Design of a novel metal binding peptide by molecular dynamics simulation to sequester Cu and Zn ions

Heavy metal toxicity has serious adverse effects on the environment. The metal sequestering characteristics of a novel metal binding peptide (Glu-Cys)(11) Gly+linker+hexahistidine (EC(11):His(6)) was investigated to determine if it can absorb Cu(2+) or Zn(2+) cations. Molecular dynamics simulations were carried out using a model of 6 Cu(2+) or Zn(2+) and other ions enclosed in a fully hydrated simulation box with the designed peptide. Totally, 240 nano second (ns) simulations were done in three phases. Results showed that the selected linker is able to separate two domains of this peptide and that the carboxyl oxygens of Glu residues of EC(11) in the designed peptide can absorb these ions. Sequestration of Cu(2+) or Zn(2+) ions by the designed peptide does not change overall tertiary and secondary structures of peptide.