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CPP: Fachverband Chemische Physik und Polymerphysik

CPP 21: French-German Session: Simulation Methods and Modeling of Soft Matter III

CPP 21.6: Talk

Tuesday, March 10, 2026, 11:00–11:15, ZEU/0255

Insights into phenylalanine self-assembly and its modulation by nucleotides from molecular dynamics simulations. — •Mattia Borriello — Ruhr-Universität Bochum

Phenylalanine (Phe) can aggregate in water into various fibrillar structures, which is relevant to diseases like phenylketonuria. The precise molecular structure of these aggregates is still unknown, and although they dissolve in the presence of nucleotides such as ATP, the mechanism behind this disassembly remains unclear. We use molecular dynamics simulations to gain new insights on Phe cluster structure, understand which interactions drive this process and how nucleotides can modulate it.

Parallel tempering simulations of Phe in water in zwitterionic form have been performed varying concentration and temperature. Analysis of the trajectories revealed a strong tendency to aggregate in two ordered structures. One is characterized by a tubular shape, while the other by an alternating motif. Cluster stabilization is mainly electrostatic for smaller aggregates, while apolar interactions become significant as the size of the clusters grows.

The same computational approach has been extended to systems containing Phe and NaCl or different nucleotides, such as ATP, ADP and AMP. While NaCl showed a limited influence on aggregation, nucleotides can inhibit cluster formation and disrupt pre-existing aggregates. Our findings provide molecular-level insight into both the structural organization of Phe assemblies and into the mechanisms through which nucleotides modulate their stability.

Keywords: Phenylalanine; Nucleotides; Molecular Dynamics; amyloid; self-assembly