User:Stephen Mills/Secondary Structure: Helices
From Proteopedia
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Biochemistry Tutorial #2 - Secondary Structure (Part 1)
The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on helices and sheets.
Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.
You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.
Other things you can do:
- To rotate: left drag
- To Zoom: scroll button or shift + left drag
- To Translate: ctrl + right drag
- Right click to bring up an options menu
Helices
In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just like spiral staircases, helices come in different forms, depending on how tightly twisted the mainchain is. The form of a helix can be described by parameters such as the number of steps (amino acids) it takes to complete a turn (a 360o rotation around the long axis of the helix), and how far you travel along the helix axis in one complete turn. Helices can also be left-handed or right-handed. For proteins composed of L-amino acids, helices are almost always right-handed (a notable exception is the type I poly-proline helix). Although several types of helix form are possible, two regular helices are very common in proteins: the α-helix and the 310-helix.
The α-helix
α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
- Dihedral angles: Φ ~ -60o, φ ~ -45o
- Repeat (number of residues per turn) = 3.6
- Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
- Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
- Pitch (translation along axis per turn) = 5.4 Angstroms (= 0.54 nm = Repeat x Rise)
The helix shown below is a 19 amino acid chain in α-helical conformation.
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All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.
to go back to the initial view.
to show the helix in a space-filling representation. This representation shows the atoms with a radius that is approximately correct.
to show only the polypeptide mainchain (NH, Cα, and C=O).
Identify the N- and C-termini.
You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).
Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, to zoom in and look down the helix axis from the N-terminal end.
What is in the middle of the helix?
Now,
to see the helix in a space-filling representation.
Now, answer that question again - what is in the middle of the helix?
H-Bonding in α-helices
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I'll reset the structure for you. Now, look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?
The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).
You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').
The atoms of each amino side chain have been colored light blue to show them more clearly.
What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: or ).
The 310-helix
310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
- Dihedral angles: Φ ~ -49o, φ ~ -26o
- Repeat (number of residues per turn) = 3.0
- Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
- Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
- Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)
The helix shown below is a 19 amino acid chain in 310-helical conformation.
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All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.
to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.
You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.
The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).
to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.
H-Bonding in 3-10 Helices
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I've zoomed back out and turned on the hydrogen bonds for the mainchain. Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). to zoom in and you should be able to see this more clearly.
The atoms of each amino side chain have been colored light blue to show them more clearly.
As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): or .
What is the identity of the N-terminal amino acid?
What is the identity of the C-terminal amino acid?
Write down these answers so that you can submit them to your instructor at the end of this tutorial.
Click here to go on to part 2 of this tutorial.
Click here to go back to the main Tutorial page.
Files for 3D printer
An protein alpha helix in different representations by Marius Mihasan
