Turns in Proteins
From Proteopedia
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== Beta Turns == | == Beta Turns == | ||
| - | There are several different classes<ref>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?doc=TRUE&pdbcode=n/a&template=doc_p_bturns.html Characteristics of β-turn classes]</ref> of β-turns with all types 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 (i + 3) is the major force maintaining the conformation of the bend in the chain, but 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. | + | There are several different classes<ref name=beta>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?doc=TRUE&pdbcode=n/a&template=doc_p_bturns.html Characteristics of β-turn classes]</ref> of β-turns with all types 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 (i + 3) is the major force maintaining the conformation of the bend in the chain, but 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/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. | 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. | ||
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=== Examples === | === Examples === | ||
| - | + | Examples of four of the nine classes<ref name=beta/> 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. Notice that class IV B turns do not have a hydrogen bone, and that is because with the presence of a cis Pro the backbone atoms of the first and fourth residues are not in position to form a hydrogen bond. Other green links reveal Ramachandran plots which show the phi and psi positions of the second and third residues. | |
<span style="font-size:150%; color:red;"> | <span style="font-size:150%; color:red;"> | ||
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</td> | </td> | ||
<td> | <td> | ||
| - | Residue 2: φ = , ψ = | + | Residue 2: φ = +56°, ψ = -117° |
| - | <br /> Residue 3: φ = | + | <br /> Residue 3: φ = -125°, ψ = +19° |
<br /> <scene name='Turns_in_Proteins/' target='3'>Hydrogen bond</scene> present | <br /> <scene name='Turns_in_Proteins/' target='3'>Hydrogen bond</scene> present | ||
<br /> <scene name='Turns_in_Proteins/' target='3'>Initial scene</scene> | <br /> <scene name='Turns_in_Proteins/' target='3'>Initial scene</scene> | ||
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</td> | </td> | ||
<td> | <td> | ||
| - | Residue 2: φ = | + | Residue 2: φ = -53°, ψ = +131° |
| - | <br /> Residue 3: φ = | + | <br /> Residue 3: φ = +78°, ψ = -10° |
<br /> <scene name='Turns_in_Proteins/2mhr_63-66b/1' target='6'>Hydrogen bond</scene> present | <br /> <scene name='Turns_in_Proteins/2mhr_63-66b/1' target='6'>Hydrogen bond</scene> present | ||
<br /> <scene name='Turns_in_Proteins/2mhr_63-66/2' target='6'>Initial scene</scene> | <br /> <scene name='Turns_in_Proteins/2mhr_63-66/2' target='6'>Initial scene</scene> | ||
</td> | </td> | ||
<td> | <td> | ||
| + | Residue 2: φ = +47°, ψ = -122° | ||
| + | <br /> Residue 3: φ = -94°, ψ = +2° | ||
</td> | </td> | ||
<td> | <td> | ||
Revision as of 17:56, 11 May 2011
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Turns are classified as a type of secondary structure, and therefore they have an ordered, repetitive structure. This article describes β-turns and γ-turns and defines and illustrates their ordered, repetitive structures.
Contents |
Beta Turns
There are several different classes[1] of β-turns with all types 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 (i + 3) is the major force maintaining the conformation of the bend in the chain, but 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
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. Notice that class IV B turns do not have a hydrogen bone, and that is because with the presence of a cis Pro the backbone atoms of the first and fourth residues are not in position to form a hydrogen bond. Other green links reveal Ramachandran plots which show the phi and psi positions of the second and third residues.
To re-align the models, reload this page.
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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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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.
