Turn (biochemistry)

Last updated March 06, 2024

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 C^α atoms of two residues separated by a few (usually 1 to 5) peptide bonds are close (less than 7 Å [0.70 nm ]).^[1] The proximity of the terminal C^α 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 C^α-distance definitions are equivalent.

Types of turns

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 → i ± 4).
In a β-turn (the most common form), by three bonds (i → i ± 3).
In a γ-turn, by two bonds (i → i ± 2).
In a δ-turn, by one bond (i → i ± 1), which is sterically unlikely.
In a π-turn, by five bonds (i → i ± 5).

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	φ_i + 1	ψ_i + 1	φ_i + 2	ψ_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

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 C^α 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^[4] 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 (i, i + 1)double turn. Multiple turns (up to sevenfold) occur commonly in proteins.^[5] 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.

Related Research Articles

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<span class="mw-page-title-main">Beta sheet</span> Protein structural motif

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<span class="mw-page-title-main">Protein structure prediction</span> Type of biological prediction

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A 3₁₀ helix is a type of secondary structure found in proteins and polypeptides. Of the numerous protein secondary structures present, the 3₁₀-helix is the fourth most common type observed; following α-helices, β-sheets and reverse turns. 3₁₀-helices constitute nearly 10–15% of all helices in protein secondary structures, and are typically observed as extensions of α-helices found at either their N- or C- termini. Because of the α-helices tendency to consistently fold and unfold, it has been proposed that the 3₁₀-helix serves as an intermediary conformation of sorts, and provides insight into the initiation of α-helix folding.

<span class="mw-page-title-main">Beta hairpin</span>

The beta hairpin is a simple protein structural motif involving two beta strands that look like a hairpin. The motif consists of two strands that are adjacent in primary structure, oriented in an antiparallel direction, and linked by a short loop of two to five amino acids. Beta hairpins can occur in isolation or as part of a series of hydrogen bonded strands that collectively comprise a beta sheet.

Alpha sheet is an atypical secondary structure in proteins, first proposed by Linus Pauling and Robert Corey in 1951. The hydrogen bonding pattern in an alpha sheet is similar to that of a beta sheet, but the orientation of the carbonyl and amino groups in the peptide bond units is distinctive; in a single strand, all the carbonyl groups are oriented in the same direction on one side of the pleat, and all the amino groups are oriented in the same direction on the opposite side of the sheet. Thus the alpha sheet accumulates an inherent separation of electrostatic charge, with one edge of the sheet exposing negatively charged carbonyl groups and the opposite edge exposing positively charged amino groups. Unlike the alpha helix and beta sheet, the alpha sheet configuration does not require all component amino acid residues to lie within a single region of dihedral angles; instead, the alpha sheet contains residues of alternating dihedrals in the traditional right-handed (α_R) and left-handed (α_L) helical regions of Ramachandran space. Although the alpha sheet is only rarely observed in natural protein structures, it has been speculated to play a role in amyloid disease and it was found to be a stable form for amyloidogenic proteins in molecular dynamics simulations. Alpha sheets have also been observed in X-ray crystallography structures of designed peptides.

Peptide plane flipping is a type of conformational change that can occur in proteins by which the dihedral angles of adjacent amino acids undergo large-scale rotations with little displacement of the side chains. The plane flip is defined as a rotation of the dihedral angles φ,ψ at amino acids i and i+1 such that the resulting angles remain in structurally stable regions of Ramachandran space. The key requirement is that the sum of the ψ_i angle of residue i and the φ_i+1 angle of residue i+1 remain roughly constant; in effect, the flip is a crankshaft move about the axis defined by the C^α-C¹ and N-C^α bond vectors of the peptide group, which are roughly parallel. As an example, the type I and type II beta turns differ by a simple flip of the central peptide group of the turn.

