Turn (biochemistry) explained

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

Definition

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).[1] 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 of turns

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

Ideal angles for different β-turn types.[3] [4] [5] Types VIa1, VIa2 and VIb turns are subject to the additional condition that residue i + 2(*) must be a cis-proline.
Type φi + 1 ψi + 1 φi + 2 ψi + 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°*
IVturns excluded from all the above categories

Turns are 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[6] (I, II, II′, I′) suffice to describe all possible beta turns. All four occur frequently in proteins but I is most common, followed by II, I′ and II′ in that order.

Loops

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

Multiple turns

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 to 4 and residues 2 to 5 form a turn; in such a case, one speaks of an double turn. Multiple turns (up to sevenfold) occur commonly in proteins. Beta bend ribbons are a different type of multiple turn.

Hairpins

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.

Flexible linkers

Turns are sometimes found within flexible linkers or loops connecting protein domains. Linker sequences vary in length and are typically rich in polar uncharged amino acids. Flexible linkers allow connecting domains to freely twist and rotate to recruit their binding partners via protein domain dynamics. They also allow their binding partners to induce larger scale conformational changes by long-range allostery.[8] [9] [10]

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 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. The non-native isomers of many X−Pro peptide bonds in turns also have little or no effect on folding.

Beta turn prediction methods

Over the years, many beta turn prediction methods have been developed. Recently, Dr. Raghava's Group developed BetaTPred3 method which predicts a complete beta turn rather than individual residues falling into a beta turn. The method also achieves good accuracy and is the first method which predicts all 9 types of beta turns. Apart from prediction, this method can also be used to find the minimum number of mutations required to initiate or break a beta turn in a protein at a desired location.

See also

External links

Literature

These references are ordered by date.

Notes and References

  1. Rose . GD . Gierasch . LM . Smith . JA . Turns in peptides and proteins. . Advances in Protein Chemistry . 1985 . 37 . 1–109 . 10.1016/s0065-3233(08)60063-7 . 2865874. 978-0-12-034237-2 .
  2. Toniolo . C . Intramolecularly hydrogen-bonded peptide conformations. . CRC Critical Reviews in Biochemistry . 1980 . 9 . 1 . 1–44 . 10.3109/10409238009105471 . 6254725.
  3. Venkatachalam . CM . Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. . Biopolymers . October 1968 . 6 . 10 . 1425–36 . 10.1002/bip.1968.360061006 . 5685102. 2027.42/37819 . 5873535 . free .
  4. Richardson . JS . The anatomy and taxonomy of protein structure. . Advances in Protein Chemistry . 1981 . 34 . 167–339 . 10.1016/s0065-3233(08)60520-3 . 7020376. 978-0-12-034234-1 .
  5. Hutchinson . EG . Thornton . JM . A revised set of potentials for beta-turn formation in proteins. . Protein Science . December 1994 . 3 . 12 . 2207–16 . 10.1002/pro.5560031206 . 7756980. 2142776 .
  6. Venkatachalam. CM. Stereochemical criteria for polypeptides and proteins. V. Conformations of a system of three linked peptide units.. Biopolymers. 1968. 6. 10. 1425–1436. 10.1002/bip.1968.360061006. 5685102. 2027.42/37819. 5873535 . free.
  7. Sibanda . BL . Blundell . TL . Thornton . JM . Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. . Journal of Molecular Biology . 20 April 1989 . 206 . 4 . 759–77 . 10.1016/0022-2836(89)90583-4 . 2500530.
  8. Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff CM, Hipps KW, Ausio J, Nissen MS, Reeves R, Kang C, Kissinger CR, Bailey RW, Griswold MD, Chiu W, Garner EC, Obradovic Z . Intrinsically disordered protein . Journal of Molecular Graphics & Modelling . 19 . 1 . 26–59 . 2001 . 11381529 . 10.1016/s1093-3263(00)00138-8 . 10.1.1.113.556 .
  9. Book: Bu Z, Callaway DJ . Proteins move! Protein dynamics and long-range allostery in cell signaling . 83 . 163–221 . 2011 . 21570668 . 10.1016/B978-0-12-381262-9.00005-7 . 9780123812629 . Advances in Protein Chemistry and Structural Biology . Protein Structure and Diseases .
  10. Compiani M, Capriotti E . Computational and theoretical methods for protein folding . Biochemistry . 52 . 48 . 8601–24 . Dec 2013 . 24187909 . 10.1021/bi4001529 . dead . https://web.archive.org/web/20150904053433/https://biofold.org/emidio/pages/documents/papers/Compiani_Biochemistry2013.pdf . 2015-09-04 .

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