Introduction History Experiment of Ramachandran Structure of protein Primary structure Secondary structure Tertiary structure Quaternary structure Peptide bond is rigid & planar Torsion angle (Φ and Ψ) Ramachandran plot For helices For β strands Significance of Ramachandran plot Conclusion Reference

1. RAMACHANDRAN MAP
By
KAUSHAL KUMAR SAHU
Assistant Professor (Ad Hoc)
Department of Biotechnology
Govt. Digvijay Autonomous P. G. College
Raj-Nandgaon ( C. G. )

2. Introduction
History
Experiment of Ramachandran
Structure of protein
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Peptide bond is rigid & planar
Torsion angle (Φ and Ψ)
Ramachandran plot
For helices
For β strands
Significance of Ramachandran plot
Conclusion
Reference
SYNOPSIS

3. HISTORY
Corey & Pauling (1953) determined the ideal value for the entire
backbone bond length and bond angles.
G. N. Ramachandran et.al. (1963) determined the values for the
pairs of dihedral angles about the Cα atoms, which are limited by
steric constraints.
Ramachandran biggest contribution was his correct proposal for
the triple helical structure of “collagen”.
Ramachandran used computer models of small polypeptides to
systematically vary φ and ψ with the objective of finding stable
conformations.

4. EXPERIMENT OF RAMACHANDRAN
The possibilities of protein conformation were based on
certain assumptions.
Peptide bond is rigid and do not allow rotation.
The molecule may be rotated about the other single
bond in the backbone that is the N- Cα bond and Cα-C’
bond.
All atoms are represented as hard sphere, there being
no chance of inter-penetration.
There are no other attractive or repulsive forces.
(Gupta, 2005)

5. Ramachandran solved one of the first protein fiber structure,
the triple-coil of collagen,
The peptide bond is planar and trans, then the conformation
of the protein backbone can be described by the φ and ψ dihedral
angles.
He analyzed all the steric clashes in the protein backbone as
a function φ and ψ.

6. He showed that the allowed values of φ and ψ (gray) broke in
to broadly three regions, which are known as α ,αL , and β.
Fig-1: -The Ramachandran map
(www.activorcorporation.net/ramachandran)

7. STRUCTURE OF PROTEINS
Primary structure: -
The linear sequence of amino acids forming the backbone of
proteins (polypeptides).
Peptide bond is formed by the amino acid linked by carboxyl group
of one amino acid with the α-amino group of another amino acid.
Fig-2: -Primary structure of protein
(www.activorcorporation.net)

8. Secondary structure: -
The spatial arrangement of protein by twisting or folding of
the polypeptide chain.
Linus Pauling and Robert Corey predict the existence of
these secondary structure in 1951.
The most common secondary structure are α-helix & β-
sheet.

9. 1. α-helix :-
The α-helix is the most common spiral structure of protein.
A α-helix can be right handed (clockwise) or left handed (anticlockwise).
The amino acid residues in a α-helix have conformation with φ = -60 and ψ =
– 45 to – 50.
Fig-3: -Secondary structure (α-
helix) of protein
(www.nature.com/.../images/importance_f3.gif)

10. 2. β- Pleated sheet: -
In β-Conformation, the backbone of the polypeptide chain is extended
in to a zigzag structure.
There two types of β-Pleated sheet i.e. parallel and antiparallel.
Fig-4: -Secondary structure (β- Pleated sheet )of protein
(www.nature.com/.../images/importance_f3.gif)

11. Tertiary structure: -
The three dimensional arrangement of protein is referred to
as tertiary structure.
This type of arrangement ensures stability of the molecule.
Fig-5: - The structure of Myoglobin
(Nelson & Cox, 2005)

12. Quaternary structure: -
Some of the proteins are composed of two or more
polypeptide chains referred as subunits & form the spatial
arrangement.
Fig-6: - The structure of Hemoglobin.
(http://trc.ucdavis.edu/biosci10v/bis10v/week2/2webimages/0143.gif)

13. PEPTIDE BOND IS RIGID AND PLANAR
The interaction of amino group of one amino acid with carboxyl group of another
amino acid results in the formation of an amide linkage known as peptide bond.
The amide C-N bond in a peptide is somewhat shorter than the C-N bond in a
simple amine and that atoms associated with the bond are coplanar.
This indicated a resonance or partial sharing of pairs of electrons between the
carbonyl oxygen atom and the amide nitrogen.
The oxygen has partial negative charge and nitrogen a partial positive charge
setting up a small electric dipole.
Fig-7: - Peptide bond has double bond character due to resonance.
(Nelson & Cox, 2005)

14. PEPTIDE BOND IS RIGID AND PLANAR
Fig-8: -Trans and Cis forms of peptide bond.
(www.nature.com/.../images/importance.gif)
Two configurations are possible for a planar peptide bond.
This preference for trans over cis can be explained by the fact
that steric clashes between group attached to the Cα atoms
hinders formation of cis form, but do not occur in trans
configuration.
Rotation in a peptide chain is permitted about Cα-N and Cα-C
bonds.

