User:Robert Dutnall/Sandbox 1 alpha helix
From Proteopedia
Contents |
Biochemistry Tutorial #2 - Secondary Structure
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
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
An 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 (= 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 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.
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 ).
An 310-helix
310-helices 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 (0.15 nm)
- Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
- Pitch (translation along axis per turn) = 6.0 Angstroms (= Repeat x Rise)
The helix shown below is a 19 amino acid chain in α-helical conformation.
|
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).
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.
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 ).
