Proteins, also known as polypeptides, are linear or branching polymers of amino acids connected by covalent peptide bonds. The creation of a covalent amide bond between the α-amino group of one amino acid and the α-carboxyl group of the next amino acid involves the loss of a water molecule in the peptide bond formation mechanism. It is a type of a condensation reaction and an endergonic process, with ∆G0 ≈ +21kg/mol.
In 1930s, Linus Pauling and Robert Corey discovered the conformational restrictions on a polypeptide chain using X-ray investigations of amino acid structures. Because of the resonance interactions that led to the peptide bond's 40% double-bond nature, the peptide bond was determined to be rigid and planar. The peptide C-N bond (1.33 Armstrong) was found to be shorter than the C-N single bond (1.49 Armstrong).
It was later discovered that the differential in electronegativity between Oxygen and Nitrogen was to blame. Due to the fact that Oxygen is more electronegative than Nitrogen, Oxygen has a partial negative charge whereas Nitrogen has a partial positive charge, setting up a small dipole moment. Due to the rigid planar configuration of the peptide bond, all the 6 atoms of 2 amino acids i.e., Cα, C, O, N, H, Cα) all lie at the same plane.
The peptide bond conformations are due to the Torsion angles, also called as dihedral angles or even rotation angles. Let us assume a system of 4 atoms- A, B, C & D that is projected onto a plane normal to B-C. The angle between A-B and C-D is described as the torsion angle about bond B-C. As previously stated, a peptide linkage has a partial double-bond character, which restricts rotation about this bond. There are two conceivable configurations observed: cis and trans.
Following 2 successive α -carbon atoms are on the same side of the peptide bond in the cis form. The two subsequent α-carbon atoms lie on opposing sides of the peptide bond in the trans configuration. The trans configuration outnumbers the cis configuration by a factor of 1000. The development of the cis configuration is hampered by steric clashes between groups linked to the α-carbon atoms, whereas they do not occur in the trans configuration.
The (N- Cα) and the (Cα-C) bonds are pure single bonds called as φ (phi) and ψ (psi) respectively. When the polypeptide chain is completely stretched, both of these angles, and, are defined as 180°.
Now, what does the Ramachandran plot signify? These two angles can theoretically have any value between +180° and –180° (i.e., 360° of rotation for each). However, due to the physical collisions of atoms in 3-dimensional space, not all combinations are conceivable in reality. These physical clashes are called as Steric Interference.
G. N. Ramachandran was the first to identify the allowed values for φ and ψ. These allowed values may be seen on a two-dimensional figure called a Ramachandran plot, which is displayed between and on the x- and y-axes, respectively.
The white regions correspond to the sterically disallowed regions and the dark blue regions imply the allowed regions due to lack of steric hindrance. The amino acid with the shortest side chain, glycine, is substantially less sterically limited than the other amino acid residues. As a result, its permitted range of φ and ψ. covers a wider region of the Ramachandran plot. Polypeptide chains frequently adopt conformations at glycine residues that are sterically forbidden to other residues. Because the side chains of the D- and L-form amino acids are orientated differently with regard to the CO group, they have different allowed φ and ψ angles.
The Ramachandran plot is divided into 4 quadrants: the upper left quadrant is occupied by the parallel and anti-parallel β-sheets and the upper right quadrant by the left-handed α helix. The lower left quadrant is occupied by the right-handed α helix.
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