User:Robert Dutnall/Sandbox 1 sheets
From Proteopedia
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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.
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All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white).
to show only the polypeptide mainchain (NH, Cα, and C=O).
Identify the N- and C-termini of each strand.
As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.
to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane. to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.
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 long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?
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).
You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet. This means that hydrogen bonds can be made between the strands of the sheet.
You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.
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 each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. to color the side chains along one strand blue-purple-blue-purple...etc. If we apply this to all the sheets () you can see that all the amino acids on one face of the sheet are blue, and on the other are purple.
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.
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.
