4. The area of allowed regions in the Ramachandran map will be least for

   (1) Gly

   (2) L—Ala

   (3) L-Pro

   (4) α-methyl L-Valine

Which Amino Acid Has the Least Allowed Region in the Ramachandran Map?

The Ramachandran plot is a graphical representation of the allowed dihedral angles (ϕ and ψ) for amino acids in a polypeptide chain. The size of the allowed region varies based on the steric hindrance imposed by the side chain.

Correct Answer:

The correct answer is:

(4) α-Methyl L-Valine

Why Does α-Methyl L-Valine Have the Least Allowed Region?

α-Methyl L-Valine has a bulky α-methyl (-CH₃) group attached to the α-carbon, further increasing steric hindrance. This restricts its flexibility more than other amino acids, limiting its allowable phi (ϕ) and psi (ψ) angles.

Comparison of Allowed Regions in the Ramachandran Plot

1. Glycine (Gly) – Most Allowed Region

• Smallest side chain (-H), highest flexibility.
• Appears in multiple regions of the Ramachandran plot.
• Found in turns and flexible loops of proteins.

2. L-Alanine (L-Ala) – Moderately Allowed Region

• Contains a methyl (-CH₃) group, which provides some steric hindrance.
• Occupies α-helix and β-sheet regions but is still relatively flexible.

3. L-Proline (L-Pro) – Highly Restricted Region

• Has a cyclic side chain that locks its phi (ϕ) angle at ~-60°.
• Found mainly in β-turns and collagen structures.

4. α-Methyl L-Valine – Least Allowed Region

• Bulky α-methyl (-CH₃) group increases steric clash.
• Extremely limited phi (ϕ) and psi (ψ) flexibility.
• Least tolerated in α-helices and β-sheets.

Impact on Protein Structure

1. Protein Folding and Stability

• Flexible amino acids like glycine enable tight turns.
• Bulky amino acids like α-methyl L-valine introduce rigidity.

2. Secondary Structure Formation

• α-Helices: Favor smaller side chains like alanine.
• β-Sheets: Can accommodate valine but struggle with bulky α-methyl groups.
• Loops & Turns: Prefer glycine or proline for flexibility.

Conclusion

In the Ramachandran map, α-methyl L-valine has the least allowed region due to high steric hindrance. This makes it less common in α-helices and β-sheets, impacting protein folding and structure. Understanding these restrictions is crucial in molecular biology and protein engineering.