User:Karsten Theis/turns

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A '''beta turn''' is a secondary structure element consisting of four consecutive amino acids (or three consecutive peptide planes). The geometry of turns correspond to a change in the direction of the polypeptide backbone, with a short distance between the first and fourth alpha carbon. This allows them to connect alpha helices and beta strands at the surface of a globular protein. Of the six main chain hydrogen bonding partners of a turn, a maximum of two are engaged in hydrogen bonding, and turns are rarely found in the hydrophobic core.
+
A '''beta turn''' is a secondary structure element consisting of four consecutive amino acids (or three consecutive peptide planes). The geometry of turns correspond to a change in the direction of the polypeptide backbone, with a short distance between the first and fourth alpha carbon.
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<ref>doi:10.3390/ijms232012314</ref>
+
==Concepts you can explore here==
-
==Exploring turns==
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# A beta turn is a secondary structure element distinct from (but sometimes overlapping with) alpha helices and beta strands
-
<StructureSection load='' size='500' side='right' caption='' scene='10/1072233/Turn/7'>The interactive Jmol window shows a turn (reload original <scene name='10/1072233/Turn/6'>conformation</scene>) that you can explore and modify with the buttons below. Four consecutive amino acids may form a beta turn if the alpha carbon atoms of the first and the fourth residue are in close proximity (less than 7.5 Angstrom). This also happens in alpha helices and 3(10) helices, and these are not considered a beta turn.
+
# Beta turns consist of stretches of four amino acids making a sharp turn, with a short distance between the first and last alpha carbon
 +
# Beta turns typically occur near the surface of globular proteins, often connecting helices and strands
 +
# There are multiple types of beta turns, distinguished by the torsion angles of the second and third residue
 +
# Glycine and proline occur relatively often in beta turns and play distinct special roles
 +
 
 +
See the discussion tab for learning and teaching notes.
 +
 
 +
==Turns in 3D==
 +
<!-- -->
 +
&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;Phi&emsp;<jmol>
 +
<jmolButton>
 +
<script>set echo top center; color echo white; rotate BRANCH {68.CA} {68.N} 10; ang = angle({67.C},{68.N},{68.CA},{68.C})%0; echo "phi2 is @{ang}"</script>
 +
<text>+</text>
 +
</jmolButton>
 +
</jmol> 2 <jmol>
 +
<jmolButton>
 +
<script>rotate BRANCH {68.CA} {68.N} -10; ang = angle({67.C},{68.N},{68.CA},{68.C})%0; echo "phi2 is @{ang}"</script>
 +
<text>−</text>
 +
</jmolButton>
 +
</jmol>&emsp;&emsp;<jmol>
 +
<jmolButton>
 +
<script>rotate BRANCH {69.N}{69.CA} 10; ang = angle({68.C},{69.N},{69.CA},{69.C})%0; echo "phi3 is @{ang}"</script>
 +
<text>+</text>
 +
</jmolButton>
 +
</jmol> 3 <jmol>
 +
<jmolButton>
 +
<script>rotate BRANCH {69.N}{69.CA} -10; ang = angle({68.C},{69.N},{69.CA},{69.C})%0; echo "phi3 is @{ang}"</script>
 +
<text>−</text>
 +
</jmolButton>
 +
</jmol> <jmol>
 +
<jmolButton>
 +
<script>save state ~one;
 +
plot ramachandran; select 2.1 and 68; label 2; select 2.1 and 69; label 3; delay 5; restore state ~one</script>
 +
<text>Ramachandran</text>
 +
</jmolButton>
 +
</jmol>
 +
 
