Ramachandran plot by Krunal Chodvadiya

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Ramachandran plot for structural validation of protein will give information whether your protein or model protein is allowed or not in three dimensional point of view.

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Ramachandran plot by Krunal Chodvadiya

  1. 1. Ramachandran plot By Krunal Chodvadiya 10MBT001
  2. 2. Ramachandran plot  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, is a way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure.  Plot of φ vs. ψ  The conformations of peptides are defined by the values of φ and ψ.
  3. 3.  Each peptide bond has partial double-bond character due to resonance and cannot rotate.  Three bonds separate sequential C in a polypeptide chain. The N-C and C – C bonds can rotate, with bond angles designated φ and ψ respectively. The peptide C-N bond is not free to rotate.  Other single bonds in the backbone may also be rotationally hindered, depending on the size and charge of the side chain R groups.
  4. 4. Both φ and ψ increases as the carbonyl and amide nitrogen (respectively) rotate clockwise.
  5. 5. • By convention, both φ and ψ are defined as 00 when the two peptide bonds flanking that C carbon are in the same plane. • In a protein, this conformation is prohibited by steric overlap between an carbonyl oxygen and an amino hydrogen atom.
  6. 6. Ramachandran plot for L-Ala residues. • Conformations deemed possible are those that involve little or no steric interference, based on calculations using known van der Waals radii and bond angles.
  7. 7. • The areas shaded dark blue reflect conformations that involve no steric overlap and thus are fully allowed. • Medium blue indicates conformations allowed at the extreme limits for unfavorable atomic contacts. • lightest blue area reflects conformations that are permissible if a little flexibility is allowed in the bond angles. • Unshaded portion indicates sterically disallowed conformations
  8. 8. values of φ and ψ for various allowed 20 structures Every type of secondary structure can be completely described by the bond angles φ and ψ at each residue.
  9. 9. The structure of cytochrome C shows many segments of helix and the Ramachandran plot shows a tight grouping of φ = -60 and psi = -45 to -50. -helix cytochrome C Ramachandran plot
  10. 10. Similarly, repetitive values in the region of φ = -110 to -140 and ψ = +110 to +135 give beta sheets. The structure of plastocyanin is composed mostly of beta sheets; the Ramachandran plot shows values in the –110, +130 region: beta-sheet plastocyanin Ramachandran plot
  11. 11. Glycine Ramachandran Plot Because its side chain, a single hydrogen atom, is small, a Gly residue can take part in many conformations that are sterically forbidden for other amino acids.
  12. 12. Proline Ramachandran Plot The range for Pro residues is greatly restricted because φ is limited by the cyclic side chain to the range of -35 to -85.
  13. 13. Significance  A Ramachandran plot can be used in 2 somewhat different ways. i. 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. ii. 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.
  14. 14. Thank you

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