Turns in Proteins

From Proteopedia

proteopedia linkproteopedia link

spinqualitylabelsall models PDB ID 1abb Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Since turns are classified as a type of secondary structure, they have an ordered, repetitive structure. There are about six different classes of β-turns with all of them containing four residues, but each class has a different range of psi and phi values for the second and third residues. Pro and Gly are commonly found in positions two and three, respectively, because their unique side chains permit a sharp bend in the peptide chain. A hydrogen bond formed between the backbond atoms of residues one and four is the major force maintaining the conformation of the bend in the chain, and in one class a Pro in the third position has the cis configuration which maintains the sharp bend without the aid of a hydrogen bond.

Seven β-turns are shown as blue traces in myohemerytherin in the scene to the right. () 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 (marked with yellow star) does not have a hydrogen bond, but it does have Pro in a cis configuration. of turn 5-8 with cis configuration marked with two halos, the bonds of both carbon and nitrogen project to the same side of the peptide bond. Observe that with the other peptide bonds they project to opposite sides.

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

Examples from Myohemerytherin

Class IV B	Class I	Class I	Class II
spinqualitylabelsall models PDB ID 2mhr 5-8.pdb Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image	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 84-87.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
Residue 2: φ = -135°, ψ = +112°    Residue 3: φ = -63°, ψ = +163°     at position 3	Residue 2: φ = -66°, ψ = -19°    Residue 3: φ = -91°, ψ = -1°     present	Residue 2: φ = -62°, ψ = -28°    Residue 3: φ = -93°, ψ = -9°     present	Residue 2: φ = -56°, ψ = +126°    Residue 3: φ = +78°, ψ = +1°     present
spinqualitylabelsall models PDB ID 2mhr 88-91 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image	spinqualitylabelsall models PDB ID 2mhr 63-66 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image	spinqualitylabelsall models PDB ID 2mhr 67-70 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
Residue 2: φ = -89°, ψ = +142°    Residue 3: φ = -76°, ψ = +135°     at position 3	Residue 2: φ = -58°, ψ = -40°    Residue 3: φ = -83°, ψ = 0°     present	Residue 2: φ = -70°, ψ = -25°    Residue 3: φ = -109°, ψ = +29°     present