In 1976 only 56 protein structures were available in the PDB cite(bernstein1977), yet tertiary structure had already been generally classified into four secondary structure classes cite(levitt1976) and three different 'folding units' or supersecondary structures cite(lesk2001), speculated to be the 'building blocks' of tertiary structure cite(levitt1976,chothia1977). The prevalence of common secondary and supersecondary structures in proteins is explained by the thermodynamic stability conferred by these protein conformations cite(chothia1984,finkelstein1987). Thus, for any given amino-acid sequence, only a few stable secondary and supersecondary conformations are available. For a protein to reliably assume a functional topology in a biological system, these structural units can be converged on over the course of evolution as consistent `means to an overall functional end'. Proteins are amino acid chains, made up from 20 different L-α-amino acids, also referred to as residues, that fold into unique three-dimensional protein structures. ...
Secondary structure is defined by the phi and psi angles of the backbone atoms of the amino acid residues, and the hydrogen bonds between main chain atoms.
Classic units of supersecondarystructure include the alpha-alpha unit (two antiparallel alpha-helices joined by a 'hairpin' bend changing the chain direction by 180°); the beta-beta unit (two antiparallel strands connected by a hairpin); and the beta-alpha-beta unit (two parallel strands, separated by an alpha-helix antiparallel to them, with 2 hairpins separating the three secondary structures).
Quaternary structure is the subject of a later chapter of the course.
The secondary structure of a protein is the 3D arrangement of amino acid residues that are relatively near one another in the linear sequence (Stryer (1988)).
Secondary structure is created by hydrogen bonding between the alpha-amide groups and alpha-carbonyl groups of the backbone, to enable globular proteins to retain a minimum energy conformation (Chothia (1984)), and common patterns occur in the majority of proteins, despite vastly dissimilar overall structures.
Protein structure is often divided into four classes: ‘all-alpha‘ have only alpha-helical structures, ‘all-ß‘ have only ß-sheet structures, ‘alpha+ß‘ have both alpha-helices and ß-sheets but the two types of structure are in different sections of the linear sequence, and ‘alpha/ß‘ have both structures mixed along the protein chain (Levitt and Chothia (1976)).
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