Exploring Serine-lysine Peptide Aggregation in Water and Interaction with Inorganic Surfaces Using Molecular Dynamics

Abstract

This project is a combined experimental and computational study of peptide aggregation mechanism and biomineralization phenomena among serine-lysine (S-K) peptides, a series of small artificial peptides composed of serine and lysine residues solely with varied sequences. Inspired by the richness of both lysine and serine amino acids in biomineralization activities, four different S-K peptides were designed to examine their specific qualities for aggregation in water as well as roles in titania (TiO2) or silica (SiO2) precipitation. To mimic the experimental counterparts, TiO2 and SiO2 under neutral condition are chosen as the inorganic surface models here. Considering the time limitation and possible driving force, we applied our new enhanced sampling method (PBmetaD-PF) with identical components to provide new molecular-level insight into the aggregation process and structures. In second part, we did reweighting and clustering analysis to find out dominant states and structures for each system, and investigated their interaction with inorganic surfaces after testing their stability respectively. Different binding forces between the two metal oxide surfaces were studied and discussed in detail.