Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterise an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into -sheet-like stacks with strongly favorable monomer association free energies of .

Aggregation at high-pH produces disordered aggregates destabilised by Coulombic repulsion between negatively charged Asp termini (). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markov process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly.