Part:BBa_K3561018
G5Q7
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 have incorporated a glutamine residue at position 5, glutamine was reported as a strong binder, glutamine residues were also found in the active sites of various palladium binding proteins, suggesting an active role in binding. We wish to explore its effects in this peptide.
This peptide has an isoelectric point of 6.0, a molecular weight of 0.80 kDa and hydrophobicity of 16.68. The serine residue at positions 3 and 7 are reported to be important in binding with palladium(Chiu et al., 2010). The tryptophan residue at position 4 is reported to reduce palladium(Chiu et al., 2010). The amino acid sequence of the peptide is QQSWGIS.
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 2.54 nm and 0.76 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 twelve 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 0.32 nm and 0.09 nm respectively. Radius of gyration (Rg) measures the compactness of the protein structure. The average and standard deviation of the Rg were 0.59 nm and 0.046 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 -164952 KJ/mol and 579 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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