Self-assembly of peptide scaffolds in biosilica formation: computer simulations of a coarse-grained model

The self-assembly of model peptides is studied using Brownian dynamics computer simulations. A coarse-grained, bead-spring model is designed to mimic silaffins, small peptides implicated in the biomineralization of certain silica diatom skeletons and observed to promote the formation of amorphous silica nanospheres in vitro. The primary characteristics of the silaffin are a 15 amino acid hydrophilic backbone and two modified lysine residues near the ends of the backbone carrying long polyamine chains. In the simulations, the model peptides self-assemble to form spherical clusters, networks of strands, or bicontinuous structures, depending on the peptide concentration and effective temperature. The results indicate that over a broad range of volume fractions (0.05-25%) the characteristic structural lengthscales fall in the range 12-45 nm. On this basis, we suggest that self-assembled structures act as either nucleation points or scaffolds for the deposition of 10-100 nm silica-peptide building blocks from which diatom skeletons and synthetic nanospheres are constructed.