Ramachandran Plot | easy explanation

The Ramachandran Plot • It also provides an overview of allowed and disallowed regions of torsion angle values – serve as an important indicator of the quality of protein three-dimensional structures • Torsion angles are among the most important local structural parameters that control protein folding. Torsion angles • The backbone of a protein has three different torsion angles • Describe the rotations of the polypeptide backbone around the bonds between • N-Cα (called Phi, φ) • Cα-C (called Psi, ψ) and • The omega-angle (ω) - around the peptide bond between C and N • ω-bond has a slightly double-bond character and is therefore almost always 180 degrees. The Ramachandran Plot In a polypeptide the main chain N-Calpha and Calpha-C bonds relatively are free to rotate. These rotations are represented by the torsion angles phi and psi, respectively • G N Ramachandran used computer models of small polypeptides to systematically vary phi and psi with the objective of finding stable conformations. Torsion angles • Torsion angles are dihedral angles, which are defined by 4 points in space • In proteins the two torsion angles phi and psi describe the rotation of the polypeptide chain around the two bonds on both sides of the C alpha atom. The Ramachandran Plot • Ability to predict the Ramachandran angles for a particular protein, provide ability to predict its 3D folding • The reason is that these angles provide the flexibility required for the polypeptide backbone to adopt a certain fold, since ω is essentially flat and fixed to 180 degrees – This is due to the partial double-bond character of the peptide bond which; – restricts rotation around the C-N bond, placing two successive alpha-carbons and C, O, N and H between them in one plane – Thus, rotation of the protein chain can be described as rotation of the peptide bond planes relative to each other. Protein backbone The psi angle is the angle around the -CA-C- bond- can rotate in 3600 (-180-+180) +ve angle clockwise rotation The omega angle is the angle around the -C-N- bond (i.e. the peptide bond) The protein backbone can be described in terms of the phi, psi and omega torsion angles of the bonds: The phi angle is the angle around the -N-CA- bond - can rotate in 3600 (-180 to +180) +ve angle clockwise rotation. The Ramachandran Plot In a polypeptide the main chain N-Calpha and Calpha-C bonds relatively are free to rotate. These rotations are represented by the torsion angles phi and psi, respectively • G N Ramachandran used computer models of small polypeptides to systematically vary phi and psi with the objective of finding stable conformations • For each conformation, the structure was examined for close contacts between atoms • Atoms were treated as hard spheres with dimensions corresponding to their van der Waals radii • Therefore, phi and psi angles which cause spheres to collide correspond to sterically disallowed conformations of the polypeptide backbone. Steric limits of psi and phi angles • Atoms take up space • Same space can not be occupied by more than one atom • Atoms connected by covalent bonds • These bonds can not be broken- only rotation • Only two angles in a residue rotate- psi and phi • Physical clashes of atoms in 3D space make many combinations not possible