Understanding the Structural and Binding Properties of Collagen: A Theoretical Perspective

The change in the stability and conformational dynamics of a collagen-like microfibril segment (CMS), 23 amino acid residues long (around 5[3(GLY-X-Y)8]), as a result of the interaction with water, formaldehyde, and gallic acid is studied by performing a series of nanosecond molecular dynamics simulations. Major changes in the conformation of CMS occur when interacting with water while in the other solutions: (1) pure formaldehyde, (2) 8.0% (v/v) formaldehyde/water, and (3) 1.4% (v/v) gallic acid/water; the variation is less evident. Possible CMS/modifying agents' binding sites are evidenced by the analysis of radial distribution functions, coordination number, and H-bonding network. In particular, in the case of formaldehyde a high preference for ARG, LYS, and GLN residues is found. Gallic acid molecules preferably bind to PRO and HPR residues. The examination of average interaction energies per residue and their van der Waals and electrostatic components confirms the results obtained with the structural analysis. Furthermore, both van der Waals and electrostatic terms are important for the stabilization of the CMS. This is especially noted when CMS interacts with gallic acid. A comparison between calculated and available experimental findings is proposed. The agreement is very satisfactory, thus validating the computational approach to these systems.