5. The ϕ and Ψ values of a ß-strand composed of all D- amino acids will mainly occupy which quadrant in the Ramachandran plot?

   (1) upper left

   (2) upper right

   (3) lower left

   (4) lower right

Ramachandran Plot Quadrant for β-Strands of D-Amino Acids

The Ramachandran plot helps visualize the allowed conformations of amino acids based on their ϕ (phi) and Ψ (psi) angles. The positioning of β-strands in this plot depends on whether the amino acids are L- or D-forms.

Correct Answer:

The correct answer is:

(2) Upper right

Why Do β-Strands of D-Amino Acids Occupy the Upper Right Quadrant?

• In proteins made of L-amino acids, β-strands typically appear in the upper left quadrant of the Ramachandran plot.
• D-amino acids are mirror images of L-amino acids, causing their ϕ and Ψ angles to be inverted.
• This inversion places D-amino acid β-strands in the upper right quadrant.

Comparison of Quadrants in the Ramachandran Plot

1. Upper Left Quadrant (L-Amino Acid β-Strands & Collagen Helices)

• Typical location of L-amino acid β-strands.
• Includes some collagen-like structures.

2. Upper Right Quadrant (D-Amino Acid β-Strands)

• Occupied by β-strands of D-amino acids due to reversed dihedral angles.
• Rarely found in naturally occurring proteins but seen in synthetic peptides.

3. Lower Left Quadrant (Right-Handed α-Helices for L-Amino Acids)

• Contains α-helices of L-amino acids.
• Stabilized by hydrogen bonding.

4. Lower Right Quadrant (Left-Handed α-Helices for D-Amino Acids)

• Mirror image of lower left quadrant.
• Contains α-helices of D-amino acids.

Impact on Protein Structure

1. Synthetic Peptides and Drug Design

• D-amino acids are often used in drug development to create more stable peptides.
• Their unique placement in the Ramachandran plot affects folding and bioactivity.

2. Protein Engineering and Stability

• Switching L-amino acids to D-amino acids can alter structural properties.
• Can lead to increased resistance to enzymatic degradation.

Conclusion

β-strands composed of D-amino acids appear in the upper right quadrant of the Ramachandran plot, as their dihedral angles are mirrored compared to L-amino acids. This distinction is essential in protein engineering, synthetic biology, and drug development.