Download Secondary structure

Secondary Structure of Proteins
The term secondary stricture refer to the common regular folding
pattern of polypeptide backbone.
Some physicochemical principles which act as guide lines for the
determination of three dimensional conformation of proteins:
1. Oxygen has the highest electronegativity.
2. Availability of lone pair of electron on Nitrogen.
3. The oxygen and hydrogen atom of the peptide bonds have the
potential for hydrogen bonding.
4. Bulky groups on side chains of amino acid residues in
polypeptide cause steric hindrance when present close to
gather.
5. Hydrophobic residues try to be together away from water.
6. +ive or –ive charge on side chains can stabilize or destabilize
the higher order structures.
Nature of the Peptide Bond:
In 1930s and 1940s Linus Pauling and Robert Corey analyzed amino acids
and dipeptide structures by X-ray crystallography. Their main
observations were:
1. The C-N bond in peptide group is 0.13 Ao shorter than the regular C-N
single bond (indicating partial double bond character).
2. The C=O bond is 0.02 Ao longer than the regular C=O double bond in
aldehydes and ketones (partial single bond character)
These observations suggested that there is a resonance or partial
sharing of two pairs of electrons between the carbonyl oxygen and
the amide nitrogen. Oxygen has partial –ive charge and Nitrogen
has partial +ive charge.
Thus the peptide bond is a rigid planer structure stabilized with –
85kJ/mole resonance energy. With only a few exception, all the peptide
groups assume trans conformation i.e. Ca atoms are on the opposite
sides of the peptide bond.
Polypeptide backbone conformation:
Based on the fact that peptide bond is a planer and rigid structure,
the poly peptide backbone conformation will depend mainly on the
torsion angle or rotation angles about
Ca-N bond ( f angle) and
Ca-C bond ( j angle)
Whenever there is a possibility of free rotation of groups across a
bond, amongst all the possibilities only those conformations are
most stable where there is minimum steric hindrance.
Ramchandran Plot:
•Using the Van Der Waals distances for various inter-atomic contacts
to asses the steric hindrance Ramchandran calculated the rotation
angles which would allow the most stable conformation with little or
no hinderance.
•Both rotation angles can be platted against each other, and stable
conformations can be predicted based on the amino acid residues.
•When crystal structures of many proteins were determined by X-ray
crystallography, the rotation angles obtained from these studies were
found to be matching with the predicted allowed rotation angles.
Ramchandran Plot for L-Ala residues
Helical Structures
With the information already obtained such as ;
The rigid and planer nature of peptide bond,
Allowed conformations using torsion angles and
X-ray result of keratin protein obtained by Willium Astbury, who
observed that a regular structure was occurring in keratin that
reapeated everu 5.15 to 5.2 Ao.
Pauling and Corey proposed the helical conformation which they
called a helix.
In this structure the polypeptide backbone is is tightly wound
around an imaginary axis. The side chain R groups of AA
residues protrude outward from the helical backbone.
The repeating unit is a turn of helix (3.6 amino acids) with the
periodicity of 5.4 Ao
Characteristics of a helics:
Polypeptide chains containing L-aminoacid residues make righr
handed helices. Therefore all the a helical conformations in living
systems are right handed.
No of AA per turn (n)……3.6
Distance traveled in one turn (pitch) p
5.4 Ao
Torsion angles f= -57 o and j= -47o
Hydrogen bonding between the C=O group of nth AA residue to the NH group of the n+4th AA residue in peptide.
Polypeptide with D-AA residue make left handed a helics
f= +57 o and j= +47o Rest of the parameters are same as for right
handed helics.
Effect of amino acid sequence on the stability of a
helix
Constrains that affect the stability of a helix
1. The electrostatic repulsion or attraction between the
successive AA residues with charged R groups
2. The bulkiness of the adjecent R group.
3. Interaction between the side chains spaced 3 or 4 AA apart
4. Occurrence of Pro and glycine.
5. The interaction of the amino acid residues at the ends of the
helical segment and the electrical dipole inherent to the a
helix
Interaction
between the R
group of AA three
residue apart in
an a helix
The electric dipole
of a helix
The b-conformation or b-sheets
Pauling and Corey (1951) proposed a second type of repititive
structure they called “b-conformation”.
This is more extended conformation of polypeptide chains.
In this structure, the polypeptide chain is extended in a zigzag
fashion rather than in helical form.
The zigzag polypeptide chains are arranged side by side like
pleats and hydrogen bonds are formed between the adjacent
segment of the chain.
The R group of the side chain protrude in opposite side creating
an alternating pattern.
Parallel b-conformation: with adjacent polypeptide chains
Having same amino to carboxy terminus orientation.
Anti-parallel b-conformation: with adjacent polypeptide
chains having opposite amino to carboxy terminus orientation.
When two or more beta sheets are layered closely together within a
Protein the R groups of amino acid residues on touching surfaces
must be small for example silk fibroin or spider web fibroin which
Have beta sheet structure have very high content of Gly and Ala.