The term "secondary structure" denotes the configurational relationship between residues which are about 3–4 amino acids apart in the linear sequence (Box 1). Secondary and tertiary levels of protein structure are preserved by noncovalent forces or bonds like hydrogen bonds, electrostatic bonds, hydrophobic interactions and van der Waals forces.

 i. A hydrogen bond is a weak electrostatic attraction between one electronegative atom like O or N and a hydrogen atom covalently linked to a second electronegative atom. Hydrogen atoms can be donated by -NH (imidazole, indole, peptide); -OH (serine, threonine) and -NH2 (arginine, lysine). Hydro gen accepting groups are COO— (aspartic, glutamic) C=O (peptide); and S–S (disulphide).

ii. Electrostatic bonds (ionic bonds): Positive charges are donated by epsilon amino group of lysine, guanidinium group of arginine and imidazolium group of histidine. Negative charges are provided by beta and gamma carboxyl groups of aspartic and glutamic acids.

iii. Hydrophobic bonds are formed by inter actions between nonpolar hydrophobic side chains by eliminating water molecules. This serves to hold lipophilic side chains together.

iv. The van der Waals forces are very weak, but collectively contribute maximum towards the stability of protein structure.

2-A. Alpha helix

 Pauling (Nobel prize, 1954) and Corey described the alpha-helix and beta-pleated sheet structures of polypeptide chains in 1951.

 i. The alpha-helix is the most common and stable conformation for a polypeptide chain. In proteins like hemoglobin and myoglobin, the alpha-helix is abundant, whereas it is virtually absent in chymotrypsin.

 ii. The alpha helix is a spiral structure (Fig. 1). The polypeptide bonds form the back-bone and the side chains of amino acids extend outward.

Fig1. Structure of alpha helix

 iii. The structure is stabilized by hydrogen bonds between NH and C=O groups of the main chain.

iv. Each turn is formed by 3.6 residues. The distance between each amino acid residue (translation) is 1.5 Å.

 v. The alpha-helix is generally right handed. Left handed alpha helix is rare, because amino acids found in proteins are of L-variety, which exclude left handedness. Proline and hydroxy proline will not allow the formation of alpha-helix.

2-B. Beta-pleated sheet

i. The polypeptide chains in beta-pleated sheet is almost fully extended. The distance between adjacent amino acids is 3.5Å.

 ii. It is stabilized by hydrogen bonds between NH and C=O groups of neighboring polypeptide segments.

iii. Adjacent strands in a sheet can run in the same direction with regard to the amino and carboxy terminal ends of the polypeptide chain (parallel) or in opposite direction (anti parallel beta sheet) (Fig. 2). Beta-pleated sheet is the major structural motif in proteins like silk Fibroin (anti parallel), Flavodoxin (parallel) and Carbonic anhydrase (both).

Fig2. Structure of beta-pleated sheet

iv. Beta bends may be formed in many proteins by the abrupt U-turn folding of the chain. Intrachain disulfide bridges stabilize these bends.

 2-C. Collagen helix It is a triple helical structure found in collagen.

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مواضيع ذات صلة

Brown Adipose Tissue Promotes Thermogenesis

Hormones Regulate Fat Mobilization

Adipose Tissue is The Main Store of Triacylglycerol in The Body

Classification of Proteins

Precipitation Reactions of Proteins

Study of Protein Structure

Imbalance in the Rate of Triacylglycerol Formation & Export Causes Fatty Liver

The Liver Plays A Central Role in Lipid Transport & Metabolism

HDL Takes Part in Both Lipoprotein Triacylglycerol & Cholesterol Metabolism

Tertiary Structure of Proteins

Primary Structure of Proteins

Chylomicrons & Very-low Density Lipoproteins are Rapidly Catabolized