Paper Citing NAMD - Abstract
Chiu, Chi-cheng; Dieckmann, Gregg R.; Nielsen, Steven O.
Role of Peptide-Peptide Interactions in Stabilizing Peptide-Wrapped Single-Walled Carbon Nanotubes: A Molecular Dynamics Study
BIOPOLYMERS, 92:156-163, 2009
Single-walled carbon nanotubes (SWNTs) have unique properties and are projected to have a major impact in nanoscale electronics, materials science, and nanomedicine. Yet, these potential applications are hindered by the need for sample purification to separate SWNTs from each other and from metallic catalyst and amorphous carbon present in as-synthesized samples. Common purification strategies involve dispersing SWNTs as individual tubes in aqueous solution. Towards this end, a designed helical peptide was shown to be excellent at dispersing SWNTs. However, the molecular details of the peptide-SWNT and peptide-peptide interactions await elucidation. Here we explore these molecular interactions using fully atomistic molecular dynamics simulations of peptide-wrapped SWNTs. We characterize the interactions by measuring the aromatic residue-to-SWNT surface distance, the peptide amphiphilicity, the peptide-SWNT crossing angle, the peptide-SWNT contact area, the peptide helix axis-to-axis distance, and the inter-peptide hydrogen bonding. We find that the peptides collectively tilt with respect to the SWNT long axis, are alpha-helical, and form interpeptide hydrogen bonds through their lysine and glutamate residues, which helps to stabilize the multipeptide/SWNT complex. All hydrophobic residues interact with the SWNT and are sequestered from water. The picture that emerges from this study gives insight into subsequent peptide design. (C) 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 156-163, 2009.
