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Turn (biochemistry)



A turn is an element of secondary structure in proteins.

According to the most common definition, a turn is defined by the close approach of two Cα atoms (< 7 Å), when the corresponding residues are not involved in a regular secondary structure element such as an alpha helix or beta sheet.

Additional recommended knowledge

Contents

Types of turns

Turns are grouped by their hydrogen bonding and by their backbone dihedral angles.

At the level of hydrogen bonds, the nomenclature is similar to that of helices.

  • A β-turn (the most common form) is characterized by hydrogen bond(s) in which the donor and acceptor residues are separated by three residues (i \rightarrow i\pm 3 H-bonding).
  • A γ-turn is characterized by hydrogen bond(s) in which the donor and acceptor residues are separated by two residues (i \rightarrow i\pm 2 H-bonding).
  • An α-turn is characterized by hydrogen bond(s) in which the donor and acceptor residues are separated by four residues (i \rightarrow i\pm 4 H-bonding).
  • A π-turn is characterized by hydrogen bond(s) in which the donor and acceptor residues are separated by five residues (i \rightarrow i\pm 5 H-bonding).

Finally, an ω-loop is a catch-all term for a longer loop with no internal hydrogen bonding.

Strictly speaking, a turn is defined by the close approach (< 7 Å) of Cα atoms and need not have a well-formed hydrogen bond. Thus, it is more correct to define a β-turn by the close approach of Cα atoms of residues separated by three peptide bonds, a γ-turn by the close approach of Cα atoms of residues separated by two peptide bonds, etc. In most cases, the H-bonding and Cα-distance definitions are equivalent.

Within each hydrogen-bonding type, turns may be classified by their backbone dihedral angles. 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 \left( 75^{\circ}, -65^{\circ} \right) and an inverse form with dihedral angles \left( -75^{\circ}, 65^{\circ} \right). 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 \mathrm{I}^{\prime} β-turns.

Hairpins vs. diverging turns

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.

However, turns can cause less drastic changes in direction and may connect regular secondary structure elements that do not interact with each other. Such turns are called diverging turns.

Role in protein folding

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 fostering 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

References

  • Venkatachalam CM (1968) "Stereochemical Criteria for Polypeptides and Proteins. V. Conformation of a System of 3 Linked Peptide Units", Biopolymers, 6, 1425-1436.
  • Némethy G and Printz MP. (1972) "The γ-Turn, a Possible Folded Conformation of the Polypeptide Chain. Comparison with the β-Turn", Macromolecules, 5, 755-758.
  • Lewis PN, Momany FA and Scheraga HA. (1973) "Chain Reversals in Proteins.", Biochim. Biophys. Acta, 303, 211-229.
  • Toniolo C. (1980) "Intramolecularly Hydrogen-Bonded Peptide Conformations", CRC Crit. Rev. Biochem., 9, 1-44.
  • Richardson JS. (1981) "The anatomy and taxonomy of protein structure", Adv. Protein Chem., 34, 167-339.
  • Rose GD, Gierasch LM and Smith JA. (1985) "Turns in peptides and proteins", Adv. Protein Chem., 37, 1-109.
  • Milner-White EJ and Poet R. (1987) "Loops, bulges, turns and hairpins in proteins", TIBS, 12, 189-192.
  • Wilmot CM and Thornton JM. (1988) "Analysis and Prediction of the Different Types of β-Turn in Proteins", J. Mol. Biol., 203, 221-232.
  • Milner-White EJ. (1990) "Situations of Gamma-turns in Proteins: Their Relation ot Alpha-helices, Beta-sheets and Ligand Binding Sites", J. Mol. Biol., 216, 385-397.
  • Pavone V, Gaeta G, Lombardi A, Nastri F, Maglio O, Isernia C, and Saviano M. (1996) "Discovering Protein Secondary Structures: Classification and Description of Isolated α-Turns", Biopolymers, 38, 705-721.
  • Rajashankar KR and Ramakumar S. (1996) "π-Turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence", Protein Sci., 5, 932-946.


Protein secondary structure
Helices: α-helix | 310 helix | π-helix | β-helix | Polyproline helix | Collagen helix
Extended: β-strand | Turn | Beta hairpin | Beta bulge | α-strand
Supersecondary: Coiled coil | Helix-turn-helix | EF hand
Secondary structure propensities of amino acids
Helix-favoring: Methionine | Alanine | Leucine | Glutamic acid | Glutamine | Lysine
Extended-favoring: Threonine | Isoleucine | Valine | Phenylalanine | Tyrosine | Tryptophan
Disorder-favoring: Glycine | Serine | Proline | Asparagine | Aspartic acid
No preference: Cysteine | Histidine | Arginine
←Primary structure Tertiary structure→
 
This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Turn_(biochemistry)". A list of authors is available in Wikipedia.
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