β turns are the most common form of turns—a type of non-regular secondary structure in proteins that cause a change in direction of the polypeptide chain. They are very common motifs in proteins and polypeptides. Each consists of four amino acid residues. They can be defined in two ways:

By the possession of an intra-main-chain hydrogen bond between the CO of residue i and the NH of residue i+3;
By having a distance of less than 7Å between the Cα atoms of residues i and i+3.

Schellman loops are commonly occurring structural features of proteins and polypeptides. Each has six amino acid residues with two specific inter-mainchain hydrogen bonds and a characteristic main chain dihedral angle conformation. The CO group of residue i is hydrogen-bonded to the NH of residue i+5, and the CO group of residue i+1 is hydrogen-bonded to the NH of residue i+4. Residues i+1, i+2, and i+3 have negative φ (phi) angle values and the phi value of residue i+4 is positive. Schellman loops incorporate a three amino acid residue RL nest, in which three mainchain NH groups form a concavity for hydrogen bonding to carbonyl oxygens. About 2.5% of amino acids in proteins belong to Schellman loops. Two websites are available for examining small motifs in proteins, Motivated Proteins: ; or PDBeMotif:.

The Asx turn is a structural feature in proteins and polypeptides. It consists of three amino acid residues in which residue i is an aspartate (Asp) or asparagine (Asn) that forms a hydrogen bond from its sidechain CO group to the mainchain NH group of residue i+2. About 14% of Asx residues present in proteins belong to Asx turns.

<span class="mw-page-title-main">Beta bend ribbon</span>

The beta bend ribbon, or beta-bend ribbon, is a structural feature in polypeptides and proteins. The shortest possible has six amino acid residues arranged as two overlapping hydrogen bonded beta turns in which the carbonyl group of residue i is hydrogen-bonded to the NH of residue i+3 while the carbonyl group of residue i+2 is hydrogen-bonded to the NH of residue i+5. In longer ribbons, this bonding is continued in peptides of 8, 10, etc., amino acid residues. A beta bend ribbon can be regarded as an aberrant 310 helix (3/10-helix) that has lost some of its hydrogen bonds. Two websites are available to facilitate finding and examining these features in proteins: Motivated Proteins; and PDBeMotif.

Beta bulge loops are commonly occurring motifs in proteins and polypeptides consisting of five to six amino acids. There are two types: type 1, which is a pentapeptide; and type 2, with six amino acids. They are regarded as a type of beta bulge, and have the alternative name of type G1 beta bulge. Compared to other beta bulges, beta bulge loops give rise to chain reversal such that they often occur at the loop ends of beta hairpins; hairpins of this sort can be described as 3:5 or 4:6. Two websites are available for finding and examining β bulge loops in proteins, Motivated Proteins: and PDBeMotif:.

