User:Robert Dutnall/Sandbox 1 sheets
From Proteopedia
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=β-strands and β-sheets= | =β-strands and β-sheets= | ||
| - | The second major secondary structure element is the β-sheet. β- | + | The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus). |
| - | + | Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180<sup>o</sup>) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands). | |
| - | Parallel β- | + | ==Parallel β-sheet== |
| + | Parallel β-sheets are composed of β-strand that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120<sup>o</sup>, φ ~ +105<sup>o</sup>. | ||
| - | The | + | The sheet shown below is composed of three strands in parallel orientation. |
| - | <Structure load=' | + | <Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/parallel_load/1'/> |
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. | 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. | ||
| - | <scene name='User:Robert_Dutnall/Sandbox_1_sheets/ | + | <scene name='User:Robert_Dutnall/Sandbox_1_sheets/parallel_mainchain/1'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). |
| - | Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/ | + | Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/parallel_mainchain_labels/1'>Click here to see if you were correct.</scene> |
<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> 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). | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> 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). | ||
Revision as of 20:25, 26 August 2011
Contents |
Biochemistry Tutorial #2 - Secondary Structure
Part Two
β-strands and β-sheets
The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).
Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).
Parallel β-sheet
Parallel β-sheets are composed of β-strand that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.
The sheet shown below is composed of three strands in parallel orientation.
|
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 of each strand.
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 ).
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.
|
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.
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 .
Click here to go on to back to the first part of this tutorial.
