Given below are statements related to protein structures:
A. The dihedral angles of an amino acid X in Acetyl-x- N-Methyl amide in the Ramachandran plot, occur in very small but equal areas in the left and right quadrants. It can be concluded that X is not one of the 20-coded amino acids.
B. The dihedral angles of a 20-residue peptide are represented in the Ramachandran plot. It is possible to conclude that the peptide does not have a proline.
C. Two proteins can have a similar fold even if they do not share significant similarity in their primary structure.
D. On denaturation of a protein by urea, the interactions that would be disrupted are ionic bonds and van der Waal’s interaction but not disulfide bonds.
Choose the combination with ALL CORRECT answers:

(1) A, B, C
(2) A, C, D
(3) B, C, D
(4) A, B, D

Understanding Protein Structures: Ramachandran Plot and Structural Stability

Protein structures are fundamental to biological functions. By analyzing dihedral angles, Ramachandran plots, and folding stability, we gain insights into protein conformation and stability. Below, we analyze key structural aspects of proteins and evaluate which statements about protein structures are correct.

Correct Answer:

The correct combination of statements is (2) A, C, D.

Explanation of the Statements

Statement A: Ramachandran Plot and Non-Coded Amino Acids ✅ Correct

• The Ramachandran plot maps allowed and disallowed dihedral angles for amino acids.
• If an amino acid X appears in small but equal regions in both left and right quadrants, it is likely not one of the 20-coded amino acids.
• Non-standard amino acids (e.g., D-amino acids or exotic synthetic analogs) may have such distributions.

Statement B: Absence of Proline in a Peptide via Ramachandran Plot ❌ Incorrect

• Proline has a unique cyclic structure, restricting ϕ (phi) angles and clustering in specific Ramachandran regions.
• However, absence of data points in proline-allowed regions does not confirm lack of proline, as other factors (e.g., structural flexibility) influence the data.

Statement C: Similar Fold Despite Different Primary Sequences ✅ Correct

• Protein folding depends on secondary and tertiary interactions.
• Even if two proteins have low sequence similarity, they may adopt the same structural fold due to conserved folding patterns.
• Example: Convergent evolution leads to structural similarities in unrelated proteins.

Statement D: Protein Denaturation and Interaction Disruptions ✅ Correct

• Urea disrupts hydrogen bonding and non-covalent interactions (e.g., ionic bonds and van der Waals interactions).
• Disulfide bonds, being covalent, are not broken by urea alone, but require reducing agents (e.g., β-mercaptoethanol).

Biological Importance of Protein Structure Analysis

1. Role of Ramachandran Plot in Protein Folding

• Helps predict secondary structures (e.g., α-helices, β-sheets).
• Identifies disallowed conformations, indicating steric clashes.
• Useful in protein modeling and computational biology.

2. Structural Similarity and Evolution

• Diverse proteins can evolve similar functional folds, enabling functional conservation despite sequence variations.
• Example: Serine proteases (e.g., trypsin and chymotrypsin) share a fold despite sequence divergence.

3. Protein Denaturation Mechanisms

• Heat, urea, pH shifts, and detergents affect different bonds:
  • Hydrogen bonds → Disrupted by temperature and urea.
  • Ionic bonds → Weakened by pH changes.
  • Disulfide bonds → Require reducing agents.

Conclusion

Understanding protein structures, Ramachandran plots, and denaturation mechanisms is essential for biochemistry, molecular biology, and drug design. The correct answer (A, C, D) highlights key insights into non-coded amino acids, protein folding, and stability.