Useful Notes on the Structure of Proteins

The primary structure is thus a complete description of the covalent connection of protein. Sanger, et al., 1955, established the sequence in insulin which contains fifty-one amino-acids. Later, the primary structure of ribonuclease, an enzyme containing 124 amino-acids, was elucidated by Stein et al.

Secondary structure:

The secondary structure of proteins refers to the spatial arrangement of the polypeptide chains as a result of hydrogen bond formation.

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The secondary structure is a direct conse­quence of the sequential arrangement of the amino-acids in the poly­peptide chain. The a-helix and the 3-pleated sheet are best examples of secondary structure (Pauling, Cory et al., 1951).

The ?-helix is a rod-like structure. “Hi; tightly coiled polypep­tide chain forms the inner part of the ion and the aide chains extend outward in a helical array.

The a-helix is stabilized by hydrogen bonds between the NH and CO groups of the main chain. The CO group of each amino-acid is hydrogen bonded to the NH group of the amino-acid that is situated four residues ahead in the linear sequence.

Thus, all the main-chain CO and NH groups are hydrogen-bonded. Each residue is related to the next one by a translation of 5A along the helix axis and a rotation of* 100°, which gives 3.6 amino-acid residues per turn of helix.

Thus, amino-acids spaced three or four apart in the linear sequence are spatially quite close to one another in and a-helix. In contrast, amino-acids two apart in the linear sequence are situated on opposite sides of the helix and so are unlikely to make contact.

The pitch of the a-helix is 5-4A, the product of the translation (1-5A) and the number of residues per turn (3 6).

The screw-sense of a helix can be right-handed or left-handed; the a-helices found in proteins are right-handed.

The ?-pleated sheet structure of protein differs markedly from the a-helix in that it is a sheet rather than a rod.

The polypeptide chain in the ?-pleated sheet is almost fully extended rather than being tightly coiled as in the a-helix.

Adjacent amino-acids in a polypeptide chain occur every 36A, in contrast to 1-5A for the a-helix, and every amino-acid residue is rotated 180° with respect to adjacent ones.

The ?-pleated sheet is stabilized by hydrogen bonds between NH and CO groups in different polypeptide chains where as in the a-helix the hydrogen bonds are between NH and CO groups in the same poly­peptide chain.

A configuration of this type is not possible with amino-acids other than glycine because side chains (instead of hydrogen atoms) attached to the a-carbon could not be accommodated. Silk fibroin, a member of the class of ?-keratins rich in alanine or serine, is an exam­ple of a protein with a related structure.

A somewhat more complex type of molecular organization is illustrated by the protein collagen.

Collagen consists of three poly­peptide chains with parallel orientation but with the glycine of every triplet of amino-acids displaced one residue compared to the register of the other two chains.

The three chains are wound around in a coil so that hydrogen bonding occurs between the glycine residues in adja­cent chains.

While the a-carbons of the glycine residues tend to be oriented toward each other and the centre of the three-stranded unit, the other two-thirds of the amino-acid residues are oriented with the amino acid side chains facing outward.

The pyrrolidine rings of proline and hydroxyproline tend to be closely packed, pro­ducing a helical ridge on the outer surface of the molecule. Adjacent amino-acids residue in a chain occur 2 86A apart and are rotated108A.’

Tertiary structure:

When a long peptide chain, with or without a helix, is coiled and variously fojded in itself, the resulting highly specific three-dimensional configuration of the protein is termed as the tertiary structure. This tertiary structure is found especially in the case of globular proteins.

Tertiary structure results from various weak molecular forces within the protein and from interactions between the protein and the solvent water.

Disulphide covalent bonds and, rarely, interchain peptide bonds are responsible for the tertiary structure. Accumulating evidences suggest that hydrogen bonds and hydrophobic bonds are also involved in the tertiary structure of proteins.

Quaternary structure:

A protein is said to have quaternary structure if it is composed of several polypeptide chains which are not covalently liked to one another. Each polypeptide chain in such a protein is called as subunit.

The enzyme phosphorylase, for example, contains four subunits which are identical to each other but separately inactive catalytically.

However, when they are joined together, the en­zyme becomes active. This type of structure in which all the subunits are identical is termed as homogeneous quaternary structure. But, when the subunits are dissimilar, e.g., the tobacco mosaic virus, the struct­ure is said to be heterogeneous quarternary structure.