Turns in Proteins: Difference between revisions
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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. (<scene name='Turns_in_Proteins/2mhr_5-8c/2'>Initial scene</scene>) <scene name='Turns_in_Proteins/2mhr_114-117b/2'>Compare</scene> with a turn which has a hbond. The oxygen and nitrogen of the <scene name='Turns_in_Proteins/2mhr_88-91b/2' >cis peptide bond</scene> project from the same edge of the plane, whereas with the trans peptide bonds they project from opposite edges of the plane. The <scene name='Turns_in_Proteins/Rama_8_turns/6'>Ramachandran plot</scene> 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 [[Ramachandran Plot|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. | 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. (<scene name='Turns_in_Proteins/2mhr_5-8c/2'>Initial scene</scene>) <scene name='Turns_in_Proteins/2mhr_114-117b/2'>Compare</scene> with a turn which has a hbond. The oxygen and nitrogen of the <scene name='Turns_in_Proteins/2mhr_88-91b/2' >cis peptide bond</scene> project from the same edge of the plane, whereas with the trans peptide bonds they project from opposite edges of the plane. The <scene name='Turns_in_Proteins/Rama_8_turns/6'>Ramachandran plot</scene> 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 [[Ramachandran Plot|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 == | == Gamma Turns == | ||
γ-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.<ref name="Miner">Miner-White, EJ, et. al. ''One type of gamma turn, rather than the other, gives rise to chain reversal in proteins''. J. Mol. Bio. '''204''', 1983, pp. 777-782.</ref> Seven of these eleven turns are involved in the formation of β-hairpins which produce a reversal in the peptide chain. An example of | γ-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.<ref name="Miner">Miner-White, EJ, et. al. ''One type of gamma turn, rather than the other, gives rise to chain reversal in proteins''. J. Mol. Bio. '''204''', 1983, pp. 777-782.</ref> Seven of these eleven turns are involved in the formation of β-hairpins which produce a reversal in the peptide chain. An example of a classic γ-turn producing this effect is in <scene name='Turns_in_Proteins/2alp_classic/1'>α-lytic protease</scene> (2alp). The inverse γ-turns have mean phi and psi values at residue ''i'' + 1 of -79 and +69, respectively. In their search of proteins Miner-White, et. al. revealed that inverse γ-turns are more common than the classic because in the 54 proteins searched they found 61 inverse γ-turns, but only one formed a β-hairpins producing a reversal in the peptide chain.<ref name="Miner" /> The γ-turns are not as common as the β-turns. | ||
=== Examples === | === Examples === | ||
Revision as of 22:49, 11 July 2011
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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 Cα'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.[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. Go to calculate structure for instructions on how to run these command.
Notice that there are only five blue segments, and that is because, in two cases, one β-turn follows another one. Only five of the turns contain hydrogen bonds shown in magenta. Can you locate the cis configured Pro in the two turns without hbonds? Turns shown in without the side chains so that the backbone atoms can be seen. One can 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.
ExamplesExamples
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 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.
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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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
γ-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.[2] Seven of these eleven turns are involved in the formation of β-hairpins which produce a reversal in the peptide chain. An example of a classic γ-turn producing this effect is in (2alp). The inverse γ-turns have mean phi and psi values at residue i + 1 of -79 and +69, respectively. In their search of proteins Miner-White, et. al. revealed that inverse γ-turns are more common than the classic because in the 54 proteins searched they found 61 inverse γ-turns, but only one formed a β-hairpins producing a reversal in the peptide chain.[2] The γ-turns are not as common as the β-turns.
ExamplesExamples
in domain 2 of chain A of glycogen phosphorylase.
Notes and ReferencesNotes and References
- ↑ 1.0 1.1 Characteristics of β-turn classes
- ↑ 2.0 2.1 Miner-White, EJ, et. al. One type of gamma turn, rather than the other, gives rise to chain reversal in proteins. J. Mol. Bio. 204, 1983, pp. 777-782.