Question

why so many proteins contain  helices or  sheets as secondary structure elements in their tertiary structures?

Answer 1

1. The a -helix

The a -helix is one of two secondary structures (the other being the b -sheet) predicted and discovered by Linus Pauling in 1951. It is a right-handed helix with the following spatial parameters:

F = -57°
Y = -47°
n = 3.6 (number of residues per turn)
pitch 0.54nm (or 5.4Å)

The helix has a specific hydrogen bonding pattern, where the backbone C=O group of residue n bonds with the N-H of residue n+4. The atomic distance between the N and O measures 0.28nm. The H-bonds are almost parallel to the helix axis and the total dipole moment gives the helix a dipole moment that points from the N-term (+) to the C-term (-). This helix dipole is important in the interaction of neighboring helices in the packing of secondary structural motifs into the 3-D structure.

The core of the helix is packed. The backbone atoms are in Van der Waals contact with each other across the helix axis. A helix can be represented in its so called wheel presentation. A helical wheel is a projection in 2-D along the helix axis and displays the orientation of the side chains on a 360 degree map with respect to the side of the helix. This wheel presentation is helpful for the detection of potential amphipathic helices. Amphipathic helices have a polar and a non-polar side and this plays a crucial role in helix-helix interaction and in the interaction of small peptides that have a helical conformation with the interaction with membranes, air-water interfaces, and self-

Projecting a peptide in a -helical form onto a plane along the helix axis allows for the circular distribution of the amino acid side chain direction away from the center. If the first amino acid is hydrophobic, and then amino acid at positions 4, 5, 8, 11, 12 and 15 are hydrophobic and the rest hydrophilic, the helix obtains an amphipathic character, with the upper half of the helix being hydrophobic and the lower half being hydrophilic. The distribution of hydrophobic residues follows the loose rule that every 3rd and/or 4th residue is hydrophobic in nature.

A second type of helix is the 3₁₀ helix; a right handed helix with average torsion angles F =-49 and Y =-26. Although this helix type is rarely found as long helix, the end turn of an a -helix often adopts the conformation of a 3₁₀ helix.

2. The b -strand and b -pleated sheet

In 1952, Pauling and Corey predicted the b -pleated sheet structure as an alternative secondary structure to the a -helix in proteins. b -strands are elongated peptide segments with atomic distances from side chain n to side chain n+2 of 0.7nm.

Single b -strands are not stable structures but occur in association with neighboring strands. Thus they can be found as either parallel or anti-parallel with respect to the N- to C-terminal direction of the adjacent peptide strands.

anti-parallel N® C     parallel N® C
                   C¬ N                  N® C

Like a -helices, b -pleated sheet backbones are fully hydrogen bonded, but here the H-bonds occur between neighboring strands (intermolecular). The H-bond geometry is different in the parallel and anti-parallel conformations
More than two strands can form into sheets which form extended right-handed twists. Such extended b -pleated sheets (called super secondary structures) can often been found in the cores of proteins. Alternatively, bundles of 4 closely packed a -helices (so called a -helical bundles) are also found at the center of globular proteins.

If the b -strand contains alternating polar and non-polar residues it forms an amphipathic b -sheet. This distribution of hydrophilic and hydrophobic residues has been observed in the membrane protein porin that forms a b -barrel structure (section 2.3), where the non-polar residues stick into the hydrophobic part of the lipid membrane and the hydrophilic residues form part of the channel interior responsible for the passage of small molecules across the membrane.