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Cao C, Magalhães P, Krapp LF, Bada Juarez JF, Mayer SF, Rukes V, Chiki A, Lashuel HA, Dal Peraro M. Deep Learning-Assisted Single-Molecule Detection of Protein Post-translational Modifications with a Biological Nanopore. ACS NANO 2024; 18:1504-1515. [PMID: 38112538 PMCID: PMC10795472 DOI: 10.1021/acsnano.3c08623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
Protein post-translational modifications (PTMs) play a crucial role in countless biological processes, profoundly modulating protein properties on both spatial and temporal scales. Protein PTMs have also emerged as reliable biomarkers for several diseases. However, only a handful of techniques are available to accurately measure their levels, capture their complexity at a single molecule level, and characterize their multifaceted roles in health and disease. Nanopore sensing provides high sensitivity for the detection of low-abundance proteins, holding the potential to impact single-molecule proteomics and PTM detection, in particular. Here, we demonstrate the ability of a biological nanopore, the pore-forming toxin aerolysin, to detect and distinguish α-synuclein-derived peptides bearing single or multiple PTMs, namely, phosphorylation, nitration, and oxidation occurring at different positions and in various combinations. The characteristic current signatures of the α-synuclein peptide and its PTM variants could be confidently identified by using a deep learning model for signal processing. We further demonstrate that this framework can quantify α-synuclein peptides at picomolar concentrations and detect the C-terminal peptides generated by digestion of full-length α-synuclein. Collectively, our work highlights the advantage of using nanopores as a tool for simultaneous detection of multiple PTMs and facilitates their use in biomarker discovery and diagnostics.
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Affiliation(s)
- Chan Cao
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
- Department
of Inorganic and Analytical Chemistry, Chemistry and Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Pedro Magalhães
- Laboratory
of Molecular and Chemical Biology of Neurodegeneration, Brain Mind
Institute, School of Life Sciences, Ecole
Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Lucien F. Krapp
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Juan F. Bada Juarez
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Simon Finn Mayer
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Verena Rukes
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Anass Chiki
- Laboratory
of Molecular and Chemical Biology of Neurodegeneration, Brain Mind
Institute, School of Life Sciences, Ecole
Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Hilal A. Lashuel
- Laboratory
of Molecular and Chemical Biology of Neurodegeneration, Brain Mind
Institute, School of Life Sciences, Ecole
Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Matteo Dal Peraro
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
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2
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Chen C, Song M, Li K, Yan S, Chen M, Geng J. E. coli outer membrane protein T (OmpT) nanopore for peptide sensing. Biochem Biophys Res Commun 2023; 677:132-140. [PMID: 37586211 DOI: 10.1016/j.bbrc.2023.05.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 08/18/2023]
Abstract
Peptide detection methods with facility and high sensitivity are essential for diagnosing disease associated with peptide biomarkers. Nanopore sensing technology had emerged as a low cost, high-throughput, and scalable tool for peptide detection. The omptins family proteins which can form β-barrel pores have great potentials to be developed as nanopore biosensor. However, there are no study about the channel properties of E. coli OmpT and the development of OmpT as a nanopore biosensor. In this study, the OmpT biological nanopore channel was constructed with a conductance of 1.49 nS in 500 mM NaCl buffer and a three-step gating phenomenon under negative voltage higher than 100 mV and then was developed as a peptide biosensor which can detect peptide without the interfere of ssDNA and dNTPs. The OmpT constructed in this study has potential application in peptide detection, and also provides a new idea for the detection of peptides using the specific binding ability of protease.
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Affiliation(s)
- Chuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China; School of Pharmacy, North Sichuan Medical College, Nanchong, 637000, China
| | - Mengxiao Song
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Shixin Yan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Mutian Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China; Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 641400, China.
