38. Following are statements related to peptide/protein conformation.
    A. The circular dichroism spectra of collagen and a protein in α-helical conformation will be identical.
    B. The allowed region for the dihedral angles ϕ, Ψ in Gly, spans a large area in the
    Ramachandran map. This can be drastically reduced by substituting the two hydrogens with methyl groups.
    C. Proline has high frequency of occurrence in β- turns.
    D. In a β-hairpin structure, the dihedral angles ϕ, Ψ of amino acids flanking the β-turn region will be 60⁰, -30⁰, respectively.

    Choose the combination with both INCORRECT statements.
    (1) B and C
    (2) A and B
    (3) A and D
    (4) C and D

Understanding Peptide and Protein Conformation

Protein conformation is determined by various factors such as circular dichroism (CD), dihedral angles (ϕ, Ψ), and structural motifs like β-turns and β-hairpins. Understanding these properties is crucial for structural biology and CSIR NET Life Science aspirants.

Correct Answer:

The correct option is (3) A and D.

Explanation:

(A) The Circular Dichroism Spectra of Collagen and a Protein in α-Helical Conformation Will Be Identical ❌

• Circular dichroism (CD) spectroscopy is used to analyze protein secondary structure.
• The CD spectra of collagen and α-helical proteins are different.
  • Collagen has a triple-helical structure, leading to a distinct CD spectrum.
  • α-helical proteins have a characteristic double minimum at 208 nm and 222 nm.
• Since their spectra are not identical, this statement is incorrect.

(B) The Allowed Region for the Dihedral Angles ϕ, Ψ in Gly Spans a Large Area in the Ramachandran Map. This Can Be Drastically Reduced by Substituting the Two Hydrogens with Methyl Groups ✅

• Glycine (Gly) has no side chain, allowing greater flexibility in dihedral angles (ϕ, Ψ).
• The Ramachandran plot for Gly shows a larger allowed region compared to other amino acids.
• Substituting both hydrogens with methyl groups (forming α,α-dimethylglycine) restricts backbone flexibility, drastically reducing the allowed region.
• Since this statement is correct, it is not part of the correct answer.

(C) Proline Has High Frequency of Occurrence in β-Turns ✅

• Proline has a rigid cyclic structure, making it ideal for β-turns.
• It helps stabilize sharp turns in protein structures.
• Since this statement is correct, it is not part of the correct answer.

(D) In a β-Hairpin Structure, the Dihedral Angles ϕ, Ψ of Amino Acids Flanking the β-Turn Region Will Be 60°, -30° ❌

• β-Hairpin structures contain antiparallel β-strands connected by a β-turn.
• The correct dihedral angles for β-strands flanking a β-turn are typically ϕ ≈ -120° and Ψ ≈ 120°, not 60° and -30°.
• Since this statement is incorrect, it is part of the correct answer.

Thus, the correct combination of incorrect statements is A and D (Option 3).

Nearby Topics for Better Understanding

1. Circular Dichroism (CD) Spectroscopy for Protein Secondary Structure

2. Ramachandran Map and Amino Acid Flexibility

• Shows allowed ϕ and Ψ angles for different amino acids.
• Glycine has the largest allowed region due to high flexibility.
• Proline has a restricted region due to its rigid ring structure.

3. β-Turns and β-Hairpin Structures

• β-Turns allow for abrupt direction changes in proteins.
• Proline and Glycine are commonly found in β-turns.
• β-Hairpins consist of two antiparallel β-strands connected by a turn.

Conclusion

Understanding peptide and protein conformation requires knowledge of secondary structures, dihedral angles, and circular dichroism spectra. Mastering these concepts is essential for CSIR NET Life Science aspirants.