Turns in Proteins

From Proteopedia

Revision as of 11:16, 9 July 2011

Turns are classified as a type of secondary structure, but unlike helices and sheets which have ordered, repetitive structures, turns only have ordered structures. 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 psi and phi 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.

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.

In two cases one β-turn follows another one so the blue traces are longer, and five of the turns contain hydrogen bonds shown in magenta. Turns shown in without the side chains so that the backbone atoms can be seen. One can now clearly see that the hydrogen bonds are positioned between the first and the fourth residues of the turn and involve backbone atoms.

The colors the spheres for the helices but not for the turns.

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 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.

To re-align the models, reload this page.

Notice that class IV B turns do not have a hydrogen bond, and that is because with the presence of a cis peptide bond the backbone atoms of the are not in position to form a hydrogen bond; with a turn in which they are. The following two green links show the two class IV B turns displayed as wireframe so that you can see that the peptide bond at Pro at position 3 is cis in contrast to the other two peptide bonds which are trans: ; . The oxygen and nitrogen of the cis peptide bond project from the same side of the plane, whereas the trans peptide bonds project from opposite sides 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

γ-turns consist of three residues and contain a hydrogen bond between residues one and three. There are only two classes ^[2] of γ-turns. The γ-turns are not as common as the β-turns.

Examples

in domain 2 of chain A of glycogen phosphorylase.

Notes and References

1. ↑ ^{1.0 1.1} Characteristics of β-turn classes
2. ↑ Characteristics of γ-turn classes

External Links