Why Peptide bonds are Backbone of the Proteins
“The peptide is formed between the amino group (-NH2) of the first amino acid and Carboxyl group (-COOH) of the second amino acid by eliminating one molecule of water.” The amino acids are held together in a protein by covalent peptide bonds or linkages. These bonds are rather strong and serve as the cementing material between the individual amino acids. The peptide bonds are a type of amide bonds.
Formation of a Peptide bonds:
When the amino group of an amino acid combines with the carboxyl group of another amino acid, a peptide bond is formed. Depending on the number of amino acids molecules composing a chain, the peptide may be termed as
- Dipeptide = containing 2 amino acid units
- Tripeptide = containing 3 amino acid units
- Tetrapeptide = containing 4 amino acid units
- Oligopeptide = containing not more than 10 amino acid units
- Polypeptide = containing more than 10 amino acid units, up to 100 residues
- Macropeptides = made up of more than 100 amino acids
Salient features of Peptide bond:
The peptide bond is rigid and planar
The atoms in peptide bond is Cα-C-N-Cα.
The peptide bond is coplanar, this indicated a resonance or partial sharing of two pairs of electrons between the carbonyl oxygen and the amide nitrogen.
The 4 atoms of the peptide group (C, H, O, and N) lie in a single plane, in such a way that the oxygen atom of the carbonyl group and the hydrogen atom of the amide nitrogen are trans to each other.
The peptide bond shows partial double bond character.
Characteristics of Peptide bonds:
The peptide bond is rigid and planar with partial double bond in character. It generally exists in trans-configuration. Both –C=O and –NH groups of peptide bonds are planar and are involved in hydrogen bond formation.
1. Writing of Peptide structures (or) N and C-terminals:
Conventionally, the peptide chains are written with the free amino end (N-terminal residue) at the left, and the free carboxyl end (C-terminal residue) at the right. The amino acid sequence is read from N-terminal end to C-terminal end. Incidentally, the protein biosynthesis also starts from the N-terminal amino acid.
2. Representation of Peptide chain:
To represent the peptide structure, we must write in “Rattle Snake moving representation” from left to right across the page. The C-terminal residues forms its fangs and the N-terminal residues its rattle.
3. Shorthand to read peptides:
The amino acids in a peptide or protein are represented by the 3-letter or one letter abbreviation. This is the chemical shorthand to write proteins.
4. Naming of Peptides:
For naming peptides, the amino acid suffixes –ine (glycine), -an (tryptophan), -ate (glutamate) are changed to –yl with the exception of C-terminal amino acid. Thus a tripeptide composed of an N-terminal glutamate, a cysteine and a C-terminal glycine is called glutamyl-cysteinyl-glycine.
5. Stereochemistry of peptide chains:
All proteins are made of amino acids of L-configuration. This fixes the steric arrangement at the α-carbon atom. The dimensions of the peptide chain are known exactly.
The Peptide Bond Is Rigid and Planar:
Covalent bonds also place important constraints on the conformation of a polypeptide. In the late 1930s, Linus Pauling and Robert Corey embarked on a series of studies that laid the foundation for our present understanding of protein structure. They began with a careful analysis of the peptide bond. The α-carbons of adjacent amino acid residues are separated by three covalent bonds, arranged as Cα-C-N-Cα. X-ray diffraction studies of crystals of amino acids and of simple dipeptides and tripeptides demonstrated that the peptide C-N bond is somewhat shorter than the C-N bond in a simple amine and that the atoms associated with the peptide bond are coplanar.
This indicated a resonance or partial sharing of two pairs of electrons between the carbonyl oxygen and the amide nitrogen. The oxygen has a partial negative charge and the nitrogen a partial positive charge, setting up a small electric dipole. The six atoms of the peptide group lie in a single plane, with the oxygen atom of the carbonyl group and the hydrogen atom of the amide nitrogen Trans to each other.
From these findings Pauling and Corey concluded that the peptide C-N bonds are unable to rotate freely because of their Partial double-bond character. Rotation is permitted about the N-Cα and the Cα -C bonds. The backbone of a polypeptide chain can thus be pictured as a series of rigid planes with consecutive planes sharing a common point of rotation at Cα. The rigid peptide bonds limit the range of conformations that can be assumed by a polypeptide chain.
By convention, the bond angles resulting from rotations at Cα are labeled Φ (phi) for the N-Cα bond and ψ (psi) for the Cα-C bond. Again by convention, both Φ and ψ are defined as 1800 when the polypeptide is in its fully extended conformation and all peptide groups are in the same plane. In principle, Φ and ψ can have any value between +180 and -1800, but many values are prohibited by steric interference between atoms in the polypeptide backbone and amino acid side chains. The conformation in which both Φ and ψ are 00 is prohibited for this reason; this conformation is used merely as a reference point for describing the angles of rotation. Allowed values for Φ and ψ are graphically revealed when ψ is plotted versus Φ in a Ramachandran plot , introduced by G. N. Ramachandran (Gopalasamudram Narayan Ramachandran).