Secondary structure and backbone conformation:part 1

                               

                                                  

Peptide Torsion Angles

The figure  shows the three main chain torsion angles of a polypeptide. These are phi (F), psi (Y), and omega (W).

The planarity of the peptide bond restricts to 180 degrees in very nearly all of the main chain peptide bonds. In rare cases = 10 degrees for a cis peptide bond which usually involves proline.

The Ramachandran Plot

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

GN Ramachandran used computer models of small polypeptides to systematically vary and 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, and 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 radii. 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 a-helical and a-sheet conformations. The yellow areas show the allowed regions if slightly shorter van der Waals radii 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 a-helix.

L-amino acids cannot form extended regions of left-handed helix but occasionally 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 3₁₀ helix occurs close to the upper right of the a-helical region and is on the edge of allowed region indicating lower stability.

Disallowed regions generally involve steric hindrance between the side chain C 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.

Below is a ramachandran plot of a protein containing almost exclusively beta-strands (yellow dots) and only one helix (red dots). Note how few residues are out of the allowed regions; and note also that they are almost all Glycines (depicted with a little square instead of a cross.Observe the effect of minor Phi and Psi angle changes:

Courtesy: swissmodel expasy