RAMACHANDRAN PLOT

Gives a brief idea about protien structure and validation.

1. RAMACHANDRAN PLOT Presented by, Sabhyata Chaubey M.Sc. [ Bt] Semester- 1st Roll No. - 201810901010011 Under the guidance of Dr. N eeraj Gupta Associate Professor 1

2. 2 G.N . Ramachandran (8 October 1922 – 7 April 2001) was an Indian physicist who was known for his work that led to his creation of the Ramachandran plot for understanding peptide structure. He was the first to propose a triple-helical model for the structure of collagen. He subsequently went on to make other major contributions in biology and physics

3. WHAT EXACTLY IS A RAMACHANDRAN PLOT?? O riginally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan. Ramachandran plot- provides an easy way to view the distribution of torsion angles in a protein structure . Used to visualize the backbone of amino acid residue. Used for structural validation. 3

4. 4 RAMACHANDRAN PLOT SOFTWARES

5. A dihedral angle is the angle between two intersecting planes . In a protein chain three dihedral angles are defined as φ (phi), ψ (psi) and ω (omega ). Torsion angle- a type of dihedral angle. Torsion angles- important structural parameters that control protein folding. DIHEDRAL ANGLE 5

6. T orsion angles- φ and ψ provide the flexibility required for the polypeptide backbone to adopt a certain fold. Third torsion angle ω - flat and fixed to 180 degrees. [due to the partial double-bond character of the peptide bond, which restricts rotation around the C-N bond, placing two successive α-carbons and C, O, N and H between them in one plane .] 6

7. PEPTIDE BOND AND PHI-PSI ANGLES 7 Phi is the angle around N-C α bond Psi is the angle around C α -C’ bond

8. WORK OF RAMACHANDRAN U sed computer models of small polypeptides to vary phi and psi to find stable conformations. Atoms- treated as hard spheres with dimensions corresponding to their van der Waals radii. Allowed rotations and stable structures were checked. Therefore, psi and phi angles which cause spheres to collide corresponds to sterically disallowed conformations of polypeptide backbone. 8

9. FORBIDDEN ROTATIONS- 9

10. THE RAMACHANDRAN PLOT 10 Plot between Ramachandran angles φ (horizontal axis) and ψ (vertical axis). WHITE REGIONS: Sterically disallowed for all amino acids except glycine (lacks side chain). RED REGIONS: Allowed regions namely the α -helical and β -sheet conformations. YELLOW AREAS: Outer limits, usually allowed regions (generously allowed).

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12. 12 RED - FAVOURED REGION BROWN - ALLOWED REGION YELLOW - GENEROUSLY ALLOWED REGION

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14. AMINO ACIDS PREFERENCES Usually glycine and proline are not preferred in Ramachandran plot. The amino acids with larger side chains will show less number of allowed regions within the Ramachandran plot. Proline gives a very less number of phi and psi values since it possess five carbon ring. 14

15. APPLICATIONS OF RAMACHANDRAN PLOTS- Validation of protein structures:  Three-dimensional protein structures produced by crystallography, NMR spectroscopy and computational modelling. Improvement of structure determination methods by NMR spectroscopy: φ and ψ restraints must always be taken into account while developing tools for protein solution structure prediction. Assessing side-chains effects on the protein backbone. 15

16. REFERENCES- https:// proteinstructures.com/Structure/Structure/Ramachandran-plot.html https://en.wikipedia.org/wiki/G._N._ Ramachandran http:// proteopedia.org/wiki/index.php/Ramachandran_Plots https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061398 / 16