Molecular Driving Forces in the Self-Association of Silaffin Peptide R5 from MD Simulations

Area of Science:

• Biomineralization
• Materials Science
• Computational Chemistry

Background:

• Silaffin-R5 peptide facilitates uniform silica (SiO2) particle precipitation under mild conditions.
• Post-translational modifications (PTMs) significantly influence biomineralization processes.
• Understanding R5 peptide aggregation and its role in SiO2 formation is crucial.

Purpose of the Study:

• Investigate the mechanisms of R5 peptide aggregation and SiO2 formation.
• Elucidate the impact of PTMs and ions on R5 peptide aggregation.
• Determine the prerequisite role of peptide aggregation in biomineralization.

Main Methods:

• Molecular dynamics (MD) simulations were employed to study R5 dimer aggregation.
• Parallel bias metadynamics with partitioned families was used for efficient sampling.
• Simulations included various PTMs and different ions in solution.

Main Results:

• Peptide aggregation is a necessary precursor for silica biomineralization.
• Electrostatic interactions play a critical role in R5 dimer aggregation.
• Phosphate ions (HPO4^2-) act as bridges between wild-type R5 peptides, promoting aggregation.

Conclusions:

• R5 peptide aggregation is essential for initiating silica biomineralization.
• Electrostatic forces and specific ion interactions govern the aggregation process.
• This study provides insights into the molecular mechanisms of silica biomineralization mediated by silaffin peptides.