Turns in Proteins
From Proteopedia
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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. | 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. (<scene name='Turns_in_Proteins/ | + | Seven β-turns are shown as blue traces in myohemerytherin in the scene to the right. (<scene name='Turns_in_Proteins/Hemery1/1'>Initial scene</scene>) 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 <scene name='Turns_in_Proteins/Hemery_wf/2'>wireframe</scene> 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 <scene name='Turns_in_Proteins/Hemery_5-8b/1'>turn at residues 5-8</scene> (marked with yellow star) does not have a hydrogen bond, but it does have Pro in a cis configuration. <scene name='Turns_in_Proteins/Hemery_5-8a/2'>Isolated view</scene> 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 <scene name='Turns_in_Proteins/Hemery_5-8b/1'>turn at residues 5-8</scene> (marked with yellow star) does not have a hydrogen bond, but it does have Pro in a cis configuration. <scene name='Turns_in_Proteins/Hemery_5-8a/2'>Isolated view</scene> 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. | ||
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== Examples from Myohemerytherin == | == Examples from Myohemerytherin == | ||
| + | The seven applets below show each of the seven turns in isolation. 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 | ||
<jmol> | <jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
Revision as of 18:51, 11 March 2011
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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
The seven applets below show each of the seven turns in isolation. 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
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Residue 2: φ = -135°, ψ = +112°
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Residue 2: φ = -66°, ψ = -19°
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Residue 2: φ = -62°, ψ = -28°
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Residue 2: φ = -56°, ψ = +126°
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Residue 2: φ = -89°, ψ = +142°
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Residue 2: φ = -58°, ψ = -40°
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Residue 2: φ = -70°, ψ = -25°
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