Difference between revisions of "Part:BBa K3561018"
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<span class='h3bb'>Sequence and Features</span> | <span class='h3bb'>Sequence and Features</span> | ||
<partinfo>BBa_K3561018 SequenceAndFeatures</partinfo> | <partinfo>BBa_K3561018 SequenceAndFeatures</partinfo> | ||
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| + | <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. | ||
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| + | 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. | ||
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| + | 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. | ||
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| + | More details of how our molecular dynamics is run can be found on our team wiki. | ||
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| + | [[File:BBa K3561018 radius of gyration 18.jpg|800px]] | ||
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| + | [[File:BBa K3561018 distance 18.jpg|800px]] | ||
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| + | [[File:BBa K3561018 RMSD 18.jpg|800px]] | ||
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| + | [[File:BBa K3561018 total energy 18.jpg|800px]] | ||
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Revision as of 14:06, 21 October 2020
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.
