Turn (biochemistry)

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A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.

Definition[edit]

According to the most common definition,[1] a turn is a structural motif where the Cα atoms of two residues separated by few (usually 1 to 5) peptide bonds are in close approach (< 7 Å), while the corresponding residues do not form a regular secondary structure element such as an alpha helix or beta sheet. Contrary to helices, the backbone dihedral angles are not (roughly) constant for all the residues in the turn.

Although the close approach of the two terminal Cα atoms is usually correlated with the forming of one or two hydrogen bonds between the corresponding residues, such hydrogen bond is not strictly required in the definition of the turn. That said, in most cases the H-bonding and Cα-distance definitions are equivalent.

Types of turns[edit]

Tight turns[edit]

Scheme of β turns (type I and type II)

Turns are classified[2] according to the separation between the two end residues:

  • In an α-turn the end residues are separated by four peptide bonds (i \rightarrow i\pm 4).
  • In a β-turn (the most common form), by three bonds (i \rightarrow i\pm 3).
  • In a γ-turn, by two bonds (i \rightarrow i\pm 2).
  • In a δ-turn, by one bond (i \rightarrow i\pm 1) (sterically unlikely).
  • In a π-turn, by five bonds (i \rightarrow i\pm 5).
Ideal angles for different \beta-turn types.[3] Types VIa1, VIa2 and VIb turns are subject to the additional condition that residue (i+2)(*) must be a cis-proline.
Type \phi_{i+1} \psi_{i+1} \phi_{i+2} \psi_{i+2}
I -60 -30 -90 0
II -60 120 80 0
VIII -60 -30 -120 120
I' 60 30 90 0
II' 60 -120 -80 0
VIa1 -60 120 -90 0*
VIa2 -120 120 -60 0*
VIb -135 135 -75 160*
IV

turns excluded from all the above categories

Within each type, turns may be further classified by their backbone dihedral angles (see Ramachandran plot). A turn can be converted into its inverse turn (also called its mirror-image turn) by changing the sign on all of its dihedral angles. (The inverse turn is not a true mirror image since the chirality of the Cα atoms is maintained.) 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 β-turn have been identified, varying mainly 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 usually distinguished with a prime, e.g., type I and type I' β-turns. However, if an i->i+3 hydrogen bond is taken as the criterion for turns, the four categories of Venkatachalam[4] (I, II, II', I') suffice[5] to describe all possible β-turns.

Loops[edit]

An ω-loop is a catch-all term for a longer, extended or disordered loop without fixed internal hydrogen bonding.

Multiple turns[edit]

In many cases, one or more residues are involved in two partially overlapping turns. For example, in a sequence of 5 residues, both residues 1-4 and residues 2-5 form a turn; in such a case, one speaks of a (I, I+1) double turn. Multiple turns (up to 7-fold) occur in proteins, and they are found to be more common than single turns.[6] Beta bend ribbons are a different type of multiple turn.

Hairpins[edit]

A hairpin is a special case of a turn, in which the direction of the protein backbone reverses and the flanking secondary structure elements interact. For example, a β-hairpin connects two hydrogen-bonded, antiparallel β-strands. (a rather confusing name, since a β-hairpin may contain many types of turns - α,β,γ, etc.)

β-hairpins may be classified according to the number of residues that make up the turn - that is, that are not part of the flanking β-strands.[7] If this number is X or Y (according to two different definitions of β sheets) the β hairpin is defined as X:Y

Role in protein folding[edit]

Two hypotheses have been proposed for the role of turns in protein folding. In one view, turns play a critical role in folding by bringing together and enabling or allowing interactions between regular secondary structure elements. This view is supported by mutagenesis studies indicating a critical role for particular residues in the turns of some proteins. Also, nonnative isomers of X-Pro peptide bonds in turns can completely block the conformational folding of some proteins. In the opposing view, turns play a passive role in folding. This view is supported by the poor amino-acid conservation observed in most turns. Also, non-native isomers of many X-Pro peptide bonds in turns have little or no effect on folding.

See also[edit]

External links[edit]

Notes[edit]

  1. ^ see Rose et al. 1985 in the References
  2. ^ Toniolo 1980
  3. ^ Venkatachalam 1968; Richardson 1981; Hutchinson and Thornton 1994
  4. ^ Venkatachalam, CM (1968). "Sterochemical criteria for polypeptides and proteins. V. Conformations of a system of three linked peptide units.". Biopolymers 6 (10): 1425–1436. doi:10.1002/bip.1968.360061006. PMID 5685102. 
  5. ^ Richardson, JS. "The anatomy and taxonomy of protein structure". Adv Protein Chem 34: 167–339. doi:10.1016/s0065-3233(08)60520-3. 
  6. ^ Hutchinson 1994, p 2213
  7. ^ Sibanda 1989

References[edit]

These references are ordered by date.