Methods

Correct folding study of target protein

1. Primer design for adding flanking regions which contained restriction sites for adding HER2 to pET28a which contains His-tag.
2. PCR to add the above mentioned flanking regions to HER2.
3. A restriction digestion was done on pET28a plasmid with the enzymes NheI-HF and NotI-HF simultaneously.
4. The PCR product obtained was also subjected to restriction digestion by the same enzymes.
5. Both the digests were run on a gel to confirm restriction digestion and a gel extraction was performed to get them back.
6. Now both the products were pooled together in the molar ratio of 1 part of pET28a to 2.5 parts of HER2 and an overnight ligation was performed with T4 ligase. the concentration was determined using a nanodrop.
7. These ligated products were then electroporated into Escherichia coli GB05 which were streaked onto kanamycin plates for selection.
8. These plates were checked for colonies and overnight cultures were setup from selected colonies.
9. A plasmid prep was performed on these o\n cultures to extract the pET28a-HER2 plasmid, following which a restriction digestion was performed with the enzymes NheI-HF and NotI-HF and run on a gel to confirm if the ligation was correct.
10. After this the plasmids extracted were sent for sequencing to double check if the ligated products were correct.
11. After finding that the sequences were correct, the plasmid pET28a-HER2 was electroporated into E. coli BL21 for protein expression.
12. A plasmid prep, a restriction digestion and a gel electrophoresis were done in tandem to confirm that the plasmids electroporated were correct.
13. After this 4 litre cultures were started from which protein extraction was performed.
14. The proteins extracted were subjected to affinity chromatography using a column with Ni which was specific to His tag.
15. The elution form the affinity column was subjected to size exclusion chromatography which gave 4 distinct peaks of which only three were selected and one was excluded as it was the peak for imidazole.
16. The elutes of the three peaks were subjected to CD (circular dichorism) spectroscopy which gave similar results to all three (majority alpha helices).
17. The deconvolution results were then compared with that from PDB to analyse if the protein has been folded correctly.
18. In addition a Blue Native PAGE was performed to detect if the different peaks were actually multimers of the same protein.

Structure analysis of our targets and their interactions

Investigation of P3 threshold for E. coli resistance

Conversion of BACTH into an iGEM standard and analysis of function

Set up of flow system