The Ramachandran plot graphically shows which combination of torsional angles phi (φ) and psi (Ψ) of amino acid residues contained in a peptide are possible. Examination of the plot below shows that only certain regions of the conformational space are permissible. Why are all the theoretical combinations of φ and Ψ not possible?

(1) Two atoms cannot occupy the same space
(2) The geometry of the peptide bond that links two amino acid residues restricts φ and Ψ and angles
(3) Beta sheets and alpha helices determine the allowed regions of conformational space.
(4) The tertiary fold of polypeptides restricts conformational space

Understanding Restrictions in the Ramachandran Plot: Why All φ and Ψ Angles Are Not Possible

The Ramachandran plot graphically represents the backbone torsional angles (φ and Ψ) of amino acid residues in proteins. It highlights permissible and restricted regions of conformational space, showing why only certain angle combinations occur in real protein structures.

Correct Answer:

The correct answer is:

(1) Two atoms cannot occupy the same space.

Why Are All Theoretical φ and Ψ Combinations Not Possible?

• The primary reason is steric hindrance, which means that two atoms cannot occupy the same space simultaneously.
• Certain φ and Ψ angles cause atoms to clash, making these conformations physically impossible.
• Only sterically favorable conformations are allowed, explaining the distinct regions in the Ramachandran plot.

Analysis of Other Answer Choices

2. The Geometry of the Peptide Bond Restricts φ and Ψ Angles (Partially Correct but Not the Main Reason)

• The peptide bond is planar due to partial double-bond character, restricting rotation around the C’-N bond.
• However, this only affects local flexibility and does not fully explain why many φ and Ψ angles are disallowed.

3. Beta Sheets and Alpha Helices Determine Allowed Conformational Space (Incorrect)

• The Ramachandran plot influences the formation of α-helices and β-sheets, not the other way around.
• These structures arise because of favorable φ and Ψ angles, not as a cause of restricted regions.

4. The Tertiary Fold of Polypeptides Restricts Conformational Space (Incorrect)

• The Ramachandran plot is based on local backbone angles and does not consider long-range tertiary folding interactions.
• Secondary structure constraints exist even in isolated peptides, showing that steric clashes are the primary limiting factor.

Biological Significance of Restricted φ and Ψ Angles

1. Protein Folding and Stability

• The allowed φ and Ψ angles influence protein folding pathways and native structure stability.
• Incorrect angles can lead to misfolding and aggregation.

2. Secondary Structure Formation

• The Ramachandran plot predicts whether a residue is likely to be part of an α-helix, β-sheet, or β-turn.

3. Structural Validation of Proteins

• Structural biologists use the Ramachandran plot to verify protein models.
• If residues fall in disallowed regions, the structure may need correction.

Conclusion

The main reason why all φ and Ψ angles are not possible is steric hindrance, as two atoms cannot occupy the same space. This restriction defines allowed conformational regions and governs protein structure and function.