Alanine

Alanine is not just an amino acid with a smallest side chain. This is also the parent structure for the other 17 amino acids, only proline and glycine have different backbone architecture. The alanine and its derivatives all share common backbone features: there is one hydrogen-bond donor (NH), one hydrogen bond acceptor (C=O), one chiral center (with L-configuration). These features create the world dominated by the α-helix. Alanine is the father of the α-helix, the amino acid with the highest propensity to form this secondary structure.

Because alanine is a generic structure, other amino acids in the protein structure can be substituted with Ala with little to no consequences in the secondary structure fold. This approach is known as the alanine scan. One can one-by-one exchange the amino acids of interest with alanine, and observe the changes in the function. Thereby one can figure out, which side-chain function is involved in the function, whereas the folding will most likely remain unperturbed. The alanine scan is possible due to the fact that other 17 amino acids are built on the alanine core structure, otherwise a substitution would simply ruin the folding.

It is somehow surprising though, that polyalanine does not necessarily fold into an α-helix, but may tend to fold into an extended helix, the polyproline-II helix. This fact has a large significance for our understanding of the unfolded state in proteins.

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