The collagen molecule, also known as the “tropocollagen”, is part of larger collagen aggregates such as fibrils. The whole molecule is approximately 300 nm long and 1.5 nm in diameter.
Triple helix structure of collagen
Individually there are three polypeptide strands. These are called alpha chains and each of them has a conformation of a left-handed helix. An alpha helix is a different structure with a right handed conformation.
Further the three left-handed helices are twisted together into a right-handed coiled coil, forming a triple helix or "super helix". The final cooperative quaternary structure stabilized by numerous hydrogen bonds.
In type I collagen, and possibly all fibrillar collagens if not all collagens, each of the triple helices forms a right-handed super-super-coil that is referred to as the collagen microfibril.
Thereafter, each of the microfibril is interdigitated or intercalated with its neighboring microfibrils. This strengthens the structure of the individual molecules.
Arrangement of amino acids in collagen
Collagen contains specific amino acids – Glycine, Proline, Hydroxyproline and Arginine. These amino acids have a regular arrangement in each of the three chains of these collagen subunits. The sequence often follows the pattern Gly-Pro-X or Gly-X-Hyp, where X may be any of various other amino acid residues. Proline or hydroxyproline constitute about 1/6 of the total sequence.
Glycine accounts for 1/3 of the sequence meaning that approximately half of the collagen sequence is not glycine, proline or hydroxyproline. In addition, the regular repetition and high glycine content is found in only a few other fibrous proteins, such as silk fibroin.
In silk 75-80% is -Gly-Ala-Gly-Ala- with 10% serine, and elastin is rich in glycine, proline, and alanine (Ala), whose side group is a small, inert methyl group. High glycine contents are not found in globular proteins except in very short sections of their sequence. Because glycine is the smallest amino acid with no side chain, it plays a unique role in fibrous structural proteins.
Collagens do not contain chemically reactive side groups unlike in enzymes and transport proteins. Collagen determines cell phenotype, cell adhesion, tissue regulation and infrastructure and its non-proline rich regions have cell or matrix association/regulation roles.
Left handed helices are formed because of the high content of proline and hydroxyproline rings, with their geometrically constrained carboxyl and (secondary) amino groups along with abundance of glycine. The left handed helices are formed without any intrachain hydrogen bonding.
Cross linkages in collagen
The tensile strength of collagen depends on the formation of covalent intermolecular cross-links between the individual protein subunits. The fibril containing collagens in higher vertebrates (types I, II, III, V and XI) are cross-linked through a mechanism based on the reactions of aldehydes generated enzymically from lysine (or hydroxylysine) side-chains by lysyl oxidase.
Certain other collagen types (e.g., collagen type IX of cartilage) are also cross-linked by the lysyl oxidase mechanism.