Energy Barriers of Peptide Translocation in Nanopores: Insights from MD Simulations

Solid-state nanopores offer label-free protein sensing potential, but rational design is hindered by limited quantitative understanding of pore geometry's impact on translocation energetics. To address this, the influence of Si₃N₄ nanopore thickness and radius on a model peptide's translocation free energy landscape was systematically examined via all-atom molecular dynamics simulations and potential of mean force calculations. Close matching between pore thickness and the peptide's maximum extended length was found to induce significant conformational entropy loss and desolvation energy barriers, yielding a peak free energy barrier. During peptide translocation, a critical pore radius was identified, at which an anomalous surge in the energy barrier was observed. This "critical matching effect" forces the peptide into a highly ordered, stretched conformation, triggering substantial entropy penalties, hydration shell stripping, and moderate electrostatic interactions, thereby forming a distinct "most unfavorable conformation window". The free energy barrier height is determined by the tripartite coupling of conformational freedom, solvent accessibility, and charge interactions. Consequently, a "geometry-conformation matching" nanopore design paradigm is proposed, enabling targeted free energy barrier enhancement through precise dimensional matching for intelligent protein sieving and signal modulation. This mechanism establishes a universal theoretical foundation for optimizing next-generation nanopore sensors and biomolecular separation membranes while pioneering new pathways for manipulating biomolecular transport in nanoconfined spaces, with significant implications for precision diagnostics and targeted drug delivery.