1
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Mayse L, Wang Y, Ahmad M, Movileanu L. Real-Time Measurement of a Weak Interaction of a Transcription Factor Motif with a Protein Hub at Single-Molecule Precision. ACS NANO 2024; 18:20468-20481. [PMID: 39049818 PMCID: PMC11308778 DOI: 10.1021/acsnano.4c04857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
Transcription factors often interact with other protein cofactors, regulating gene expression. Direct detection of these brief events using existing technologies remains challenging due to their transient nature. In addition, intrinsically disordered domains, intranuclear location, and lack of cofactor-dependent active sites of transcription factors further complicate the quantitative analysis of these critical processes. Here, we create a genetically encoded label-free sensor to identify the interaction between a motif of the MYC transcription factor, a primary cancer driver, and WDR5, a chromatin-associated protein hub. Using an engineered nanopore equipped with this motif, WDR5 is probed through reversible captures and releases in a one-by-one and time-resolved fashion. Our single-molecule kinetic measurements indicate a weak-affinity interaction arising from a relatively slow complex association and a fast dissociation of WDR5 from the tethered motif. Further, we validate this subtle interaction by determinations in an ensemble using single nanodisc-wrapped nanopores immobilized on a biolayer interferometry sensor. This study also provides the proof-of-concept for a sensor that reveals unique recognition signatures of different protein binding sites. Our foundational work may be further developed to produce sensing elements for analytical proteomics and cancer nanomedicine.
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Affiliation(s)
- Lauren
A. Mayse
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
| | - Yazheng Wang
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
| | - Mohammad Ahmad
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
| | - Liviu Movileanu
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, 114 Life Sciences Complex, Syracuse, New York 13244, United States
- The
BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States
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2
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Ratinho L, Bacri L, Thiebot B, Cressiot B, Pelta J. Identification and Detection of a Peptide Biomarker and Its Enantiomer by Nanopore. ACS CENTRAL SCIENCE 2024; 10:1167-1178. [PMID: 38947203 PMCID: PMC11212137 DOI: 10.1021/acscentsci.4c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 07/02/2024]
Abstract
Until now, no fast, low-cost, and direct technique exists to identify and detect protein/peptide enantiomers, because their mass and charge are identical. They are essential since l- and d-protein enantiomers have different biological activities due to their unique conformations. Enantiomers have potential for diagnostic purposes for several diseases or normal bodily functions but have yet to be utilized. This work uses an aerolysin nanopore and electrical detection to identify vasopressin enantiomers, l-AVP and d-AVP, associated with different biological processes and pathologies. We show their identification according to their conformations, in either native or reducing conditions, using their specific electrical signature. To improve their identification, we used a principal component analysis approach to define the most relevant electrical parameters for their identification. Finally, we used the Monte Carlo prediction to assign each event type to a specific l- or d-AVP enantiomer.
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Affiliation(s)
- Laura Ratinho
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 95000, Cergy, France
| | - Laurent Bacri
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025, Evry-Courcouronnes, France
| | - Bénédicte Thiebot
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 95000, Cergy, France
| | - Benjamin Cressiot
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 95000, Cergy, France
| | - Juan Pelta
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025, Evry-Courcouronnes, France
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3
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Yang J, Pan T, Xie Z, Yuan W, Ho HP. In-tube micro-pyramidal silicon nanopore for inertial-kinetic sensing of single molecules. Nat Commun 2024; 15:5132. [PMID: 38879544 PMCID: PMC11180207 DOI: 10.1038/s41467-024-48630-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 05/06/2024] [Indexed: 06/19/2024] Open
Abstract
Electrokinetic force has been the major choice for driving the translocation of molecules through a nanopore. However, the use of this approach is limited by an uncontrollable translocation speed, resulting in non-uniform conductance signals with low conformational sensitivity, which hinders the accurate discrimination of the molecules. Here, we show the use of inertial-kinetic translocation induced by spinning an in-tube micro-pyramidal silicon nanopore fabricated using photovoltaic electrochemical etch-stop technique for biomolecular sensing. By adjusting the kinetic properties of a funnel-shaped centrifugal force field while maintaining a counter-balanced state of electrophoretic and electroosmotic effect in the nanopore, we achieved regulated translocation of proteins and obtained stable signals of long and adjustable dwell times and high conformational sensitivity. Moreover, we demonstrated instantaneous sensing and discrimination of molecular conformations and longitudinal monitoring of molecular reactions and conformation changes by wirelessly measuring characteristic features in current blockade readouts using the in-tube nanopore device.
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Affiliation(s)
- Jianxin Yang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tianle Pan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhenming Xie
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wu Yuan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China.
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4
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Jia W, Ouyang Y, Zhang S, Zhang P, Huang S. Nanopore Identification of L-, D-Lactic Acids, D-Glucose and Gluconic Acid in the Serum of Human and Animals. SMALL METHODS 2024:e2400664. [PMID: 38864527 DOI: 10.1002/smtd.202400664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/30/2024] [Indexed: 06/13/2024]
Abstract
DL-Lactic acid and D-glucose are important human health indicators. Their aberrant levels in body fluids may indicate a variety of human pathological conditions, suggesting an urgent need of daily monitoring. However, simultaneous and rapid analysis of DL-lactic acid and D-glucose using a sole but simple sensing system has never been reported. Here, an engineered Mycobacterium smegmatis porin A (MspA) nanopore is used to simultaneously identify DL-lactic acid and D-glucose. Highly distinguishable nanopore event features are reported. Assisted with a custom machine learning algorithm, direct identification of DL-lactic acid and D-glucose is performed with human serum, demonstrating its sensing reliability against complex and heterogeneous samples. This sensing strategy is further applied in the analysis of different animal serum samples, according to which gluconic acid is further identified. The serum samples from different animals report distinguishable levels of DL-lactic acid, D-glucose and gluconic acid, suggesting its potential applications in agricultural science and breeding industry. This sensing strategy is generally direct, rapid, economic and requires only ≈µL of input serum, suitable for point of care testing (POCT) applications.
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Affiliation(s)
- Wendong Jia
- 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
| | - Yusheng Ouyang
- 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
| | - Panke Zhang
- 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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5
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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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6
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Thyashan N, Ghimire ML, Lee S, Kim MJ. Exploring single-molecule interactions: heparin and FGF-1 proteins through solid-state nanopores. NANOSCALE 2024; 16:8352-8360. [PMID: 38563277 DOI: 10.1039/d4nr00274a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Detection and characterization of protein-protein interactions are essential for many cellular processes, such as cell growth, tissue repair, drug delivery, and other physiological functions. In our research, we have utilized emerging solid-state nanopore sensing technology, which is highly sensitive to better understand heparin and fibroblast growth factor 1 (FGF-1) protein interactions at a single-molecule level without any modifications. Understanding the structure and behavior of heparin-FGF-1 complexes at the single-molecule level is very important. An abnormality in their formation can lead to life-threatening conditions like tumor growth, fibrosis, and neurological disorders. Using a controlled dielectric breakdown pore fabrication approach, we have characterized individual heparin and FGF-1 (one of the 22 known FGFs in humans) proteins through the fabrication of 17 ± 1 nm nanopores. Compared to heparin, the positively charged heparin-binding domains of some FGF-1 proteins translocationally react with the pore walls, giving rise to a distinguishable second peak with higher current blockade. Additionally, we have confirmed that the dynamic FGF-1 is stabilized upon binding with heparin-FGF-1 at the single-molecule level. The larger current blockades from the complexes relative to individual heparin and the FGF-1 recorded during the translocation ensure the binding of heparin-FGF-1 proteins, forming binding complexes with higher excluded volumes. Taken together, we demonstrate that solid-state nanopores can be employed to investigate the properties of individual proteins and their complex interactions, potentially paving the way for innovative medical therapies and advancements.
