Amphiphilic peptide binding on crystalline vs. amorphous silica from molecular dynamics simulations

• Published in: Molecular physics 2019-12, Vol.117 (23-24), p.3642-3650
• Main Authors: Sampath, Janani, Pfaendtner, Jim
• Format: Article
• Language: English
• Subjects: amphiphilic peptide; Binding; Cluster analysis; Crystal structure; Crystallinity; INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Leucine; Lysine; metadynamics; metal oxide surface; Molecular dynamics; Peptides; Silicon dioxide
• ISSN: 0026-8976; 1362-3028
• DOI: 10.1080/00268976.2019.1657192

The leucine-lysine amphiphilic peptide LKα14 has been used to study fundamental driving forces in processes such as peptide-surface binding and biomineralization. Here, we employ molecular dynamics (MD) simulations in tandem with replica exchange metadynamics to probe the binding mechanism and thermodynamics of LKα14 on silica. We also investigate the effect that the nature of the silica surface - crystalline vs. amorphous, has on the binding properties and peptide-surface conformations. We find that water adsorbs differently on both surfaces; it forms a denser interfacial layer on the crystalline surface, compared to the amorphous surface. This causes the peptide to bind more strongly on the amorphous surface than the crystalline surface. Cluster analysis shows that the peptide adopts a helical conformation at both surfaces, with a greater distribution of states on the crystalline surface. Peptide binding is primarily through lysine interactions, in line with prior experimental results.