Beyond the Static Caliper: Dynamical Translocases and the Mathematical Imperative for Single-Molecule Proteomics

Abstract

The advent of single-molecule nanopore sequencing established a powerful platform for modern genomics by using static biological pores to report the translocation of canonical nucleic acids, enabling rapid, accessible nucleic acid analysis. However, extending this strategy to single-molecule proteomics has stalled against a fundamental biophysical bottleneck. Current efforts in nanopore proteomics attempt to retrofit these static, spatial "caliper" biological nanopores (e.g., -hemolysin, MspA, CsgG, aerolysin) for protein sequencing despite the immense steric, charge, and conformational heterogeneity of proteins. Unlike the chemically uniform, polyanionic phosphodiester backbone of DNA, the proteome contains isosteric and isobaric variants that confound purely volumetric measurements made by static pores. To address this bottleneck, we propose the application of dynamical translocases - naturally evolved, protein-handling nanomachines (e.g., the anthrax toxin protective antigen). Unlike static pores that rely on passive diffusion, dynamical translocases employ target-docking clamp architectures that achieve low nanomolar sensitivity. Active-site conformational dynamics generate high-dimensional kinetic fingerprints that enable molecular discrimination during translocation. By coupling dynamical translocases with Physics-Informed Machine Learning (PIML), we demonstrate that amino-acid side-chain-dependent thermodynamic friction can be mathematically decoded, enabling >90% accurate classification of chemically distinct amino acid classes and doing so label-free without the artificial DNA-handles required by legacy platforms.