochemistry and Molecular Biology, Facultat de Medicina, Av. Can Domènech s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Catalonia, Spain.

Journal of Chemical Information and Modeling
|January 17, 2025
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Summary

Cell-penetrating peptides (CPPs) internalize into cells through complex mechanisms. Computational simulations reveal how peptide properties and membrane composition, including cholesterol and charge, influence internalization barriers and bilayer interactions.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Membrane Biophysics

Background:

  • Cell-penetrating peptides (CPPs) are crucial for cellular delivery.
  • Understanding CPP internalization mechanisms is vital for drug development.
  • Early peptide-membrane interactions dictate cellular uptake efficiency.

Purpose of the Study:

  • To investigate the early mechanisms of peptide-bilayer interactions during CPP internalization.
  • To analyze the influence of membrane composition on peptide translocation.
  • To characterize the distinct interaction modes of different CPP types.

Main Methods:

  • Combined adaptive Steered Molecular Dynamics (aSMD) and conventional Molecular Dynamics (cMD) simulations.
  • Studied three distinct membrane compositions: neutral lipids, lipids with cholesterol, and charged lipids with cholesterol.
  • Analyzed energy barriers and disruption mechanisms for cationic (Arg9), amphiphilic (MAP), and hydrophobic (TP2) CPPs.

Main Results:

  • Cholesterol and negative charges on lipids increase energy barriers for peptide crossing.
  • Hydrophobic CPPs (TP2) insert into the bilayer, while cationic CPPs (Arg9) form pores.
  • Amphiphilic CPPs (MAP) exhibit both hydrophobic insertion and pore formation behaviors.
  • Distinct CPP types interact differently with lipid bilayers.

Conclusions:

  • Computational approaches provide significant insights into CPP-membrane interactions.
  • Membrane composition critically affects CPP internalization pathways.
  • Findings aid in designing CPPs with enhanced cell penetration capabilities.