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Affiliation(s)
- Navod Thyashan
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, 75205, USA.
| | - Madhav L Ghimire
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, 75205, USA.
| | - Sangyoup Lee
- Bionic Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul, Republic of Korea.
| | - Min Jun Kim
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, 75205, USA.
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7
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Yao G, Ke W, Xia B, Gao Z. Nanopore-based glycan sequencing: state of the art and future prospects. Chem Sci 2024; 15:6229-6243. [PMID: 38699252 PMCID: PMC11062086 DOI: 10.1039/d4sc01466a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Sequencing of biomacromolecules is a crucial cornerstone in life sciences. Glycans, one of the fundamental biomolecules, derive their physiological and pathological functions from their structures. Glycan sequencing faces challenges due to its structural complexity and current detection technology limitations. As a highly sensitive sensor, nanopores can directly convert nucleic acid sequence information into electrical signals, spearheading the revolution of third-generation nucleic acid sequencing technologies. However, their potential for deciphering complex glycans remains untapped. Initial attempts demonstrated the significant sensitivity of nanopores in glycan sensing, which provided the theoretical basis and insights for the realization of nanopore-based glycan sequencing. Here, we present three potential technical routes to employ nanopore technology in glycan sequencing for the first time. The three novel technical routes include: strand sequencing, capturing glycan chains as they translocate through nanopores; sequential hydrolysis sequencing, capturing released monosaccharides one by one; splicing sequencing, mapping signals from hydrolyzed glycan fragments to an oligosaccharide database/library. Designing suitable nanopores, enzymes, and motors, and extracting characteristic signals pose major challenges, potentially aided by artificial intelligence. It would be highly desirable to design an all-in-one high-throughput glycan sequencer instrument by integrating a sample processing unit, nanopore array, and signal acquisition system into a microfluidic device. The nanopore sequencer invention calls for intensive multidisciplinary cooperation including electrochemistry, glycochemistry, engineering, materials, enzymology, etc. Advancing glycan sequencing will promote the development of basic research and facilitate the discovery of glycan-based drugs and disease markers, fostering progress in glycoscience and even life sciences.
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Affiliation(s)
- Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- School of Life Science and Technology, Shanghai Tech University 201210 Shanghai China
- Lingang Laboratory 200031 Shanghai China
| | - Wenjun Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 528400 Zhongshan China
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8
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Zhao C, Wang Y, Chen C, Zhu Y, Miao Z, Mou X, Yuan W, Zhang Z, Li K, Chen M, Liang W, Zhang M, Miao W, Dong Y, Deng D, Wu J, Ke B, Bao R, Geng J. Direct and Continuous Monitoring of Multicomponent Antibiotic Gentamicin in Blood at Single-Molecule Resolution. ACS NANO 2024; 18:9137-9149. [PMID: 38470845 DOI: 10.1021/acsnano.4c00302] [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: 03/14/2024]
Abstract
Point-of-care monitoring of small molecules in biofluids is crucial for clinical diagnosis and treatment. However, the inherent low degree of recognition of small molecules and the complex composition of biofluids present significant obstacles for current detection technologies. Although nanopore sensing excels in the analysis of small molecules, the direct detection of small molecules in complex biofluids remains a challenge. In this study, we present a method for sensing the small molecule drug gentamicin in whole blood based on the mechanosensitive channel of small conductance in Pseudomonas aeruginosa (PaMscS) nanopore. PaMscS can directly detect gentamicin and distinguish its main components with only a monomethyl difference. The 'molecular sieve' structure of PaMscS enables the direct measurement of gentamicin in human whole blood within 10 min. Furthermore, a continuous monitoring device constructed based on PaMscS achieved continuous monitoring of gentamicin in live rats for approximately 2.5 h without blood consumption, while the drug components can be analyzed in situ. This approach enables rapid and convenient drug monitoring with single-molecule level resolution, which can significantly lower the threshold for drug concentration monitoring and promote more efficient drug use. Moreover, this work also lays the foundation for the future development of continuous monitoring technology with single-molecule level resolution in the living body.
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Affiliation(s)
- Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Yu Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Chen Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Yibo Zhu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zhuang Miao
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xingyu Mou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Weidan Yuan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhihao Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Mutian Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Weibo Liang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wenqian Miao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuhan Dong
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Dong Deng
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, 610041 China
| | - Jianping Wu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Bowen Ke
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Rui Bao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
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9
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Dorey A, Howorka S. Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics. Nat Chem 2024; 16:314-334. [PMID: 38448507 DOI: 10.1038/s41557-023-01322-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 07/14/2023] [Indexed: 03/08/2024]
Abstract
Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost and portability. This label-free method for sequencing at the single-molecule level is an achievement on its own. However, nanopores also show promise for the technologically even more challenging sequencing of polypeptides, something that could considerably benefit biological discovery, clinical diagnostics and homeland security, as current techniques lack portability and speed. Here we survey the biochemical innovations underpinning commercial and academic nanopore DNA/RNA sequencing techniques, and explore how these advances can fuel developments in future protein sequencing with nanopores.
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Affiliation(s)
- Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
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10
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Rockett T, Almahyawi M, Ghimire ML, Jonnalagadda A, Tagliaferro V, Seashols-Williams SJ, Bertino MF, Caputo GA, Reiner JE. Cluster-Enhanced Nanopore Sensing of Ovarian Cancer Marker Peptides in Urine. ACS Sens 2024; 9:860-869. [PMID: 38286995 PMCID: PMC10897939 DOI: 10.1021/acssensors.3c02207] [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] [Received: 10/19/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024]
Abstract
The development of novel methodologies that can detect biomarkers from cancer or other diseases is both a challenge and a need for clinical applications. This partly motivates efforts related to nanopore-based peptide sensing. Recent work has focused on the use of gold nanoparticles for selective detection of cysteine-containing peptides. Specifically, tiopronin-capped gold nanoparticles, trapped in the cis-side of a wild-type α-hemolysin nanopore, provide a suitable anchor for the attachment of cysteine-containing peptides. It was recently shown that the attachment of these peptides onto a nanoparticle yields unique current signatures that can be used to identify the peptide. In this article, we apply this technique to the detection of ovarian cancer marker peptides ranging in length from 8 to 23 amino acid residues. It is found that sequence variability complicates the detection of low-molecular-weight peptides (<10 amino acid residues), but higher-molecular-weight peptides yield complex, high-frequency current fluctuations. These fluctuations are characterized with chi-squared and autocorrelation analyses that yield significantly improved selectivity when compared to traditional open-pore analysis. We demonstrate that the technique is capable of detecting the only two cysteine-containing peptides from LRG-1, an emerging protein biomarker, that are uniquely present in the urine of ovarian cancer patients. We further demonstrate the detection of one of these LRG-1 peptides spiked into a sample of human female urine.
