title: A theoretical study on the stability of CNT encased cyclic peptide beyond hydrogen bond cut-off.
abstract: The Carbon nanotubes (CNT) are potential candidate for many biomedical applications especially in targeted drug delivery for cancer diseases. However, the use of CNT has limitations due to its insolubility in aqueous media. The self-assembly of cyclic peptide encased on the CNT has enhanced its dispersion in aqueous medium which extend their applications as antibacterial and drug delivery agents. To understand this process, an attempt has been made to investigate the dynamics and stability of trimer cyclic peptide encasing with CNT using classical molecular dynamics. The model cyclic peptide monomer constitutes 14 series of amino acids viz.; (cyclo-[(D-ARG-L-VAL-D-ARG-L-THR-D-AGR-L-LYS-D-GLY-L-ARG-D-ARG-L-ILE-D-ARG-L-ILE-D-PRO-L-PRO)]). Each cyclic peptide in the assembly stacking far apart at approximately 15 Å each other beyond hydrogen bond cut-off distance. The trimer was observed to be stable only over 10 ns of entire MD trajectory. But when there is electrostatic interaction between cyclic peptides at 6.5 Å distance then assembly is stable for entire 50 ns. Our result reveals that for a stable assembly, beyond the hydrogen bond cut-off distance, the electrostatic interaction plays significant role.
authors.affiliation: a Department of Chemistry , Bharathiar University , Coimbatore 641046 , India.
authors.forename: Subramanian
authors.initials: S
authors.lastname: Vidhyasankar
authors.affiliation: a Department of Chemistry , Bharathiar University , Coimbatore 641046 , India.
authors.forename: Nallasamy
authors.initials: N
authors.lastname: Dharmaraj
authors.affiliation: b Department of Physics , Bharathiar University , Coimbatore 641046 , India.
authors.forename: Ponmalai
authors.initials: P
authors.lastname: Kolandaivel
mesh_terms: D000465:Algorithms; D006860:Hydrogen Bonding; D008962:Models, Theoretical; D037742:Nanotubes, Carbon / Q000737:chemistry*; D010456:Peptides, Cyclic / Q000737:chemistry*; D055550:Protein Stability
chemical_list: D037742:Nanotubes, Carbon; D010456:Peptides, Cyclic
keywords: MM/PBSA; WCA; collective variable; cyclic peptide; encasing; free energy; hydrogen bond; molecular dynamic simulation; single-wall carbon nanotube