Secondary Structure:

How was this knowledge obtained? Through the study of keratins, which are fibrous, insoluble proteins derived from ectodermal (skin) cells.

Keratins come in two types:
alpha-keratins - rich in cystiene, plus most of common amino acids
beta-keratins - no Cys or S-S, rich in Gly, Ala, Ser

X-ray analysis: In 1930, Astbury (England) carried out experiments on proteins. The alpha-keratins produced a diffraction pattern which indicated a repeating unit of 0.50-0.55 nm ===> a-helix
When stretched (hot and moist) = repeat distance increased to
0.65-0.70 nm
(similar to beta-keratin) ===> -pleated sheet

Also available at this time were detailed X-ray structures of di- and tripeptides.

The Puzzle:

R.B. Corey and Linus Pauling (U.S.) studied all of these data using precise molecular models.

In 1951:
They constructed a model by coiling the peptide backbone along one axis, a constraint imposed by the planarity of the peptide bond. This model gave a repeat distance of 0.50-0.55 nm or approximately 3.6 amino acid residues per turn.

They had applied Okam's razor and arrived at the simplest arrangement, which was the alpha helix. The rise per residue is 0.15 nm, which also corresponded to the observed diffraction patterns.

This structure also permits formation of intrachain hydrogen bonds between successive coils of the helix and these are oriented to give maximum bond strength!

Nomenclature for helices

There is a second nomenclature, shown above in parenthesis, called the nN system, where n is the number of residues per turn and N is the number of atoms in a hydrogen-bonded loop.

The Ramachandran plot

In the study of protein conformation, we consider with two angles:

psi (C-C bond) and phi, (C-N bond)

G. N. Ramachandran, and his collegues in India constructed a correlation diagram which represents the various structures possible along with those that are actually found.

The angles phi and psi are set at 180 degrees when the peptide is fully extended and the N and carbonyl oxygens are alternating.

The Ramachandran plot shows the areas of stable, allowed conformations, circles indicate conformations of specific known structures. All other areas, and the conformations they represent, are disallowed. The areas of disallowed structures are due in part to collision of the van der Waals radii of the carbonyl oxygens and peptide nitrogens.

L-Amino acids can form either right or left handed helices; right is, however, more stable. Alpha helices found in all proteins to date are right-handed (the screw sense is defined from N --> C along the peptide sequence).

Beta-pleated sheets:
1. Two kinds = parallel and antiparallel (silk fibroin)

2. Found in globular proteins in combinations with alpha-helix

Collagen = the most abundant protein on higher vertebrates 1/3 or more of body protein (tendons, bones, ligaments)

Vitamin C is involved in the hydroxylation reaction for proline and lysine

Has great strength but little capacity to stretch; athletic injuries occur because of this property.

Gets more brittle with age because of cross-linking (a type of aldol condensation). As a result, tendons are more easily broken, as are bones also, and skin loses elasticity.

Optical Activity:

Carl Djerassi (of Stanford) worked extensively with this technique along with developing the birth-control pill.

Native proteins are more dextrorotatory than the sum of their amino acids (i.e. total optical rotation = rotation of individual amino acids + rotation of the alpha helix).

A circular dichroism (CD) machine is often used to estimate the percentage of helix in a protein before an X-ray crystal structure is available. It does so by measuring the extent to which a circularly polarized light beams (of both screw senses) are absorbed.