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Affiliation(s)
- Thomas
W. Rockett
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Mohammed Almahyawi
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- King
Fahd Medical Research Center, King Abdulaziz
University, Jeddah 21589, Saudi Arabia
| | - Madhav L. Ghimire
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Aashna Jonnalagadda
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Victoria Tagliaferro
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Sarah J. Seashols-Williams
- Department
of Forensic Sciences, Virginia Commonwealth
University, Richmond, Virginia 23284, United States
| | - Massimo F. Bertino
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Gregory A. Caputo
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Joseph E. Reiner
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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11
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Zhang S, Cao Z, Fan P, Sun W, Xiao Y, Zhang P, Wang Y, Huang S. Discrimination of Disaccharide Isomers of Different Glycosidic Linkages Using a Modified MspA Nanopore. Angew Chem Int Ed Engl 2024; 63:e202316766. [PMID: 38116834 DOI: 10.1002/anie.202316766] [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] [Received: 11/05/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
Disaccharides are composed of two monosaccharide subunits joined by a glycosidic linkage in an α or β configuration. Different combinations of isomeric monosaccharide subunits and different glycosidic linkages result in different isomeric disaccharide products. Thus, direct discrimination of these disaccharide isomers from a mixture is extremely difficult. In this paper, a hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore conjugated with a phenylboronic acid (PBA) adapter was applied for disaccharide sensing, with which three most widely known disaccharides in nature, including sucrose, lactose and maltose, were clearly discriminated. Besides, all six isomeric α-D-glucopyranosyl-D-fructoses, differing only in their glycosidic linkages, were also well resolved. Assisted by a custom machine learning algorithm, a 0.99 discrimination accuracy is achieved. Nanopore discrimination of disaccharide isomers with different glycosidic linkages, which has never been previously demonstrated, is inspiring for nanopore saccharide sequencing. This sensing capacity was also applied in direct identification of isomaltulose additives in a commercial sucrose-free yogurt, from which isomaltulose, lactose and L-lactic acid were simultaneously detected.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - 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
| | - Yunqi Xiao
- 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
| | - Yuqin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
- Institute for the Environment and Health, Nanjing University Suzhou Campus, Suzhou, 215163, 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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12
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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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13
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Greive SJ, Bacri L, Cressiot B, Pelta J. Identification of Conformational Variants for Bradykinin Biomarker Peptides from a Biofluid Using a Nanopore and Machine Learning. ACS NANO 2024; 18:539-550. [PMID: 38134312 DOI: 10.1021/acsnano.3c08433] [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: 12/24/2023]
Abstract
There is a current need to develop methods for the sensitive detection of peptide biomarkers in complex mixtures of molecules, such as biofluids, to enable early disease detection. Moreover, to our knowledge, there is currently no detection method capable of identifying the different conformations of a peptide biomarker differing by a single amino acid. Single-molecule nanopore sensing promises to provide this level of resolution. In order to be able to identify these differences in a biofluid such as serum, it is necessary to carefully characterize electrical parameters to obtain specific signatures of each biomarker population observed. We are interested here in a family of peptide biomarkers, kinins such as bradykinin and des-Arg9 bradykinin, that are involved in many disabling pathologies (allergy, asthma, angioedema, sepsis, or cancer). We show the proof of concept for direct identification of these biomarkers in serum at the single-molecule level using a protein nanopore. Each peptide exhibits two unique electrical signatures attributed to specific conformations in bulk. The same signatures are found in serum, allowing their discrimination and identification in a complex mixture such as biofluid. To extend the utility of our experimental results, we developed a principal component analysis approach to define the most relevant electrical parameters for their identification. Finally, we used semisupervised classification to assign each event type to a specific biomarker at physiological serum concentration. In the future, single-molecule scale analysis of peptide biomarkers using a powerful nanopore coupled with machine learning will facilitate the identification and quantification of other clinically relevant biomarkers from biofluids.
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Affiliation(s)
| | - Laurent Bacri
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Benjamin Cressiot
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, F-95000 Cergy, France
| | - Juan Pelta
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, F-95000 Cergy, France
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14
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Stuber A, Schlotter T, Hengsteler J, Nakatsuka N. Solid-State Nanopores for Biomolecular Analysis and Detection. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:283-316. [PMID: 38273209 DOI: 10.1007/10_2023_240] [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: 01/27/2024]
Abstract
Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.
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Affiliation(s)
- Annina Stuber
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Tilman Schlotter
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Julian Hengsteler
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland.
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15
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Yu Q, Zhang L, Jiang M, Xiao L, Xiang Y, Wang R, Liu Z, Zhou R, Yang M, Li C, Liu M, Zhou X, Chen S. An NIR Fluorescence Turn-on and MRl Bimodal Probe for Concurrent Real-time in vivo Sensing and Labeling of β-Galactosidase. Angew Chem Int Ed Engl 2023; 62:e202313137. [PMID: 37766426 DOI: 10.1002/anie.202313137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023]
Abstract
To realize sensing and labeling biomarkers is quite challenging in terms of designing multimodal imaging probes. In this study, we developed a novel β-galactosidase (β-gal) activated bimodal imaging probe that combines near-infrared (NIR) fluorescence and magnetic resonance imaging (MRI) to enable real-time visualization of activity in living organisms. Upon β-gal activation, Gal-Cy-Gd-1 exhibits a remarkable 42-fold increase in NIR fluorescence intensity at 717 nm, allowing covalent labeling of adjacent target enzymes or proteins and avoiding molecular escape to promote probe accumulation at the tumor site. This fluorescence reaction enhances the longitudinal relaxivity by approximately 1.9 times, facilitating high-resolution MRI. The unique features of Gal-Cy-Gd-1 enable real-time and precise visualization of β-gal activity in live tumor cells and mice. The probe's utilization aids in identifying in situ ovarian tumors, offering valuable assistance in the precise removal of tumor tissue during surgical procedures in mice. The fusion of NIR fluorescence and MRI activation through self-immobilizing target enzymes or proteins provides a robust approach for visualizing β-gal activity. Moreover, this approach sets the groundwork for developing other activatable bimodal probes, allowing real-time in vivo imaging of enzyme activity and localization.
