Membrane partitioning of peptide aggregates: coarse-grained molecular dynamics simulations

Yu Hsien Lien, Dhani Ram Mahato, Felix Hoppe-Seyler, Wolfgang B. Fischer*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


Coarse-grained molecular dynamics (CGMD) simulation technique (MARTINI force field) is applied to monitor the aggregation of helical peptides representing the transmembrane sequence and its extension of bone marrow stromal cell antigen 2 (BST-2). One of the peptides is coupled with a protein transducing domain (PTD) of nine arginine residues (R9) at its N-terminal side as well as a peptide, pep11**, which has been shown to bind to human papilloma virus 16 (HPV16) E6 oncoprotein. A short hydrophobic stretch of the transmembrane domain (TMD) of BST-2 aggregates the fastest and inserts into a lipid membrane. An aggregate of R9-pep11** attaches to the membrane via simultaneous contact of many arginine residues. Monomers from the aggregates of the shortest of the hydrophobic TMDs dissolve into the opposing leaflet when the aggregate spans the bilayer. A ‘flipping’ of the individual monomeric peptides is not observed. Communicated by Ramaswamy H. Sarma.

Original languageEnglish
Pages (from-to)524-532
Number of pages9
JournalJournal of Biomolecular Structure and Dynamics
Issue number2
StatePublished - 22 Jan 2020


  • helical rods
  • membrane activity
  • molecular dynamics simulations
  • molecular recognition
  • Peptides
  • self-assembly


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