Difference between revisions of "Part:BBa K3561004"
 
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[[File:BBa K3561004 distance 4.jpg|800px]]
 
[[File:BBa K3561004 distance 4.jpg|800px]]
  
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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 1.93 nm and 0.26 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 nine times the length.  
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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 1.93 nm and 0.262 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 nine times the length.  
  
 
The consistent distance of the tryptophan’s nitrogen and the Pd (II) indicates the four designed peptides can sequester the Pd (II) ion.  
 
The consistent distance of the tryptophan’s nitrogen and the Pd (II) indicates the four designed peptides can sequester the Pd (II) ion.  
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[[File:BBa K3561004 RMSD 4.jpg|800px]]
 
[[File:BBa K3561004 RMSD 4.jpg|800px]]
  
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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 0.08 nm respectively. Radius of gyration (Rg) measures the compactness of the protein structure. The average and standard deviation of the Rg were 0.76 nm and 0.03 nm respectively.
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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 0.318 nm and 0.0769 nm respectively. Radius of gyration (Rg) measures the compactness of the protein structure. The average and standard deviation of the Rg were 0.758 nm and 0.0343 nm respectively.
 
The small deviation in RMSD and Rg shows that the peptide was stable.
 
The small deviation in RMSD and Rg shows that the peptide was stable.
 
   
 
   
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[[File:BBa K3561004 total energy 4.jpg|800px]]
 
[[File:BBa K3561004 total energy 4.jpg|800px]]
  
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Total energy of the system showed conservation of energy. The average and standard deviation of the total energy were -297372 KJ/mol and 778.5 KJ/mol respectively.
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Total energy of the system showed conservation of energy. The average and standard deviation of the total energy were -297000 KJ/mol and 779 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.
 
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.  
 
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.  
  
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===Shaking Flask Cultivations===
 
 
<h2>Reference</h2>
 
<h2>Reference</h2>
 
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.
 
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.

Latest revision as of 15:34, 26 October 2020


W3W4A6C11

This peptide is expected to be a palladium reducing peptide. This peptide is modified by our team from the palladium binding peptide A6C11 (Coppage et al., 2013). We have incorporated a tryptophan residue into the peptide as it was reported that tryptophan is capable of reducing palladium (Chiu et al., 2010). We chose 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 would also like to investigate what effects will there have if we inserted the tryptophan residue at different positions.

This peptide has an isoelectric point of 9.0, a molecular weight of 1.43 kDa and hydrophobicity of 37.71. The alanine residue at position 6 has a minimal binding with palladium while the cysteine residue at position 11 has a strong binding with palladium, it was suggested that this may have higher efficiency(Coppage et al., 2013). The serine and threonine residues at position 2 and 10 are also reported to be important in binding with palladium(Sarikaya et al., 2003). The amino acid sequence of the peptide is TSWWVAPTLRCL.

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.

Coppage, et al. “Exploiting Localized Surface Binding Effects to Enhance the Catalytic Reactivity of Peptide-Capped Nanoparticles.” Journal of the American Chemical Society, U.S. National Library of Medicine, 2013, pubmed.ncbi.nlm.nih.gov/23865951/.

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

DI;, Tan YN;Lee JY;Wang. Uncovering the Design Rules for Peptide Synthesis of Metal Nanoparticles. 2010, pubmed.ncbi.nlm.nih.gov/20355728/. 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 K3561004 distance 4.jpg

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 1.93 nm and 0.262 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 nine times the length.

The consistent distance of the tryptophan’s nitrogen and the Pd (II) indicates the four designed peptides can sequester the Pd (II) ion.


BBa K3561004 radius of gyration 4.jpg BBa K3561004 RMSD 4.jpg

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 0.318 nm and 0.0769 nm respectively. Radius of gyration (Rg) measures the compactness of the protein structure. The average and standard deviation of the Rg were 0.758 nm and 0.0343 nm respectively. The small deviation in RMSD and Rg shows that the peptide was stable.


BBa K3561004 total energy 4.jpg

Total energy of the system showed conservation of energy. The average and standard deviation of the total energy were -297000 KJ/mol and 779 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.