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Revision as of 22:12, 28 August 2011

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 ≠ 180^o) 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-strands that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120^o, φ ~ +105^o.

The sheet shown below is composed of three strands in parallel orientation. All the atoms are shown (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, with each strand running left-to-right (N- to C-terminus).

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.

You are looking roughly edge-on to the flat plane of the sheet and 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 freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands () you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

Anti-Parallel β-sheet

Anti-parallel β-sheets are composed of β-strands that alternate in direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120^o, φ ~ +105^o.

The sheet shown below is composed of three strands in anti-parallel orientation. All the atoms are shown (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, with each strand running left-to-right (N- to C-terminus).

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.

You are looking roughly edge-on to the flat plane of the sheet and 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 freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands () you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

Click here to go on to back to the first part of this tutorial.