Molecular dynamics simulations of peptides on calcite surface

Abstract

A series of molecular dynamics (MD) simulations has been carried out to investigate the interaction between peptides and a calcite surface in water. A 16-amino acid and a 17-amino acid peptide have been built and three different configurations for each peptide are used as starting configurations. The dynamic behaviour of these peptides has been investigated by calculating their radii of gyration and distribution of dihedral angles. For comparison, the simulations of peptides in vacuum and water have also been carried out. The simulations indicate that these peptides generally have strong interactions with the calcite surface and the peptides changed their configuration to favour this interfacial interaction. Continuum electrostatic calculations based on the Poisson–Boltzmann Equation (PBE) have also confirmed strong electrostatic interactions between the peptides and the calcite surface. The results suggest that the peptides can control calcite crystallisation and that the strong electrostatic interactions between the peptides and the calcite surfaces dominate the interfacial interactions.

Keywords:

• molecular simulation
• peptide
• biomineralisation
• calcite
• surface

Acknowledgements

M.Y. and J.H.H. acknowledge funding from the EPSRC under Grant No. GR/S80103/01 and M.Y. and S.L.S.S. acknowledge funding from Maersk Olie og Gas. Computer resources were provided by the Danish Center for Scientific Computing (DCSC) and the MOTT facility (EPSRC Grant No. GR/S84415/01), run by the STFC e-Science Centre. We also thank Colin L. Freeman (University of Sheffield, UK) for the helpful discussions.