Difference between revisions of "Part:BBa K3843001:Design"

Revision as of 17:51, 18 October 2021

Affinity-improved PEA-binding salmon trypsin (1UTM+)

Design Notes

• * REPLACE ABOVE SEQUENCE WITH IMPROVED SEQUENCE * *

To obtain the affinity-improved sequence, the original protein was first computationally mutated at every residue to every amino acid. Then, the stability of the mutated protein was assessed through overall energy scoring of the lone protein using Rosetta. Ultimately, only mutations occurring near the PEA-binding site were considered, as these mutations were most likely to affect binding. Next, the protein's binding affinity to phenylethylamine was assessed using ligand docking in AutoDock Vina as well as molecular dynamics simulations in GROMACS, which returned an energy score for the phenylethylamine+1UTM complex; lower energy scores indicated a higher binding affinity. The mutant with the highest binding affinity, where the mutation was in the active site of the protein, was chosen as the improved version of 1UTM. Combining multiple mutations by this process, the final affinity-improved 1UTM included the following mutations: LIST MUTATIONS

Source

The original sequence of this part was obtained from GenBank: https://www.ncbi.nlm.nih.gov/nuccore/X70071

With that said, the sequence of this part is a mutated version, obtained through computational rational protein design, as described above.

References