Evaluation of the binding mechanism of human defensin 5 in a bacterial membrane: A simulation study

Tadsanee Awang, Phoom Chairatana, Ranjit Vijayan, Prapasiri Pongprayoon

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)


Human α-defensin 5 (HD5) is a host-defense peptide exhibiting broad-spectrum antimicrobial activity. The lipopolysaccharide (LPS) layer on the Gram-negative bacterial membrane acts as a barrier to HD5 insertion. Therefore, the pore formation and binding mechanism remain unclear. Here, the binding mechanisms at five positions along the bacterial membrane axis were investigated using Molecular Dynamics. (MD) simulations. We found that HD5 initially placed at positions 1 to 3 moved up to the surface, while HD5 positioned at 4 and 5 remained within the membrane interacting with the middle and inner leaflet of the membrane, respectively. The arginines were key components for tighter binding with 3-deoxy-d-manno-octulosonic acid (KDO), phosphates of the outer and inner leaflets. KDO appeared to retard the HD5 penetration.

Original languageEnglish
Article number12401
JournalInternational journal of molecular sciences
Issue number22
Publication statusPublished - Nov 1 2021


  • Antimicrobial peptides
  • Human defensin 5
  • Lipopolysaccharide
  • Molecular dynamics simulations

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry


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