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3
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Zhang L, Burns N, Ji Z, Sun S, Deutscher SL, Carson WE, Guo P. Nipple fluid for breast cancer diagnosis using the nanopore of Phi29 DNA-packaging motor. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2023; 48:102642. [PMID: 36581256 PMCID: PMC10035634 DOI: 10.1016/j.nano.2022.102642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/14/2022] [Accepted: 12/02/2022] [Indexed: 12/27/2022]
Abstract
Detection of cancer in its early stage is a challenging task for oncologists. Inflammatory breast cancer has symptoms that are similar to mastitis and can be mistaken for microbial infection. Currently, the differential diagnosis between mastitis and Inflammatory breast cancer via nipple aspirate fluid (NAF) is difficult. Here, we report a label-free and amplification-free detection platform using an engineered nanopore of the phi29 DNA-packaging motor with biomarker Galectin3 (GAL3), Thomsen-Friedenreich (TF) binding peptide as the probe fused at its C-terminus. The binding of the biomarker in NAF samples from breast cancer patients to the probe results in the connector's conformational change with a current blockage of 32 %. Utilization of dwell time, blockage ratio, and peak signature enable us to detect basal levels of biomarkers from patient NAF samples at the single-molecule level. This platform will allow for breast cancers to be resolved at an early stage with accuracy and thoroughness.
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Affiliation(s)
- Long Zhang
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Zhouxiang Ji
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Steven Sun
- OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Susan L Deutscher
- Department of Biochemistry, University of Missouri, Harry S. Truman Memorial VA Hospital, Columbia, MO 65211, USA.
| | - William E Carson
- OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
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4
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Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions. Comput Struct Biotechnol J 2022; 20:6120-6137. [PMID: 36420155 PMCID: PMC9672130 DOI: 10.1016/j.csbj.2022.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022] Open
Abstract
The International Society of RNA Nanotechnology and Nanomedicine (ISRNN) serves to further the development of a wide variety of functional nucleic acids and other related nanotechnology platforms. To aid in the dissemination of the most recent advancements, a biennial discussion focused on biomotors, viral assembly, and RNA nanobiotechnology has been established where international experts in interdisciplinary fields such as structural biology, biophysical chemistry, nanotechnology, cell and cancer biology, and pharmacology share their latest accomplishments and future perspectives. The results summarized here highlight advancements in our understanding of viral biology and the structure-function relationship of frame-shifting elements in genomic viral RNA, improvements in the predictions of SHAPE analysis of 3D RNA structures, and the understanding of dynamic RNA structures through a variety of experimental and computational means. Additionally, recent advances in the drug delivery, vaccine design, nanopore technologies, biomotor and biomachine development, DNA packaging, RNA nanotechnology, and drug delivery are included in this critical review. We emphasize some of the novel accomplishments, major discussion topics, and present current challenges and perspectives of these emerging fields.
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Liu Y, Zhang S, Wang Y, Wang L, Cao Z, Sun W, Fan P, Zhang P, Chen HY, Huang S. Nanopore Identification of Alditol Epimers and Their Application in Rapid Analysis of Alditol-Containing Drinks and Healthcare Products. J Am Chem Soc 2022; 144:13717-13728. [PMID: 35867993 DOI: 10.1021/jacs.2c04595] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alditols, which have a sweet taste but produce much lower calories than natural sugars, are widely used as artificial sweeteners. Alditols are the reduced forms of monosaccharide aldoses, and different alditols are diastereomers or epimers of each other and direct and rapid identification by conventional methods is difficult. Nanopores, which are emerging single-molecule sensors with exceptional resolution when engineered appropriately, are useful for the recognition of diastereomers and epimers. In this work, direct distinguishing of alditols corresponding to all 15 monosaccharide aldoses was achieved by a boronic acid-appended hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore (MspA-PBA). Thirteen alditols including glycerol, erythritol, threitol, adonitol, arabitol, xylitol, mannitol, sorbitol, allitol, dulcitol, iditol, talitol, and gulitol (l-sorbitol) could be fully distinguished, and their sensing features constitute a complete nanopore alditol database. To automate event classification, a custom machine-learning algorithm was developed and delivered a 99.9% validation accuracy. This strategy was also used to identify alditol components in commercially available "zero-sugar" drinks and healthcare products, suggesting their use in rapid and sensitive quality control for the food and medical industry.
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Affiliation(s)
- Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zhenyuan Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Wen Sun
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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6
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Zhang M, Chen C, Zhang Y, Geng J. Biological nanopores for sensing applications. Proteins 2022; 90:1786-1799. [PMID: 35092317 DOI: 10.1002/prot.26308] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/27/2021] [Accepted: 01/27/2022] [Indexed: 02/05/2023]
Abstract
Biological nanopores are proteins with transmembrane pore that can be embedded in lipid bilayer. With the development of single-channel current measurement technologies, biological nanopores have been reconstituted into planar lipid bilayer and used for single-molecule sensing of various analytes and events such as single-molecule DNA sensing and sequencing. To improve the sensitivity for specific analytes, various engineered nanopore proteins and strategies are deployed. Here, we introduce the origin and principle of nanopore sensing technology as well as the structure and associated properties of frequently used protein nanopores. Furthermore, sensing strategies for different applications are reviewed, with focus on the alteration of buffer condition, protein engineering, and deployment of accessory proteins and adapter-assisted sensing. Finally, outlooks for de novo design of nanopore and nanopore beyond sensing are discussed.
