Part:BBa_K3561021

SVTQNKY(Sarikaya et al., 2003)

This part is a reported palladium binding peptide. It is used as a library peptide in our project to act as a template for our mutations. The results of molecular dynamics for our modified peptides are also compared with this peptide. This palladium binding peptide was also used by team St Andrew's in 2012 (BBa_K925005).

This peptide has an isoelectric point of 9.7, a molecular weight of 0.84kDa and hydrophobicity of 5.86. The serine and threonine residues at positions 1 and 3 are reported to be important in the binding of palladium(Sarikaya et al., 2003).

References

Sarikaya, et al. “Molecular Biomimetics: Nanotechnology through Biology.” Nature News, Nature Publishing Group, 2003, www.nature.com/articles/nmat964.

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  COMPATIBLE WITH RFC[21]
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]

Modelling

From our molecular dynamics, we were able to determine the distance of the peptide from the palladium ion, the radius of gyration, the RMSD score and the total energy of the system.

We can compare the bond lengths of our peptides with the distances reported by previous literature to evaluate the attraction between the palladium ion and the peptide. The distance should also stay consistent.

The radius of gyration represent the compactness of the peptide, the peptide is generally more stable if the standard deviation is smaller. RMSD measures the average distance each atom deviated from the start of the simulation. A small deviation in RMSD indicates a stable structure.

We have also evaluated the total energy of the system during the simulation, if the total energy of the system varies a lot, it indicates that the law of energy conservation has not been fulfilled and further in vitro analysis is required to prove its reducing ability.

More details of how our molecular dynamics is run can be found on our team wiki.

The root mean square deviation (RMSD) of peptide backbone atoms measures the structure of the peptide throughout the simulation. The average and standard deviation of the RMSD were 0.179 nm and 0.08 nm respectively. Radius of gyration (Rg) measures the compactness of the protein structure. The average and standard deviation of the Rg were 0.55 nm and 0.047 nm respectively. The small deviation in RMSD and Rg shows that the peptide was stable.

Total energy of the system showed conservation of energy. The average and standard deviation of the total energy were -195233 KJ/mol and 632 KJ/mol respectively. The average and standard deviation were very close to our expected values from simulations of Cu2+ and Zn2+ ion binding peptides¹. This proves our system fulfils the law of energy conservation.

However, we must acknowledge that in silico molecular modelling cannot fully represent the experimental environment. Further in vitro analysis is required to prove the binding and reducing ability of this part.

Reference

1. Mahnam, K., Saffar, B., Mobini-Dehkordi, M., Fassihi, A., & Mohammadi, A. (2014). Design of a novel metal binding peptide by molecular dynamics simulation to sequester Cu and Zn ions. Research in pharmaceutical sciences, 9(1), 69–82.