CONTRIBUTION
Background
iGEM team 2012 St_Andrews designed a peptide with Pd binding properties, BBa_K925005. However, no characterisation was carried out. Our team decided to carry out an in silico simulation to predict the peptide’s functionality and evaluate its stability.
Method
The structure of the Pd binding peptide designed by St Andrews was predicted by using I-TASSER. The peptide was solvated in water model spc216. The Molecular Dynamics (MD) simulation was performed using GROMACS 2020.3.
MD results
The interaction between the peptide and Pd was analysed through 4 aspects.
The distance of the O in hydroxyl group between threonine and Pd were evaluated for 80ns. The average and standard deviation of the distance were 2.286150981nm and 0.45291467nm respectively.
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 0.2429242nm and 0.036509137nm respectively. The small RMSD shows that the peptide was stable.
Radius of gyration (Rg) measures the compactness of the protein structure. The average and standard deviation of the Rg were 1.867476428nm and 0.015650297nm respectively.
Total energy of the system showed conservation of energy. The average and standard deviation of the total energy were -808423.6426 KJ/mol and 1443.8496 KJ/mol respectively.
Conclusion
The PdTagGST consists of a glutathione S-transferase protein, in which the molecular size (24.35 kilodaltons) is relatively larger than that of the palladium peptide (0.84 kilodaltons) proposed by St_Andrews. The intermolecular force between the Pd (II) ions and the Pd peptide may be weakened, as the larger sized GST may exhibit a stronger molecular interaction with Pd (II) ions. Therefore, the distance between the expected binding residue, threonine, and the Pd (II) ions was larger than expected. Further in vitro analysis is required to prove the binding ability of this part.