Peptide Bonds & Structure

Ramachandran Plots

Summary

The Ramachandran plot maps the allowed backbone conformations of proteins by plotting the φ (phi) and ψ (psi) dihedral angles. Due to steric clashes, only certain regions of φ-ψ space are accessible, corresponding to defined secondary structures like α-helices, β-sheets, and turns.

Key Points

  • 1φ (phi) and ψ (psi) angles define backbone conformation
  • 2Steric clashes limit accessible conformational space
  • 3Distinct regions correspond to α-helices, β-sheets, and other structures
  • 4Essential tool for protein structure validation

The Ramachandran plot is one of the most fundamental tools in structural biology, providing a visual map of the conformational space available to protein backbones.

The Dihedral Angles

Each amino acid residue in a protein chain is characterized by two key backbone dihedral angles:

- φ (phi): Rotation around the N-Cα bond

- ψ (psi): Rotation around the Cα-C bond

The third angle, ω (omega), describes rotation around the peptide bond itself and is typically fixed at ~180° (trans) due to resonance.

Steric Constraints

Not all combinations of φ and ψ are physically possible. Steric clashes between atoms limit the accessible conformational space:

1. Backbone atoms (carbonyl oxygen, amide hydrogen) collide at certain angle combinations

2. Cβ atoms of side chains create additional restrictions

3. Glycine, lacking a side chain, has the most conformational freedom

4. Proline, with its cyclic side chain, has the most restricted angles

Allowed Regions

The Ramachandran plot reveals distinct clusters corresponding to secondary structures:

Right-Handed α-Helix Region

  • φ ≈ -60°, ψ ≈ -45°
  • Tight, right-handed spiral with 3.6 residues per turn
  • Most common secondary structure element

    • β-Sheet Region

  • φ ≈ -120° to -140°, ψ ≈ +120° to +140°
  • Extended conformation allowing strand interactions
  • Both parallel and antiparallel arrangements

    • Left-Handed Helix Region

  • φ ≈ +60°, ψ ≈ +45°
  • Energetically less favorable
  • Rare, except for glycine residues

    • Polyproline II (PPII) Region

  • φ ≈ -75°, ψ ≈ +145°
  • Extended left-handed helix
  • Common in collagen and unfolded states

    • Practical Applications

    Structure Validation

    Ramachandran plots are essential for validating experimentally determined protein structures:

    - Good structures: >95% of residues in favored regions

    - Outliers suggest errors or genuine unusual conformations

  • Standard quality metric for PDB depositions

    • Secondary Structure Assignment

    The plot directly reveals:

  • Which residues adopt α-helical conformations
  • Which residues are in β-strand conformations
  • Location of turns and loops

    • Glycine and Proline Exceptions

    - Glycine: Separate plot with expanded allowed regions

    - Proline: Restricted to specific regions due to pyrrolidine ring

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