New insights into the interaction of sugarcane cystatin (CaneCPI-5) with the surface of hydroxyapatite through molecular dynamics simulations.

Abstract

Introduction: This study conducted a molecular dynamics simulation to elucidate the interactions in silico between a sugarcane cystatin (CaneCPI-5) and hydroxyapatite, aiming to deepen the understanding of its potential role in modulating the dental enamel demineralization process.

Methods: The CaneCPI-5 protein structure was modeled using homology with SWISS-MODEL, based on the multicystatin template PDB-ID 4LZI. Molecular dynamics simulations were conducted with the protein positioned randomly in a box containing a hydroxyapatite surface (001 face). Molecular dynamics simulations were then carried out for 500 ns with control of temperature and pressure using the GROMACS package. The free energy of interaction between CaneCPI-5 and the hydroxyapatite surface was calculated using the MM/GBSA method based on trajectory frames.

Results: For several initial orientations, the protein rapidly migrated to anchor to the surface, ensuring minimal distance between its amino acid residues and the surface. Most residues interacting with the surface phosphates were positively charged. Arginine 81, alanine 105 and arginine 107 were found to be key residues. During the simulations, similar values were observed for all orientations in terms of root-mean-square deviation, radius of gyration, and root mean square fluctuation. The free energy calculation showed strong protein-hydroxyapatite interactions, except for one of the initial orientations.

Conclusion: This study demonstrates that CaneCPI-5 has affinity for hydroxyapatite surfaces, with positively charged residues, particularly arginine. The stable binding observed throughout the simulations suggests that this protein may contribute to mechanisms that influence the integrity of dental enamel in demineralizing conditions.