Collagen side-chains

Sarkar, S. K., Hiyama, Y., Niu, C. H., Young, P. E., Gerig, J. T., and Torchia, D. A. (1987). Molecular dynamics of collagen side chains in hard and soft tissues. A multinuclear magnetic resonance study. Biochemistry 26, 6793-6800. 

Figure 14.2 Models of a collagen-like peptide with a mutation Gly to Ala in the middle of the peptide (orange). Each polypeptide chain is folded into a polyproline type II helix and three chains form a superhelix similar to part of the collagen molecule. The alanine side chain is accommodated inside the superhelix causing a slight change in the twist of the individual chains, (a) Space-filling model, (b) Ribbon diagram. Compare with Figure 14.1c for the change caused by the alanine substitution. (Adapted from J. Bella et al.. Science 266 75-81, 1994.)...

It is known that native collagen contains tripeptide sequences which, because of being homopolypeptides, are not able to give rise to triple-helical tertiary structures (e.g. Gly-Pro-Leu, Gly-Pro-Ser). The reason for this and for the above-mentioned low thermostability of the synthetic homopolypeptides is presumably to be found in the fact that in the case of the model peptides with their monotonously repeated tripeptide sequences, special interactions between the side chains of the different amino acid residues as postulated by Ward and Mason are no more possible157). 

Ti values may occur with such native biopolymers as ribonuclease A, deoxyribonucleic acid, and collagen, whose molecular motions are restricted, but, as yet, high values have not been observed for polysaccharides in solution, or for gels, in which these motional-restriction effects may be equivalent, or less marked. However, an extensive relaxation-study by Levy and coworkers68 on poly(n-alkyl methacrylates) may serve as a model for future experiments on polysaccharides, as this type of molecule has a main chain and side chains, albeit more mobile than those in polysaccharides. 

The availability of high-resolution structures of peptides EKG, T3-785, IBP, and G991-G1032, which include residues other than Pro and Hyp in the X and Y positions, offers the opportunity to investigate the conformation and interactions of side chains from residues typically found within the collagen triple helix. In the peptide with an EKG tripeptide sequence, the Lys and Glu residues did not form direct intermolecular or intramolecular ion pairs, even though such pairs are sterically feasible. ... 

The Pro side chain (R group), is unique in that it incorporates the terminal amino group in the side chain. The incorporation of this amine group into a five-membered pyrrolidine ring, constrains the rotational freedom around the N—Ca bond in Pro to a specific rotational angle. This has important consequences for the protein structures in which Pro participates, for example, collagen. ... 

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