Sequencing of α-Synuclein Intrinsically Disordered Protein in MoS ₂ Nanopores

α-synuclein is an intrinsically disordered protein composed of 140 amino acids that adopts multiple conformations and is prone to aggregate into β-sheet-rich structures, which are hallmarks of Parkinson’s disease. Moreover, missense mutations in α-synuclein are related to familial forms of this neurodegenerative disorder, making their detection at the single-molecule level essential. Recently, protein sequencing using solid-state nanopores has emerged as a powerful, label-free approach for single-molecule sensing with high sensitivity. Atomically thin two-dimensional materials, such as MoS2, provide ideal platforms for sequencing applications due to their ultimate thinness and enhanced spatial resolution. However, protein sequencing using 2D materials remains challenging because of rapid translocation speeds, which limit the observation time per molecule. Here, we present the sequencing of a full-length protein through a 2D solid-state nanopore. We performed extensive all-atom classical molecular dynamics simulations in explicit solvent of the complete translocation of the wild-type α-synuclein protein and two pathogenic mutants, i.e. A30P and E46K, through single-layer MoS2 nanopores. From the simulated ionic current traces, we identified distinct blockade levels and transient fluctuations and characterized their depth and duration along the protein sequence across multiple temporal and sequence-length scales. These blockades span approximately 40% of the total sequence of α-synuclein protein, preventing full amino acid resolution. Nonetheless, short sequence motifs comprising 1–3 residues still yield distinctive current signatures. Furthermore, we analyzed the volume properties of amino acids inside the pore and identified characteristic blockade fingerprints differentiating the wild-type from the mutant proteins. These pioneering results pave the way for future experimental studies, offering a roadmap for validating 2D nanopore-based protein sequencing and biomarker detection with single-molecule resolution.