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Affiliation(s)
- Ming Zhang
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Chen Chen
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Yanjing Zhang
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Jia Geng
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
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7
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Zhang L, Burns N, Jordan M, Jayasinghe L, Guo P. Macromolecule sensing and tumor biomarker detection by harnessing terminal size and hydrophobicity of viral DNA packaging motor channels into membranes and flow cells. Biomater Sci 2021; 10:167-177. [PMID: 34812812 DOI: 10.1039/d1bm01264a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Biological nanopores for single-pore sensing have the advantage of size homogeneity, structural reproducibility, and channel amenability. In order to translate this to clinical applications, the functional biological nanopore must be inserted into a stable system for high-throughput analysis. Here we report factors that control the rate of pore insertion into polymer membrane and analyte translocation through the channel of viral DNA packaging motors of Phi29, T3 and T7. The hydrophobicity of aminol or carboxyl terminals and their relation to the analyte translocation were investigated. It was found that both the size and the hydrophobicity of the pore terminus are critical factors for direct membrane insertion. An N-terminus or C-terminus hydrophobic mutation is crucial for governing insertion orientation and subsequent macromolecule translocation due to the one-way traffic property. The N- or C-modification led to two different modes of application. The C-terminal insertion permits translocation of analytes such as peptides to enter the channel through the N terminus, while N-terminus insertion prevents translocation but offers the measurement of gating as a sensing parameter, thus generating a tool for detection of markers. A urokinase-type Plasminogen Activator Receptor (uPAR) binding peptide was fused into the C-terminal of Phi29 nanopore to serve as a probe for uPAR protein detection. The uPAR has proven to be a predictive biomarker in several types of cancer, including breast cancer. With an N-terminal insertion, the binding of the uPAR antigen to individual peptide probe induced discretive steps of current reduction due to the induction of channel gating. The distinctive current signatures enabled us to distinguish uPAR positive and negative tumor cell lines. This finding provides a theoretical basis for a robust biological nanopore sensing system for high-throughput macromolecular sensing and tumor biomarker detection.
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Affiliation(s)
- Long Zhang
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute; James Comprehensive Cancer Center; College of Medicine; The Ohio State University, Columbus, OH 43210, USA.
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute; James Comprehensive Cancer Center; College of Medicine; The Ohio State University, Columbus, OH 43210, USA.
| | - Michael Jordan
- Oxford Nanopore Technologies Ltd, Gosling Building, Edmund Halley Road, Oxford Science Park, Oxford, OX4 4DQ, UK
| | - Lakmal Jayasinghe
- Oxford Nanopore Technologies Ltd, Gosling Building, Edmund Halley Road, Oxford Science Park, Oxford, OX4 4DQ, UK
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute; James Comprehensive Cancer Center; College of Medicine; The Ohio State University, Columbus, OH 43210, USA.
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8
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Motone K, Cardozo N, Nivala J. Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis. iScience 2021; 24:103032. [PMID: 34527891 PMCID: PMC8433247 DOI: 10.1016/j.isci.2021.103032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Proteins carry out life's essential functions. Comprehensive proteome analysis technologies are thus required for a full understanding of the operating principles of biological systems. While current proteomics techniques suffer from limitations in sensitivity and/or throughput, nanopore technology has the potential to enable de novo protein identification through single-molecule sequencing. However, a significant barrier to achieving this goal is controlling protein/peptide translocation through the nanopore sensor for processive strand analysis. Here, we review recent approaches that use a range of techniques, from oligonucleotide conjugation to molecular motors, aimed at driving protein strands and peptides through protein nanopores. We further discuss site-specific protein conjugation chemistry that could be combined with these translocation approaches as future directions to achieve single-molecule protein detection and sequencing of native proteins.
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Affiliation(s)
- Keisuke Motone
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Nicolas Cardozo
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Jeff Nivala
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
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