Turns in Proteins
From Proteopedia
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Turns are classified as a type of secondary structure, but unlike helices and sheets which have ordered, repetitive structures, turns only have ordered structures, but like helices and sheets they can be classified by the values of the torsional angles of the Cα's. This article describes β-turns and γ-turns and illustrates their ordered structures.
Beta Turns
All β-turns contain four residues and are divided into classes based on the range of their phi and psi values for the second and third residues.[1] Most classes have a hydrogen bond between the backbond atoms of residues one(i) and four (i + 3), and this attraction is the major force maintaining the conformation of the bend in the chain, but in several classes a Pro in the third position (i + 2) has the cis configuration which produces a conformation which can not form a hydrogen bond (hbonds).
Seven β-turns are shown as blue traces in myohemerytherin in the scene to the right (). There are only five blue segments because, in two cases, one β-turn follows another one. Only five of the turns contain hydrogen bonds shown in magenta. As explained in Calculate structure, the calculate structure command does not detect beta turns which have a Pro in the cis configuration and lack a hbond. Since the command has this limitation, the initial scene was produced by manually selecting and coloring the turns and forming the hbonds. the results of the calculate structure command.
For reasons explained in the Introduction of Calculate structure, the command to form hbonds of secondary structures was not included in the construction of the above scene, but they can be displayed in any scene by doing the following: click on the Jmol frank, in the main menu click on Console, in the bottom box of the console enter the command: calculate hbonds structure and then click Run.
Also, if any Proteopedia scene shows the secondary structure and it does not show the beta turns highlighted in blue, the beta turns can be shown in blue by following the above procedure but enter select protein; calculate structure; cartoon; color structure into the bottom box of the console.
Shown in so that one can see the hydrogen bonds are positioned between the first and the fourth residues of the turn and involve backbone atoms. Can you locate the cis configured Pro in the two turns without hbonds? (Ramachandran Plot).
Examples
Examples of four of the nine classes[1] of β-turns are shown below with two examples of each of the four classes. The turns were cut from either myohemerytherin (2mhr.pdb) or domain 2 of glycogen phosphorylase chain A (1abb.pdb). Compare the shapes of the turns and observe the differences in the phi (φ) and psi (ψ) values of the second and third residues. Checking the synchronize box will permit you to rotate all the turns by rotating any one of the turns with the mouse.
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| Class I | Class II | Class III | Class IV B | ||||||||||||||||||||||||
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Residue 2: φ = -66°, ψ = -19°
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Residue 2: φ = -56°, ψ = +126°
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Residue 2: φ = +56°, ψ = -117°
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Residue 2: φ = -135°, ψ = +112°
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Residue 2: φ = -70°, ψ = -25°
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Residue 2: φ = -53°, ψ = +131°
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Residue 2: φ = +47°, ψ = -122°
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Residue 2: φ = -89°, ψ = +142°
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Turn 2mhr 5-8, classIVB, is shown in the applet on the right. Notice that it does not have a hydrogen bond and that the backbone atoms of the first and fourth residues are not in position to form a hydrogen bond because the presence of a cis peptide bond. () with a turn which has a hbond. The oxygen and nitrogen of the project from the same edge of the plane, whereas with the trans peptide bonds they project from opposite edges of the plane. The of the eight turns shown above. Two residues of each turn are plotted giving a total of 16 points. Hover the cursor over a sphere to identify the residue name and number. Realize that, in most cases, the spheres that are of the same class and are close to each other are not part of the same turn. Notice that Gly is the only residue in a disallowed region since other residues at those positions could not generate the angles necessary to form the turn and that Pro is the third residue in both class IVB turns.
Gamma Turns
Gamma turns consist of three residues and contain a hydrogen bond between residues one and three. In a search of 54 proteins nine proteins were found to have eleven classic γ-turns, and these eleven turns had mean phi and psi values at residue i + 1 of +75.0 and -64, respectively.[2] Seven of these eleven turns are involved in the formation of β-hairpins which produce a reversal in the peptide chain. Several examples of β-hairpins follow:
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- ; - Unusual because it has two hbonds.
- ;
The inverse γ-turns have mean phi and psi values at residue i + 1 of -79 and +69, respectively. In their search of 54 proteins Miner-White, et. al. found 61 inverse γ-turns, but only one formed a β-hairpin producing a reversal in the peptide chain.[2] Example of an from proteinase A. Compare the structures of a classic and an inverse turns in the two applets below. The direction of rotation of the orange and violet planes with respect to the yellow plane is opposite for the two turns. As a result of this the backbone nitrogens and oxygens of the two turns are mirror images of each other.
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Notes and References
- ↑ 1.0 1.1 Characteristics of β-turn classes
- ↑ 2.0 2.1 Miner-White, EJ, et. al. One type of gamma turn, rather than the other, gives rise to chain reversal in proteins. J. Mol. Bio. 204, 1983, pp. 777-782.
