User:Karsten Theis/turns

Role in protein folds

The repetitive secondary structure elements (alpha helices and beta strands) go in a single direction. Turns change the direction of the main chain, allowing them to connect alpha helices and beta strands at the surface of a globular protein. Of the six main chain hydrogen bonding partners of a turn, a maximum of two are engaged in hydrogen bonding, and turns are rarely found in the hydrophobic core. Below are three different protein folds highlighting the role of turns and their positions within a fold.

Turns in an all-alpha protein

In this protein, you can see beta turns connecting the anti-parallel alpha helices. You can on the turn shown in the initial scene (and used below to explore conformations).

Turns in an all-beta protein

In this , you can see beta turns connecting the strands of anti-parallel beta sheets. Two antiparallel beta strands directly connected by a turn is called a . In this case, residues 1 and 4 of the turn are also part of the strands. This overlap of secondary structure assignment is common, but residues 2 and 3 of the turn are never part of a strand or an helix, by definition.

Turns in an alpha/beta protein

In this , you can see beta turns connecting helices and strands. The beta sheet is a barrel of parallel strands, as you can see if you turn on the cartoon representation with the buttons below.

The buttons below alow you to change the background color, spin the molecule, change the style and turn on the Ramachandran plot for 10 seconds.

Exploring torsion angles of turns

The interactive Jmol window shows a (residues 67-70 of the 2hmr structure shown previously) that you can explore. Four consecutive amino acids are said to form a beta turn if the alpha carbon atoms of the first and the fourth residue are in close proximity (less than 7.0 or 7.5 Angstrom^[1]). However, this also happens in alpha helices and 3(10) helices, and these are not classified as beta turn.

In the structure fragment shown, the alpha carbon atoms are numbered 1 through 4 (relative numbering, sometimes also given as n, n+1, n+2, n+3), and the distance between the carbonyl oxygen and the amide hydrogen is indicated (dashed line and magnitude). Side chains are truncated to just show the beta carbon, and residues 1 and 4 have some main chain omitted for clarity.

Another way of looking at it is that turns consist of three , whose relative orientation is determined by the phi/psi angles of residue 2 and 3.

The buttons below allow you to modify the conformation of the turn by changing the relevant torsion angles. To get a low energy conformation, you want a good hydrogen bond, i.e. carbonyl oxygen, amide hydrogen and nitrogen colinear , and want to avoid any clashes, e.g. carbonyl oxygen too close to beta carbon of the side chains.

Excercise 1

Turns have been classified into different types in different ways, but most classifications include type I, type II, and type I' ^[2]. Try to use the buttons to make a type I turn with the features shown below. This is the most common beta turn (more than one third are of this type). Are there any clashes? How is the different from an alpha helix (where all carbonyl groups are pointing in the same direction)?

Before you start, make sure a single turn is displayed in the Jmol window on the right ().

Phi  2    3

Psi  2    3    

Excercise 2

And now try to get a type I prime conformation, as shown below. This turn is rare (about 4% of beta turns are of this type). Hint: the pepflip button might serve as a bit of a shortcut. Why is that? Are there any clashes? If you had to choose, would you place a glycine at position 2 or position 3?

Before you start, make sure a single turn is displayed in the Jmol window on the right ().

Phi  2    3

Psi  2    3    

Exercise 3

Compare and contrast the two turns we discussed, and compare them to alpha helix and beta sheet. Clicking the buttons will preserve the orientation of the 2->3 peptide plane while adjusting the torsion angles. You can press the last button to rotate the entire molecules as a rigid body (different from the pepflip button above, which changes torsion angles).

Before you start, make sure a single turn is displayed in the Jmol window on the right ().

Here are some possible things to discuss: the orientation of the carbonyl groups, hydrogen bonding patterns, potential clashes of side chains with the main chain secondary structure conformation, regions of the Ramachandran plot, distance of certain pairs of atoms, cis and trans peptides (what?).

Role of glycine and proline

Glycine is the only amino acid lacking a side chain, allowing for a larger range of favorable phi/psi combinations. Proline, on the other hand, has a severely restricted range of phi torsion angles because it forms a five-membered ring involving the side chain and the main chain nitrogen. This allows these two amino acids to fulfil special roles in beta turns.

We will look at two examples from myohemethryin. The first shows a type II turn with . A side chain in position 3 would clash with the carbonyl group of the central peptide plane of the turn, so a glycine in the position avoids a clash. Position 2 would be a good fit for a proline, but is a different amino acid in this case.

In the , we have a proline in position 3 and a cis-peptide between position 2 and 3. The cis-peptide has a shorter distance between alpha carbons (3.04 instead of 3.76 angstroms), making for a very tight turn. There is no hydrogen bond between residue 1 and 4 in this case. Beta turns involving a cis-peptide are classified as type VI.

You can explore more turns at betaturn.com, which allows you to browse for turns of a specific type, and contains a lot of information and explanations.