Molecular Dynamics Study of a Nanotube-Binding Amphiphilic Helical Peptide at Different Water/Hydrophobic Interfaces

Many potential applications of single-walled carbon nanotubes (SWNTs) require that they be isolated from one another. This may be accomplished through covalent or noncovalent SWNT functionalization. The noncovalent approach preserves the intrinsic electrical, optical, and mechanical properties of SWNTs and can be achieved by dispersing SWNTs in aqueous solution using surfactants, polymers, or biomacromolecules like DNA or polypeptides. The designed amphiphilic helical peptide nano-1, which contains hydrophobic valine and aromatic phenylalanine residues for interaction with SWNTs and glutamic acid and lysine residues for water solubility, has been shown to debundle and disperse SWNTs, although the details of the peptide-SWNT interactions await elucidation. Here we use fully atomistic molecular dynamics simulations to investigate the nano-1 peptide at three different water/hydrophobic interfaces: water/oil, water/graphite, and water/SWNT. The amphiphilic nature of the peptide is characterized by its secondary structure, peptide-water hydrogen bonding, and peptide-hydrophobic surface van der Waals energy. We show that nano-1 has reduced amphiphilic character at the water/oil interface because the peptide helix penetrates into the hydrophobic phase. The peptide alpha-helix cannot match its hydrophobic face to the rigid planar graphite surface without partially unfolding. In contrast, nano-1 can curve on the SWNT surface in an alpha-helical conformation to simultaneously maximize its hydrophobic contacts with the SWNT and its hydrogen bonds with water. The molecular insight into the peptide conformation at the various hydrophobic surfaces provides guidelines for future peptide design.