Bioinformatics Protein Structure Structure Analysis

Turns Secondary Structure of Proteins

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According to one definition a turn is a structural motif where the Cα atoms of two residues separated by a few (usually 1 to 5) peptide bonds are close (less than 7 Å ). The proximity of the terminal Cα atoms often correlates with formation of an inter main chain hydrogen bond between the corresponding residues. Such hydrogen bonding is the basis for the original, perhaps better known, turn definition. In many cases, but not all, the hydrogen-bonding and Cα-distance definitions are equivalent.

Types

Turns are classified according to the separation between the two end residues:

  • In an α-turn the end residues are separated by four peptide bonds (i → i ± 4).
  • In a β-turn (the most common form), by three bonds (i → i ± 3).
  • In a γ-turn, by two bonds (i → i ± 2).
  • In a δ-turn, by one bond (i → i ± 1), which is sterically unlikely.
  • In a π-turn, by five bonds (i → i ± 5).

Turns are further classified by their backbone dihedral angles . A turn can be converted into its inverse turn (in which the main chain atoms have opposite chirality) by changing the sign on its dihedral angles. Thus, the γ-turn has two forms, a classical form with (φ, ψ) dihedral angles of roughly (75°, −65°) and an inverse form with dihedral angles (−75°, 65°). At least eight forms of the beta turn occur, varying in whether a cis isomer of a peptide bond is involved and on the dihedral angles of the central two residues. The classical and inverse β-turns are distinguished with a prime, e.g., type I and type I′ beta turns. If an i → i + 3 hydrogen bond is taken as the criterion for turns, the four categories of 

β-Turns 

All β-turns have four residues and are divided into classes based on the range of their phi and psi values for the second and third residues. Most classes have a hydrogen bond between the backbone atoms of residues.

Gamma Turns 

Gamma turns consist of three residues and contain a hydrogen bond between residues one and three. Several examples of β-hairpins follow:

  • Alpha-Lytic protease; Isolated turn
  • Proteinase A; Isolate Turn
  • Thermolysin; Isolated turn – Unusual because it has two hydrogen bonds.
  • Flavodoxin; Isolated turn

Turns are located primarily on the protein surface and accordingly contain polar and charged residues. Antibody recognition, phosphorylation, glycosylation, hydroxylation, and intron/exon splicing are found frequently at or adjacent to turns. 

Definitions of turns can be grouped into two classes;

  • Reference, based on stereochemical templates
  • Requirement for a hydrogen bond and working

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