Classical molecular dynamics (MD) simulation has been carried out in an explicit solvent environment to understand the interaction between the single walled carbon nanotube (SWCNT) and α-helix. A polyalanine peptide consisting of 40 alanine residues has been chosen as the model for the α-helix (PA(40)). Results reveal that the SWCNT induces conformational changes in PA(40). Furthermore, breakage of hydrogen bonds in the chosen model peptides has been observed, which leads to conformational transitions (α → turns) in different parts of the PA(40). Owing to these transitions, regions of different structural and energetic stability are generated in PA(40) which enable the PA(40) to curl around the surface of the SWCNT. The overall observations obtained from the MD simulations are not significantly influenced by the starting geometry and the choice of the force field. Although the qualities of structural information obtained from the MD simulation using ff03 and OPLS are different, the overall observation derived from the ff03 is similar to that of OPLS. Results from the MD simulation on the interaction of the α-helical fragment of the SNARES protein with the SWCNT elicit that the amino acid composition influences the interaction pattern. The wrapping of the α-helical fragment of the SNARES onto the SWCNT is similar to that of PA(40). Overall, there is a considerable decrease in the helical content of peptides upon interaction with SWCNTs, in agreement with the experimental findings.

In this study, an attempt has been made to understand the interaction between collagen like peptides (CPs) with a gold nanosurface (AuNS) using a classical molecular dynamics simulation. Results reveal that the adsorption of CPs onto the gold surface depends on the amino acid composition of the collagen like peptides. It is evident from the findings that the Hyp residue of collagen interacts favorably with the AuNS. It is interesting to note that the model CP without a Hyp residue does not adsorb well on the surface. Results indicate that gold nanosurfaces or gold nanoparticles can be exploited to detect breast cancer due to the increased content of Hyp residues in the Gly-XAA-YAA triplet of collagen in breast cancer tissues. These results provide useful information for designing collagen based scaffolds for tissues engineering applications.