 +
&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;Psi&emsp;<jmol>
 +
<jmolButton>
 +
<script>rotate BRANCH {68.C}{68.CA} 10; ang = angle({68.N},{68.CA},{68.C},{69.N})%0; echo "psi2 is @{ang}"</script>
 +
<text>+</text>
 +
</jmolButton>
 +
</jmol> 2 <jmol>
 +
<jmolButton>
 +
<script>rotate BRANCH {68.C}{68.CA} -10; ang = angle({68.N},{68.CA},{68.C},{69.N})%0; echo "psi2 is @{ang}"</script>
 +
<text>−</text>
 +
</jmolButton>
 +
</jmol>&emsp;&emsp;<jmol>
 +
<jmolButton>
 +
<script>rotate BRANCH {69.CA}{69.C} 10; ang = angle({69.N},{69.CA},{69.C},{70.N})%0; echo "psi3 is @{ang}"</script>
 +
<text>+</text>
 +
</jmolButton>
 +
</jmol> 3 <jmol>
 +
<jmolButton>
 +
<script>rotate BRANCH {69.CA}{69.C} -10; ang = angle({69.N},{69.CA},{69.C},{70.N})%0; echo "psi3 is @{ang}"</script>
 +
<text>−</text>
 +
</jmolButton>
 +
</jmol>&emsp;&emsp;&emsp;<jmol>
 +
<jmolButton>
 +
<script>original = {all}.xyz.all;rotate BRANCH {68.CA}{68.C} 180;rotate BRANCH {69.N}{69.CA} 180;rotate COMPARE {all} @original;echo ""
 +
</script>
 +
<text>pepflip</text>
 +
</jmolButton>
 +
</jmol>
 +
<StructureSection load='' size='350' side='right' caption='' scene='10/1072233/Turn_2mhr/2'>
 +
===Basic features===
 +
The interactive Jmol window on the right shows a beta turn (<scene name='10/1072233/Turn_2mhr/2'>reload initial scene</scene>) indicating the short distance between the first and the fourth alpha carbon. Because of this short distance, the polypeptide takes a sharp turn, sometimes also called a reverse turn. There are many types of beta turns, and they differ in the phi and psi angles of residues two and three. Some turns feature a <scene name='10/1072233/Turn_2mhr/4'>hydrogen bond</scene> between residues one and four (like the one shown here) and others don't.
 +
 
 +
===Beta turns in the context of other secondary structures===
 +
The repetitive secondary structure elements (alpha helices and beta strands) go in a single direction. Turns change the direction of the main chain, allowing them to connect alpha helices and beta strands at the surface of a globular protein. Of the six main chain hydrogen bonding partners of a turn, a maximum of two are engaged in hydrogen bonding, and turns are rarely found in the hydrophobic core. Below are three different protein folds highlighting the role of turns and their positions within a fold.
 +
 
 +
====Turns in an all-alpha protein====
 +
 
 +
In this <scene name='10/1072233/Alpha_2hmr/4'>myohemerythrin</scene> protein, you can see beta turns connecting the anti-parallel alpha helices. You can <jmol><jmolLink>
 +
<script>
 +
view1 = script("show moveto")[11][0];
 +
select (67-70 and mainchain) or (68-69 and *.CB);
 +
moveto 0.5 { 396 918 -22 24.97} 132.25 0.0 0.0 {27.01119230769231 33.81188461538462 10.03376923076923} 43.963541342342076 {0 0 0} 0 0 0 3.0 0.0 0.0;
 +
wireframe 0.3;
 +
color cpk;
 +
select 67-70;
 +
backbone off;
 +
delay 0.5;
 +
moveto 1.0 { 455 178 -872 110.43} 935.76 0.0 0.0 {26.793 33.036 8.6745} 44.96343106192573 {0 0 0} 0 0 0 3.0 0.0 0.0;
 +
slab on
 +
slab 60
 +
delay 6;
 +
select 67-70; backbone 0.4; wireframe off;
 +
slab off;
 +
script inline @{"moveto 1.0" + view1};
 +
</script>
 +
<text>zoom in</text>
 +
</jmolLink>
 +
</jmol> on the turn shown in the initial scene (and used below to explore conformations).
 +
 
