Validating protein structures Background: Most protein structures are determined based on x‐ray crystallographic data. The primary sequence of the protein is matched with the electron density map, and the individual amino acids are placed within the structure as closely as possible. After all the amino acids are positioned, the quality of the assigned structure can be measured with several tools. One of the most common tools is the Ramachandran plot. Instructions: Read the passage below about the use of Ramachandran plots to validate protein structural assignments. Learning Goal: To learn how Ramachandran plots graphically represents dihedral angles of individual amino acids to predict the validity of a proposed protein structure and folding. The Ramachandran plot is one of the primary methods for validating proposed protein structures based on x‐ray crystallographic data. The plot compares selected dihedral angles in each amino acid found within the proposed protein. The key dihedral angles for each amino acid are located along the backbone of the protein and are labeled φ (phi), ψ (psi), and ω (omega). To repeat, each amino acid residue contributes three rotatable bonds and three distinct dihedral angles to the backbone of a peptide chain.
Published on May 6, 2014