Question

Peptide: YCQKWMWTCDSARKCCEGPVCRPWCKKII

Imagine conducting the following experiment. Take a sample of the native folded peptide and measure the amount of peptide required to inhibit the activity of a potassium channel, say the Kv4.2 channel, by 50%. We will call this value the IC₅₀ value. For our peptide, IC₅₀ = 5 nM for the Kv4.2 channel. Treat the peptide with a mixture of 2-mercaptoethanol and guanidine hydrochloride. Remove the 2-mercatoethanol and then the guanidine hydrochloride to allow the peptide to refold. Treat the Kv4.2 channel with the refolded peptide and measure the IC₅₀ value. If the IC₅₀ value is now 250 nM, does this peptide sequence obey the Anfinsen dogma? Explain.

Answer 1

In the given scenario, the IC50 value of the refolded peptide increased 50 fold than the native peptide. This indicates that the peptide sequence does not obey Anfinsen dogma.

Anfinsen dogma:

The native folded structure of the protein is the thermodynamically most stable conformation and protein folding is purely based on the amino acid sequence.

So, according to Anfinsen, if a protein is denatured by 2-mercatoethanol or guanidine hydrochloride, the unfolded protein should regain the native conformation once the denaturants are removed from the environment and regain its activity.

In the present scenario, the peptide has an IC50 of 5nM to inhibit the activity of Kv4.2 channel. After denaturation and removal of the denaturing agents, 2-mercatoethanol and guanidine hydrochloride, the refolded peptide has an IC50 of 250nM which indicates that the refolded peptide does not have the inhibitory activity of the native folded peptide. This loss of inhibitory activity may have occurred due to incorrect refolding of the peptide and random disulfide bond formation leading to misfolded peptide.

According to Anfinsen dogma, the refolded peptide should have the same IC50 as the native folded peptide. Hence, this peptide does not obey Anfinsen dogma.