RAMACHANDRAN PLOT One is to show in principle which values of and angles are possible for an amino-acid residue in a protein. ..pptx

This presentation is based on Ramachandran plot, which uses computer models of small polypeptides to systematically vary phi and psi with the objective of finding stable conformations. Plotting the torsional angles in this way graphically shows which combination of angles are possible.

1. CC10 PRESENTATION ON RAMACHANDRAN PLOT NAME- SAKSHI PRIYA CLASS- M.Sc.- II SEMESTER- III SESSION-21-23

2. INTRODUCTION

3. PRIMARY STRUCTURE OF PROTEIN The amino acids in  polypeptides  are held together by peptide bonds.   A dipeptide  is formed by a reaction between the α-carboxyl and α-amino groups of two amino acids . Each peptide has an amino terminus,  conventionally written on the left side, and a carboxyl terminus,  written on the right side . The peptide bond is not ionizable , but it can form hydrogen bonds. Therefore  peptides and proteins  tend to be water soluble.

4. Partial-Double Bond of Peptide Bond X-ray diffraction studies of crystals of amino acids and of simple dipeptides and tri-peptides showed that the peptide C—N bond is somewhat shorter NORMAL C-N BOND LENGTH- 1.45 A C=N LENGTH- 1.28A C-N BOND IN PEPTIDE- 1.33A

5. TYPES OF BOND IN AMINO ACIDS The figure below shows the three main chain torsion angles of a polypeptide . Phi (Φ; C, N, C α , C ) psi (Ψ; N, C α , C, N) are on either side of the C α  atom and omega (ω; C α , C, N, C α ) describes the angle of the peptide bond. While Φ and Ψ have considerable rotational freedom, ω is planar. This is a result of the partial double bond character of the peptide bond which is caused by resonance effects

6. CONFIGURATION OF BONDS

7. ROTATIONS OF φ   AND   ϕ BONDS The rotation angles for the two planes are called phi (f) and psi(y) are analogous to the torsion angles in the acyl chains of fatty acid. They can vary from -180° to +180°. The R group substituent attached to the alpha C can also rotate around the alpha C and the beta C of the side chain. This angle is defined as chi. Other rotations also occur within the side chain. We will concentrate on phi (f) and psi(y) angles in this section.

8. A protein can now be thought of as a series of linked sequences of rigid, planar peptide units which can rotate around phi/psi angles. When the chain is fully extended (as shown in the links above), phi/psi are 180 °. When phi (f) and psi(y) equal 0o, the two peptide bonds flanking the alpha Cs are in the same plane

9. RAMACHANDRAN PLOT

10. INTRODUCTION 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 , It is a way to visualize energetically allowed regions for backbone  dihedral angles  ψ against φ of  amino acid  residues in  protein structure .

11. Life of R amachandran 1922:  G N Ramachandran was born on October 8 . 1942 :  Became a student of the Indian Institute of Science in Bangalore . 1942 :  Completed his master’s degree in Physics from IISc . 1947 :  Completed the DSc degree, his thesis paper under Sir C V Raman . 1947 :  Went to Cambridge for PhD . 1949 :  Returned from Cambridge to join as assistant professor of Physics in IISc , Bangalore . 1952 :  Joined Madras University as head of Physics department . 1954 :   Proposed and published triple helical structure of collagen . 1963 :  The Ramachandran Plot was published . 1970 :  Set up the molecular biophysics unit at the IISc , Bangalore . 1971 :  Quit Madras University to join IISc , Bangalore again . 1971 :  Study on convolution- backprojection algorithms in X-Ray tomography was published . 1998 :  His wife Rajalakshmi passed away . 2001 :   Ramachandran breathed his last on July 4.

12. Awards and Recognition G . N. Ramachandran was a loved and respected scientist during his tenure both in IISc , Bangalore and Madras University. Some awards which he received for his scientific contributions are: Shanti Swarup Bhatnagar Award for contribution in the field of Physics in India in 1961. Fellowship of the Royal Society of London. Ewald Prize from the International Union of Crystallography for his outstanding contribution to crystallography in the year 1999.

13. RAMACHANDRAN PLOT G.N Ramachandran used computer models of small polypeptides to systematically vary phi and psi with the objective of finding stable conformations. G.N Ramachamdran plots the phi value on the X-axis and the psi value on the Y-axis. Plotting the torsional angles in this way graphically shows which combination of angles are possible . 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. .

14. RED REGION- ALLOWED REGION ( NO STERIC HINDERANCE). i.e.- ALPHA HELIX AND BETA SHEET. YELLOW REGION- OUTER LIMIT WHITE REGION- STERICALLY DISALLOWED FOR ALL EXCEPT- GLYCINE.

15. Individual residue distributions . Shown are individual Ramachandran plots of each of the 20 residue types as well as Xpr (i.e. pre-Pro). Glycine , by far the most flexible amino acid, is the only amino acid that truly populates the β′ portion of the ε region.

16. RAMACHANDRAN PLOT FOR SECONDARY STRUCTURE OF PROTEIN

17. Applications of Ramachandran plot There are two alternative ways to use a Ramachandran plot. One is to show in principle which values of and angles are possible for an amino-acid residue in a protein. The second is to display the empirical distribution of data points observed in a single structure (as seen at the right) used for structure validation, or in a database of multiple structures (as in the lower 3 plots at left ). In either scenario, outlines for the supposedly favoured locations are frequently shown.

18. REFERENCE https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061398 / https:// www.sciencedirect.com/topics/medicine-and-dentistry/peptide-bond https:// swissmodel.expasy.org/course/text/chapter1.htm https://chem.libretexts.org/Under_Construction/Purgatory/Book%3A_Biochemistry_Online_(Jakubowski)/04%3A_Protein_Structure/4.3%3A_Understanding_Protein_Conformation/C1._ Main_Chain_Conformations https://www.nature.com/articles/nsb0601_489#:~: text=His%20discovery%20of%20the%20triple,Watson%20and%20Crick's%20discovery%20of https:// www.iloveindia.com/indian-heroes/gn-ramachandran.html https:// proteopedia.org/wiki/index.php/Ramachandran_Plots https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061398 / https://unacademy.com/content/csir-ugc/study-material/life-sciences/ramachandran-plot-in-biology /