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Thursday, April 03, 2008

Ramachandran Plots


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Protein Structure
The peptide bond has considerable double-bond character and this prevents rotation around that bond in the polypeptide chain. Adjacent amino acids can adopt different configurations by rotation around the two other bonds in the backbone. The angle of the bond between the nitrogen atom (blue) and the α-carbon atom (black) is &Phi (phi) and the angle of the bond between the α-carbon atom and the carbonyl carbon atom (grey) is Ψ (psi) [The Peptide Bond]. These angles are measured in degrees where 180° is the angle of the bonds when all of the atoms of both residues lie in the most extended conformation. Rotation in one direction is positive so the values go from 0° to 180° and in the other direction they go from 0° to -180°. (180° = -180° in this notation.)

Most of the amino acid residues in a given protein are found in some form of secondary structure such as α helix, β strands, or turns.

The Φ and Ψ bond angles for each residue in the α-helical structure are very similar as shown on the left. This is why the structure is so regular. Similarly, the Φ and Ψ bond angles for every residue in a β strand are similar. Since the residues in a β stand are in an extended form, the Φ and Ψ angles in this conformation are close to 180°.

For any given protein, you can plot all of the bond angles for every pair of residues. These can be plotted on a diagram called a Ramachandran plot, named after the biophysicist G.N. Ramachandran (1922 - 2001). Such a plot shows that most of the residues in β strands have similar bond angles that cluster in a region near the top left-hand corner of the diagram. Similarly, residues in a right-handed α helix have very similar bond angles around Ψ=-45°, Φ=+45°.

The residues in Type II turns also have very characteristic bond angles. Some regions of the Ramachandran plot will be empty because of steric clashes between the oxygen atoms [see The Peptide Bond]. These regions are mostly located in the lower right-hand corner of the plot.

Let's look at some specific examples. One of the proteins we saw in the slideshow was an all-α protein called human serum albumin [PDB 1BJ5]. Another was an all-β protein called Jack bean conconavalin A [PDB 1CON].

If you click on the PDB numbers of these proteins you will be directed to the Protein DataBase (PDB) entry for these proteins. Click on "Structural Analysis" then "Geometry" in the left-hand sidebar of these PDB entries to see the link to "Ramachandran plot." This will take you to the two diagrams shown below for Human serum albumin (left) and Jack bean conconavalin A (right).

The Ψ and Φ angles of every residue in the protein are plotted. Note that for the all-α protein (left) almost all the angles cluster around the region identified as α helix. Similarly, for the all-β proteins (right) the angles cluster in the upper left-hand corner of the plot where you expect to find residues in β strands.

Large regions of the plot are empty indicating that many conformations are disallowed for steric or thermodynamic reasons. The point is that the number of conformations of polypeptides in solution is not infinitely large. Most residues cluster in regions of secondary structure (α helix, β strands, turns). These are thermodynamically stable structures and polypeptides will spontaneously adopt these secondary structures very rapidly.

The overall conformation of a polypeptide then depends on the arrangement of secondary structure motifs relative to each other. Even at this level, there are preferred motifs such as β barrels and α helix bundles.


Alex said...


Larry Moran said...

Thanks Dunbar.

Anonymous said...

Not sure if you will see this or not given the date it was posted originally, but this was incredibly helpful. Thank you so much!

Unknown said...

thank you!! well explained!!

Unknown said...

Nice explanation, I would like to add that amino acids like glycine and proline have different Ramachandran plot owing to their non-canonical structure.

On a side note, this year also marks completion of 50 years of Ramachandran plot. Read more here:

sudhakar Malla said...

nice explanation.. helped me a lot.. thank u sir.

Unknown said...

I think there is a slight confusion in the following sentence
" the angle of the bond between the α-carbon atom and the
carbonyl carbon atom (grey) is Ψ (psi) [The Peptide Bond]."
That is not the peptide bond.