Diverse Roles of Nucleotides in Tuning Metal-Ion-Stabilized Intermediates of Amino Acid Aggregate via Phosphate Multiplicity and Salt-Triggered Fusion.

Supramolecular assemblies regulated by small biomolecules, such as nucleotides, provide key insights into biological organization, particularly in protein aggregation, which is linked to neurodegenerative diseases. While the role of nucleotides as a stabilizer and biological hydrotrope is well-established, their interaction with biological assembly is inherently paradoxical. Furthermore, the interaction of nucleotides with the transient intermediates of self-assembly of proteins and peptides remains largely unexplored. Here, l-phenylalanine (Phe) is employed as a minimal model to investigate nucleotide-mediated regulation in both native and metal-stabilized assemblies. In native Phe assemblies, ATP and ADP exhibit a concentration-dependent disruption of fibrillar morphology, whereas AMP offers a minimal influence. In contrast, within cation-mediated metastable assemblies, nucleotides actively redirect the assembly pathways. Phosphate multiplicity dictates structural outcomes: ATP and ADP stabilize compact spherical-like architectures, while AMP promotes fibrillar aggregates. Mechanistic analysis, supported by imaging techniques and zeta potential, reveals synergistic contributions from multivalent phosphate interaction and nucleoside-mediated interactions.