title: Designing new surfactant peptides for binding to carbon nanotubes via computational approaches.
abstract: The non-covalent interaction between single-walled carbon nanotube and surfactant peptides makes them soluble in biological media to be used in nano-medicine, drug delivery and gene therapy. Pervious study has shown that two important parameters in binding peptides into nanotubes are hydrophobic effect and the number of aromatic amino acids. Ten surfactant peptides with the length of eight residue, including Lys, Trp, Tyr, Phe and Val, were designed to investigate the important parameters in binding peptides to a (6, 6) carbon nanotube. 500ns MD simulation was performed for free surfactant peptides in water or near to a nanotube. Our results have indicated that the binding affinity of peptides to nanotube increases with the increase of aromatic residue content. Also, among aromatic residues, the peptides containing Trp residues have higher binding affinity to nanotube compared to the peptides with Phe or Tyr residue. Steric hindrance between bulky aromatic residues in peptide sequence has negative influence in binding peptide to nanotube, and in designing a surfactant peptide, the number and distance of aromatic residue and polarity of them should be taken into account. Our results also show that in docking peptides to nanotube, full-flexible docking leads to incorrect results.
authors.affiliation: Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran; Department of Biophysics, Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran.
authors.forename: Alireza
authors.initials: A
authors.lastname: Mansouri
authors.affiliation: Department of Biology, Faculty of Science, University of Shahrekord, Shahrekord, Iran. Electronic address: mahnam.karim@sci.sku.ac.ir.
authors.forename: Karim
authors.initials: K
authors.lastname: Mahnam
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D037742:Nanotubes, Carbon / Q000737:chemistry*; D009842:Oligopeptides / Q000737:chemistry*; D013501:Surface-Active Agents / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D037742:Nanotubes, Carbon; D009842:Oligopeptides; D013501:Surface-Active Agents
keywords: Carbon nanotubes; Docking; MM-PBSA binding free energy; Molecular dynamics simulation; Steric hindrance; Surfactant peptide