11.ramachandran plot
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A Ramachandran plot visualizes the backbone of amino acid residues by plotting the possible phi and psi dihedral angles, which were originally developed by Ramachandran et al. in 1963. It shows favored, allowed, and generously allowed regions based on analysis of protein crystal structures. Two high density regions correspond to alpha helices and beta sheets. Ramachandran plots are used for protein structure validation and show amino acid preferences and distributions observed in protein data bank structures.
![Work of Ramachandran
A Ramachandran plot (also known as a
Ramachandran diagram or a [φ,ψ] plot),
originally developed in 1963 by G. N.
Ramachandran, C. Ramakrishnan, and V.
Sasisekharan
Initially proposed a modelled structure on
collagen as a two bonded system based on the
formation of two inter hydrogen bonds between
their structures](https://image.slidesharecdn.com/11-150314133251-conversion-gate01/85/11-ramachandran-plot-3-320.jpg)
11.ramachandran plot
- 2. Ramachandran plot – to visualize the backbone of aminoacid residues Used for structural validation and to calculate the possible phi and psi angles that accounts for the aminoacid residues Done by several software namely WHATIF RAMACHANDRAN PLOT
- 3. Work of Ramachandran A Ramachandran plot (also known as a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan Initially proposed a modelled structure on collagen as a two bonded system based on the formation of two inter hydrogen bonds between their structures
- 4. The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined (myoglobin, in 1960) Now, many decades later, there are tens of thousands of high-resolution protein structures determined by X-ray crystallography and deposited in the Protein Data Bank (PDB)
- 5. Basics of map Parameter – torsion angle System used – protein chain consisting of amino acid side chains Ramachandran angles – phi and psi A B C D B C A D
- 6. Peptide Bond & Phi-Psi Angles Phi is the angle around the N-Ca bond Psi is the angle around the Ca-C’ bond
- 7. Principle within the formation Using the analysis of crystal structure data. Two limiting condition was approached - normal limits - outer limits Using phi and psi angles conformation of linked peptide units are calculated This gave three results (color variations)
- 8. The red, brown, and yellow regions represent the favored, allowed, and "generously allowed" regions
- 9. Distribution over the map The distribution of phi and psi angles for a total of 9,156 amino acid residues from 4,413 protein chains, based on crystallographic data 2 areas where the density of points is high (1) Around phi= -60° and psi= -60° corresponds to the a-helix (2) Around phi= -90° and psi= -120° corresponds to the b-structure
- 10. Aminoacid preferences Usually glycine and proline are not peffered in ramachandran plot. Glycine has only a hydrogen atom for its side chain, with a much smaller van der Waals radius than the CH3, CH2, or CH group that starts the side chain of all other amino acids. Hence it is least restricted. The aminoacids with larger side chains will show less number of allowed region within the ramachandran plot. Proline gives a very less number of phi and psi values since the possess five carbon ring.
- 11. USES A Ramachandran plot can be used in two ways. ● One is to show in theory which values, or conformations, of the ψ and φ angles are possible for an amino-acid residue in a protein. ● A second is to show the empirical distribution of datapoints observed in a single structure in usage for structure validation, or else in a database of many structures