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Affiliation(s)
- Qiao Yu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, P. R. China
| | - Lei Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Mou Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, P. R. China
| | - Long Xiao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yunhui Xiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Ruifang Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhaoqing Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Rui Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Shizhen Chen
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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16
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Lucas FLR, Finol-Urdaneta RK, Van Thillo T, McArthur JR, van der Heide NJ, Maglia G, Dedecker P, Strauss O, Wloka C. Evidence of Cytolysin A nanopore incorporation in mammalian cells assessed by a graphical user interface. NANOSCALE 2023; 15:16914-16923. [PMID: 37853831 DOI: 10.1039/d3nr01977b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Technologies capable of assessing cellular metabolites with high precision and temporal resolution are currently limited. Recent developments in the field of nanopore sensors allow the non-stochastic quantification of metabolites, where a nanopore is acting as an electrical transducer for selective substrate binding proteins (SBPs). Here we show that incorporation of the pore-forming toxin Cytolysin A (ClyA) into the plasma membrane of Chinese hamster ovary cells (CHO-K1) results in the appearance of single-channel conductance amenable to multiplexed automated patch-clamp (APC) electrophysiology. In CHO-K1 cells, SBPs modify the ionic current flowing though ClyA nanopores, thus demonstrating its potential for metabolite sensing of living cells. Moreover, we developed a graphical user interface for the analysis of the complex signals resulting from multiplexed APC recordings. This system lays the foundation to bridge the gap between recent advances in the nanopore field (e.g., proteomic and transcriptomic) and potential cellular applications.
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Affiliation(s)
| | - Rocio K Finol-Urdaneta
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
- Electrophysiology Facility for Cell Phenotyping and Drug Discovery, Wollongong, NSW 2522, Australia
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Toon Van Thillo
- Lab for Nanobiology, Department of Chemistry, KU Leuven, Belgium.
| | - Jeffrey R McArthur
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, Groningen, The Netherlands
| | - Peter Dedecker
- Lab for Nanobiology, Department of Chemistry, KU Leuven, Belgium.
| | - Olaf Strauss
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, A Corporate Member of Freie Universität, Humboldt-University, The Berlin Institute of Health, Berlin, Germany.
| | - Carsten Wloka
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, A Corporate Member of Freie Universität, Humboldt-University, The Berlin Institute of Health, Berlin, Germany.
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17
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Straathof S, Di Muccio G, Yelleswarapu M, Alzate Banguero M, Wloka C, van der Heide NJ, Chinappi M, Maglia G. Protein Sizing with 15 nm Conical Biological Nanopore YaxAB. ACS NANO 2023; 17:13685-13699. [PMID: 37458334 PMCID: PMC10373527 DOI: 10.1021/acsnano.3c02847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Nanopores are promising single-molecule tools for the electrical identification and sequencing of biomolecules. However, the characterization of proteins, especially in real-time and in complex biological samples, is complicated by the sheer variety of sizes and shapes in the proteome. Here, we introduce a large biological nanopore, YaxAB for folded protein analysis. The 15 nm cis-opening and a 3.5 nm trans-constriction describe a conical shape that allows the characterization of a wide range of proteins. Molecular dynamics showed proteins are captured by the electroosmotic flow, and the overall resistance is largely dominated by the narrow trans constriction region of the nanopore. Conveniently, proteins in the 35-125 kDa range remain trapped within the conical lumen of the nanopore for a time that can be tuned by the external bias. Contrary to cylindrical nanopores, in YaxAB, the current blockade decreases with the size of the trapped protein, as smaller proteins penetrate deeper into the constriction region than larger proteins do. These characteristics are especially useful for characterizing large proteins, as shown for pentameric C-reactive protein (125 kDa), a widely used health indicator, which showed a signal that could be identified in the background of other serum proteins.
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Affiliation(s)
- Sabine Straathof
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Giovanni Di Muccio
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Maaruthy Yelleswarapu
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Melissa Alzate Banguero
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Carsten Wloka
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, A Corporate Member of Freie Universität, Humboldt-University, The Berlin Institute of Health, Berlin 10178, Germany
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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18
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Chingarande RG, Tian K, Kuang Y, Sarangee A, Hou C, Ma E, Ren J, Hawkins S, Kim J, Adelstein R, Chen S, Gillis KD, Gu LQ. Real-time label-free detection of dynamic aptamer-small molecule interactions using a nanopore nucleic acid conformational sensor. Proc Natl Acad Sci U S A 2023; 120:e2108118120. [PMID: 37276386 PMCID: PMC10268594 DOI: 10.1073/pnas.2108118120] [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: 05/18/2021] [Accepted: 04/14/2023] [Indexed: 06/07/2023] Open
Abstract
Nucleic acids can undergo conformational changes upon binding small molecules. These conformational changes can be exploited to develop new therapeutic strategies through control of gene expression or triggering of cellular responses and can also be used to develop sensors for small molecules such as neurotransmitters. Many analytical approaches can detect dynamic conformational change of nucleic acids, but they need labeling, are expensive, and have limited time resolution. The nanopore approach can provide a conformational snapshot for each nucleic acid molecule detected, but has not been reported to detect dynamic nucleic acid conformational change in response to small -molecule binding. Here we demonstrate a modular, label-free, nucleic acid-docked nanopore capable of revealing time-resolved, small molecule-induced, single nucleic acid molecule conformational transitions with millisecond resolution. By using the dopamine-, serotonin-, and theophylline-binding aptamers as testbeds, we found that these nucleic acids scaffolds can be noncovalently docked inside the MspA protein pore by a cluster of site-specific charged residues. This docking mechanism enables the ion current through the pore to characteristically vary as the aptamer undergoes conformational changes, resulting in a sequence of current fluctuations that report binding and release of single ligand molecules from the aptamer. This nanopore tool can quantify specific ligands such as neurotransmitters, elucidate nucleic acid-ligand interactions, and pinpoint the nucleic acid motifs for ligand binding, showing the potential for small molecule biosensing, drug discovery assayed via RNA and DNA conformational changes, and the design of artificial riboswitch effectors in synthetic biology.
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Affiliation(s)
- Rugare G. Chingarande
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Kai Tian
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Yu Kuang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Aby Sarangee
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Chengrui Hou
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Emily Ma
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Jarett Ren
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Sam Hawkins
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Joshua Kim
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Ray Adelstein
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Sally Chen
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Kevin D. Gillis
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Li-Qun Gu
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
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19
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Jeong KB, Ryu M, Kim JS, Kim M, Yoo J, Chung M, Oh S, Jo G, Lee SG, Kim HM, Lee MK, Chi SW. Single-molecule fingerprinting of protein-drug interaction using a funneled biological nanopore. Nat Commun 2023; 14:1461. [PMID: 37015934 PMCID: PMC10073129 DOI: 10.1038/s41467-023-37098-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/01/2023] [Indexed: 04/06/2023] Open
Abstract
In drug discovery, efficient screening of protein-drug interactions (PDIs) is hampered by the limitations of current biophysical approaches. Here, we develop a biological nanopore sensor for single-molecule detection of proteins and PDIs using the pore-forming toxin YaxAB. Using this YaxAB nanopore, we demonstrate label-free, single-molecule detection of interactions between the anticancer Bcl-xL protein and small-molecule drugs as well as the Bak-BH3 peptide. The long funnel-shaped structure and nanofluidic characteristics of the YaxAB nanopore enable the electro-osmotic trapping of diverse folded proteins and high-resolution monitoring of PDIs. Distinctive nanopore event distributions observed in the two-dimensional (ΔI/Io-versus-IN) plot illustrate the ability of the YaxAB nanopore to discriminate individual small-molecule drugs bound to Bcl-xL from non-binders. Taken together, our results present the YaxAB nanopore as a robust platform for label-free, ultrasensitive, single-molecule detection of PDIs, opening up a possibility for low-cost, highly efficient drug discovery against diverse drug targets.