 +
====Turns in an all-beta protein====
 +
In this <scene name='10/1072233/Agglutinin/3'>agglutinin protein</scene>, you can see beta turns connecting the strands of anti-parallel beta sheets. Two antiparallel beta strands directly connected by a turn is called a <jmol><jmolLink>
 +
<script>spin off; moveto 1.0 { 788 -362 -499 99.91} 404.55 0.0 0.0 {48.10615151515151 42.74112121212122 9.030939393939395} 37.460536158500446 {0 0 0} 0 0 0 3.0 0.0 0.0; delay 0.5; set zshade on; select protein; backbone -0.5;
 +
</script>
 +
<text>beta hairpin structure</text>
 +
</jmolLink>
 +
</jmol>. In this case, residues 1 and 4 of the turn are also part of the strands. This overlap of secondary structure assignment is common, but residues 2 and 3 of the turn are never part of a strand or an helix, by definition.
 +
 
 +
====Turns in an alpha/beta protein====
 +
 
 +
In this <scene name='10/1072233/Tim/3'>TIM barrel protein</scene>, you can see beta turns connecting helices and strands. The beta sheet is a barrel of parallel strands, as you can see if you turn on the cartoon representation with the buttons below.
 +
 
 +
The buttons below alow you to change the background color, spin the molecule, change the style and turn on the Ramachandran plot for 10 seconds.
 +
<jmol>
 +
<jmolButton>
 +
<script>background white</script>
 +
<text>white</text>
 +
</jmolButton>
 +
</jmol> <jmol>
 +
<jmolButton>
 +
<script>background black</script>
 +
<text>black</text>
 +
</jmolButton>
 +
</jmol> <jmol>
 +
<jmolButton>
 +
<script>spin y -50</script>
 +
<text>fastspin</text>
 +
</jmolButton>
 +
</jmol> <jmol>
 +
<jmolButton>
 +
<script>spin off</script>
 +
<text>spin off</text>
 +
</jmolButton>
 +
</jmol> <jmol>
 +
<jmolButton>
 +
<script>select protein; cartoon on; backbone off</script>
 +
<text>cartoon</text>
 +
</jmolButton>
 +
</jmol> <jmol>
 +
<jmolButton>
 +
<script>select protein; backbone 0.5; cartoon off</script>
 +
<text>trace</text>
 +
</jmolButton>
 +
</jmol> <jmol>
 +
<jmolButton>
 +
<script>set zshade on; set zshadepower 2</script>
 +
<text>zshade</text>
 +
</jmolButton>
 +
</jmol> <jmol>
 +
<jmolButton>
 +
<script>save state ~one;
 +
plot ramachandran; delay 10; restore state ~one</script>
 +
<text>rama</text>
 +
</jmolButton>
 +
</jmol>
 +
 
 +
===Exploring torsion angles of turns===
 +
 
 +
The interactive Jmol window shows a <scene name='10/1072233/Turn_2mhr/1'>turn</scene> (residues 67-70 of the [[2hmr]] structure shown previously) that you can explore. Four consecutive amino acids are said to form a beta turn if the alpha carbon atoms of the first and the fourth residue are in close proximity (less than 7.0 or 7.5 Angstrom<ref>PMID:36293166</ref>). However, this also happens in alpha helices and 3(10) helices, and these are not classified as beta turn.
In the structure fragment shown, the alpha carbon atoms are numbered 1 through 4 (relative numbering, sometimes also given as n, n+1, n+2, n+3), and the distance between the carbonyl oxygen and the amide hydrogen is indicated (dashed line and magnitude). Side chains are truncated to just show the beta carbon, and residues 1 and 4 have some main chain omitted for clarity.
In the structure fragment shown, the alpha carbon atoms are numbered 1 through 4 (relative numbering, sometimes also given as n, n+1, n+2, n+3), and the distance between the carbonyl oxygen and the amide hydrogen is indicated (dashed line and magnitude). Side chains are truncated to just show the beta carbon, and residues 1 and 4 have some main chain omitted for clarity.
-
To get a low energy conformation, you want a good hydrogen bond, i.e. carbonyl oxygen, amide hydrogen and nitrogen colinear <jmol>
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Another way of looking at it is that turns consist of three <jmol><jmolLink>
 +
<script>
 +
draw ID p68a polygon [{68.CA} {69.H} {69.CA}] color blue;
 +
draw ID p68b polygon [{68.CA} {69.CA} {68.O}] color red;
 +
draw ID p67a polygon [{67.CA} {68.H} {68.CA}] color blue;
 +
draw ID p67b polygon [{67.CA} {68.CA} {67.O}] color red;
 +
draw ID p69a polygon [{69.CA} {70.H} {70.CA}] color blue;
 +
draw ID p69b polygon [{69.CA} {70.CA} {69.O}] color red;
 +
delay 2; hide protein; delay 5; display protein; delay 1; draw ID p* delete;
 +
</script>
 +
<text>peptide planes</text>
 +
</jmolLink>
 +
</jmol>, whose relative orientation is determined by the phi/psi angles of residue 2 and 3.
 +
 
