Part:BBa_K3561017
Q7 (Chiu et al., 2010)
This peptide is a palladium reducing peptide. It is used in this project as a library peptide, this peptide's performance in molecular dynamics and reducing efficiency will be used as a standard to compare with our own designed peptides. This peptide has an isoelectric point of 6.0, a molecular weight of 0.84 kDa and hydrophobicity of 19.50. The serine residues at positions 3 and 7 are reported to contribute to the binding ability of the peptide and the tryptophan residue at position 4 is able to reduce palladium(Chiu et al., 2010). The amino acid sequence of this peptide is QQWPIS.
References
Chiu, et al. Size-Controlled Synthesis of Pd Nanocrystals Using a Specific Multifunctional Peptide. 2010, pubmed.ncbi.nlm.nih.gov/20648291/.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE 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 distance of the N in indole group between threonine and Pd was evaluated for 80ns. The average and standard deviation of the distance were 1.99 nm and 0.591 nm respectively. Pd-N bond length in Dichlorido{2,6-diisopropyl-N-[(S)- pyrrolidin-2-ylmethyl]aniline-j2 N,N0}- palladium (II) is 2.040 Å1 and the four peptides have an average distance around ten times the length. The inconsistent distance of the tryptophan’s nitrogen and the Pd (II) indicates the four designed peptides cannot sequester the Pd (II) ion.
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 0.339 nm and 0.0647 nm respectively. Radius of gyration (Rg) measures the compactness of the protein structure. The average and standard deviation of the Rg were 0.621 nm and 0.0476 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 -92100 KJ/mol and 446 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.
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