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

Abstract

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

Keywords:

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

Acknowledgements

DRM acknowledges a Taiwan scholarship from the Ministry of Education of Taiwan. We are grateful to the National Center for High-performance Computing Taiwan for computer time and facilities. YHL and DRM contributed equally to this work.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

WBF thanks the Ministry of Science and Technology Taiwan [MOST-104-2112-M-010-001-MY3], Taiwan, for financial support.