15. The bond angles resulting from rotation at Cα are labeled φ (phi) for Cα-N
bond and ψ (psi) for Cα-C bond.
Both φ and ψ are defined as 180°, φ and ψ can have any value between -
180° and +180°,
But many values are prohibited by steric interference between atoms in
the polypeptide backbone and amino acid side chains.
Allowed values for φ and ψ can be shown graphically by simple plotting φ
versus ψ, an arrangement known as Ramachandran plot.
PEPTIDE BOND IS RIGID AND PLANAR
Fig-9: - Peptide bond is rigid & planar
(Nelson & Cox, 2005)

16. TORSION ANGLE (Φ and Ψ)
Described the polypeptide backbone conformation
A torsion angle (or dihedral angle) is an angle around a bond which
defines the shape of a protein backbone.
A proteins 3- D structure can be uniquely defined by sequence of torsion
angles along its chain, called φ (phi) and ψ (psi).
The angle of rotation of the Cα –N bond is called φ angle and that of the
Cα – C bond is called ψ angle.
These are the only degrees of freedom, the conformation of the whole
main chain of the polypeptide is completely determined when the φ and ψ
angles for each amino acid are defined.

17. TORSION ANGLE (Φ and Ψ)
Described the polypeptide backbone conformation
Φ and Ψ can have any value between - 180°
and + 180°, but many values of φ and ψ are
prohibited by steric interference between atoms
in the polypeptide backbone and the amino acid
side chains.
The conformation in which φ and ψ are both
0° is prohibited for this reason (steric
interference).
This conformation is used merely as a
reference point for describing the angles of
rotation.
Fig-10: - The Torsional degrees of freedom in a peptide unit.
(Voet & Voet, 2005)

18. RAMACHANDRAN PLOT
A Ramachandran plot developed by Gopalasamudram Narayana
Ramachandran, is a way to visualize dihedral angle φ and ψ of amino acid
residues in protein structure.
G.N. Ramachandran used computer models of small polypeptides to
systematically vary φ and ψ with the objective of finding stable conformations.
Atoms were treated as hard spheres with dimensions corresponding to their
Vander waals radii.
Conformations deemed possible are those that involve little or no steric
interference, based on calculations using known Vander waals radii and bond
angles.

19. The Gly residue, which is less srterically hindered, exhibits a much
broader range of allowed conformations because Gly has an H-atom,
with a small Vander waal radii instead of a methyl group at the β
position.
RAMACHANDRAN PLOT
Fully allowed
At limits of
allowability
Fig 11:-Ramachandran Plot for Polyglycine
(Voet & Voet, 2005)

20. RAMACHANDRAN PLOT
The allowed ranges for branched amino acid residues such as Val, Ile,
and Thr are somewhat smaller than for Ala.
Ramachandran plot for Proline shows only a very limited no. of possible
combinations of φ and ψ because presence of a five membered ring which
prevent the rotation about the Cα-N bond, which fixes φ at about -35° to -85°.
Pro
Fig-12: - Ramachandran plot for
L-Ala residues.
(Nelson & Cox, 2005)

21. RAMACHANDRAN PLOT FOR HELICS
Both right and left handed helices lies in the regions of allowed
conformations in the Ramachandran diagram.
However, right handed helices are energetically more favorable
because there is less steric clash between the side chains and the
backbone.
Essentially all α helices found in proteins are right handed.
Fig-13: -Ramachandran Diagram for Helices.
(Stryer, 2006)

22. RAMACHANDRAN PLOT FOR β STRANDS
The β-sheet is almost fully extended rather than being tightly coiled
as in the α helices.
The red area shows the sterically allowed conformations of the
extended, β strand like structures.
Fig-14: -Ramachandran Diagram for
β-stands.
(Stryer, 2006)

23. SIGNIFICANCE OF RAMACHANDRAN PLOT
Ramachandran plot was the first verification tool for protein structures.
It displays the dihedral angles φ (phi) and ψ (psi) of all residues.
It is a very powerful tool to identify errors in protein structures.
It has become a standard tool in determining the protein structure and in
defining secondary structures in terms of α -helices and β sheet contents.
It allows the display of distribution of residues in the protein in terms of
their φ and ψ angles.
The region in the plot helps in identifying residues that are in allowed and
disallowed regions of the Ramachandran plot.

24. CONCLUSION
The atomic description of biological molecules in computational simulations
have promoted significant advances in the comprehension of the biological process
as well as proposed new insights in the design of molecules to satisfy specific
properties.
Ramachandran described proteins through graph on the basis of their structure,
size, shape, mass and weight.
Different proteins which moderate between these characters are found scattered
in the graph.
The Ramachandran plot was conceived as a theoretical means of predicting the
allowed conformational space of a single amino acid in a peptide.
The Ramachandran plot has proven itself as an unequalled tool in understanding
the conformational space available for proteins and in analysis of newly
determined protein structures.

25. REFERENCE
S.no. Name of the Book Author Year & Edition
1 Principles of Biochemistry Nelson & Cox 2005, 4th edition
2 Fundamentals of
Biochemistry
Dr. J.L. Jain 2005, 6th edition
3 Biochemistry Voet & Voet 2005, 4th edition
4 Biochemistry Lubert Stryer 2006, 5th edition
5 Biochemistry U. Satyanarayana 2007, 3rd revised
edition
6 Molecular biology & genetic
engineering
P. K. Gupta 2005, 3rd reprint
edition
Search engine (internet):- Websites:- www.answerforyou.com
www.google.co.in www.kbiotech.com
www.wikipedia.com www.nature.com