A phage library displaying random 8-residue peptides is sorted for binding to Re

Question

A phage library displaying random 8-residue peptides is sorted for binding to Receptor O. The phage library represent 25,600,000,000 possible peptides. The selected phage all have sequences of the form XFYXXSLI, where X is any amino acid. Isolated peptide sequence = XFYXXSLI (X = Any amino acid). The presence of any amino acid at these positions indicates that these amino acid positions are not important for the interaction.

One of the selected phage from the problem above displays a peptide with the sequence SFYDNSLI. Predict the results of an alanine scan of this peptide? Explain.

Explanation / Answer

Alanine scanning is a molecular biology technique used to determine the importance/significance of a specific amino acid residue in a polypeptide to its structure or function. This is typically achieved by changing a specific amino acid to alanine and observe the effect the protein structure and function.

In this technique, alanine is used because

i. It is not bulky

ii. It is non-reactive

iii. Its methyl group mimics side chains of many of the other amino acids.

In the given experiment,

Consensus sequence = XFYXXSLI

So, first, fourth and fifth amino acid positions are dispensible.

If we replace these (first, fourth and fifth) amino acids with alanine, Kd values would not change.

If we replace the other (excluding first, fourth and fifth) amino acids with alanine, Kd values would not change (Most like increase. However, the decrease can also be seen in a few cases).

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