Turns in Proteins

spinqualitylabelsall models PDB ID 2mhr Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

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 C_α's. This article describes β-turns and γ-turns and illustrates their ordered structures.

Beta TurnsBeta Turns

All β-turns contain four residues and are divided into classes based on the range of their psi and phi values for the second and third residues. 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.

Seven β-turns are shown as blue traces in myohemerytherin in the scene to the right (). This scene was produced by manually selecting and coloring the turns and forming the hydrogen bonds (hbonds).

Jmol 12.0 (As of July 2011 Proteopedia is running in Jmol 11.8.) has a command, calculate structure, which locates the turns by computation and a command, calculate hbonds structure, which displays the hbonds involved in secondary structures. Until Protepedia is upgraded to ver. 12 any page can be run in the signed ver. 12 by appending "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" to the url of the page and reloading the page. The user must give permission for the signed version of Jmol to open, and when it does it has a red frank, whereas in the unsigned version it is grey. Click on the Jmol frank, in the main menu click on Console, in the bottom box of the console enter the commands:

select protein; calculate structure; cartoon; color structure; calculate hbonds structure

and then click Run.

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. (If you ran the above series of commands in ver. 12, hbonds in only these five turns are displayed.) Can you locate the cis configured Pro in the two turns without hbonds? Turns shown in (If you are using ver. 12, run calculate hbonds structure in the console after clicking the green link.) without the side chains so that the backbone atoms can be clearly seen. One can see that the hydrogen bonds are positioned between the first and the fourth residues of the turn and involve backbone atoms.

The (Ramachandran Plot) colors the spheres for the helices but not for the turns.

ExamplesExamples

Examples of four of the nine classes 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 and psi 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
spinqualitylabelsall models PDB ID 2mhr 12-15.pdb Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image	spinqualitylabelsall models PDB ID 2mhr 114-117.pdb Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image	spinqualitylabelsall models PDB ID 1abb 636-639.pdb Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image	spinqualitylabelsall models PDB ID 2mhr 5-8.pdb Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
Residue 2: φ = -66°, ψ = -19°    Residue 3: φ = -91°, ψ = -1°	Residue 2: φ = -56°, ψ = +126°    Residue 3: φ = +78°, ψ = +1°	Residue 2: φ = +56°, ψ = -117°    Residue 3: φ = -125°, ψ = +19°	Residue 2: φ = -135°, ψ = +112°    Residue 3: φ = -63°, ψ = +163°
spinqualitylabelsall models PDB ID 2mhr 67-70 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image	spinqualitylabelsall models PDB ID 1abb 610-613.pdb Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image	spinqualitylabelsall models PDB ID 1abb 693-696.pdb Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image	spinqualitylabelsall models PDB ID 2mhr 88-91 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
Residue 2: φ = -70°, ψ = -25°    Residue 3: φ = -109°, ψ = +29°	Residue 2: φ = -53°, ψ = +131°    Residue 3: φ = +78°, ψ = -10°	Residue 2: φ = +47°, ψ = -122°    Residue 3: φ = -94°, ψ = +2°	Residue 2: φ = -89°, ψ = +142°    Residue 3: φ = -76°, ψ = +135°

spinqualitylabelsall models PDB ID 2mhr Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

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 TurnsGamma 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. 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:

• ;
• ;
• ; - 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. 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 with respect to the yellow plane of the orange and violet planes 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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spinqualitylabelsall models Classic gamma turn; Thermolysin (25-27) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

spinqualitylabelsall models Inverse gamma turn; Proteinase A (113-115) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image