Question

What is the Ramachandran plot and how are the bond angles used to understand protein structure?

Answer 1

A Ramachandran plot (also known as a Ramachandran diagram ), originally developed in 1963 by G.N.Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles psi against phi of amino acid residues in protein structure.

A Ramachandran plot can be used in two somewhat different ways. One is to show in theory which values, or conformations of the psi and phi angles are possible for an amino-acid residue in a protein (as at top right). A second is to show the empirical distribution of data points observed in a single structure (as at right, here) in usage for structure validation or else in a database of many structures (as in the lower 3 plots at left). Either case is usually shown against outlines for the theoretically favored regions.

In a polypeptide the main chain N-C alpha and C alpha-C bonds relatively are free to rotate. These rotations are represented by the torsion angles phi and psi, respectively.

G N Ramachandran used computer models of small polypeptides to systematically vary phi and psi with the objective of finding stable conformations.

For each conformation, the structure was examined for close contacts between atoms. Atoms were treated as hard spheres with dimensions corresponding to their van der Waals radii. Therefore, phi and psi angles which cause spheres to collide correspond to sterically disallowed conformations of the polypeptide backbone.

In the diagram above the white areas correspond to conformations where atoms in the polypeptide come closer than the sum of their van der Waals radi. These regions are sterically disallowed for all amino acids except glycine which is unique in that it lacks a side chain. The red regions correspond to conformations where there are no steric clashes, i.e., these are the allowed regions namely the alpha-helical and beta-sheet conformations. The yellow areas show the allowed regions if slightly shorter van der Waals radi are used in the calculation, i.e., the atoms are allowed to come a little closer together. This brings out an additional region which corresponds to the left-handed alpha-helix.

L-amino acids cannot form extended regions of left-handed helix but occassionally individual residues adopt this conformation. These residues are usually glycine but can also be asparagine or aspartate where the side chain forms a hydrogen bond with the main chain and therefore stabilises this otherwise unfavourable conformation. The 3(10) helix occurs close to the upper right of the alpha-helical region and is on the edge of allowed region indicating lower stability.

Disallowed regions generally involve steric hindrance between the side chain C-beta methylene group and main chain atoms. Glycine has no side chain and therefore can adopt phi and psi angles in all four quadrants of the Ramachandran plot. Hence it frequently occurs in turn regions of proteins where any other residue would be sterically hindered.