 +
The buttons below allow you to modify the conformation of the turn by changing the relevant torsion angles. To get a low energy conformation, you want a good hydrogen bond, i.e. carbonyl oxygen, amide hydrogen and nitrogen colinear <jmol>
<jmolLink>
<jmolLink>
<script>
<script>
Line 15: Line 182:
spacefill 30%;
spacefill 30%;
selectionHalos on;
selectionHalos on;
-
delay 0.5;
+
delay 1.5;
selectionHalos off;
selectionHalos off;
spacefill off
spacefill off
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spacefill 30%;
spacefill 30%;
selectionHalos on;
selectionHalos on;
-
delay 0.5;
+
delay 1.5;
selectionHalos off;
selectionHalos off;
spacefill off
spacefill off
Line 43: Line 210:
spacefill 30%;
spacefill 30%;
selectionHalos on;
selectionHalos on;
-
delay 0.5;
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delay 1.5;
selectionHalos off;
selectionHalos off;
spacefill off;
spacefill off;
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</jmolLink>
</jmolLink>
</jmol> of the side chains.
</jmol> of the side chains.
 +
 +
====Excercise 1====
 +
 +
Turns have been classified into different types in different ways, but most classifications include type I, type II, and type I' <ref>PMID: 3184187</ref>. Try to use the buttons to make a type I turn with the features shown below. This is the most common beta turn (more than one third are of this type). Are there any clashes? How is the different from an alpha helix (where all carbonyl groups are pointing in the same direction)?
 +
 +
Before you start, make sure a single turn is displayed in the Jmol window on the right (<scene name='10/1072233/Turn_2mhr/1'>reload</scene>).
Phi&emsp;<jmol>
Phi&emsp;<jmol>
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<script>rotate BRANCH {69.N}{69.CA} -10</script>
<script>rotate BRANCH {69.N}{69.CA} -10</script>
<text>−</text>
<text>−</text>
 +
</jmolButton>
 +
</jmol> <jmol>
 +
<jmolButton>
 +
<script>save state ~one;
 +
plot ramachandran; select 2.1 and 68; label 2; select 2.1 and 69; label 3; delay 5; restore state ~one</script>
 +
<text>Ramachandran</text>
</jmolButton>
</jmolButton>
</jmol>
</jmol>
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</jmolButton>
</jmolButton>
</jmol>
</jmol>
- 
-
===Excercise 1===
 
- 
-
Try to use the buttons to make a type 1 turn with the features shown below. This is the most common beta turn (about one third are of this type). Are there any clashes? How is the different from an alpha helix (where all carbonyl groups are pointing in the same direction)?
 
