Peptide Aggregation in Solution and Interaction with Inorganic Surfaces: A Metadynamics Investigation

Silaffin peptides that regulate the process of biomineralization in organisms like diatoms are interesting as their ability to generate intricate mineral morphologies at ambient conditions could be harnessed to produce precise materials from non-biological molecules. A phenomenon central to this process is peptide aggregation – prior studies show that different aggregates are associated with different mineral morphologies. We employ all-atom molecular dynamics (MD) simulations to study the aggregation of R5 peptide, a 19 amino acid residue of silaffin that precipitates silica in vitro. In order to access relevant time scales, we enhance our sampling by using a recent variation of the metadynamics approach, metadynamic metainference, which guides average simulation behavior towards experimental structures obtained from NMR. Another relevant aspect of biomineralization is the interaction of peptides with mineral surfaces and the effect that amino acid modification has on peptide-surface binding. By implementing MD simulations enhanced by parallel-bias metadynamics, we generate complex free energy landscapes, which helps elucidate peptide-mineral structure-property relationships.