Ramachandran plot – Biochemistry (Notes and PPT)

It was given by scientist Gopalasamudram Narayana Ramachandran (G.N. Ramachandran) in the field of biochemistry which improved our understanding of the protein conformation.

What does it explains?

Ramachandran plot explains the values of the psi and phi angles between the amino acid which forms the different conformations of proteins.

It explains various aspects of protein chemistry, discussed one by one:

  • Types of protein structure
  • Dihedral angles
  • Steric hindrance
  • Stability of proteins

The points mentioned above are explained one by one:

  • Types of protein structure Have you ever thought, how the chain of amino acids acquire these different configuration?  How these different configurations of proteins remain stabilized? Ramachandran plot explains both points, the primary; secondary, tertiary and quaternary structure in proteins is acquired by the changing shapes of the different angles those are acquired by the different carbon and hydrogen atoms present in the amino acid structures. These changing are called dihedral angles.
  • Dihedral angles- When two atoms or angles rotate around a common plane they are called as dihedral angles. The carbon, hydrogen and nitrogen atoms of each amino acid have 3 angles between them. Phi between N-Cα which can have values from -180 degree to +180 degree, same psi between C-Cα which can have values from -180 degree to +180 degree, last angle omega between the peptide bonded c=0 and N whose value can only be either 180 degree or 0 degree because peptide bond have double bond character which makes it rigid to move in the plane. These phi and psi dihedral angles determine the conformation of a polypeptide chain.
  • Characteristics of dihedral angles- rotation occur only at single bonds (psi and phi):
  • Peptide bond does not rotate because of its partial double bond character.
  • Rotation is affected by the size of R-chain of amino acid and complexity of R-chain of amino acid.

Both these effects cause the steric hinderance.

  • Steric hindrancesteric- bulky, hinderance- to stop. The rotation of the dihedral angles can be affected by the steric hinderance between the atoms of the amino acids. Steric hinderance basically restricts the rotation of the phi and psi angles, which restricts the value of these phi and psi angles.
  • Stability of proteins- The stability of different structure of proteins is;
  • Primary structure.                    
  • Secondary structure.
  • Tertiary structure.
  • Quaternary structure.   

The stability of protein structure increases from primary to quaternary structure due to decrease in the entropy.

Test yourself

Questions:

1) What is a dihedral angle?

2) What is the decreasing order of entropy of protein structures?

3) What is steric hinderance?

4) What are different characteristics of dihedral angles?

5) How the rotation of dihedral angles can be affected?

Published by yamini1520

I believe in being real.

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