Mechanical elasticity of proline-rich and hydroxyproline-rich collagen-like triple-helices studied using steered molecular dynamics

Abstract

Identity of the amino acids in Gly-X-Y repetitive motives governs biomechanical features of collagen such as elasticity in the extracellular matrix. Proline and hydroxyproline are the most abundant residues at the X and Y sites of collagen repetitive motives, respectively. However, their effects on the elasticity of collagen have not been identified. Here, we investigated the molecular mechanics of five different proline-rich collagens with Gly-Pro-Y repetitive motives, four hydroxyproline-rich collagens with Gly-X-Hyp repetitive motives as well as a collagen with Gly-Pro-Hyp repetitive motif, focusing on molecular stiffness and elasticity. The proteins were virtually built and stiffness, Young's modulus, cross-sectional radius, intermolecular and protein-solvent hydrogen bonds of the collagens were investigated using steered molecular dynamic simulation. Results showed a higher stiffness and Young's moduli of the proline-rich collagens compared to the hydroxyproline-rich collagens. Young's modulus of the proline-rich collagens was negatively correlated with the cross-sectional radius. There was no significant difference between the proline-rich and the hydroxyproline-rich collagen from the point of view of intermolecular and protein-water hydrogen bonds. However, a decreased and an increased number of protein-water hydrogen bonds in response to stretching was found for the proline-rich and the hydroxyproline-rich collagens respectively. Interestingly, the collagen with Gly-Pro-Hyp repetitive motif showed an intermediate stiffness, Young's moduli and cross-sectional radius. The collagen also had a lower number of intermolecular and protein -water hydrogen bonds when compared to the proline-rich and hydroxproline-rich collagens. These results suggest that the presence of proline in the structure of collagen reduces elasticity and increases stiffness, whereas presence of hydroxyproline increases elasticity of the collagen. We conclude that any codon substitution in the collagen genes causing alteration of proline and/or hydroxyproline residues may result in drastic collagen deficiency.

Keywords: Collagen; Elasticity; Hydroxyproline; Proline; Stiffness; Young's modulus.