[[Image:Beta_turn_type_I.png|500px]]
[[Image:Beta_turn_type_I.png|500px]]
-
 
+
====Excercise 2====
-
 
+
-
===Excercise 2===
+
And now try to get a type I prime conformation, as shown below. This turn is rare (about 4% of beta turns are of this type). Hint: the pepflip button might serve as a bit of a shortcut. Why is that? Are there any clashes? If you had to choose, would you place a glycine at position 2 or position 3?
And now try to get a type I prime conformation, as shown below. This turn is rare (about 4% of beta turns are of this type). Hint: the pepflip button might serve as a bit of a shortcut. Why is that? Are there any clashes? If you had to choose, would you place a glycine at position 2 or position 3?
Line 115: Line 288:
[[Image:Beta_turn_type_I_prime.png|500px]]
[[Image:Beta_turn_type_I_prime.png|500px]]
 +
Before you start, make sure a single turn is displayed in the Jmol window on the right (<scene name='10/1072233/Turn_2mhr/3'>reload</scene>).
Phi&emsp;<jmol>
Phi&emsp;<jmol>
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<script>rotate BRANCH {69.N}{69.CA} -10</script>
<script>rotate BRANCH {69.N}{69.CA} -10</script>
<text>−</text>
<text>−</text>
 +
</jmolButton>
 +
</jmol> <jmol>
 +
<jmolButton>
 +
<script>save state ~one;
 +
plot ramachandran; select 2.1 and 68; label 2; select 2.1 and 69; label 3; delay 5; restore state ~one</script>
 +
<text>Ramachandran</text>
</jmolButton>
</jmolButton>
</jmol>
</jmol>
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Psi&emsp;<jmol>
Psi&emsp;<jmol>
<jmolButton>
<jmolButton>
-
<script>rotate BRANCH {68.C}{68.CA} 10</script>
+
<script>rotate BRANCH {68.C}{68.CA} 10;
 +
</script>
<text>+</text>
<text>+</text>
</jmolButton>
</jmolButton>
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-
===Exercise 3===
+
====Exercise 3====
Compare and contrast the two turns we discussed, and compare them to alpha helix and beta sheet. Clicking the buttons will preserve the orientation of the 2->3 peptide plane <jmol>
Compare and contrast the two turns we discussed, and compare them to alpha helix and beta sheet. Clicking the buttons will preserve the orientation of the 2->3 peptide plane <jmol>
<jmolLink>
<jmolLink>
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<text>(☼)</text>
<text>(☼)</text>
</jmolLink>
</jmolLink>
-
</jmol> while adjusting the torsion angles. You can press the last button to flip the entire molecules as a rigid body (different from the pepflip button above, which changes torsion angles).
+
</jmol> while adjusting the torsion angles. You can press the last button to rotate the entire molecules as a rigid body (different from the pepflip button above, which changes torsion angles).
 +
 
