Structural features of proteins

The structural organization of proteins follows a hierarchical order: from the specific order of amino acids forming the polypeptide chain (primary sequence), to local organization of polypeptide stretches (secondary structure elements), followed by the overall spatial, three-dimensional protein organization (tertiary structure), and finally the interactions between various folded chains (quaternary structure). The three-dimensional spatial arrangement adopted by the protein is defined by three dihedral angles, ω, φ, ψ, which describe the rotation of the backbone atoms about the C-N', N-Ca, and Ca-C bonds, respectively, and determine the relative orientation of the groups forming the protein backbone. The allowed φ and ψ angles that the backbone of a polypeptide chain can adopt are limited within specific ranges summarized by the "Ramachandran plot." Residues located in different types of secondary structure have different φ/ψ combinations and hydrogen bond patterns between the carbonyl oxygen and the amide hydrogen of the amino acids. The most common types of secondary structure elements are helices, parallel and antiparallel pleated ß-sheets, and ß-turns. They can also combine forming structural motifs that constitute portions of the overall tertiary structure and are often related to specific functional features. Different combinations of secondary structure elements and motifs form structural domains. The latter are the fundamental units of the tertiary structure, and comprise parts of the polypeptide chain that are structurally independent and can fold separately. Each structural domain can be classified according to its content of a-helices and ß-sheets, and their relative location. At this simplest level of classification, the types of folds are grouped into four main classes: a, ß, a/ß, and a + ß classes. A fifth class is formed by protein domains that have little if any secondary structure. Many proteins can assemble into multimeric proteins composed of two or more monomers, defining a quaternary structure.