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Secondary Structure of a Protein

The primary structure of protein tells us only about the sequence of amino acids in the protein chain. It tells us nothing about the shape or conformation of the molecule. Most of the bonds in protein molecules being single bonds, these can assume infinite number of shapes due to the free rotation about single bonds. From a variety of physical measurements, it has, however, been found that each protein has only a single three dimensional conformation. teh fixed configuration of a polypeptide skeleton is referred to a the secondary structure of a protein.

Secondary structure of protein tells us about:

1. The manner in which the protein chain is folded and bent.

2. The nature of bonds which stabilize this structure.

 

What is the Secondary Structure of a Protein?

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Based on the nature of the hydrogen bonding, whether it is intra or inter molecular, Pauling and Corey, in 1951, identified two regular types of secondary structures of protein.
  • α - Helix and
  • β- Pleated sheet

Alpha Helix

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Early x-ray diffraction studies conducted by William Astbury in 1930s, of fibrous proteins such as hair and wool, showed a major periodicity or repeat unit of 5.0 to 5.5 Å, indicating some regularity in the structure of these proteins.

According to Linus Pauling and Robert Corey, polypeptide chains in the same proteins are coiled up like a spiral staircase to form a helix. This can be visualized as a spring coiled about an imaginary cylinder. The spring may be right handed, or left handed. It is however, invariably found to be right handed. The spiral that is right-handed, is called as α-helix. In their helical structure, NH group in one unit is linked to the carbonyl oxygen of the third unit by hydrogen bonding. This hydrogen bonding between different units is responsible for holding the helix in position. On an average there are about four amino acid units in each turn (gyre) of the helix.

The model building experiments have shown that an α- helix can form with either D or L- amino acids. However, the residues must all be of one stereo isomer, the dextro- amino acid disrupts the regular protein structure having Laevo-amino acids, and vice versa.

Formation preference of such helix considered against the other possible conformations in the nature are usually expected and in part the α helix makes the exact usage of the hydrogen bonds internally. Wool fiber is flexible and could be stretched twice its length without any breakage. These fibres returns to its normal length as the tension is released. On stretching, the hydrogen bonding along the turns of the α - helix starts breaking whereas the covalent bonds remain intact. On release of tension, these hydrogen bonds are re-formed and the helical shape is restored.

Destabilization of α -helical conformations by certain amino acid residues can occur in various ways.
  1. A sharp bend is created by a propyl residue has its α-N atom in a rigid ring system. It does not participate in the α-helical structure.
  2. Since the negatively charged side chains repel each other in a sequence of aspartyl and/or glutamyl residue, the α-helical structure can be destabilized.
  3. Glycine contains a small hydrogen atom as an R group. It can destabilize the alpha helical structure too, because of the lack of a side chain on glycine allows for a great degree of rotation about the amino acid's α- carbon. Hence, conformations other than a helical bond angles are possible.
  4. Because of steric hindrance imposed by the bulky R groups in a cluster of isoleucyl residues, the helical conformation is disrupted.

Beta Pleated Sheet

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There are some proteins, like gamma globulin, in which there is no helical structure. In proteins like hemoglobin and myoglobin, certain regions of the polypeptide chain are helical while remaining portions possess a random configuration.

In proteins like silk fibroin and β - keratin, the polypeptide chains are aligned side by side in a sheet like arrangement. Hydrogen bonds between the adjacent chains stabilize them. This type of structure is called as a β-pleated sheet.

There are two types of β - pleated sheet. If the N-terminal end of polypeptides participating chains lie on the same edge and with all C- terminal on the opposite edge, the structure is better known as Parallel - β -pleated sheet.

Anti parallel β-pleated sheet
is one in which the chain directions get alternated resulting in these alternating chains having their N-terminal ends lying on same side with the C - terminal ends lie on the opposite edge. In a silk fiber, the polypeptide chains are aligned in a sheet-like arrangement and are held together very tightly by hydrogen bonding. Silk fiber, therefore, is very strong, but resists stretching. Silk fibroin has an anti parallel sheet structure.

Determination of secondary structure of protein

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The secondary structure of protein is determined by using:

a. NMR spectroscopy analysis.

b. Infra -red analysis.

Since secondary structure is a three dimensional structure, and apart from the two structures, alpha helical and the beta pleated sheet, there are other forms of secondary structure too, it is very difficult to arrive at a proper determination of secondary structure.

Apart from the two important secondary structures of protein, there are other types, like:


a. Random coil - This structure results due to the bulky residue in the polypeptide chain. It does not have a specific conformation.

b. γ - helix - This resembles slightly the helical structure, with no inter atomic contact between two strands. It is a highly hydrogen bonded structure.

Comparing Alpha Helical and Beta Pleated Sheet

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Pauling and Corey identified a second type of repetitive, minimum-energy or stable conformation, which they named β-pleated sheet.
  • The formation of β-pleated sheet depends upon the intermolecular hydrogen bonding, although the intra-molecular hydrogen bonds are also present.
  • The pleated sheet is formed by the parallel alignment of a number of polypeptide chain alternatively project above and below the plane of the sheet, leading to a two-residue repeat unit.
  • The β-sheet structures are quite common in nature and are favored by the presence of amino acids, glycine, and alanine.
  • Silk and certain synthetic fibers such as nylon and orlon are composed of β-structures.
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