Peptide Bonds & Structure

Secondary Structure Hydrogen Bonding

Summary

Hydrogen bonds between backbone amide groups (N-H···O=C) are the defining interactions that stabilize protein secondary structures. The geometry and periodicity of these bonds distinguish α-helices, β-sheets, and other regular structural elements.

Key Points

  • 1Backbone N-H···O=C bonds stabilize secondary structures
  • 2α-Helices: i → i+4 hydrogen bonding pattern
  • 3β-Sheets: inter-strand bonds (parallel or antiparallel)
  • 4Hydrogen bond cooperativity enhances structural stability

Hydrogen bonding between backbone atoms is the molecular glue that holds protein secondary structures together, creating the regular patterns observed in virtually all folded proteins.

The Backbone Hydrogen Bond

The canonical backbone hydrogen bond forms between:

- Donor: Amide nitrogen (N-H) of one residue

- Acceptor: Carbonyl oxygen (C=O) of another residue

Bond Characteristics

- Distance: N···O typically 2.8-3.2 Å

- Angle: N-H···O ideally ~160-180°

- Energy: ~2-7 kcal/mol per bond

- Cooperativity: Networks of H-bonds are stronger than isolated bonds

α-Helix Hydrogen Bonding

The α-helix features a characteristic hydrogen bonding pattern:

Bonding Pattern

- Each C=O group bonds to the N-H 4 residues ahead (i → i+4)

- Creates a right-handed helix with 3.6 residues per turn

  • Helix pitch of approximately 5.4 Å

    • Structural Consequences

  • All backbone H-bond donors and acceptors are satisfied internally

    • - Helix dipole: Partial positive charge at N-terminus, negative at C-terminus

  • Side chains project outward from the helical axis
  • Proline disrupts helices (no N-H donor)

    • Helix Variants

    - 3₁₀-Helix: i → i+3 bonding, tighter winding

    - π-Helix: i → i+5 bonding, wider and rare

    β-Sheet Hydrogen Bonding

    β-Sheets form through inter-strand hydrogen bonds:

    Antiparallel β-Sheets

  • Strands run in opposite directions

    • - H-bonds are perpendicular to strand direction

  • Slightly more stable due to optimal H-bond geometry

    • Parallel β-Sheets

  • Strands run in same direction

    • - H-bonds are angled relative to strand direction

  • Slightly weaker individual bonds

    • Structural Features

    - Pleated appearance due to tetrahedral Cα geometry

  • Side chains alternate above and below the sheet plane
  • Twist is common, especially in larger sheets

    • β-Turns and Loops

    Turns allow the polypeptide chain to reverse direction:

    Type I β-Turn

  • H-bond from residue i C=O to residue i+3 N-H
  • Most common turn type
  • Specific φ/ψ angles for residues i+1 and i+2

    • Type II β-Turn

  • Same H-bonding pattern as Type I
  • Different φ/ψ angles
  • Glycine often at position i+2

    • Hydrogen Bond Networks in Stability

    Cooperativity

    - H-bonds in secondary structures exhibit positive cooperativity

  • Adding one H-bond strengthens existing bonds
  • Partially explains nucleation-propagation in helix formation

    • Solvent Competition

  • Water molecules compete for backbone H-bond sites
  • Secondary structures must be more favorable than water interactions
  • Contributes to the marginal stability of proteins
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