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Affiliation(s)
- Ki-Baek Jeong
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Minju Ryu
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jin-Sik Kim
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Minsoo Kim
- Department of Physics, Sungkyunkwan University, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Jejoong Yoo
- Department of Physics, Sungkyunkwan University, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Minji Chung
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sohee Oh
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Gyunghee Jo
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Seong-Gyu Lee
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, Daejeon, 34141, Republic of Korea.
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi, 16419, Republic of Korea.
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20
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Kim D, Byun S, Pu Y, Huh H, Jung Y, Kim S, Lee KY. Design of a Current Sensing System with TIA Gain of 160 dBΩ and Input-Referred Noise of 1.8 pA rms for Biosensor. SENSORS (BASEL, SWITZERLAND) 2023; 23:3019. [PMID: 36991734 PMCID: PMC10051069 DOI: 10.3390/s23063019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
This paper proposes a high-gain low-noise current signal detection system for biosensors. When the biomaterial is attached to the biosensor, the current flowing through the bias voltage is changed so that the biomaterial can be sensed. A resistive feedback transimpedance amplifier (TIA) is used for the biosensor requiring a bias voltage. Current changes in the biosensor can be checked by plotting the current value of the biosensor in real time on the self-made graphical user interface (GUI). Even if the bias voltage changes, the input voltage of the analog to digital converter (ADC) does not change, so it is designed to plot the current of the biosensor accurately and stably. In particular, for multi-biosensors with an array structure, a method of automatically calibrating the current between biosensors by controlling the gate bias voltage of the biosensors is proposed. Input-referred noise is reduced using a high-gain TIA and chopper technique. The proposed circuit achieves 1.8 pArms input-referred noise with a gain of 160 dBΩ and is implemented in a TSMC 130 nm CMOS process. The chip area is 2.3 mm2, and the power consumption of the current sensing system is 12 mW.
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Affiliation(s)
- Donggyu Kim
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sungjun Byun
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Younggun Pu
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Hyungki Huh
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Yeonjae Jung
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Seokkee Kim
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Kang-Yoon Lee
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
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21
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Bošković F, Zhu J, Tivony R, Ohmann A, Chen K, Alawami MF, Đorđević M, Ermann N, Pereira-Dias J, Fairhead M, Howarth M, Baker S, Keyser UF. Simultaneous identification of viruses and viral variants with programmable DNA nanobait. NATURE NANOTECHNOLOGY 2023; 18:290-298. [PMID: 36646828 PMCID: PMC10020084 DOI: 10.1038/s41565-022-01287-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/07/2022] [Indexed: 05/31/2023]
Abstract
Respiratory infections are the major cause of death from infectious disease worldwide. Multiplexed diagnostic approaches are essential as many respiratory viruses have indistinguishable symptoms. We created self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target selection via toehold-mediated strand displacement and rapid readout via nanopore sensing. Here we show that this platform can concurrently identify several common respiratory viruses, detecting a panel of short targets of viral nucleic acids from multiple viruses. Our nanobait can be easily reprogrammed to discriminate viral variants with single-nucleotide resolution, as we demonstrated for several key SARS-CoV-2 variants. Last, we show that the nanobait discriminates between samples extracted from oropharyngeal swabs from negative- and positive-SARS-CoV-2 patients without preamplification. Our system allows for the multiplexed identification of native RNA molecules, providing a new scalable approach for the diagnostics of multiple respiratory viruses in a single assay.
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Affiliation(s)
- Filip Bošković
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Ran Tivony
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Milan Đorđević
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Niklas Ermann
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Joana Pereira-Dias
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | | | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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22
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Liang L, Qin F, Wang S, Wu J, Li R, Wang Z, Ren M, Liu D, Wang D, Astruc D. Overview of the materials design and sensing strategies of nanopore devices. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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23
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Ying YL, Hu ZL, Zhang S, Qing Y, Fragasso A, Maglia G, Meller A, Bayley H, Dekker C, Long YT. Nanopore-based technologies beyond DNA sequencing. NATURE NANOTECHNOLOGY 2022; 17:1136-1146. [PMID: 36163504 DOI: 10.1038/s41565-022-01193-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/02/2022] [Indexed: 06/16/2023]
Abstract
Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the portability, lower costs and long reads of these methods. Nanopore applications, however, extend far beyond nucleic acid sequencing. In this Review, we present an overview of the broad applications of nanopores in molecular sensing and sequencing, chemical catalysis and biophysical characterization. We highlight the prospects of applying nanopores for single-protein analysis and sequencing, single-molecule covalent chemistry, clinical sensing applications for single-molecule liquid biopsy, and the use of synthetic biomimetic nanopores as experimental models for natural systems. We suggest that nanopore technologies will continue to be explored to address a number of scientific challenges as control over pore design improves.
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Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Zheng-Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Shengli Zhang
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Yujia Qing
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Amit Meller
- Faculty of Biomedical Engineering, Technion-IIT, Haifa, Israel.
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China.
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24
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Huang G, Voorspoels A, Versloot RCA, van der Heide NJ, Carlon E, Willems K, Maglia G. PlyAB Nanopores Detect Single Amino Acid Differences in Folded Haemoglobin from Blood. Angew Chem Int Ed Engl 2022; 61:e202206227. [PMID: 35759385 PMCID: PMC9541544 DOI: 10.1002/anie.202206227] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Indexed: 01/04/2023]
Abstract
The real‐time identification of protein biomarkers is crucial for the development of point‐of‐care and portable devices. Here, we use a PlyAB biological nanopore to detect haemoglobin (Hb) variants. Adult haemoglobin (HbA) and sickle cell anaemia haemoglobin (HbS), which differ by just one amino acid, were distinguished in a mixture with more than 97 % accuracy based on individual blockades. Foetal Hb, which shows a larger sequence variation, was distinguished with near 100 % accuracy. Continuum and Brownian dynamics simulations revealed that Hb occupies two energy minima, one near the inner constriction and one at the trans entry of the nanopore. Thermal fluctuations, the charge of the protein, and the external bias influence the dynamics of Hb within the nanopore, which in turn generates the unique ionic current signal in the Hb variants. Finally, Hb was counted from blood samples, demonstrating that direct discrimination and quantification of Hb from blood using nanopores, is feasible.
