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Design of a Novel Metal Binding Peptide by Molecular Dynamics Simulation to Sequester Cu and Zn Ions



Mahnam K1 ; Saffar B2, 3 ; Mobinidehkordi M2, 3 ; Fassihi A4 ; Mohammadi A2
Authors
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Authors Affiliations
  1. 1. Biology Department, Faculty of Science, Shahrekord University, Shahrekord, I.R., Iran
  2. 2. Genetics Department, Faculty of Science, Shahrekord University, Shahrekord, I.R., Iran
  3. 3. Research Institute of Biotechnology, Shahrekord University, Shahrekord, I.R., Iran
  4. 4. Department of Medicinal Chemistry, Isfahan Bioinformatic Research Center, Isfahan University of Medical Sciences, Isfahan, I.R., Iran

Source: Research in Pharmaceutical Sciences Published:2014

Abstract

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 (EC11:His 6) was investigated to determine if it can absorb Cu2+ or Zn2+ cations. Molecular dynamics simulations were carried out using a model of 6 Cu2+ or Zn2+ 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 EC11 in the designed peptide can absorb these ions. Sequestration of Cu2+ or Zn2+ ions by the designed peptide does not change overall tertiary and secondary structures of peptide.
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