User:Karsten Theis/turns
From Proteopedia
(Difference between revisions)
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</jmol> | </jmol> | ||
| + | ===Excercise 1=== | ||
Try to use the buttons to make a type 1 turn with the features shown below. Are there any clashes? How is the different from an alpha helix (where all carbonyl groups are pointing in the same direction)? | Try to use the buttons to make a type 1 turn with the features shown below. Are there any clashes? How is the different from an alpha helix (where all carbonyl groups are pointing in the same direction)? | ||
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[[Image:Beta_turn_type_I.png|500px]] | [[Image:Beta_turn_type_I.png|500px]] | ||
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| - | + | ===Excercise 2=== | |
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And now try to get a type I prime conformation, as shown below. 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. 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? | ||
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[[Image:Beta_turn_type_I_prime.png|500px]] | [[Image:Beta_turn_type_I_prime.png|500px]] | ||
| - | <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 = 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> | ||
| - | <text>Type I prime</text> | ||
| - | </jmolButton> | ||
| - | </jmol><jmol> | ||
| - | <jmolButton> | ||
| - | <script>rotate X 180</script> | ||
| - | <text>flip along x-axis</text> | ||
| - | </jmolButton> | ||
| - | </jmol> | ||
Phi <jmol> | Phi <jmol> | ||
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</jmolButton> | </jmolButton> | ||
</jmol> | </jmol> | ||
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Psi <jmol> | Psi <jmol> | ||
<jmolButton> | <jmolButton> | ||
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</jmol> | </jmol> | ||
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| + | ===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 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). | ||
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| + | <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 = -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> | ||
| + | <text>Type I</text> | ||
| + | </jmolButton> | ||
| + | </jmol> <jmol> | ||
| + | <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> | ||
| + | <text>(alpha helix)</text> | ||
| + | </jmolButton> | ||
| + | </jmol> <jmol> | ||
| + | <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> | ||
| + | <text>(beta strand)</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 = 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> | ||
| + | <text>Type I prime</text> | ||
| + | </jmolButton> | ||
| + | </jmol> <jmol> | ||
| + | <jmolButton> | ||
| + | <script>rotate X 180</script> | ||
| + | <text>flip along x-axis</text> | ||
| + | </jmolButton> | ||
| + | </jmol> | ||
. | . | ||
Revision as of 21:13, 7 February 2025
A beta turn is a secondary structure element consisting of four consecutive amino acids (or three peptide planes). The geometry of turns correspond to a change in the direction of the polypeptide backbone, 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.
Exploring turns
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