Paper Citing NAMD - Abstract
Chiu, Chi-cheng; Maher, Marie C.; Dieckmann, Gregg R.; Nielsen, Steven O.
Molecular Dynamics Study of a Carbon Nanotube Binding Reversible Cyclic Peptide
ACS NANO, 4:2539-2546, MAY 2010
Many potential biological applications of single-walled carbon nanotubes (SWNTs) require their dispersion in aqueous conditions. Recently, Dieckmann et al, designed a series of reversible cyclic peptides (RCPs) which exist in linear or cyclized states through controlled formation of an intramolecular disulfide bond between terminal Cys residues. These RCP-Cys peptides have been shown to disperse SWNTs in aqueous solution and form peptide/SWNT complexes which are stable against dilution. However, the detailed molecular interactions between the peptide and the SWNT in an aqueous environment remain unexplored. Here, fully atomistic molecular dynamics simulations were used to study the effect of RCP-Cys at the water/SWNT interface. We show that the peptide SWNT association is thermodynamically favorable through free energy calculations. Furthermore, we analyze the structure and energetics of the possible beta-sheet-like ring stacking that can form on the SWNT through peptide backbone hydrogen bonding. Our results reveal the thermodynamic driving force for the formation of an ordered, self-assembled RCP-Cys/SWNT complex, which provides insight into peptide design strategies for future applications.
