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A collagen molecule consists of three polypeptide chains arranged in a parallel triple-helix. The individual polypeptide chains are called alpha-chains, and although each is helical they only have this conformation when associated with two other alpha chains; they should not be confused with alpha-helices. There are at least 9 distinct alpha chains; most are approximately 1000 amino acids in length. This results in a diameter of 14 Å and a length of about 300nm for a single collagen molecule.
The helical conformation of each chain is dependent on the fact that every thirdresidue is a Gly, and that the sequence is rich in Pro. A larger side chain than Gly would prevent the close contact of the three chains. About half of the Pro side chains are hydroxylated; the resulting residue Hydroxproline is referred to as "Hyp". The structure is stabilised by hydrogen bonds between the backbone amide of a Gly residue and the backbone carbonyl of residue X, where the sequence is represented by a repeat of -Gly-X-Y-. Collagen I, which constitutes 90% of the collagen in a mammal, consists of a heterotrimer where 2 of the alpha-chains are identical.
Here is a model collagen structure. This consists of the repeated sequence Gly-Pro-Pro in each of the 3 alpha-chains, subjected to an energy minimization procedure. Hydrogen bonds between the backbone atoms of the 3 alpha-chains are indicated. This model can be seen with RasMol by clicking here .
Here is a space-filling model of the triple-helix.
The alpha-chains are initially synthesized in the form of precursors called pro-alpha-chains, which have globular sequences called extension peptides at each end. The C-terminal extension peptides (approximately 300 residues long) of three chains associate, forming disulphide cross-links, and the triple helix forms in a zipper-fashion giving procollagen. Collagen results from the cleavage of the extension peptide domains.
Collagen type I forms collagen fibrils. Collagen molecules are arranged head-to-tail, with a 35nm gap between each, in a staggered bundle as shown. All the molecules point in the same direction. The -OH groups of hydroxyproline are involved in hydrogen bonds between chains, while interactions between other side chains are thought to be important in formation of fibrils from a number of individual molecules. Charged and uncharged residues are found to be periodically clustered along the sequence of collagen I every 234 residues, which is equivalent to 67 nm; while the gap between staggered molecules in a fibril is the same distance. This suggests that the collagen molecules are aligned such that the maximum electrostatic and hydrophobic interactions occur between different molecules.
The diagram here indicates interactions between alpha-chains in two different molecules. Again this is taken from a model structure, of the Smith collagen microfibril arrangement in which 5 triple helices are involved in a left-handed superhelical arrangement which is postulated to be repeated throughout the fibril. Only two of the five collagen molecules are shown here. All the alpha-chains consist of a repeated Gly-Pro-Hyp sequence. Three Hyp residues are highlighted forming hydrogen bonds between individual collagen molecules, rather than within them.
Here is an end-on view of the superheilx. Click here to see the whole structure.
Silk fibroin, tropomyosin and keratin are other fibrous proteins which are rich in glycine. Details of these can be found under the Glycine Group's section on Glycine in Structure.
Examine the crystal structure of actin. The actin molecule is complexed with deoxyribonuclease I; actin is the larger of the two (select Colour:chains). Consider how the shape of this molecule might relate to its ability to polymerize.
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