User:Stephen Mills/Secondary Structure: Sheets

From Proteopedia

1 Biochemistry Tutorial #2 - Secondary Structure (Part 2)
2 β-strands and β-sheets
3 Parallel β-sheet
4 H-bonds in Parallel Sheets
5 Anti-Parallel β-sheet
6 H-bonds in antiparallel sheets
7 A mixed β-sheet

Biochemistry Tutorial #2 - Secondary Structure (Part 2)

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?

H-bonds in Parallel Sheets

Hydrogen bonds have now been added to the structure. The hydrogen bonds connect backbone NH groups of one strand with the C=O groups of another. 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 the NH and C=O groups are parallel to plane of the sheet and lie opposite each other in pairs. 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 ~ -150^o, φ ~ +135^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 of each strand (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. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain. The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet and lie opposite each other so that they can make hydrogen bonds.

H-bonds in antiparallel sheets

I'll reset the structure and add hydrogen bonds. 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 between the strands of the sheet.

You should 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, but if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

Two of the strands in this sheet are connected by a β-turn. to show the β-turn. The carbon atoms of the amino acids that define the turn have been colored orange. The turn allows a segment of polypeptide to reverse direction in a short distance. In this case it also allows two strands to interact in an antiparallel fashion. Is this a Type I or Type II β-turn? (Write down your answer so you can submit it to your instructor) Here are a couple of links that might help you figure this out. NKU tutorial and UVM COMET.

In this view, some of the residues at the turn have been omitted and you are looking roughly edge-on to the flat plane of the sheet. Sidechains have been added and the atoms of each amino side chain have been colored blue or purple in an alternating fashion.

The side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction (above the plane, below the plane, above the plane...) so you should be able to see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

A mixed β-sheet

The sheet shown below is composed of four strands. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white). This is a mixed β-sheet. Some of the strands are parallel, some are antiparallel.