Part:BBa_K3561019

W3W4Q7

This peptide is expected to be a palladium reducing peptide. This peptide is modified by our team from the palladium reducing peptide Q7(Chiu et al., 2010). We implemented a double tryptophan structure at residues 3 and 4 as it was said that a double tryptophan is more effective than a single tryptophan structure in gold(Tan et al., 2010). We would like to investigate whether a double tryptophan will be more effective in palladium. We also want to investigate what effects will there have if we inserted the tryptophan residue at different positions.

This peptide has an isoelectric point of 6.0, a molecular weight of 0.94 kDa and hydrophobicity of 30.65. The serine residue at positions 7 is reported to be important in binding with palladium(Chiu et al., 2010). The tryptophan residue at positions 3 and 4 are reported to reduce palladium(Chiu et al., 2010). The amino acid sequence of the peptide is QQWWPIS.

References

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

DI;, Tan YN;Lee JY;Wang. Uncovering the Design Rules for Peptide Synthesis of Metal Nanoparticles. 2010, pubmed.ncbi.nlm.nih.gov/20355728/.

Chiu, et al. Size-Controlled Synthesis of Pd Nanocrystals Using a Specific Multifunctional Peptide. 2010, pubmed.ncbi.nlm.nih.gov/20648291/.

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.