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In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, [1] is a way to visualize energetically allowed regions for backbone dihedral angles ( also called as torsional angles , phi and psi angles ) ψ ...
In a protein chain three dihedral angles are defined: ω (omega) is the angle in the chain C α − C' − N − C α, φ (phi) is the angle in the chain C' − N − C α − C' ψ (psi) is the angle in the chain N − C α − C' − N (called φ′ by Ramachandran)
All torsion angles are reported in degrees. Torsion angles are a very useful indicator of the stereochemistry and the stereochemical quality of a protein structure, with most high-quality proteins exhibiting a relatively tight clustering of phi/psi angles and relatively little deviation in the omega angles. [10]
Proteins will have limitations on their folding abilities by the restricted bending angles or conformations that are possible. These allowable angles of protein folding are described with a two-dimensional plot known as the Ramachandran plot, depicted with psi and phi angles of allowable rotation. [20]
Nests are defined by the conformation of the main chain atoms, namely the phi, psi dihedral angles of the first two amino acids in the nest. For a typical (RL) nest phi i =-90°; psi i =0°; phi i+1 =80°; psi i+1 =20°. Nests vary in their degree of concavity.
PREDITOR was designed to exploit these experimental observations and to help NMR spectroscopists easily predict protein torsion angles from chemical shift assignments. Specifically, PREDITOR accepts protein sequence and/or chemical shift data as input and generates torsion angle predictions for phi, psi, omega and chi-1 angles.
The most common simplification is to assume ideal bond lengths and bond angles. However, this still leaves the phi-psi angles of the backbone, and up to four dihedral angles for each side chain, leading to a worst case complexity of k 6*n possible states of the protein, where n is the number of residues and k is the number of discrete states ...
For example, a polypeptide of 100 residues will have 200 different phi and psi bond angles, two within each residue. If each of these bond angles can be in one of three stable conformations, the protein may misfold into a maximum of 3 200 different conformations (including any possible folding redundancy), not even considering the peptide ...