20. The following are four statements on the peptides/proteins conformation:

    A. Glycine has a largest area of conformationally allowed space in the Ramachandran plot of Φ and Ψ
    B. A 20-residue peptide that is acetylated at the N-terminus and amidated at the C- terminus has Φ = -60⁰ (±5), Ψ = -30⁰(±5) for all the residues. It can be concluded that conformation of the peptide is helix-turn-strand
    C. The allowed values of Φ, Ψ for amino acids in a protein are not valid for short peptide
    D. A peptide Acetyl-A₁ – A₂ -A₃ -A₄-CONH₂ (A-A₄ are amino acids) adopts well defined ß-turn. The dihedral angles of A₂ and A₃ determined the type of ß- turn
    Choose the combination of correct statements.

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

Protein Structure and Ramachandran Plot Analysis

Understanding protein structures is essential in biochemistry, as it provides insights into protein folding, stability, and function. The Ramachandran plot is a crucial tool used to determine the conformational space of amino acids in proteins.

Correct Answer:

The correct option is:

(3) A and D

Explanation of Statements

1. Glycine and the Ramachandran Plot (Statement A – Correct)

• Glycine is unique among amino acids because it lacks a bulky side chain, allowing for greater flexibility in dihedral angles (Φ, Ψ).
• This results in glycine having the largest conformationally allowed space in the Ramachandran plot.

2. Peptide Conformation (Statement B – Incorrect)

• A peptide with Φ = -60° and Ψ = -30° in all residues is characteristic of an α-helix.
• The described helix-turn-strand conformation is not consistent with these angles.

3. Short Peptides and Ramachandran Plot (Statement C – Incorrect)

• While the Ramachandran plot applies broadly to proteins, its allowed Φ, Ψ values are still valid for short peptides.
• Thus, this statement is incorrect.

4. β-Turns and Peptide Conformation (Statement D – Correct)

• β-turns are a common structural motif in proteins, allowing for tight turns in the backbone.
• The dihedral angles of residues A2 and A3 determine the type of β-turn adopted by the peptide.

Biological Significance of Protein Conformation

1. Role of Amino Acids in Protein Folding

• Each amino acid contributes uniquely to the stability and flexibility of proteins.
• Glycine enhances flexibility, while proline restricts movement, often forming β-turns.

2. Structural Insights Using Ramachandran Plot

• The Ramachandran plot helps predict protein secondary structures, distinguishing α-helices, β-strands, and turns.
• It is a vital tool in structural bioinformatics and molecular modeling.

3. Applications in Drug Design

• Understanding protein conformations helps in drug discovery and protein engineering.
• Structural knowledge assists in developing inhibitors for diseases linked to protein misfolding, such as Alzheimer’s and Parkinson’s.

Conclusion

The Ramachandran plot and protein conformation play a key role in understanding peptide folding. Glycine’s flexibility and β-turn formation significantly influence protein structure. Mastering these concepts is essential for biochemistry, molecular biology, and pharmaceutical sciences.