1
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Zhu L, Wu H, Xu Z, Guo L, Zhao J. Analysis of the effect of cations on protein conformational stability using solid-state nanopores. Analyst 2024; 149:3186-3194. [PMID: 38639484 DOI: 10.1039/d4an00248b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The conformation of proteins is closely related to their biological functions, and it is affected by many factors, including the type of cations in solution. However, it is difficult to detect the conformational changes of a protein in situ. As a single-molecule sensing technology, nanopores can convert molecular structural information into analyzable current signals within a reasonable time range. Herein, we detect and analyze the effects of two different types of monovalent cations (Na+ and Li+) on a model protein bovine serum albumin (BSA) conformation using SiNx nanopores with different diameters. The quantitative analysis results show that the excluded volume of BSA in LiCl salt solutions is larger than the value in NaCl solution, indicating that Li+ is more prone to unfolding the proteins and making them unstable. This study demonstrated that nanopores enable the in situ detection of the structure of proteins at the single-molecule level and provide a new approach for the quantitative analysis of proteins.
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Affiliation(s)
- Libo Zhu
- School of Medical Imaging, Wannan Medical College, Wuhu, 241002, China.
| | - Hongwen Wu
- Jiangxi Institute of Respiratory Disease, the First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Zhengyuan Xu
- School of Medical Imaging, Wannan Medical College, Wuhu, 241002, China.
| | - Lanying Guo
- School of Medical Imaging, Wannan Medical College, Wuhu, 241002, China.
| | - Jinsong Zhao
- School of Medical Imaging, Wannan Medical College, Wuhu, 241002, China.
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2
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Meyer N, Torrent J, Balme S. Characterizing Prion-Like Protein Aggregation: Emerging Nanopore-Based Approaches. SMALL METHODS 2024:e2400058. [PMID: 38644684 DOI: 10.1002/smtd.202400058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/10/2024] [Indexed: 04/23/2024]
Abstract
Prion-like protein aggregation is characteristic of numerous neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases. This process involves the formation of aggregates ranging from small and potentially neurotoxic oligomers to highly structured self-propagating amyloid fibrils. Various approaches are used to study protein aggregation, but they do not always provide continuous information on the polymorphic, transient, and heterogeneous species formed. This review provides an updated state-of-the-art approach to the detection and characterization of a wide range of protein aggregates using nanopore technology. For each type of nanopore, biological, solid-state polymer, and nanopipette, discuss the main achievements for the detection of protein aggregates as well as the significant contributions to the understanding of protein aggregation and diagnostics.
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Affiliation(s)
- Nathan Meyer
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, Cedex 5, Montpellier, 34095, France
- INM, University of Montpellier, INSERM, Montpellier, 34095, France
| | - Joan Torrent
- INM, University of Montpellier, INSERM, Montpellier, 34095, France
| | - Sébastien Balme
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, Cedex 5, Montpellier, 34095, France
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3
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Gonzalez Solveyra E, Perez Sirkin YA, Tagliazucchi M, Szleifer I. Orientational Pathways during Protein Translocation through Polymer-Modified Nanopores. ACS NANO 2024; 18:10427-10438. [PMID: 38556978 DOI: 10.1021/acsnano.3c11318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein translocation through nanopores holds significant promise for applications in biotechnology, biomolecular analysis, and medicine. However, the interpretation of signals generated by the translocation of the protein remains challenging. In this way, it is crucial to gain a comprehensive understanding on how macromolecules translocate through a nanopore and to identify what are the critical parameters that govern the process. In this study, we investigate the interplay between protein charge regulation, orientation, and nanopore surface modifications using a theoretical framework that allows us to explicitly take into account the acid-base reactions of the titrable amino acids in the proteins and in the polyelectrolytes grafted to the nanopore surface. Our goal is to thoroughly characterize the translocation process of different proteins (GFP, β-lactoglobulin, lysozyme, and RNase) through nanopores modified with weak polyacids. Our calculations show that the charge regulation mechanism exerts a profound effect on the translocation process. The pH-dependent interactions between proteins and charged polymers within the nanopore lead to diverse free energy landscapes with barriers, wells, and flat regions dictating translocation efficiency. Comparison of different proteins allows us to identify the significance of protein isoelectric point, size, and morphology in the translocation behavior. Taking advantage of these insights, we propose pH-responsive nanopores that can load proteins at one pH and release them at another, offering opportunities for controlled protein delivery, separation, and sensing applications.
