Turns in Proteins: Difference between revisions
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<Structure load='2mhr' size='500' frame='true' align='right' caption='' scene='Turns_in_Proteins/Hemery/4' /> | <Structure load='2mhr' size='500' frame='true' align='right' caption='' scene='Turns_in_Proteins/Hemery/4' />__NOTOC__ | ||
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 C<sub>α</sub>'s. This article describes β-turns and γ-turns and illustrates their ordered structures. | 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 C<sub>α</sub>'s. This article describes β-turns and γ-turns and illustrates their ordered structures. | ||
== Beta Turns == | == Beta Turns == | ||
All β-turns contain four residues and are divided into classes based on the range of their [[Psi and Phi Angles|psi | All β-turns contain four residues and are divided into classes based on the range of their [[Psi and Phi Angles|phi and psi]] values for the second and third residues.<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> 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 (hbonds). | ||
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>). | 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>). There are only five blue segments because, in two cases, one β-turn follows another one. Only five of the turns contain hydrogen bonds shown in magenta. As explained in [[Calculate structure]], the '''calculate structure''' command does not detect beta turns which have a Pro in the cis configuration and lack a hbond. Since the command has this limitation, the initial scene was produced by manually selecting and coloring the turns and forming the hbonds. <scene name='Turns_in_Proteins/Calculate_structure/2'>Show</scene> the results of the '''calculate structure''' command. | ||
<blockquote> | <blockquote>For reasons explained in the Introduction of [[Calculate structure]], the command to form hbonds of secondary structures was not included in the construction of the above scene, but they can be displayed in any scene by doing the following: click on the Jmol frank, in the main menu click on Console, in the bottom box of the console enter the command: <span style='background-color:yellow;'>calculate hbonds structure</span> and then click Run. | ||
</blockquote> | |||
<blockquote>Also, if any Proteopedia scene shows the secondary structure and it does not show the beta turns highlighted in blue, the beta turns can be shown in blue by following the above procedure but enter <span style='background-color:yellow;'>select protein; calculate structure; cartoon; color structure</span> into the bottom box of the console. | |||
</blockquote> | </blockquote> | ||
Shown in <scene name='Turns_in_Proteins/Hemery_wf/5'>wireframe</scene> so that one can see the hydrogen bonds are positioned between the first and the fourth residues of the turn and involve backbone atoms. Can you locate the cis configured Pro in the two turns without hbonds? <scene name='Turns_in_Proteins/Rama_2mhr/1'>Ramachandran plot</scene> ([[Ramachandran Plot]]). | |||
{{Clear}} | {{Clear}} | ||
=== 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 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. | 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 domain 2 of glycogen phosphorylase chain A (1abb.pdb). Compare the shapes of the turns and observe the differences in the phi (φ) and psi (ψ) 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. | ||
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<jmolCheckbox> | <jmolCheckbox> | ||
<target>all</target> | <target>all</target> | ||
<scriptWhenChecked>set syncMouse on;sync | <scriptWhenChecked>set syncMouse on;sync 1,2,3,4,5,6,7,8 on; </scriptWhenChecked> | ||
<scriptWhenUnchecked>sync * off;</scriptWhenUnchecked> | <scriptWhenUnchecked>sync * off;</scriptWhenUnchecked> | ||
<text>Synchronize the 8 models for rotation with the mouse. </text> | <text>Synchronize the 8 models for rotation with the mouse. </text> | ||
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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#Plot regions limited by steric hindrance|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#Plot regions limited by steric hindrance|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 == | ||
Gamma 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. A <scene name='Turns_in_Proteins/ | Gamma 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. Several examples of β-hairpins follow: | ||
* <scene name='Turns_in_Proteins/2alp_classic/3'>Alpha-Lytic protease</scene>; <scene name='Turns_in_Proteins/2alp_classic2/2'>Isolated turn</scene> | |||
* <scene name='Turns_in_Proteins/Proteinase_a/4'>Proteinase A</scene>; <scene name='Turns_in_Proteins/Proteinase_a2/3'>Isolate Turn</scene> | |||
* <scene name='Turns_in_Proteins/Thermolysin/2'>Thermolysin</scene>; <scene name='Turns_in_Proteins/Thermolysin2/2'>Isolated turn</scene> - Unusual because it has two hbonds. | |||
* <scene name='Turns_in_Proteins/Flavodoxin/1'>Flavodoxin</scene>; <scene name='Turns_in_Proteins/Flavodoxin2/1'>Isolated turn</scene> | |||
The inverse γ-turns have mean phi and psi values at residue ''i'' + 1 of -79 and +69, respectively. In their search of 54 proteins Miner-White, et. al. found 61 inverse γ-turns, but only one formed a β-hairpin producing a reversal in the peptide chain.<ref name="Miner" /> Example of an <scene name='Turns_in_Proteins/2sga_inverse/2'>inverse gamma turn</scene> from proteinase A. Compare the structures of a classic and an inverse turns in the two applets below. The direction of rotation of the orange and violet planes with respect to the yellow plane is opposite for the two turns. As a result of this the backbone nitrogens and oxygens of the two turns are mirror images of each other. | |||
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<Structure load='8tln' size='500' frame='true' align='left' caption='Classic gamma turn; Thermolysin (25-27)' scene='Turns_in_Proteins/8tln_classic/ | |||
<Structure load='2sga' size='500' frame='true' align='right' caption='Inverse gamma turn; Proteinase A (113-115)' scene='Turns_in_Proteins/2sga_inverse2/ | <span style="font-size:125%; color:red;"> | ||
<jmol> | |||
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<target>all</target> | |||
<scriptWhenChecked>set syncMouse on;sync 10,11 on; </scriptWhenChecked> | |||
<scriptWhenUnchecked>sync * off;</scriptWhenUnchecked> | |||
<text>Synchronize the 2 models for rotation with the mouse. </text> | |||
</jmolCheckbox> | |||
</jmol></span> | |||
To re-align the models, reload this page. | |||
<Structure load='8tln' size='500' frame='true' align='left' caption='Classic gamma turn; Thermolysin (25-27)' scene='Turns_in_Proteins/8tln_classic/6' /> | |||
<Structure load='2sga' size='500' frame='true' align='right' caption='Inverse gamma turn; Proteinase A (113-115)' scene='Turns_in_Proteins/2sga_inverse2/6' /> | |||
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==Notes and References== | ==Notes and References== | ||
<references /> | <references /> | ||