Difference between revisions of "Part:BBa K3843001:Design"
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===Design Notes=== | ===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. Next, the protein's binding affinity to phenylethylamine was assessed using 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. The mutation and evaluation process was repeated once more to obtain a double mutant of 1UTM. | 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. Next, the protein's binding affinity to phenylethylamine was assessed using 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. The mutation and evaluation process was repeated once more to obtain a double mutant of 1UTM. | ||
Revision as of 05:41, 1 October 2021
Affinity-improved PEA-binding salmon trypsin (1UTM+)
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
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. Next, the protein's binding affinity to phenylethylamine was assessed using 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. The mutation and evaluation process was repeated once more to obtain a double mutant of 1UTM.
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.