Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles

Abdallah Sayyed-Ahmad, Himanshu Khandelia, Yiannis Kaznessis

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


We present relative binding free energy calculations for six antimicrobial peptide-micelle systems, three peptides interacting with two types of micelles. The peptides are the scorpion derived antimicrobial peptide (AMP), IsCT and two of its analogues. The micelles are dodecylphosphatidylcholine (DPC) and sodium dodecylsulphate (SDS) micelles. The interfacial electrostatic properties of DPC and SDS micelles are assumed to be similar to those of zwitterionic mammalian and anionic bacterial membrane interfaces, respectively. We test the hypothesis that the binding strength between peptides and the anionic micelle SDS can provide information on peptide antimicrobial activity, since it is widely accepted that AMPs function by binding to and disrupting the predominantly anionic lipid bilayer of the bacterial cytoplasmic membrane. We also test the hypothesis that the binding strength between peptides and the zwitterionic micelle DPC can provide information on peptide haemolytic activities, since it is accepted that they also bind to and disrupt the zwitterionic membrane of mammalian cells. Equilibrium structures of the peptides, micelles and peptide-micelle complexes are obtained from more than 300ns of molecular dynamics simulations. A thermodynamic cycle is introduced to compute the binding free energy from electrostatic, non-electrostatic and entropic contributions. We find relative binding free energy strengths between peptides and SDS to correlate with the experimentally measured rankings for peptide antimicrobial activities, and relative free energy binding strengths between peptides and DPC to correlate with the observed rankings for peptide haemolytic toxicities. These findings point to the importance of peptide-membrane binding strength for antimicrobial activity and haemolytic activity.

Original languageEnglish (US)
Pages (from-to)986-997
Number of pages12
JournalMolecular Simulation
Issue number10-11
StatePublished - Sep 2009

Bibliographical note

Funding Information:
This work was supported by a grant from the NIH (GM 070989). The authors gratefully acknowledge the computational support from the Minnesota Supercomputing Institute. This work also was partially supported by the National Computational Science Alliance under TG-MCA04N033. A. Sayyed-Ahmad also appreciates the partial funding from the Consortium for Bioinformatics and Computational Biology, University of Minnesota, Minneapolis.


  • Antimicrobial peptides
  • Binding free energy calculations
  • IsCT
  • Molecular dynamics simulations


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