Difference between revisions of "Part:BBa K3561017"
Line 15: Line 15:
 
<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
 
<partinfo>BBa_K3561017 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K3561017 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 K3561017 radius of gyration 17.jpg|800px]]
 +
 +
[[File:BBa K3561017 distance 17.jpg|800px]]
 +
 +
[[File:BBa K3561017 RMSD 17.jpg|800px]]
 +
 +
[[File:BBa K3561017 total energy 17.jpg|800px]]
 +
 +
  
  

Revision as of 14:05, 21 October 2020


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


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.


BBa K3561017 radius of gyration 17.jpg

BBa K3561017 distance 17.jpg

BBa K3561017 RMSD 17.jpg

BBa K3561017 total energy 17.jpg