Protein Secondary Structure

Protein Secondary Structure

In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure.

Secondary structure can be formally defined by the hydrogen bonds of the biopolymer, as observed in an atomic-resolution structure. In proteins, the secondary structure is defined by the patterns of hydrogen bonds between backbone amino and carboxyl groups. In nucleic acids, the secondary structure is defined by the hydrogen bonding between the nitrogenous bases. The hydrogen bonding patterns may be significantly distorted, which makes an automatic determination of secondary structure difficult.

The secondary structure may be also defined based on the regular pattern of backbone dihedral angles in a particular region of the Ramachandran plot; thus, a segment of residues with such dihedral angles may be called a helix, regardless of whether it has the correct hydrogen bonds. The secondary structure may be also provided by crystallographers in the corresponding PDB file.

The rough secondary-structure content of a biopolymer (e.g., "this protein is 40% α-helix and 20% β-sheet.") can often be estimated spectroscopically. For proteins, a common method is far-ultraviolet (far-UV, 170-250 nm) circular dichroism. A pronounced double minimum at 208 and 222 nm indicate α-helical structure, whereas a single minimum at 204 nm or 217 nm reflects random-coil or β-sheet structure, respectively. A less common method is infrared spectroscopy, which detects differences in the bond oscillations of amide groups due to hydrogen-bonding. Finally, secondary-structure contents may be estimated accurately using the chemical shifts of an unassigned NMR spectrum.

Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang at Stanford in 1952.