The secondary structure of a
protein is an interesting phenomenon. When a protein
folds, it is believed that stretches of the
primary sequence pre-assemble into structures such as
alpha helices or
beta strands. This is the first and fastest process of protein folding. These secondary structural elements then join together in various patterns forming the
tertiary fold.
Alpha helices look like winding staircases of amino acids, while
beta sheets look like flat surfaces (generally). Whether a region of a protein forms a helix or a sheet is determined by many different factors, which are still under investigation today.
To a large extent, the primary sequence is a contributing factor because specific amino acids have propensities to form helices over sheets, or vice versa. Given these known propensities, people have tried to predict secondary structure as a preliminary solution to the protein folding problem. Sophisticated rule based algorithms have been implemented in neural nets which are becoming better and better at achieving success.
See also:
primary structure
tertiary structure
quaternary structure