References

↑ Rose, GD; Gierasch, LM; Smith, JA (1985). "Turns in peptides and proteins". Advances in Protein Chemistry. 37: 1–109. doi:10.1016/s0065-3233(08)60063-7. ISBN 978-0-12-034237-2. PMID 2865874.
↑ Toniolo, C (1980). "Intramolecularly hydrogen-bonded peptide conformations". CRC Critical Reviews in Biochemistry. 9 (1): 1–44. doi:10.3109/10409238009105471. PMID 6254725.
↑ Venkatachalam, CM (October 1968). "Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units". Biopolymers. 6 (10): 1425–36. doi:10.1002/bip.1968.360061006. hdl: 2027.42/37819 . PMID 5685102. S2CID 5873535.
1 2 Richardson, JS (1981). "The anatomy and taxonomy of protein structure". Advances in Protein Chemistry. 34: 167–339. doi:10.1016/s0065-3233(08)60520-3. ISBN 978-0-12-034234-1. PMID 7020376.
1 2 Hutchinson, EG; Thornton, JM (December 1994). "A revised set of potentials for beta-turn formation in proteins". Protein Science. 3 (12): 2207–16. doi:10.1002/pro.5560031206. PMC 2142776 . PMID 7756980.
↑ Venkatachalam, CM (1968). "Stereochemical criteria for polypeptides and proteins. V. Conformations of a system of three linked peptide units" (PDF). Biopolymers. 6 (10): 1425–1436. doi:10.1002/bip.1968.360061006. hdl: 2027.42/37819 . PMID 5685102. S2CID 5873535.
↑ Sibanda, BL; Blundell, TL; Thornton, JM (20 April 1989). "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. 206 (4): 759–77. doi:10.1016/0022-2836(89)90583-4. PMID 2500530.
↑ 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 (2001). "Intrinsically disordered protein". Journal of Molecular Graphics & Modelling. 19 (1): 26–59. CiteSeerX 10.1.1.113.556 . doi:10.1016/s1093-3263(00)00138-8. PMID 11381529.
↑ Bu Z, Callaway DJ (2011). "Proteins move! Protein dynamics and long-range allostery in cell signaling". Protein Structure and Diseases. Advances in Protein Chemistry and Structural Biology. Vol. 83. pp. 163–221. doi:10.1016/B978-0-12-381262-9.00005-7. ISBN 9780123812629. PMID 21570668.
↑ Compiani M, Capriotti E (Dec 2013). "Computational and theoretical methods for protein folding" (PDF). Biochemistry. 52 (48): 8601–24. doi:10.1021/bi4001529. PMID 24187909. Archived from the original (PDF) on 2015-09-04.

External links

Literature

These references are ordered by date.

Venkatachalam CM. (1968). "Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units". Biopolymers. 6 (10): 1425–36. doi:10.1002/bip.1968.360061006. hdl: 2027.42/37819 . PMID 5685102.
Némethy, George; Printz, Morton P. (1972). "The $\gamma$ -Turn, a Possible Folded Conformation of the Polypeptide Chain. Comparison with the β-Turn". Macromolecules. 5 (6): 755–758. doi:10.1021/ma60030a017.
Lewis PN, Momany FA, Scheraga HA (1973). "Chain reversals in proteins". Biochim Biophys Acta. 303 (2): 211–29. doi:10.1016/0005-2795(73)90350-4. PMID 4351002.
Toniolo C.; Benedetti, Ettore (1980). "Intramolecularly hydrogen-bonded peptide conformations". CRC Crit Rev Biochem. 9 (1): 1–44. doi:10.3109/10409238009105471. PMID 6254725.
Richardson JS. (1981). "The anatomy and taxonomy of protein structure". Advances in Protein Chemistry. 34: 167–339. doi:10.1016/S0065-3233(08)60520-3. ISBN 9780120342341. PMID 7020376.
Rose GD, Gierasch LM, Smith JA (1985). "Turns in peptides and proteins". Advances in Protein Chemistry. 37: 1–109. doi:10.1016/S0065-3233(08)60063-7. ISBN 9780120342372. PMID 2865874.
Milner-White EJ, Poet R (1987). "Loops, bulges, turns and hairpins in proteins". Trends Biochem Sci. 12: 189–192. doi:10.1016/0968-0004(87)90091-0.
Wilmot CM, Thornton JM (1988). "Analysis and prediction of the different types of beta-turn in proteins". J Mol Biol. 203 (1): 221–32. doi:10.1016/0022-2836(88)90103-9. PMID 3184187.
Sibanda, B.L.; Blundell, T.L.; Thornton, J.M. (1989). "Conformation of β-hairpins in protein structures:: A systematic classification with applications to modelling by homology, electron density fitting and protein engineering". Journal of Molecular Biology. 206 (4): 759–777. doi:10.1016/0022-2836(89)90583-4. PMID 2500530.
Milner-White, E (1990). "Situations of gamma-turns in proteinsTheir relation to alpha-helices, beta-sheets and ligand binding sites". J. Mol. Biol. 216 (2): 385–397. doi:10.1016/S0022-2836(05)80329-8. PMID 2254936.
Hutchinson, E.G.; Thornton, J.M. (1994). "A revised set of potentials for β-turn formation in proteins". Protein Science. 3 (12): 2207–2216. doi:10.1002/pro.5560031206. PMC 2142776 . PMID 7756980.
Pavone V, Gaeta G, Lombardi A, Nastri F, Maglio O, Isernia C, Saviano M (1996). "Discovering protein secondary structures: classification and description of isolated alpha-turns". Biopolymers. 38 (6): 705–21. doi:10.1002/(SICI)1097-0282(199606)38:6<705::AID-BIP3>3.0.CO;2-V. PMID 8652792.
Rajashankar KR, Ramakumar S (1996). "Pi-turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence". Protein Sci. 5 (5): 932–46. doi:10.1002/pro.5560050515. PMC 2143406 . PMID 8732765. Archived from the original on 2009-05-24.
Shapovalov, M; Vucetic, S; Dunbrack RL, Jr (March 2019). "A new clustering and nomenclature for beta turns derived from high-resolution protein structures". PLOS Computational Biology. 15 (3): e1006844. Bibcode:2019PLSCB..15E6844S. doi: 10.1371/journal.pcbi.1006844 . PMC 6424458 . PMID 30845191.</ref>

