Properties and origins of protein secondary structure

Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local correlations along the protein chain. Using this definition and a simple model for proteins, the forces driving the formation of secondary structure are explored. The relative role of energy and entropy are examined. Recent work has indicated that compaction is sufficient to create secondary structure. We test this hypothesis, using simple nonlattice protein models.