9. The regions of phi, psi space occupied by well characterized protein secondary structures are marked on a Ramachandran plot as shown above. Which of the following statements is CORRECT?

(1) A- right handed α helix, B- ß strand, C- left handed α helix, D- collagen,
(2) A- ß strand, B- right handed α helix, C- left handed α helix, D- collagen,
(3) A- collagen, B- right handed α helix, C- left handed α helix, D- ß strand,
(4) A- left handed α helix, B- ß strand, C-collagen, D- right handed α helix

Understanding Secondary Structure Regions in the Ramachandran Plot

The Ramachandran plot is a graphical representation of the allowed dihedral angles (φ and Ψ) of amino acids in a protein. It provides insights into different secondary structures such as α-helices, β-strands, and collagen conformations.

Correct Answer:

The correct answer is:

(1) A- right-handed α-helix, B- β-strand, C- left-handed α-helix, D- collagen.

Explanation of Ramachandran Plot Regions

The Ramachandran plot divides the φ and Ψ angle space into specific regions where different secondary structures occur:

1. Right-Handed α-Helix (A)

• Located in the bottom-left quadrant of the plot.
• Typical φ ≈ -60° and Ψ ≈ -45°.
• Most common helix found in proteins.

2. β-Strand (B)

• Located in the upper-left quadrant.
• Typical φ ≈ -120° and Ψ ≈ 120°.
• Forms the extended structure of β-sheets.

3. Left-Handed α-Helix (C)

• Found in the upper-right quadrant.
• Typical φ ≈ 60° and Ψ ≈ 30°.
• Less common but observed in certain polypeptides.

4. Collagen (D)

• Located near φ ≈ -60° and Ψ ≈ 135°.
• Forms a triple-helical structure unique to collagen.

Biological Significance of Secondary Structure Regions

1. Role in Protein Folding

• The placement of residues in these regions determines the overall protein structure and function.
• Incorrect angles can lead to misfolding diseases.

2. Structural Validation in Protein Models

• If a residue falls outside these allowed regions, it may indicate errors in a protein structure model.

3. Design of Engineered Proteins

• Understanding secondary structure preferences helps in designing synthetic proteins and peptides.

Conclusion

The Ramachandran plot clearly maps different secondary structures based on φ and Ψ angles. The correct identification of right-handed α-helices, β-strands, left-handed α-helices, and collagen conformations is essential for understanding protein folding and stability.