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Affiliation(s)
- Gang Huang
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Aderik Voorspoels
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001, Leuven, Belgium
| | | | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Enrico Carlon
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001, Leuven, Belgium
| | | | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
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25
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Jeong KB, Kim JS, Dhanasekar NN, Lee MK, Chi SW. Application of nanopore sensors for biomolecular interactions and drug discovery. Chem Asian J 2022; 17:e202200679. [PMID: 35929410 DOI: 10.1002/asia.202200679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/04/2022] [Indexed: 11/07/2022]
Abstract
Biomolecular interactions, including protein-protein, protein-nucleic acid, and protein/nucleic acid-ligand interactions, play crucial roles in various cellular signaling and biological processes, and offer attractive therapeutic targets in numerous human diseases. Currently, drug discovery is limited by the low efficiency and high cost of conventional ensemble-averaging-based techniques for biomolecular interaction analysis and high-throughput drug screening. Nanopores are an emerging technology for single-molecule sensing of biomolecules. Owing to the robust advantages of single-molecule sensing, nanopore sensors have contributed tremendously to nucleic acid sequencing and disease diagnostics. In this minireview, we summarize the recent developments and outlooks in single-molecule sensing of various biomolecular interactions for drug discovery applications using biological and solid-state nanopore sensors.
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Affiliation(s)
- Ki-Baek Jeong
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
| | - Jin-Sik Kim
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
| | - Naresh Niranjan Dhanasekar
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 34113, Daejeon, Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 34113, Daejeon, Republic of Korea
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26
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Li W, Wang Y, Xiao Y, Li M, Liu Q, Liang L, Xie W, Wang D, Guan X, Wang L. Simultaneous Dual-Site Identification of 5 mC/8 oG in DNA Triplex Using a Nanopore Sensor. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32948-32959. [PMID: 35816657 DOI: 10.1021/acsami.2c08478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA triplex participates in delivering site-specific epigenetic modifications critical for the regulation of gene expression. Among these marks, 5mC with 8oG functions comprehensively on gene expression. Recently, few research studies have emphasized the necessity of incorporation detection of 5mC with 8oG using one DNA triplex at the same time. Herein, DNA triplex structure was designed and tailored for the site-specific identification of 5mC with 8oG by means of nanopore electroanalysis. The identification was associated with the distinguishable current modulation types caused by DNA unzipping through the nanopore in an electrical field. Results demonstrated that the epigenetic modification proximity to the latch zone or constriction area of the nanopore enables differentiation of modification series at single nucleotide resolution in one DNA triplex, at both physiological and mildly acidic environment. In addition, our nanopore method enables the kinetic and thermodynamic studies to calculate the free energy of modified DNA triplex with applied potentials. Gibbs' energy provided the direct evidence that the DNA triplex with these epigenetic modifications is more stable in acidic environment. Considering modified DNA functions significantly in gene expression, the presented method may provide future opportunities to understand incorporating epigenetic mechanisms of many dysregulated biological processes on the basis of accurate detection.
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Affiliation(s)
- Wei Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yicen Xiao
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Minghan Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Qianshan Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Liyuan Liang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wanyi Xie
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
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27
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Huang G, Voorspoels A, Versloot RCA, Van Der Heide NJ, Carlon E, Willems K, Maglia G. PlyAB Nanopores Detect Single Amino Acid Differences in Folded Haemoglobin from Blood. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Gang Huang
- University of Groningen: Rijksuniversiteit Groningen Chemical Biology NETHERLANDS
| | - Aderik Voorspoels
- KU Leuven: Katholieke Universiteit Leuven Soft Matter and Biophysics BELGIUM
| | | | | | - Enrico Carlon
- KU Leuven University: Katholieke Universiteit Leuven Soft Matter and Biophysics NETHERLANDS
| | - Kherim Willems
- Imec Integrated photonics for microscopy and biomedical imaging BELGIUM
| | - Giovanni Maglia
- Rijksuniversiteit Groningen Chemical Biology Nijenborgh 7 9747 AG Groningen NETHERLANDS
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28
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Mapping the conformational energy landscape of Abl kinase using ClyA nanopore tweezers. Nat Commun 2022; 13:3541. [PMID: 35725977 PMCID: PMC9209526 DOI: 10.1038/s41467-022-31215-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/07/2022] [Indexed: 02/06/2023] Open
Abstract
Protein kinases play central roles in cellular regulation by catalyzing the phosphorylation of target proteins. Kinases have inherent structural flexibility allowing them to switch between active and inactive states. Quantitative characterization of kinase conformational dynamics is challenging. Here, we use nanopore tweezers to assess the conformational dynamics of Abl kinase domain, which is shown to interconvert between two major conformational states where one conformation comprises three sub-states. Analysis of kinase-substrate and kinase-inhibitor interactions uncovers the functional roles of relevant states and enables the elucidation of the mechanism underlying the catalytic deficiency of an inactive Abl mutant G321V. Furthermore, we obtain the energy landscape of Abl kinase by quantifying the population and transition rates of the conformational states. These results extend the view on the dynamic nature of Abl kinase and suggest nanopore tweezers can be used as an efficient tool for other members of the human kinome. Quantitative characterization of kinase conformational dynamics remains challenging. Here, the authors show that protein nanopore tweezers allow analyzing the conformational energy landscape and ligand binding of the Abl kinase domain.
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29
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Versloot RA, Straathof SA, Stouwie G, Tadema MJ, Maglia G. β-Barrel Nanopores with an Acidic-Aromatic Sensing Region Identify Proteinogenic Peptides at Low pH. ACS NANO 2022; 16:7258-7268. [PMID: 35302739 PMCID: PMC9134492 DOI: 10.1021/acsnano.1c11455] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Biological nanopores are emerging as sensitive single-molecule sensors for proteins and peptides. The heterogeneous charge of a polypeptide chain, however, can complicate or prevent the capture and translocation of peptides and unfolded proteins across nanopores. Here, we show that two β-barrel nanopores, aerolysin and cytotoxin K, cannot efficiently detect proteinogenic peptides from a trypsinated protein under a wide range of conditions. However, the introduction of an acidic-aromatic sensing region in the β-barrel dramatically increased the dwell time and the discrimination of peptides in the nanopore at acidic pH. Surprisingly, despite the fact that the two β-barrel nanopores have a similar diameter and an acidic-aromatic construction, their capture mechanisms differ. The electro-osmotic flow played a dominant role for aerolysin, while the electrophoretic force dominated for cytotoxin K. Nonetheless, both β-barrel nanopores allowed the detection of mixtures of trypsinated peptides, with aerolysin nanopores showing a better resolution for larger peptides and cytotoxin K showing a better resolution for shorter peptides. Therefore, this work provides a generic strategy for modifying nanopores for peptide detection that will be most likely be applicable to other nanopore-forming toxins.