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[1] Rose, GD; Gierasch, LM; Smith, JA (1985). "Turns in peptides and proteins". Advances in Protein Chemistry. 37: 1–109. doi:10.1016/s0065-3233(08)60063-7. ISBN 978-0-12-034237-2. PMID 2865874.

[2] Toniolo, C (1980). "Intramolecularly hydrogen-bonded peptide conformations". CRC Critical Reviews in Biochemistry. 9 (1): 1–44. doi:10.3109/10409238009105471. PMID 6254725.

[3] Venkatachalam, CM (October 1968). "Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units". Biopolymers. 6 (10): 1425–36. doi:10.1002/bip.1968.360061006. hdl: 2027.42/37819 . PMID 5685102. S2CID 5873535.

[Richardson-4] 1 2 Richardson, JS (1981). "The anatomy and taxonomy of protein structure". Advances in Protein Chemistry. 34: 167–339. doi:10.1016/s0065-3233(08)60520-3. ISBN 978-0-12-034234-1. PMID 7020376.

[Hutchinson-5] 1 2 Hutchinson, EG; Thornton, JM (December 1994). "A revised set of potentials for beta-turn formation in proteins". Protein Science. 3 (12): 2207–16. doi:10.1002/pro.5560031206. PMC 2142776 . PMID 7756980.

[6] Venkatachalam, CM (1968). "Stereochemical criteria for polypeptides and proteins. V. Conformations of a system of three linked peptide units" (PDF). Biopolymers. 6 (10): 1425–1436. doi:10.1002/bip.1968.360061006. hdl: 2027.42/37819 . PMID 5685102. S2CID 5873535.

[7] Sibanda, BL; Blundell, TL; Thornton, JM (20 April 1989). "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. 206 (4): 759–77. doi:10.1016/0022-2836(89)90583-4. PMID 2500530.

[pmid11381529-8] 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 (2001). "Intrinsically disordered protein". Journal of Molecular Graphics & Modelling. 19 (1): 26–59. CiteSeerX 10.1.1.113.556 . doi:10.1016/s1093-3263(00)00138-8. PMID 11381529.

[pmid21570668-9] Bu Z, Callaway DJ (2011). "Proteins move! Protein dynamics and long-range allostery in cell signaling". Protein Structure and Diseases. Advances in Protein Chemistry and Structural Biology. Vol. 83. pp. 163–221. doi:10.1016/B978-0-12-381262-9.00005-7. ISBN 9780123812629. PMID 21570668.

[pmid24187909-10] Compiani M, Capriotti E (Dec 2013). "Computational and theoretical methods for protein folding" (PDF). Biochemistry. 52 (48): 8601–24. doi:10.1021/bi4001529. PMID 24187909. Archived from the original (PDF) on 2015-09-04.

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