Regensburg 2025 – scientific programme

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BP: Fachverband Biologische Physik

BP 32: Computational Biophysics II

BP 32.3: Talk

Friday, March 21, 2025, 10:00–10:15, H46

Graphite-based Bio-mimetic Nanopores for Protein Sequencing and Beyond — •Chandan K. Das and Maria Fyta — Computational Biotechnology, RWTH Aachen University, Aachen, Germany

Protein sequencing via nanopores offers a transformative approach to bioanalytics, but challenges remain, particularly in linearizing unfolded proteins and controlling translocation speed through solid-state nanopores. This study introduces a novel solution: biomimetic graphite-based nanopores designed with nanometer-sized pores featuring a constriction zone inspired by the alpha-hemolysin protein pore. All-atom molecular dynamics simulations demonstrate the nanopores’ ability to achieve ion selectivity and generate electro-osmotic flow (EOF) within the pore lumen due to tailored surface charges. This innovation enables the detection of peptides at the single amino acid level by analyzing ionic current fluctuations during peptide translocation. A critical feature of this design is its capacity to balance hydrodynamic drag, induced by EOF, with electrophoretic force (EPF), facilitating peptide linearization and extending amino acid residence time within the constriction zone. These advancements significantly enhance sequencing resolution and accuracy. Beyond protein sequencing, this technology holds potential for diverse applications, including seawater desalination via electrodialysis and renewable energy generation through salinity gradient-driven ion separation. By providing a robust computational foundation, this study advances the development of graphite-based biomimetic nanopores, offering versatile solutions for bio/nanotechnological challenges and sustainable energy innovations.

Keywords: Nanopore; Protein Sequencing; Post Translational Modification; Electrodialysis; Molecular Dynamics Simulation