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Affiliation(s)
| | | | - Gemma Stouwie
- Groningen Biomolecular Sciences
and Biotechnology Institute, University
of Groningen, Groningen, Groningen 9747AG, Netherlands
| | - Matthijs Jonathan Tadema
- Groningen Biomolecular Sciences
and Biotechnology Institute, University
of Groningen, Groningen, Groningen 9747AG, Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences
and Biotechnology Institute, University
of Groningen, Groningen, Groningen 9747AG, Netherlands
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30
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Tanimoto IMF, Cressiot B, Greive SJ, Le Pioufle B, Bacri L, Pelta J. Focus on using nanopore technology for societal health, environmental, and energy challenges. NANO RESEARCH 2022; 15:9906-9920. [PMID: 35610982 PMCID: PMC9120803 DOI: 10.1007/s12274-022-4379-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/11/2022] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
With an increasing global population that is rapidly ageing, our society faces challenges that impact health, environment, and energy demand. With this ageing comes an accumulation of cellular changes that lead to the development of diseases and susceptibility to infections. This impacts not only the health system, but also the global economy. As the population increases, so does the demand for energy and the emission of pollutants, leading to a progressive degradation of our environment. This in turn impacts health through reduced access to arable land, clean water, and breathable air. New monitoring approaches to assist in environmental control and minimize the impact on health are urgently needed, leading to the development of new sensor technologies that are highly sensitive, rapid, and low-cost. Nanopore sensing is a new technology that helps to meet this purpose, with the potential to provide rapid point-of-care medical diagnosis, real-time on-site pollutant monitoring systems to manage environmental health, as well as integrated sensors to increase the efficiency and storage capacity of renewable energy sources. In this review we discuss how the powerful approach of nanopore based single-molecule, or particle, electrical promises to overcome existing and emerging societal challenges, providing new opportunities and tools for personalized medicine, localized environmental monitoring, and improved energy production and storage systems.
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Affiliation(s)
- Izadora Mayumi Fujinami Tanimoto
- LAMBE, CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
- LuMIn, CNRS, Institut d’Alembert, ENS Paris-Saclay, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | | | | | - Bruno Le Pioufle
- LuMIn, CNRS, Institut d’Alembert, ENS Paris-Saclay, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Laurent Bacri
- LAMBE, CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
| | - Juan Pelta
- LAMBE, CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
- LAMBE, CNRS, CY Cergy Paris Université, 95000 Cergy, France
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31
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Wu Y, Gooding JJ. The application of single molecule nanopore sensing for quantitative analysis. Chem Soc Rev 2022; 51:3862-3885. [PMID: 35506519 DOI: 10.1039/d1cs00988e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.
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Affiliation(s)
- Yanfang Wu
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - J Justin Gooding
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
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32
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Abstract
Evolution has found countless ways to transport material across cells and cellular compartments separated by membranes. Protein assemblies are the cornerstone for the formation of channels and pores that enable this regulated passage of molecules in and out of cells, contributing to maintaining most of the fundamental processes that sustain living organisms. As in several other occasions, we have borrowed from the natural properties of these biological systems to push technology forward and have been able to hijack these nano-scale proteinaceous pores to learn about the physical and chemical features of molecules passing through them. Today, a large repertoire of biological pores is exploited as molecular sensors for characterizing biomolecules that are relevant for the advancement of life sciences and application to medicine. Although the technology has quickly matured to enable nucleic acid sensing with transformative implications for genomics, biological pores stand as some of the most promising candidates to drive the next developments in single-molecule proteomics.
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Affiliation(s)
- Simon Finn Mayer
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Chan Cao
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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33
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Chang AS, Tahira A, Solangi ZA, Solangi AG, Ibupoto MH, Chang F, Medany SS, Nafady A, Kasry A, Willander M, Ibupoto ZH. Pd-Co3O4-based nanostructures for the development of enzyme-free glucose sensor. BULLETIN OF MATERIALS SCIENCE 2022; 45:62. [DOI: 10.1007/s12034-021-02642-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/23/2021] [Indexed: 07/11/2023]
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34
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Wu J, Liang L, Zhang M, Zhu R, Wang Z, Yin Y, Yin B, Weng T, Fang S, Xie W, Wang L, Wang D. Single-Molecule Identification of the Conformations of Human C-Reactive Protein and Its Aptamer Complex with Solid-State Nanopores. ACS APPLIED MATERIALS & INTERFACES 2022; 14:12077-12088. [PMID: 35234028 DOI: 10.1021/acsami.2c00453] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Human C-reactive protein (CRP) is an established inflammatory biomarker and was proved to be potentially relevant to disease pathology and cancer progression. A large body of methodologies have been reported for CRP analysis, including electrochemical/optical biosensors, aptamer, or antibody-based detection. Although the detection limit is rather low until pg/uL, most of which are time-consuming and relatively expensive, and few of them provided CRP single-molecule information. This work demonstrated the nanopore-based approach for the characterization of CRP conformation under versatile conditions. With an optimized pore of 14 nm in diameter, we achieved the detection limit as low as 0.3 ng/μL, voltage polarity significantly influences the electro-osmotic force and CRP translocation behavior, and the pentameric conformation of CRP may dissociate into pro-inflammatory CRP isoforms and monomeric CRP at bias potential above 300 mV. CRP tends to translocate through nanopores faster along with the increase in pH values, due to more surface charge on both CRP and pore inner wall and stronger electro-osmotic force. The CRP could specifically bind with its aptamer of different concentrations to form complexes, and the complexes exhibited distinguishable nanopore translocation behavior compared with CRP alone. The variation of the molar ratio of aptamer significantly influences the orientation of CRP translocation. The plasma test under physiological conditions displayed the ability of the nanopore system on the CRP identification with a concentration of 3 ng/μL.
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Affiliation(s)
- Ji Wu
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Mingkun Zhang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Rui Zhu
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Zhong Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Yajie Yin
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Bohua Yin
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Ting Weng
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Shaoxi Fang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Liang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
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35
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Mayse LA, Imran A, Larimi MG, Cosgrove MS, Wolfe AJ, Movileanu L. Disentangling the recognition complexity of a protein hub using a nanopore. Nat Commun 2022; 13:978. [PMID: 35190547 PMCID: PMC8861093 DOI: 10.1038/s41467-022-28465-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
WD40 repeat proteins are frequently involved in processing cell signaling and scaffolding large multi-subunit machineries. Despite their significance in physiological and disease-like conditions, their reversible interactions with other proteins remain modestly examined. Here, we show the development and validation of a protein nanopore for the detection and quantification of WD40 repeat protein 5 (WDR5), a chromatin-associated hub involved in epigenetic regulation of histone methylation. Our nanopore sensor is equipped with a 14-residue Win motif of mixed lineage leukemia 4 methyltransferase (MLL4Win), a WDR5 ligand. Our approach reveals a broad dynamic range of MLL4Win-WDR5 interactions and three distant subpopulations of binding events, representing three modes of protein recognition. The three binding events are confirmed as specific interactions using a weakly binding WDR5 derivative and various environmental contexts. These outcomes demonstrate the substantial sensitivity of our nanopore sensor, which can be utilized in protein analytics. Nanopores are powerful tools for sampling protein-peptide interactions. Here, the authors convert a protein-based nanopore into a sensitive biosensor to characterize the complex binding of WDR5 protein to a 14-residue ligand.
