Atypical Ramachandran Plots: Videos & Practice Problems

The Ramachandran plot is a valuable tool in understanding the conformational angles of amino acids in proteins. While most amino acids exhibit similar Ramachandran plots, glycine and proline stand out due to their atypical characteristics. Glycine, with the smallest R group among all amino acids, allows for greater flexibility in its phi (φ) and psi (ψ) bond rotations. This unique feature results in a Ramachandran plot where permissible angles are present in nearly every quadrant, contrasting sharply with the other 18 amino acids, which have more restricted angles due to steric hindrance.

In a typical Ramachandran plot, the white regions indicate non-permissible angles caused by steric clashes between atoms. For glycine, however, the plot reveals that it can adopt permissible bond angles across all quadrants, making it the only amino acid capable of such versatility. This flexibility enables glycine to fit into tighter spaces within protein structures, a significant advantage in various biological contexts.

Glycine's three-letter code is Gly (or GLY), and its one-letter code is G. Understanding glycine's atypical Ramachandran plot is crucial as it highlights the importance of R group size in determining the conformational possibilities of amino acids. This knowledge will be beneficial as we explore further topics in protein structure and function.

Proline is an amino acid with a distinctive structure that significantly influences its behavior in proteins, particularly as illustrated by its Ramachandran plot. The unique feature of proline is its bulky cyclic R group, which restricts the rotations around the phi (φ) and psi (ψ) bonds. This limitation is crucial for understanding proline's role in protein structure.

Proline's three-letter code is pro and its one-letter code is P. The structure of proline can be visualized as resembling the loop of a flipped letter "P," which can aid in remembering its configuration. The R group of proline forms a pentagon-like shape, consisting of methylene groups (–CH₂–) that connect back to the nitrogen atom in the amino group. Notably, this connection results in proline having one less hydrogen atom than other amino acids, which is an important structural characteristic.

When examining proline's Ramachandran plot, the x-axis represents the phi (φ) bond angles, while the y-axis represents the psi (ψ) bond angles. The plot reveals that proline has very limited permissible bond angles, primarily confined to the upper left quadrant. Unlike glycine, which has a small R group allowing for a broader range of angles across all four quadrants, proline's bulky structure restricts it to a much narrower range. The darker regions of the plot indicate areas of permissible angles, and proline lacks significant dark shaded regions, highlighting its restricted conformational flexibility.

In summary, the comparison between proline and glycine illustrates the impact of R group size and structure on the conformational possibilities of amino acids. Glycine's small R group allows for flexibility across the Ramachandran plot, while proline's bulky cyclic structure results in a highly restricted range of permissible angles, emphasizing the importance of amino acid structure in protein folding and stability.