Molecular dynamics simulations of the proline and hydroxyproline of collagen

Abstract

Collagen is an important natural, bioactive, and abundant material in living systems. Developing collagen materials that resolve practical issues in tissue engineering is the focus of significant research. However, its properties and behavior are not sufficiently understood, not in the least because proteins undergo significant conformational changes while performing their function. Moreover, it is difficult to determine the solvent impact on the structure and interatomic bonding at the atomistic level. Molecular Dynamics (MD) simulation is a technique that can be used successfully to understand macromolecular structure-to-function relationships. This work investigates the influence of hydroxyproline and proline on hexamer and heptamer collagen structures using the GROMACS software. We applied the Amber99sb force field to conduct molecular dynamics simulations in triplicate of the collagen fragments over a trajectory of 200 ns. We studied the root mean square (RMS) distribution, hydrogen bonds, and solvent accessible surface area (SASA). The results showed proline and hydroxyproline helped to stabilize the 3-helix of collagen; hydroxyproline did so more extensively than proline did. Hydroxyproline is responsible for the formation of intermolecular hydrogen bonds. It increases the stability of the triple helical, while proline promotes the formation of the intramolecular hydrogen bonds and makes the overall structure less stable than hydroxyproline. The solvent-accessible surface area (SASA) indicates that collagen is a lipophilic polymer.