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The Ramachandran plot is a plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in a peptide. In sequence order, φ is the N(i-1),C(i),Ca(i),N(i) torsion angle and ψ is the C(i),Ca(i),N(i),C(i 1) torsion angle. The plot was developed in 1963 by G. N. Ramachandran, et. al.[1] by plotting the φ values on the x-axis and the ψ values on the y-axis, as for the image at left[2]. Plotting the torsional angles in this way graphically shows which combination of angles are possible. The torsional angles of each residue in a peptide define the geometry of its attachment to its two adjacent residues by positioning its planar peptide bond relative to the two adjacent planar peptide bonds, thereby the torsional angles determine the conformation of the residues and the peptide. Many of the angle combinations, and therefore the conformations of residues, are not possible because of steric hindrance. By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides. The scene on the right is the Ramachandran plot of ribonuclease H. Secondary structure plot regions Secondary structures of a peptide are segments of the peptide that have ordered and repetitive structure, and the repetitive structure is due to a repetitive conformation of the residues and, ultimately, repetitive values of φ and ψ. The different secondary structures can be distinguished by their range of φ and ψ values with the values of different secondary structures mapping to different regions of the Ramachandran plot. Two common examples of secondary structure are illustrated below. α-helix The scene on the right shows the axis of the α-helix rotating in the y-plane. When viewing the helix on end, observe the open center of the helix. Planes are drawn on some of the peptide bonds to emphasize that in an α-helix the planar peptide bonds rotate about the axis of the helix. The Ramachandran plot of this peptide has points clustered about the values of φ= -57o and ψ= -47o which are the average values for α-helices. Adding the values of two other helical segments demonstrates that data from all three appear in one large cluster and that the helical segments can not be distinguished by the differences in their φ and ψ values. β-sheets Display a two segment twisted β-sheet. Draw planes of the peptide bonds. Most β-sheets in globular proteins are twisted sheets which do not have flat parallel pleats. Closer view of β-sheets. The Ramachandran plot of this twisted sheet has points clustered about the values of φ= -130o and ψ= 140o which are the average values for twisted sheets. Adding the values of three other sheet segments more clearly defines the area in which values for twisted sheets are located. The number of phi and psi angles in an isolated amino acid (not in a polypeptide chain) is: A) None B) 1 C) 2 D) 3 E) 4 F) 5 The number of atoms held into a geometric plane by a peptide bond is: A) 3 B) 4 C) 5 D) 6 E) 7 F) 8 #RamachandranPlot #bioinformatics #computationalBiology #proteinFolding #aminoAcids #polypeptide #peptideBond
