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. 2014 Jan-Feb;9(1):69-82.

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

K Mahnam  1 , B Saffar  2 , M Mobini-Dehkordi  2 , A Fassihi  3 , A Mohammadi  4
Affiliations

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

K Mahnam et al. Res Pharm Sci. 2014 Jan-Feb.

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:His6) 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 EC11 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.

Keywords: Metal binding peptide; Molecular dynamics.

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Figures

Fig. 1
Fig. 1
Root mean square deviation (RMSD) of protein backbone during 80 ns MD simulation in phase
Fig. 2
Fig. 2
The kinetics and potential energies during 80 ns MD simulations in phase I.
Fig. 3
Fig. 3
Distance between center of mass EC11 of sequence from center of mass hexahistidine sequence during 80 ns MD simulation.
Fig. 4
Fig. 4
Na+ or Cl- to oxygen (of Glus of EC11) radial distribution function in phase I.
Fig. 5
Fig. 5
Ramachandran plot and plot statistics of native EC11:His6 model.
Fig. 6
Fig. 6
G-factors of some properties of final model in phase I.
Fig. 7
Fig. 7
Projection of Cα motions of EC11:His6 during 80 ns MD simulation onto its first 3 principal components in phase I.
Fig. 8
Fig. 8
Projections of EC11:His6 structures found in 80 ns MD simulation on to the 1–2 eigenvector plane in Phase I.
Fig. 9
Fig. 9
Minimum distance between Zn2+ ions and sulfur atoms of cysteines during 80 ns MD simulation in phase II.
Fig. 10
Fig. 10
Detention time for Zn2+ ions and Cu2+ ions versus distance from carboxyl oxygen of glutamic acid residues of EC11.
Fig. 11
Fig. 11
Zn2+ or Cu2+ to oxygen (of Glus of EC11) radial distribution functionsin phases II and III.
Fig. 12
Fig. 12
Minimum distances between Cu2+ ions and sulfur of cysteine residues during 80 ns MD simulation in phase III.
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