Structure of Proteins

Structure of protein is the three-dimensional arrangement of atoms in an amino acid-chain molecule. There are number of factors which determine the exact shape of a protein. These are considered in terms of four levels of strutural organization called the primary, secondary, tertiary and quartenary structures of the protein. Each succeeding level of organization is more complex than the previous one and is a direct result of the chemical features of the previous level.

Primary Structure

The primary structure of proteins refers to the sequence of amino acids held together by peptide linkages. The amino acid sequence in proteins can be determined by the methods used for peptides.

These methods have been applied to a number of proteins and several generalisations regarding the primary structure of proteins have been made. They are:
A. Proteins are made up of L-amino acids only
B. A protein may contain more than one amino acid chain. If so, the chains are usually bonded to each other at specific points by disulphide-S-S-linkages
C. Sequence of amino acids along the protein chains is essentially random. Repeating sequences within a protein molecule are not common
D. Small variations in the sequence of amino acids have pronounced effects on the chemical and physical properties of protein.

Secondary Structure

The secondary structure of a protein refers to the shape in which the long amino acid chain exists. Many proteins consist of amino acid chain coiled into a spiral known as a helix. Such a helix may be either right-or left-handed, as in the case of Screws. The right-handed helix is known as the α-helix, and the left-handed helix is known as the β-helix. It has been found that an α-helix constitutes the more stable arrangement. The spiral is held together by hydrogen bonds between N-H and C=O groups vertically adjacent to one another in the helix (shown in figure). X-Ray studies have shown that there approximately 3.6 amino acid units for turn in the helix.

α-Helix

α-helix structure was proposed in 1951 for α-keratin protein by L. Pauling and F. H. C. Crick. The α-helical structure arises due to resonance in the peptide linkage and hydrogen bonding between —NH— and >C=O groups along the protein chains.

In the α-helical structure of the protein, each turn of the helix has nearly 3.7 amino acids and it is at a distance of 5.4Å from the other. Two adjacent turns are linked by means of hydrogen bonds which involve NH group of one amino acid and the carbonyl oxygen of the fourth residue in the chain. This hydrogen bonding prevents free rotation and so the helix is rigid. Furthermore, at least three adjacent hydrogen bonds must be broken before free rotation can occur in a segment of the helix. The hydrogen bonds lie along the axis of the coil, and serve to maintain the spacing between the turns, The α-helix may be left- or right-handed. However, Moffitt (1956) deduced theoretically, that the right-handed helix is more stable than the left-handed helix. The diameter of the helix has been estimated to be about 10Å. This smaller helix in turn is a part of a larger helix; each turn of a larger helix has nearly thirteen turns of the smaller helix.

The existence of α-helical structure in proteins in the solid state has been established by X-ray analysis. It is important to note that all polypeptide chains are not capable of forming the α-helix, since the stability of this helix depends on the nature and sequence of the side-chains (R groups) in the polypeptide chains. Actually, the amount of the helix form varies in proteins, ranging from zero to about 100 per cent. The amount of helical content in a protein may be estimated by means of optical rotations, optical rotatory dispersion (ORD), and IR studies.

β-Conformation or Pleated Sheet

This conformation was also proposed by Pauling et al. (1951). In the β-conformation or pleated sheet, the polypeptide chain is extended and chains are held together by inter-molecular hydrogen bonds. Two types of pleated sheets are known, viz. parallel and anti-parallel. In parallel pleated sheet, all the polypeptide chains run in the same direction e.g. keratin, while in anti-parallel the chains run alternately in opposite directions, as in fibroin.
--- Hydrogen Bond

The existence of the pleated sheet structure in solid proteins has been confirmed by X-ray analysis. The calculated bond distance between two CHR groups on the same side of a chain is 7.2Å, while the experimental value is 7.0Å. This difference is due to the crowding caused by the side chains (R), which in turn prevents the chain from being fully extended.

Tertiary Structure

An α-helix may be considered to be a piece of a rope which is free to bend, twist, and fold. The tertiary structure of a protein refers to the final three- dimensional shape that results from the twisting, bending, and folding of the protein helix. The detailed determination of this shape has been carried out only for a few proteins.

Two major molecular shapes have been found, viz- fibrous and globular. Fibrous proteins have a large helical content and are essentially rigid molecules of rod like shape. On the othe rhand, globular proteins have a polypeptide chain which consist partly of helical sectionsand folded about the random coil section to give a spherical shape.

The tertiary structure of a protein is best determined by X-ray studies which is achieved in many years. Other methods used for elucidating the tertiary structure are viscosity measurements, diffusion, light scattering, ultracentrifuge method and electron microscopy.

Three main type of bonds are responsible for the formation of tertiary structure of a protein namely hydroge, ionic and hydrophobic. The other type of bond is the disulphide bond which maintains the tertiary structure is generally included in primary structure because of its covalent nature.

Quaternary Structure

Complex proteins are often formed from two or more amino acid chains rather than a single amino acid chain. Each chain is a complete protein with a characteristic primary, secondary, and tertiary structure. The quaternary structure refers to the way in which these amino acid chains of a complex protein are associated with each other. In such cases, the protein is known as oligomeric and the individual chains as protomers or sub-units. The association of sub-units can be disrupted by reagents which do not break covalent bonds and thus two chains joined by disulphide bonds should not be considered as two sub-units. Each sub-unit has its own primary, secondary and tertiary structures, and two or more sub-units in a given protein may have identical or different above three structures. The haemoglobin molecule is made up of four sub-units (two identical α-chains and two identical β-chains); each chain binds a haeme group and there are minor differences in folding between the α-and β-chains, which depend on differences in primary structures. The four chains are held together by Van der Waals forces (hydrophobic forces) giving the molecule a quaternary structure that resembles a sphere.

Myoglobin is an example of protein consisting of a single polypeptide chain which contains about eight straight segments (α-helices) folded in an irregular manner at the random-coil sections.

Source: Advanced Organic Chemistry By B.S.Bahal and Arun Bahl
Chemistry of Organic Natural Products Vol.1 By O.P.Agarwal