Secondary Structure Of Proteins

contents INTRODUCTION WHAT ARE PROTEINS? AMINO ACIDS: BUILDING BLOCKS OF PROTEINS STRUCTURE OF PROTEINS REFERENCES

Introduction Origin of word: Proteins are the most abundant organic molecules of the living systems. Proteins form the fundamental basis of structure and function of life. Origin of word: The term protein is derived from a Greek word proteios, meaning “holding the first place”. Berzilius (Swedish chemist) suggested the name proteins. Mulder (Dutch chemist) in 1838 used the term protein for the high molecular weight nitrogen rich substances.

What are proteins? PROTEINS may be defined as the high molecular weight, macromoecules, mixed polymers of α-amino acids joined together with peptide linkage (-CO-NH-). Proteins are the chief constituents of all living matter. They contain carbon, hydrogen, nitrogen and sulphur and some contain phosphorus also.

Amino acids:Building Blocks Of Proteins Amino acids are called as building blocks of protein. Contain two functional groups : amino and carboxyl group. Amino group is basic Carboxyl group is acidic. Side group R gives unique characterstics. Commonly found amino acids are α- amino acids.

Fig: Structure Of Amino Acid with its existence as Cation,Zwitter ion and Anion

Structure Of Proteins PROTEINS are the polymers of L- α-amino acids. The structure of proteins is rather complex which can be divided into four level of organisation: Primary structure Secondary structure Tertiary structure Quaternary structure

Fig:Structure Of Proteins

Bonds responsible for protein structure Proteins are stablised by two types of bonds:- covalent and non-covalent bonds Covalent bonds Peptide bonds Disulphide bonds Non – covalent bonds Hydrogen bonds Hydrophobic bonds Van der waals forces Electrostatic forces

Primary Structure Of Proteins Linear sequence of amino acids. Forms backbone of proteins (polypeptide), Amino acids are held together in a protein by covalent bond or linkage called as peptide bond . The primary structure of protein starts from the amino terminal (N)end and ends in the carboxyl terminal (C) end.

Fig: Primary Structure Of Proteins

Fig: Formation Of A Peptide Bond In a peptide bond the amino acid residue at the end with free α-amino group is the amino terminal (or N –terminal)residue whereas the residue at the other end , which has free a free carboxyl group ,is the carboxyl terminal (c –terminal)residue.

2) Secondary Structure Of Proteins Secondary structure is the local spatial arrangement of the main chain atoms is a selected segment of a polypeptide chain. Most common prominent secondary conformations are:- α- helix β- pleated sheet β-bends Secondary structure is the result of hydrogen bonding. The secondary structure of a polypeptide segment can be defined if the φ and Ψ angles are known for all amino acid residues in that segment.

Fig: Secondary Structures Of Proteins

The peptide bond is rigid and planar The peptide C – N bonds, because of their partial double bond character, cannot rotate freely. Rotation is permitted about the N – C (α) and the C(α) – C bonds. Peptide conformation is defined by two dihedral angles (or torsion angles) called ɸ(phi) and Ψ(psi). The important dihedral angles in a peptide defined by the three bond vectors connecting four consecutive main chain atoms: Φ involves the C(α) –N bonds Ψ involves the C (α) – C bonds Both φ and Ψ are defined as ± 180° when the polypeptide is fully extended and all peptide groups are in the same plane. In principle, φ and Ψ can have any value between -180° and +180°. Allowed values for φ and Ψ become evident when Ψ is plotted versus φ in a Ramachandran plot , introduced by G.N. Ramachandran.

Fig: Resonance in Peptide bond Fig:TORSION ANGLES IN PEPTIDE BOND

RAMCHANDRAN PLOT A Ramchandran Plot is a way to visualize backbone dihedral angles Ψ against φ of amino acid residues in protein structure. A Ramchandran Plot can be used to show which values ,or conformations, of the φ and Ψangles are possible for an amino acid residue in a protein and to show the empirical distribution of datapoints observed in a single structure. The darkest areas correspond to the core regions representing the most favourable combinations of phi-psi values. Horizontal axis – φ values Vertical axis – Ψ values Counting values -- -180° to +180° (vertical and horizontal axes)

Fig: Ramchandran Plots

1) α-helix structure It is the most common protein secondary structure given by Pauling and Corey, proposed that peptide bonds is a helical stucture called as α- HELIX. Each helical turn includes 3.6 amino acid residues. The distance between two amino acids in α-helix is 1.5Å. So the length of each helical turn is 3.6 x 1.5Å= 5.4Å. The amino acid residues in the prototypical α helix have conformations with φ = -57° and Ψ = -47°. In all proteins, the helical twist of the α helix is right handed .

Fig: Alpha Helical Structure

2) β-pleated sheet structure Second type of repetitive structure. Predicted by Pauling and Corey in 1951. In the β conformation, the backbone of the polypeptide chain is extended into zigzag rather than helical structure. In this arrangement, hydrogen bonds form between adjacent segments of polypeptide chain.

Fig: Beta Pleated Sheet

Types of β pleated sheets The polypeptide chains in the β sheets may be arranged either in : PARALLEL :- having same amino to carboxyl orientations.(φ= -119° , Ψ= +113°) ANTIPARALLEL :- having opposite amino to carboxyl orientations.(φ= -139° , Ψ= +135°) Antiparallel β-sheets is often promoted by formation of β-turns also called as β-bends or tight turns. Fig: β-turn

Fig: β-conformations of polypeptide chains Fig: ANTI-PARALLEL BETA SHEET Fig: PARALLEL BETA SHEET

3)β-turns FEATURES: Polypeptide bond has the capacity to turn called as beta turns. Found in globular proteins. Stablised by H-bond The conformation of beta bends sequence depends upon some extent of amino acid composition. Two types of beta turn based on torsion angles: TYPE I TYPE II

REFERENCES:- PRINCIPLES OF BIOCHEMISTRY (fifth edition) By: DAVID L. NELSON MICHAEL M. COX BIOCHEMISTRY By: ZUBAY