Turn (biochemistry)

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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 C^α atoms (< 7 Å), when the corresponding residues are not involved in a regular secondary structure element such as an alpha helix or beta sheet.

Contents 1 Types of turns 2 Hairpins vs. diverging turns 3 Role in protein folding 4 See also 5 References

[edit] 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 ( H-bonding).
• A γ-turn is characterized by hydrogen bond(s) in which the donor and acceptor residues are separated by two residues ( H-bonding).
• An α-turn is characterized by hydrogen bond(s) in which the donor and acceptor residues are separated by four residues ( H-bonding).
• A π-turn is characterized by hydrogen bond(s) in which the donor and acceptor residues are separated by five residues ( 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 C^α 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 C^α atoms of residues separated by three peptide bonds, a γ-turn by the close approach of C^α atoms of residues separated by two peptide bonds, etc. In most cases, the H-bonding and C^α-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 C^α atoms is maintained.) Thus, the γ-turn has two forms, a classical form with (φ, ψ) dihedral angles of roughly and an inverse form with dihedral angles . 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 β-turns.

[edit] 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.

[edit] 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.

[edit] See also

• Secondary structure

[edit] References

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• 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→