Structural Biochemistry, Proteins, Ramachandron Plot

Original hard-sphere, reduced-radius, and relaxed-tau φ,ψ regions from Ramachandran, with -180 to +180 axes (Image: Dcrjsr, CC BY 3.0)

Backbone dihedral angles φ and ψ (and ω) (Image: Dcrjsr, CC BY 3.0)

A Ramachandran plot, also known as a Ramachandran diagram or a [φ,ψ] plot, was originally developed by Gopalasamudram Ramachandran, an Indian physicist, in 1963. Ramachandran Plot is a way to visualize dihedral angles ψ against φ of amino acid residues in protein structure. Ramachandran recognized that many combinations of angles in a polypeptide chain are forbidden because of steric collisions between atoms. His two-dimensional plot shows the allowed and disfavored values of ψ and φ: three-quarters of the possible combinations are excluded simply by local steric clashes. Steric exclusion is the fact that two atoms cannot be in the same place at the same time is the powerful organizing principle that propels the use of the Ramachandran plot forward.

Torsion Angles

The two torsion angles of the polypeptide chain, also called Ramachandran angles, describe the rotations of the polypeptide backbone around the bonds between N-Cα (called Phi, φ) and Cα-C (called Psi, ψ). The Ramachandran plot provides an easy way to view the distribution of torsion angles of a protein structure. It also provides an overview of allowed and disallowed regions of torsion angle values, serving as an important factor in the assessment of the quality of protein three-dimensional structures.

Torsion angles are among the most important local structural parameters that control protein folding - essentially, if we would have a way to predict the Ramachandran angles for a particular protein, we would be able to predict its 3D structure. The reason is that these angles provide the flexibility required for folding of the polypeptide backbone, since the third possible torsion angle within the protein backbone (called omega, ω) is essentially flat and fixed to 180 degrees. This is due to the partial double-bond character of the peptide bond, which restricts rotation around the C-N bond, placing two successive alpha-carbons and C, O, N and H between them in one plane. Thus, rotation of the main chain (backbone) of a protein can be described as the rotation of the peptide bond planes relative to each other.

Regions in Ramachandran Plot

The Ramachandran Plot helps with determination of secondary structures of proteins.

• Quadrant I shows a region where some conformations are allowed. This is where rare left-handed alpha helices lie.
• Quadrant II shows the biggest region in the graph. This region has the most favorable conformations of atoms. It shows the sterically allowed conformations for beta strands.
• Quadrant III shows the next biggest region in the graph. This is where right-handed alpha helices lie.
• Quadrant IV has almost no outlined region. This conformation(ψ around -180 to 0 degrees, φ around 0-180 degrees) is disfavored due to steric clash.

Exceptions

Exception from the principle of clustering around the α-helix and β-strand regions is glycine. Glycine does not have a complex side chain, which allows high flexibility in the polypeptide chain as well as torsion angles, something normally not allowed for other amino acid residues. That is why glycine is often found in loop regions, where the polypeptide chain makes a sharp turn. This is also the reason for the high conservation of glycine residues in protein families, since the presence of turns at certain positions is a characteristic of a particular fold of a protein structure.

Another residue with special properties in terms of its torsion angles is proline. Proline, in contrast to glycine, fixes the torsion angles at values, which are very close to those of an extended conformation of the polypeptide (like in a beta-sheet). Proline is often found at the end of helices and functions as a helix disruptor.

References

• Berg, Jeremy M., John L. Tymoczko, and Lubert Stryer. "Chapter 2: Protein Composition and Structure." Biochemistry. New York: W. H. Freeman, 2007. N. pag. Print.
• "Torsion Angles and the Ramachandran Plot". http://proteinstructures.com/Structure/Structure/Ramachandran-plot.html.

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