Turn (biochemistry)

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A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction. For beta turns go to Beta turn.

Definition[edit]

According to one 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 close (< 7 Å), while the residues do not form a secondary structure element such as an alpha helix or beta sheet with regularly repeating backbone dihedral angles. Although the proximity of the terminal Cα atoms usually correlates with formation of a hydrogen bond between the corresponding residues, a hydrogen bond is not a requirement in this turn definition. That said, in many cases the H-bonding and Cα-distance definitions are equivalent.

Types of turns[edit]

Scheme of beta 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 Beta turn (much 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 (in which the main chain atoms have opposite chirality) by changing the sign on its dihedral angles. (The inverse turn is not a true enantiomer since the Cα atom chirality 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 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 Venkatachalam[4] (I, II, II', I') suffice[5] to describe all possible beta turns. All four occur frequently in proteins but I is commonest, followed by II, I' and II' in that order.

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 commonly in proteins.[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 beta 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.)

Beta 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

Beta turns at the loop ends of beta hairpins have a different distribution of types from the others; type I' is commonest, followed by types II', I and II.

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.