📐 Stereochemistry: Protein Folding & Ramachandran Plot
Protein backbone conformation is governed by rotation around two dihedral torsion angles per residue: $phi$ (phi: $N-C_alpha$) and $psi$ (psi: $C_alpha-C$), with the peptide bond itself locked in a planar trans state by partial double-bond resonance.
1. The Ramachandran Plot (G.N. Ramachandran, 1963)
Steric clashes between non-bonded atoms restrict the allowed values of $phi$ and $psi$ to distinct quadrants of conformational space:
| Conformational Region | Typical ($phi$, $psi$) Coordinates | Secondary Structure Type |
|---|---|---|
| Top Left Quadrant | $phi approx -120^circ$ to $-140^circ$ $psi approx +130^circ$ to $+150^circ$ |
$beta$-Sheets: Antiparallel $beta$-strands, Parallel $beta$-strands, Polyproline II helix, Collagen triple helix |
| Bottom Left Quadrant | $phi approx -60^circ$ $psi approx -45^circ$ |
Right-handed $alpha$-Helix ($alpha_R$): Intrachain hydrogen bond between $C=O$ of residue $i$ and $N-H$ of residue $i+4$; 3.6 residues per turn, 5.4 Å pitch |
| Top Right Quadrant | $phi approx +60^circ$ $psi approx +45^circ$ |
Left-handed $alpha$-Helix ($alpha_L$): Rare in natural proteins except for short turns or glycine residues |
| Glycine & Proline Exceptions | Glycine: symmetric across all 4 quadrants Proline: restricted to $phi approx -65^circ pm 15^circ$ |
Glycine lacks a $beta$-carbon sidechain, permitting extreme flexibility; Proline has a rigid pyrrolidine ring locking $phi$ |