 +
Before you start, make sure a single turn is displayed in the Jmol window on the right (<scene name='10/1072233/Turn_2mhr/3'>reload</scene>).
<jmol>
<jmol>
<jmolButton>
<jmolButton>
-
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -90 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; center visible</script>
+
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;
 +
rpsi2 = -30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA} @rpsi2;
 +
rphi3 = -90 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;
 +
rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3;
 +
set echo top center; echo "Type I"; color echo white</script>
<text>Type I</text>
<text>Type I</text>
</jmolButton>
</jmolButton>
</jmol> <jmol>
</jmol> <jmol>
<jmolButton>
<jmolButton>
-
<script>rphi2 = -57 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -47 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -57 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = -47 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3</script>
+
<script>rphi2 = -57 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -47 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -57 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = -47 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "alpha helix"</script>
<text>(alpha helix)</text>
<text>(alpha helix)</text>
</jmolButton>
</jmolButton>
</jmol> <jmol>
</jmol> <jmol>
<jmolButton>
<jmolButton>
-
<script>rphi2 = -49 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -26 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -49 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = -26 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3</script>
+
<script>rphi2 = -49 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -26 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -49 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = -26 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "3-10 helix"</script>
<text>(3-10 helix)</text>
<text>(3-10 helix)</text>
</jmolButton>
</jmolButton>
</jmol> <jmol>
</jmol> <jmol>
<jmolButton>
<jmolButton>
-
<script>rphi2 = -140 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 130 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -140 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 130 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3</script>
+
<script>rphi2 = -140 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 130 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -140 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 130 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "beta strand"</script>
<text>(beta strand)</text>
<text>(beta strand)</text>
</jmolButton>
</jmolButton>
</jmol> <jmol>
</jmol> <jmol>
<jmolButton>
<jmolButton>
-
<script>rphi2 = 60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = 90 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3</script>
+
<script>rphi2 = 60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = 90 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "Type I prime"</script>
<text>Type I prime</text>
<text>Type I prime</text>
</jmolButton>
</jmolButton>
</jmol> <jmol>
</jmol> <jmol>
 +
<jmolButton>
 +
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 120 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = 80 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "Type II"</script>
 +
<text>Type II</text>
 +
</jmolButton>
 +
</jmol> <jmol>
 +
<jmolButton>
 +
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -120 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 120 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "Type VIII"</script>
 +
<text>Type VIII</text>
 +
</jmolButton>
 +
</jmol>
 +
 +
<jmol>
<jmolButton>
<jmolButton>
<script>rotate X 180 180</script>
<script>rotate X 180 180</script>
-
<text>flip along x-axis</text>
+
<text>rotate along x-axis</text>
 +
</jmolButton>
 +
</jmol> <jmol>
 +
<jmolButton>
 +
<script>center visible</script>
 +
<text>center</text>
 +
</jmolButton>
 +
</jmol> <jmol>
 +
<jmolButton>
 +
<script>save state ~one;
 +
plot ramachandran; select 2.1 and 68; label 2; select 2.1 and 69; label 3; delay 5; restore state ~one</script>
 +
<text>rama</text>
</jmolButton>
</jmolButton>
</jmol>
</jmol>
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Here are some possible things to discuss: the orientation of the carbonyl groups, hydrogen bonding patterns, potential clashes of side chains with the main chain secondary structure conformation, regions of the Ramachandran plot, distance of certain pairs of atoms, cis and trans peptides (what?).
Here are some possible things to discuss: the orientation of the carbonyl groups, hydrogen bonding patterns, potential clashes of side chains with the main chain secondary structure conformation, regions of the Ramachandran plot, distance of certain pairs of atoms, cis and trans peptides (what?).
-
===Turns in an all-alpha protein===
+
===Role of glycine and proline===
-
In this <scene name='10/1072233/Alpha_2hmr/1'>myohemerythrin</scene> protein, you can see beta turns connecting the anti-parallel alpha helices.
+
Glycine is the only amino acid lacking a side chain, allowing for a larger range of favorable phi/psi combinations. Proline, on the other hand, has a severely restricted range of phi torsion angles because it forms a five-membered ring involving the side chain and the main chain nitrogen. This allows these two amino acids to fulfil special roles in beta turns.
-
===Turns in an all-beta protein===
+
We will look at two examples from myohemethryin. The first shows a type II turn with <jmol>
-
In this <scene name='10/1072233/Agglutinin/1'>agglutinin protein</scene>, you can see beta turns connecting the strands of anti-parallel beta sheets. Here is an alternate representation using <scene name='10/1072233/Agglutinin/2'>secondary structure cartoons</scene>.
+
<jmolLink>
 +
<script>source /scripts/10/1072233/Alpha_2hmr/1.spt; background black; set zshade on; delay 0.5; moveto 1.0 { 68 -995 72 143.7} 132.25 0.0 0.0 {17.7825 49.4315 12.7155} 29.587605862640846 {0 0 0} 0 0 0 3.0 0.0 0.0;;
 +
moveto 2.0 { 732 -555 394 175.75} 615.28 0.0 0.0 {15.7575 32.677 14.6085} 44.38762035414952 {0 0 0} 0 0 0 3.0 0.0 0.0;
 +
source /scripts/10/1072233/Alpha_2hmr/2.spt; background black; set zshade on;delay 0.5;draw * off
 +
</script>
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<text>glycine in position 3</text>
 +
</jmolLink>
 +
</jmol>. A side chain in position 3 would clash with the carbonyl group of the central peptide plane of the turn, so a glycine in the position avoids a clash. Position 2 would be a good fit for a proline, but is a different amino acid in this case.
 +
In the <jmol>
 +
<jmolLink>
 +
<script>source /scripts/10/1072233/Alpha_2hmr/1.spt; background black; set zshade on; delay 0.5;
 +
moveto 2.5 { -576 521 -629 104.96} 1076.13 -1.4 -15.1 {3.9860344827586216 57.429310344827584 10.870275862068969} 43.92085420330055 {0 0 0} 0 0 0 3.0 0.0 0.0;
 +
source /scripts/10/1072233/Alpha_2hmr/6.spt; delay 1.0;select visible and alpha; backbone off; color cpk; draw * off
 +
</script>
 +
<text>second example</text>
 +
</jmolLink>
 +
</jmol>, we have a proline in position 3 and a cis-peptide between position 2 and 3. The cis-peptide has a shorter distance between alpha carbons (3.04 instead of 3.76 angstroms), making for a very tight turn. There is no hydrogen bond between residue 1 and 4 in this case. Beta turns involving a cis-peptide are classified as type VI.
-
===Turns in an alpha/beta protein===
+
You can revisit <scene name='10/1072233/Alpha_2hmr/4'>myohemerythrin</scene> and <scene name='10/1072233/Agglutinin/3'>agglutinin protein</scene>and <scene name='10/1072233/Tim/3'>TIM barrel protein</scene>. Use the button below to highlight glycine (white) and proline (green) residues.
-
In this <scene name='10/1072233/Tim/1'>TIM barrel protein</scene>, you can see beta turns connecting helices and strands. Here is an alternate representation using <scene name='10/1072233/Tim/2'>secondary structure cartoons</scene>.
+
<jmol>
 +
<jmolButton>
 +
<script>select gly.ca;
 +
spacefill on;
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color white;
 +
select pro.ca;
 +
spacefill on;
 +
color green
 +
</script>
 +
<text>Glycine and Proline</text>
 +
</jmolButton>
 +
</jmol>
 +
 
