In this work we have explored dynamic properties of two protein-fragment models interacting with single-walled carbon nanotubes. The properties of custom engineered peptides have benn explored using molecular dynamics simulations to elucidate the structure and interactions with the nanotubes in aqueous environment. We have considered peptides interacting with the outer walls of nanotubes, encapsulated into nanotubes, as well as covalently bound to nanotubes through a computationally-engineered linker. The results suggest that the confined space of the nanotube and its interactions with peptides stabilizes the structure of biomacromolecules. On the other hand covalent linking of peptides to nanotubes may lead to a change in the peptide conformation. The general conclusions derived from this work may be of importance in devising new nanotube systems for peptide and drug delivery.