At –rst glance, most proteins look like a chaotic crowding of atoms. A closer look, however, reveals a complex structure organized in a hierarchical manner[3] (Figure 2.1). e –rst level of this hierarchy, referred to as the primary structure, is the ordered sequence of amino acids composing the protein chain. Certain segments within this chain tend to fold into simple shapes, such as helices, loops, etc. ese structures are referred to as secondary elements, and collectively constitute the second level of the protein hierarchy, the secondary structure. Secondary elements are local, and (except for loops) proceed along one axis of the protein chain. e overall chain tends to fold further into a three-dimensional compact tertiary structure, which constitutes the third level of the hierarchy. As explained in Chapter 1, the tertiary structure is the most stable form of the protein, since it optimizes the various attraction forces between di˜erent amino acids that compose the chain. Moreover, the tertiary structure is also the biologically active form of the protein, and its disruption renders the protein partially or completely inactive. erefore, it is o®en referred to as the native structure of the protein.