 +
 
 +
You can explore more turns at betaturn.com, which allows you to browse for turns of a specific type, and contains a lot of information and explanations.
 +
 
 +
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--!>
</StructureSection>
</StructureSection>
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Further reading
 +
* [[Turns in Proteins]]
 +
* [betaturn.com] allows you to brows a protein database for turns of different types
==References==
==References==
<references/>
<references/>

Current revision

A beta turn is a secondary structure element consisting of four consecutive amino acids (or three consecutive peptide planes). The geometry of turns correspond to a change in the direction of the polypeptide backbone, with a short distance between the first and fourth alpha carbon.

Concepts you can explore here

  1. A beta turn is a secondary structure element distinct from (but sometimes overlapping with) alpha helices and beta strands
  2. Beta turns consist of stretches of four amino acids making a sharp turn, with a short distance between the first and last alpha carbon
  3. Beta turns typically occur near the surface of globular proteins, often connecting helices and strands
  4. There are multiple types of beta turns, distinguished by the torsion angles of the second and third residue
  5. Glycine and proline occur relatively often in beta turns and play distinct special roles

See the discussion tab for learning and teaching notes.

Turns in 3D

                                                             Phi  2    3

                                                             Psi  2    3    

Drag the structure with the mouse to rotate

Further reading

  • Turns in Proteins
  • [betaturn.com] allows you to brows a protein database for turns of different types

References

  1. ↑ de Brevern AG. A Perspective on the (Rise and Fall of) Protein β-Turns. Int J Mol Sci. 2022 Oct 14;23(20):12314. PMID:36293166 doi:10.3390/ijms232012314
  2. ↑ Wilmot CM, Thornton JM. Analysis and prediction of the different types of beta-turn in proteins. J Mol Biol. 1988 Sep 5;203(1):221-32. PMID:3184187 doi:10.1016/0022-2836(88)90103-9

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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