Where would you expect to find serine and alanine in a globular protein in an aqueous solution?

Answer 1

Alanine is very hydrophobic as it is non-polar at its (medium sized) side chain. This means it will most often be found in the internal regions of a globular protein in an aqueous solution, as it will become buried during the hydrophobic collapse of the early stages of protein folding. There will be exceptions to this when the majority of amino acids near it in the polypeptide chain are hydrophilic.

Serine has a polar hydroxyl group, making it slightly hydrophilic. You would therefore expect it to appear on the surface of the protein more often, or lining aqueous channels. It is only a little hydrophilic though, so it would not be surprising to find a more even distribution of serine around both the internal regions and external surfaces of the protein. More importantly though, the hydroxyl group of serine can be very reactive, particularly in certain environments produced by surrounding amino acids. Since it is very reactive, it is a common components of the catalytic (active) site of enzymes. For example, the catalytic triad of some protease enzymes.