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Affiliation(s)
- Estefania Gonzalez Solveyra
- Instituto de Nanosistemas, Universidad Nacional de San Martín-CONICET, San Martín, Buenos Aires B1650, Argentina
| | - Yamila A Perez Sirkin
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica Analítica y Química Física y CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE). Pabellón 2, Ciudad Universitaria, C1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - Mario Tagliazucchi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica Analítica y Química Física y CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE). Pabellón 2, Ciudad Universitaria, C1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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4
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Salehirozveh M, Kure Larsen AK, Stojmenovic M, Thei F, Dong M. In-situ PLL-g-PEG Functionalized Nanopore for Enhancing Protein Characterization. Chem Asian J 2023; 18:e202300515. [PMID: 37497831 DOI: 10.1002/asia.202300515] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/03/2023] [Indexed: 07/28/2023]
Abstract
Single-molecule nanopore detection technology has revolutionized proteomics research by enabling highly sensitive and label-free detection of individual proteins. Herein, we designed a small, portable, and leak-free flowcell made of PMMA for nanopore experiments. In addition, we developed an in situ functionalizing PLL-g-PEG approach to produce non-sticky nanopores for measuring the volume of diseases-relevant biomarker, such as the Alpha-1 antitrypsin (AAT) protein. The in situ functionalization method allows continuous monitoring, ensuring adequate functionalization, which can be directly used for translocation experiments. The functionalized nanopores exhibit improved characteristics, including an increased nanopore lifetime and enhanced translocation events of the AAT proteins. Furthermore, we demonstrated the reduction in the translocation event's dwell time, along with an increase in current blockade amplitudes and translocation numbers under different voltage stimuli. The study also successfully measures the single AAT protein volume (253 nm3 ), which closely aligns with the previously reported hydrodynamic volume. The real-time in situ PLL-g-PEG functionalizing method and the developed nanopore flowcell hold great promise for various nanopores applications involving non-sticky single-molecule characterization.
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Affiliation(s)
- Mostafa Salehirozveh
- Department Of Physics And Astronomy, University of Bologna, Bologna, Italy
- Elements srl, Cesena, Italy
| | - Anne-Kathrine Kure Larsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Sino-Danish Center for Education and Research, Aarhus, Denmark
- University of the Chinese Academy of Sciences, Beijing, China
| | | | | | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Biology - Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
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5
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Meyer N, Bentin J, Janot JM, Abrao-Nemeir I, Charles-Achille S, Pratlong M, Aquilina A, Trinquet E, Perrier V, Picaud F, Torrent J, Balme S. Ultrasensitive Detection of Aβ42 Seeds in Cerebrospinal Fluid with a Nanopipette-Based Real-Time Fast Amyloid Seeding and Translocation Assay. Anal Chem 2023; 95:12623-12630. [PMID: 37587130 DOI: 10.1021/acs.analchem.3c00017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
In this work, early-stage Aβ42 aggregates were detected using a real-time fast amyloid seeding and translocation (RT-FAST) assay. Specifically, Aβ42 monomers were incubated in buffer solution with and without preformed Aβ42 seeds in a quartz nanopipette coated with L-DOPA. Then, formed Aβ42 aggregates were analyzed on flyby resistive pulse sensing at various incubation time points. Aβ42 aggregates were detected only in the sample with Aβ42 seeds after 180 min of incubation, giving an on/off readout of the presence of preformed seeds. Moreover, this RT-FAST assay could detect preformed seeds spiked in 4% cerebrospinal fluid/buffer solution. However, in this condition, the time to detect the first aggregates was increased. Analysis of Cy3-labeled Aβ42 monomer adsorption on a quartz substrate after L-DOPA coating by confocal fluorescence spectroscopy and molecular dynamics simulation showed the huge influence of Aβ42 adsorption on the aggregation process.
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Affiliation(s)
- Nathan Meyer
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
- INM UM, CNRS, INSERM, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Jeremy Bentin
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon, France
| | - Jean-Marc Janot
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Imad Abrao-Nemeir
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Saly Charles-Achille
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Maud Pratlong
- PerkinElmer, Parc Marcel Boiteux, 30200 Codolet, France
| | | | - Eric Trinquet
- PerkinElmer, Parc Marcel Boiteux, 30200 Codolet, France
| | - Veronique Perrier
- INM UM, CNRS, INSERM, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Fabien Picaud
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon, France
| | - Joan Torrent
- INM UM, CNRS, INSERM, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Sebastien Balme
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
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6
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Roelen Z, Briggs K, Tabard-Cossa V. Analysis of Nanopore Data: Classification Strategies for an Unbiased Curation of Single-Molecule Events from DNA Nanostructures. ACS Sens 2023; 8:2809-2823. [PMID: 37436112 PMCID: PMC10913896 DOI: 10.1021/acssensors.3c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Nanopores are versatile single-molecule sensors that are being used to sense increasingly complex mixtures of structured molecules with applications in molecular data storage and disease biomarker detection. However, increased molecular complexity presents additional challenges to the analysis of nanopore data, including more translocation events being rejected for not matching an expected signal structure and a greater risk of selection bias entering this event curation process. To highlight these challenges, here, we present the analysis of a model molecular system consisting of a nanostructured DNA molecule attached to a linear DNA carrier. We make use of recent advances in the event segmentation capabilities of Nanolyzer, a graphical analysis tool provided for nanopore event fitting, and describe approaches to the event substructure analysis. In the process, we identify and discuss important sources of selection bias that emerge in the analysis of this molecular system and consider the complicating effects of molecular conformation and variable experimental conditions (e.g., pore diameter). We then present additional refinements to existing analysis techniques, allowing for improved separation of multiplexed samples, fewer translocation events rejected as false negatives, and a wider range of experimental conditions for which accurate molecular information can be extracted. Increasing the coverage of analyzed events within nanopore data is not only important for characterizing complex molecular samples with high fidelity but is also becoming essential to the generation of accurate, unbiased training data as machine-learning approaches to data analysis and event identification continue to increase in prevalence.
