Analyzing Asymmetry in the Ramachandran Plot

Why isn’t the Ramachandran plot symmetric?

The Ramachandran plot is a valuable tool used in structural biology to analyze the dihedral angles between the amino acid residues in a protein. It provides information about the allowed and disallowed conformations of these angles, giving insights into the protein’s stability and folding.

The plot is not symmetric primarily due to the inherent characteristics of protein structures and their amino acid residues. Three main factors contribute to the asymmetry observed in the Ramachandran plot:

1. Steric hindrance: Protein structures rely on a delicate balance of interactions between atoms. Certain combinations of dihedral angles lead to unfavorable steric clashes, where atoms come too close to each other and experience repulsive forces. These clashes create energy barriers that prevent certain conformations from occurring, resulting in the forbidden regions of the Ramachandran plot

2. Backbone conformation: The backbone of a protein is made up of repeating units of peptide bonds, connecting amino acid residues. The arrangement and orientation of these peptide bonds influence the dihedral angles, particularly the phi (Φ) and psi (Ψ) angles, which are the most common angles represented in the Ramachandran plot. The orientation and flexibility of the peptide bonds create constraints on the dihedral angles, leading to specific patterns and distributions seen in the plot

3. Amino acid side chains: The side chains of amino acids introduce additional complexity to the Ramachandran plot. Each amino acid has unique structural characteristics and side chain properties, which can significantly affect the allowed conformations. Some side chains are bulky and can restrict certain dihedral angles, while others are more flexible, allowing a broader range of conformations. These diverse side chain properties contribute to the overall asymmetry of the Ramachandran plot

It is important to note that despite the asymmetry of the Ramachandran plot, certain regions in the plot are still populated, indicating the favorable conformations for the phi and psi angles of amino acid residues. These populated regions correspond to energetically favorable conformations that facilitate proper protein folding and stability

In summary, the Ramachandran plot is not symmetric due to a combination of steric hindrance, backbone conformational constraints, and amino acid side chain properties. It reflects the limitations and preferences dictated by the physical and chemical properties of amino acids and their interactions within a protein structure

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