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Distinguishing between Similar Miniproteins with Single-Molecule Nanopore Sensing: A Computational Study
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.ORCID iD: 0000-0003-0707-1832
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.ORCID iD: 0000-0001-7328-0400
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestra├če 85, 22607 Hamburg, Germany.ORCID iD: 0000-0003-2638-1940
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.ORCID iD: 0000-0001-5397-7753
2022 (English)In: ACS Nanoscience Au, E-ISSN 2694-2496, Vol. 2, no 2, p. 119-127Article in journal (Refereed) Published
Abstract [en]

A nanopore is a tool in single-molecule sensing biotechnology that offers label-free identification with high throughput. Nanopores have been successfully applied to sequence DNA and show potential in the study of proteins. Nevertheless, the task remains challenging due to the large variability in size, charges, and folds of proteins. Miniproteins have a small number of residues, limited secondary structure, and stable tertiary structure, which can offer a systematic way to reduce complexity. In this computational work, we theoretically evaluated sensing two miniproteins found in the human body using a silicon nitride nanopore. We employed molecular dynamics methods to compute occupied-pore ionic current magnitudes and electronic structure calculations to obtain interaction strengths between pore wall and miniprotein. From the interaction strength, we derived dwell times using a mix of combinatorics and numerical solutions. This latter approach circumvents typical computational demands needed to simulate translocation events using molecular dynamics. We focused on two miniproteins potentially difficult to distinguish owing to their isotropic geometry, similar number of residues, and overall comparable structure. We found that the occupied-pore current magnitudes not to vary significantly, but their dwell times differ by 1 order of magnitude. Together, these results suggest a successful identification protocol for similar miniproteins.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2022. Vol. 2, no 2, p. 119-127
National Category
Condensed Matter Physics
Identifiers
URN: urn:nbn:se:uu:diva-495139DOI: 10.1021/acsnanoscienceau.1c00022ISI: 001027123700001PubMedID: 37101662OAI: oai:DiVA.org:uu-495139DiVA, id: diva2:1730465
Funder
Swedish Research Council, 2017-04627Swedish Research Council, 2018-00740Swedish Research Council, 2019-03935Available from: 2023-01-24 Created: 2023-01-24 Last updated: 2023-10-09Bibliographically approved

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Cardoch, SebastianTimneanu, NicusorCaleman, CarlScheicher, Ralph H.

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