Residue Specific and Chirality Dependent Interactions between Carbon Nanotubes and Flagellin

Flagellum is a lash-like cellular appendage found in many single-celled living organisms. The flagellin protofilaments contain 11-helix dual turn structure in a single flagellum. Each flagellin consists of four sub-domains - two inner domains (D0, D1) and two outer domains (D2, D3). While inner domains predominantly consist of α-helices, the outer domains are primarily beta sheets with D3. In flagellum, the outermost sub-domain is the only one that is exposed to the native environment. This study focuses on the interactions of the residues of D3 of an R-type flagellin with 5nm long chiral (5,15) and arm-chair (12,12) single-walled carbon nanotubes (SWNT) using molecular dynamics simulation. It presents the interactive forces between the SWNT and the residues of D3 from the perspectives of size and chirality of the SWNT. It is found that the metallic (arm-chair) SWNT interacts the most with glycine and threonine residues through van der Waals and hydrophobic interactions, whereas the semiconducting (chiral) SWNT interacts largely with the area of protein devoid of glycine by van der Waals, hydrophobic interactions, and hydrogen bonding. This indicates a crucial role that glycine plays in distinguishing metallic from semiconducting SWNTs

Study of interactions between single walled carbon nanotubes and a flagellin-specific library of tripeptides

Dispersion of single walled carbon nanotube in water is hard to achieve due to the strong cohesive forces existing between them. A good dispersion of nanotubes is essential for their separation into their chirality based separation. Many surfactants like SDS have been used to create a dispersion of nanotubes and for their separation into different chiralities (zig-zag, armchair and chiral). The dual action of these surfactants is assumed to be due to their amphiphilic nature of a hydrophobic core surrounded by a hydrophilic head. The interaction of carbon nanotubes with biological molecules has been less studied hence finding peptides which can disperse the bundle or ropes of nanotube while displaying selective affinity for different kinds of nanotube can expand the small list of surfactants existing today. In this study, we create a tripepetide library from the D3 domain of flagellin (used in previous study by Macwan et al.) All the 9 tri-peptides in the library showed the presence of a middle glycine residue. Their interactions with single walled carbon nanotubes was studied using Visual Molecular Dynamics (VMD). RMSD provided quantitative and qualitative data to determine the extent and selectivity of the interactions, hence allowing us to screen the tri-peptide library to determine the tri-peptides with the best selective affinity for the nanotubes

Chirality Based Seperation of Carbon Nanotubes by Analyzing the Specific Interaction With the AMB-1 Flagellin Derived Tripeptide

Isaac et. al (2015) studied the interaction between the flagellum of AMB-1 and different chirality CNTs (m-CNT and s-CNT). The observations through Molecular Dynamics simulations demonstrated that the glycine residues in D3 domain of flagellum interacts with m-CNT whereas such an interaction with s-CNT is absent. The specific interaction of glycine with m-CNT can lead to the development of a biological method for chirality based CNT sorting. Hence, further studies were required to determine the effect of the residues flanking glycine on it’s interaction with m-CNT. The type of interactions and the extent of interaction of different combinations of polar and non-polar amino acid residues flanking glycine were conducted. Hence, the role of glycine with two flanking amino acid residues (tripeptide) is substantiated to determine it’s specific interaction with m-CNT through the study of interaction energy and RMSD of the middle glycine and the flanking residues towards the adsorption of the tripeptide onto m-CNT