Overview
This lecture covers protein secondary structure, focusing on alpha helices, beta strands/sheets, and how their backbone dihedral angles are represented on a Ramachandran plot.
Ramachandran Plot and Secondary Structure
- The Ramachandran plot shows allowed phi (Φ) and psi (Ψ) angles for amino acid residues in proteins.
- Regular secondary structures have repeating phi and psi angles, visible as clusters in specific plot regions.
- Common phi/psi values: alpha helix (~–60°, –45°), beta strand (~–150°, +150°).
- Glycine and proline have unique regions due to their side chain properties; glycine is flexible, proline’s phi angle is fixed at –60°.
- Most residues fall within allowed regions, indicating stable structures.
Types of Secondary Structure
- Regular secondary structure: Repeating phi/psi angles (e.g., alpha helix, beta strand); highly stable due to consistent hydrogen bonding patterns.
- Irregular secondary structure: Non-repeating phi/psi angles; stable but not regular; backbone hydrogen bonds still formed, but with varied partners.
- Random coil: No fixed phi/psi angles; backbone is dynamic; hydrogen bonds only with water, not within the protein.
Alpha Helix Structure
- Defined by ~–60° phi and –45° psi angles.
- 3.6 residues per turn; each turn is 5.4 Ã… long (pitch).
- Backbone carbonyl (CO) of residue n hydrogen bonds to NH of residue n+4.
- Helix core is tightly packed; side chains extend outward from the axis.
- The arrangement minimizes volume and enhances protein stability.
Beta Sheet Structure
- Defined by ~–150° phi and +150° psi angles.
- Extended, pleated conformation; every other side chain points to opposite sides of the sheet.
- Can be parallel (less common) or antiparallel (more common, more stable).
- Backbone NH forms hydrogen bonds with backbone CO of neighboring strands.
Irregular Secondary Structures and Turns
- Omega loops and beta turns are examples of irregular structures.
- Beta turns often contain proline (at position 2) and glycine (at position 3) to facilitate the tight turn.
Key Terms & Definitions
- Ramachandran plot — graphical representation of allowed backbone dihedral angles (phi and psi) in proteins.
- Phi (Φ), Psi (Ψ) angles — backbone dihedral angles determining protein secondary structure.
- Regular secondary structure — regions with repeating phi/psi angles (alpha helix, beta strand).
- Irregular secondary structure — regions with non-repeating but stable phi/psi angles.
- Random coil — disordered region, no stable phi/psi angles.
- Alpha helix — right-handed coiled secondary structure stabilized by hydrogen bonds (every 4 residues).
- Beta sheet — extended secondary structure with hydrogen bonds between strands; can be parallel or antiparallel.
Action Items / Next Steps
- Review Ramachandran plot regions for alpha helices and beta strands.
- Study hydrogen bonding patterns in alpha helices and beta sheets.
- Prepare for exam covering secondary structure (Module 5).