5.2.1.2 Secondary structure

5.2.1.2 Secondary structure

The secondary structure of a protein is the local spatial arrangement of a polypeptide's backbone atoms without  regard to the conformations of its side chains. It is formed by hydrogen bonding between the hydrogen of the peptide amide and carboxyl groups within one polypeptide chain giving rise to folding, looping or twisting of the primary structure. The most common types of secondary structure are the α-helix or a β- pleated sheet. Proline, hydroxyproline, glycine, glutamate, aspartate, arginine, lysine, isoleucine, threonine and serine are hlix-destabilising amino acids. Where ever they occurin a peptide chain, regular hydrogen bonding is interruped and the helix either shows a bend or gives place to a more flexible nonhelical segment.

 

 

                                                    Secondary Structure of Protein

 

  

i) The α-Helix

If the backbone of polypeptide is twisted by equal amount about each α-carbon, it forms a coil or helix. Difference types of helices, formed by imparting differing extent and direction of twist, are described by the number (n ) of aminoacyl residues, per turn and the pitch (P) or distance per turn that the helix rises along its axis. The α-Helices of protein contain anywhere from 4 to 50 residues (average, about 12 residues). The relevant parameters of an α-helix are n=3.6 residues per turn and p=0.54nm (5.4A). The distance along the helix axis that separates equivalent main-chain atoms of adjacent residues is 0.15nm (1.5A).

 

The aminoacyl R groups are directed outward from the helix axis minimizing mutual stearic interference. α-Helixes are stabilized by hydrogen bonding between the carboxy oxygen and the amino hydrogen 4 amino acids further along the chain. The α-helix is the lowest energy and most stable conformation for a polypeptide chain and it is formed spontaneously. These hydrogen bonds have an essentially optimal N to O distance of 28nm. Van der Waals interaction also confers additional stability. The tightly packed atoms at the core of an α-helix are in Van der Waals contact with one another across the axis of the α-helix.

Sec Strucutre alpha

 

ii) β - Pleated Sheets

The secondary structure of a protein is formed by hydrogen bonding between the hydrogen of the peptide amide and carboxyl groups within one polypeptide chain giving rise to folding, looping or twisting of the primary structure and called as β - pleated Sheets. It is present in most proteins. β-pleated sheet may be parallel or antiparallel. Adjacent polypeptide chains of antiparallel sheet proceed in opposite direction; those of parallel sheet, in the same direction. If the polypeptide chain is extended, there is no hydrogen bonding between carboxy oxygen and amino hydrogen in neighboring amino acids. If several strands lay next to each other, then hydrogen bonds are formed between these chains.

Beta related sheets

 

Proline and hydroxy proline(Hyp) interrupt the β-pleated sheet structure because their residues have no α-amide hydrogen left for hydrogen bonding with the carbonyl-O of another bond.

Last modified: Saturday, 31 March 2012, 7:09 AM