Difference between revisions of "Part:BBa K3561001"

Latest revision as of 15:52, 27 October 2020

Pd4 (Pacardo et al., 2009)

Pd4 is a 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 peptide has an isoelectric point of 11.1, a molecular weight of 1.35 kDa and hydrophobicity of 21.38. The histidine residues at positions 6 and 11 are reported to bind to palladium and arginine is reported to coordinate with palladium in the literature of which the peptide is discovered(Pacardo et al., 2009). The serine and threonine residues at positions 1 and 2 are also reported to be important in binding with palladium(Sarikaya et al., 2003). The amino acid sequence is TSNAVHPTLRHL.

References

Pacardo, et al. “Biomimetic Synthesis of Pd Nanocatalysts for the Stille Coupling Reaction.” ACS Nano, U.S. National Library of Medicine, 2009, pubmed.ncbi.nlm.nih.gov/19422199/.

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 0.293 nm and 0.0675 nm respectively. Radius of gyration (Rg) measures the compactness of the protein structure. The average and standard deviation of the Rg were 0.719 nm and 0.0484 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 -85300 KJ/mol and 436 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.

@@ Line 2: / Line 2: @@
 <partinfo>BBa_K3561001 short</partinfo>
-Pd4 is a 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 peptide has an isoelectric point of 11.1, a molecular weight of 1.35 kDa and hydrophobicity of 21.38. The histidine residues at positions 6 and 11 are reported to bind to palladium and arginine is reported to coordinate with palladium in the literature of which the peptide is discovered(Pacardo et al., 2009). The serine and threonine residues at positions 1 and 2 are also reported to be important in binding with palladium(Sarikaya et al., 2003).
+Pd4 is a 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 peptide has an isoelectric point of 11.1, a molecular weight of 1.35 kDa and hydrophobicity of 21.38. The histidine residues at positions 6 and 11 are reported to bind to palladium and arginine is reported to coordinate with palladium in the literature of which the peptide is discovered(Pacardo et al., 2009). The serine and threonine residues at positions 1 and 2 are also reported to be important in binding with palladium(Sarikaya et al., 2003). The amino acid sequence is TSNAVHPTLRHL.
-<h2>References:</h2>
+<h2>References</h2>
 Pacardo, et al. “Biomimetic Synthesis of Pd Nanocatalysts for the Stille Coupling Reaction.” ACS Nano, U.S. National Library of Medicine, 2009, pubmed.ncbi.nlm.nih.gov/19422199/.
@@ Line 15: / Line 15: @@
 <span class='h3bb'>Sequence and Features</span>
 <partinfo>BBa_K3561001 SequenceAndFeatures</partinfo>
+<h2>Modelling</h2>
+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.
+[[File:BBa K3561001 radius of gyration 1.jpeg|800px]]
+[[File:BBa K3561001 RMSD 1.jpg|800px]]
+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 0.293 nm and 0.0675 nm respectively. Radius of gyration (Rg) measures the compactness of the protein structure. The average and standard deviation of the Rg were 0.719 nm and 0.0484 nm respectively.
+The small deviation in RMSD and Rg shows that the peptide was stable.
+[[File:BBa K3561001 total energy 1.jpg|800px]]
+Total energy of the system showed conservation of energy. The average and standard deviation of the total energy were -85300 KJ/mol and 436 KJ/mol respectively.
+The average and standard deviation were very close to our expected values from simulations of Cu2+ and Zn2+ ion binding peptides<sup>1</sup>. 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.
+<h2>Reference</h2>
+. 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.