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Affiliation(s)
- Zachary Roelen
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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7
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Wei W, Chen X, Wang X. Nanopore Sensing Technique for Studying the Hofmeister Effect. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200921. [PMID: 35484475 DOI: 10.1002/smll.202200921] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/22/2022] [Indexed: 06/14/2023]
Abstract
The nanopore sensing technique is an emerging method of detecting single molecules, and extensive research has gone into various fields, including nanopore sequencing and other applications of single-molecule studies. Recently, several researchers have explored the specific ion effects in nanopore channels, enabling a unique understanding of the Hofmeister effect at the single-molecule level. Herein, the recent advances of using nanopore sensing techniques are reviewed to study the Hofmeister effect and the physicochemical mechanism of this process is attempted. The challenges and goals are also discussed for the future in this field.
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Affiliation(s)
- Weichen Wei
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Xiaojuan Chen
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Xuejiao Wang
- Fujian Provincial University Engineering Research Center of Industrial Biocatalysis, College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, China
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8
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Abrao-Nemeir I, Zaki O, Meyer N, Lepoitevin M, Torrent J, Janot JM, Balme S. Combining ionic diode, resistive pulse and membrane for detection and separation of anti-CD44 antibody. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2022.120391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Robertson JWF, Reiner JE. Highlights on the current state of proteomic detection and characterization with nanopore sensors. Proteomics 2022; 22:e2100061. [PMID: 35289091 DOI: 10.1002/pmic.202100061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Joseph W F Robertson
- Biophysical and Biomedical Research Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia, USA
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10
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Bandara YMNDY, Farajpour N, Freedman KJ. Nanopore Current Enhancements Lack Protein Charge Dependence and Elucidate Maximum Unfolding at Protein's Isoelectric Point. J Am Chem Soc 2022; 144:3063-3073. [PMID: 35143193 DOI: 10.1021/jacs.1c11540] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein sequencing, as well as protein fingerprinting, has gained tremendous attention in the electrical sensing realm of solid-state nanopores and is challenging due to fast translocations and the use of high molar electrolytes. Despite providing an appreciable signal-to-noise ratio, high electrolyte concentrations can have adverse effects on the native protein structure. Herein, we present a thorough investigation of low electrolyte sensing conditions across a broad pH and voltage range generating conductive pulses (CPs) irrespective of protein net charge. We used Cas9 as the model protein and demonstrated that unfolding is noncooperative, represented by the gradual elongation or stretching of the protein, and sensitive to both the applied voltage and pH (i.e., charge state). The magnitude of unfolding and the isoelectric point (pI) of Cas9 was found to be correlated and a critical factor in our experiments. Electroosmotic flow (EOF) was always aligned with the transit direction, whereas electrophoretic force (EPF) was either reinforcing (pH < pI) or opposing (pH > pI) the protein's movement, which led to slower translocations at higher pH values. Further exploration of higher pH values led to slowing down of protein with > 30% of the population being slower than 0.5 ms. Our results would be critical for protein sensing at very low electrolytes and to retard their translocation speed without resorting to high-bandwidth equipment.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Bioengineering, University of California, Riverside, 900 University Ave., Riverside, California 92521, United States
| | - Nasim Farajpour
- Department of Bioengineering, University of California, Riverside, 900 University Ave., Riverside, California 92521, United States
| | - Kevin J Freedman
- Department of Bioengineering, University of California, Riverside, 900 University Ave., Riverside, California 92521, United States
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11
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King S, Briggs K, Slinger R, Tabard-Cossa V. Screening for Group A Streptococcal Disease via Solid-State Nanopore Detection of PCR Amplicons. ACS Sens 2022; 7:207-214. [PMID: 34995448 DOI: 10.1021/acssensors.1c01972] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-molecule detection methods are becoming increasingly important for diagnostic applications. Practical early detection of disease requires sensitivity down to the level of single copies of the targeted biomarkers. Of the candidate technologies that can address this need, solid-state nanopores show great promise as digital sensors for single-molecule detection. Here, we present work detailing the use of solid-state nanopores as downstream sensors for a polymerase chain reaction (PCR)-based assay targeting group A streptococcus (strep A), which can be readily extended to detect any pathogen that can be identified with a short nucleic acid sequence. We demonstrate that with some simple modifications to the standard PCR reaction mixture, nanopores can be used to reliably identify strep A in clinical samples. We also discuss methodological best practices for both adapting PCR-based assays to solid-state nanopore readout and analytical approaches by which to decide on sample status.
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Affiliation(s)
- Simon King
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Robert Slinger
- Division of Microbiology and Infectious Disease, Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario K1H 8L1, Canada
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