Lecture on Alpha Helix Structure

Introduction to Protein Structure

• Proteins have four structural levels:
  • Primary structure
  • Secondary structure
  • Tertiary structure
  • Quaternary structure
• Focus of this lecture: Secondary structures
  • Types: Alpha helices, beta turns, beta pleated sheets

Focus on Alpha Helix

• Importance: Common secondary structure in proteins
• Examples: G protein-coupled receptors, transcription factors (e.g., leucine zipper motif)

Studying Alpha Helix

• X-ray Crystallography:
  • Begin with protein crystallization
  • Obtain diffraction pattern using X-rays
  • Convert to electron density map via Fourier transformation
  • Build molecular model based on the map

Alpha Helix Structure and Properties

• Discovered by Pauling and colleagues in the 1940s
• Characteristics:
  • 3.6 amino acid residues per turn
  • Stabilized by hydrogen bonding between I and I+4 amino acids
  • Dihedral angles important, plotted using Ramachandran plot
  • Right-handed helices are common

Factors Affecting Helix Stability

• Hydrogen Bonding: Crucial between I and I+4 residues
• Electrostatic Interactions:
  • Repeating charged residues can cause repulsion
  • Glutamate (negative charge) and lysine/arginine (positive charge)
• Helix Breakers:
  • Proline: Causes structural tilt, cannot form hydrogen bonds
  • Glycine: Also destabilizes the helix
• Helix Makers: Alanine, leucine, methionine

Helix Dipole and Neutralization

• Peptide bonds create a dipole with net charges
• Stabilized by opposite charges at N-terminus and C-terminus

Tools for Studying Alpha Helix

• Circular Dichroism Spectroscopy:
  • Provides structural signatures of secondary structures
  • Useful for identifying predominant structures in proteins
• Cryo-Electron Microscopy: Offers detailed structural insights

Summary

• Discussed alpha helix structure and stabilizing factors
• Explored techniques for studying alpha helices, including X-ray crystallography and circular dichroism spectroscopy

Feel free to reach out for more detailed studies on techniques like X-ray crystallography and circular dichroism spectroscopy.