Metal-Ion-Modulated Stabilization of Intermediates in Diphenylalanine and Phenylalanine Self-Assembly: Roles of Metal-Ion-Specific Salt Bridges and Hydrophobic Interactions

The self-assembly of aromatic amino acids and short peptides into fibrillar structures involves transient intermediates whose roles remain poorly understood, despite their potential involvement in cytotoxicity and disease progression. Here, we investigate the self-assembly of diphenylalanine (FF) and phenylalanine (Phe) in the presence of biologically relevant divalent metal ions: Ca 2+, Mg 2+, and Zn 2+ . These ions significantly influence the assembly pathways by stabilizing distinct intermediate structures and delaying fibril formation, particularly at higher ion concentrations. Notably, FF assemblies form long-lived microspherical structures in the presence of Ca 2+ and Mg 2+ without transitioning into fibrils. Molecular dynamics simulations provide a mechanistic interpretation of the experimental observations, from compact aggregates to multicluster states. Ca 2+ stabilizes FF cluster intermediates through salt-bridge interactions, Mg 2+ drives aggregation via hydration-mediated effects, and Zn 2+ acts through a combination of hydrophobic and salt-bridge interactions. These findings reveal the role of metal ions in the phenylalanine-rich dipeptide assembly and their potential as biomimetic materials.