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36
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Song Y, He T, Zhang Y, Yin C, Chen Y, Liu Q, Zhang Y, Chen S. Cobalt single atom sites in carbon aerogels for ultrasensitive enzyme-free electrochemical detection of glucose. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116024] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Galenkamp NS, Maglia G. Single-Molecule Sampling of Dihydrofolate Reductase Shows Kinetic Pauses and an Endosteric Effect Linked to Catalysis. ACS Catal 2022; 12:1228-1236. [PMID: 35096468 PMCID: PMC8787752 DOI: 10.1021/acscatal.1c04388] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/13/2021] [Indexed: 12/21/2022]
Abstract
![]()
The ability to sample multiple reactions
on the same single enzyme
is important to link rare intermediates with catalysis and to unravel
the role of conformational changes. Despite decades of efforts, however,
the single-molecule characterization of nonfluorogenic enzymes during
multiple catalytic turnovers has been elusive. Here, we show that
nanopore currents allow sampling the dynamic exchange between five
structural intermediates during E. coli dihydrofolate reductase (DHFR) catalysis. We found that an endosteric
effect promotes the binding of the substrate to the enzyme with a
specific hierarchy. The chemical step then switched the enzyme from
the closed to the occluded conformation, which in turn promotes the
release of the reduced cofactor NADP+. Unexpectedly, only
a few reactive complexes lead to catalysis. Furthermore, second-long
catalytic pauses were observed, possibly reflecting an off-path conformation
generated during the reaction. Finally, the free energy from multiple
cofactor binding events were required to release the product and switch
DHFR back to the reactive conformer. This catalytic fueled concerted
mechanism is likely to have evolved to improve the catalytic efficiency
of DHFR under the high concentrations of NADP+ in E. coli and might be a general feature for complex
enzymatic reactions where the binding and release of the products
must be tightly controlled.
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Affiliation(s)
- Nicole Stéphanie Galenkamp
- Groningen Biomolecular Sciences and Biotechnology (GBB) Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology (GBB) Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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38
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Liu Y, Wang K, Wang Y, Wang L, Yan S, Du X, Zhang P, Chen HY, Huang S. Machine Learning Assisted Simultaneous Structural Profiling of Differently Charged Proteins in a Mycobacterium smegmatis Porin A (MspA) Electroosmotic Trap. J Am Chem Soc 2022; 144:757-768. [PMID: 34994548 DOI: 10.1021/jacs.1c09259] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The nanopore is emerging as a means of single-molecule protein sensing. However, proteins demonstrate different charge properties, which complicates the design of a sensor that can achieve simultaneous sensing of differently charged proteins. In this work, we introduce an asymmetric electrolyte buffer combined with the Mycobacterium smegmatis porin A (MspA) nanopore to form an electroosmotic flow (EOF) trap. Apo- and holo-myoglobin, which differ in only a single heme, can be fully distinguished by this method. Direct discrimination of lysozyme, apo/holo-myoglobin, and the ACTR/NCBD protein complex, which are basic, neutral, and acidic proteins, respectively, was simultaneously achieved by the MspA EOF trap. To automate event classification, multiple event features were extracted to build a machine learning model, with which a 99.9% accuracy is achieved. The demonstrated method was also applied to identify single molecules of α-lactalbumin and β-lactoglobulin directly from whey protein powder. This protein-sensing strategy is useful in direct recognition of a protein from a mixture, suggesting its prospective use in rapid and sensitive detection of biomarkers or real-time protein structural analysis.
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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, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
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39
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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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40
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Benton JT, Bayly-Jones C. Challenges and approaches to studying pore-forming proteins. Biochem Soc Trans 2021; 49:2749-2765. [PMID: 34747994 PMCID: PMC8892993 DOI: 10.1042/bst20210706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/19/2021] [Accepted: 10/06/2021] [Indexed: 02/07/2023]
Abstract
Pore-forming proteins (PFPs) are a broad class of molecules that comprise various families, structural folds, and assembly pathways. In nature, PFPs are most often deployed by their host organisms to defend against other organisms. In humans, this is apparent in the immune system, where several immune effectors possess pore-forming activity. Furthermore, applications of PFPs are found in next-generation low-cost DNA sequencing, agricultural crop protection, pest control, and biosensing. The advent of cryoEM has propelled the field forward. Nevertheless, significant challenges and knowledge-gaps remain. Overcoming these challenges is particularly important for the development of custom, purpose-engineered PFPs with novel or desired properties. Emerging single-molecule techniques and methods are helping to address these unanswered questions. Here we review the current challenges, problems, and approaches to studying PFPs.
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Affiliation(s)
- Joshua T. Benton
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Charles Bayly-Jones
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
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41
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Suginta W, Sanram S, Aunkham A, Winterhalter M, Schulte A. The C2 entity of chitosugars is crucial in molecular selectivity of the Vibrio campbellii chitoporin. J Biol Chem 2021; 297:101350. [PMID: 34715124 PMCID: PMC8608610 DOI: 10.1016/j.jbc.2021.101350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/14/2022] Open
Abstract
The marine bacterium Vibrio campbellii expresses a chitooligosaccharide-specific outer-membrane channel (chitoporin) for the efficient uptake of nutritional chitosugars that are externally produced through enzymic degradation of environmental host shell chitin. However, the principles behind the distinct substrate selectivity of chitoporins are unclear. Here, we employed black lipid membrane (BLM) electrophysiology, which handles the measurement of the flow of ionic current through porins in phospholipid bilayers for the assessment of porin conductivities, to investigate the pH dependency of chitosugar-chitoporin interactions for the bacterium's natural substrate chitohexaose and its deacetylated form, chitosan hexaose. We show that efficient passage of the N-acetylated chitohexaose through the chitoporin is facilitated by its strong affinity for the pore. In contrast, the deacetylated chitosan hexaose is impermeant; however, protonation of the C2 amino entities of chitosan hexaose allows it to be pulled through the channel in the presence of a transmembrane electric field. We concluded from this the crucial role of C2-substitution as the determining factor for chitoporin entry. A change from N-acetylamino- to amino-substitution effectively abolished the ability of approaching molecules to enter the chitoporin, with deacetylation leading to loss of the distinctive structural features of nanopore opening and pore access of chitosugars. These findings provide further understanding of the multistep pathway of chitin utilization by marine Vibrio bacteria and may guide the development of solid-state or genetically engineered biological nanopores for relevant technological applications.
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Affiliation(s)
- Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
| | - Surapoj Sanram
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Anuwat Aunkham
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Albert Schulte
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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42
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Campos-Ferreira D, Visani V, Córdula C, Nascimento G, Montenegro L, Schindler H, Cavalcanti I. COVID-19 challenges: From SARS-CoV-2 infection to effective point-of-care diagnosis by electrochemical biosensing platforms. Biochem Eng J 2021; 176:108200. [PMID: 34522158 PMCID: PMC8428033 DOI: 10.1016/j.bej.2021.108200] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 12/25/2022]
Abstract
In January 2020, the World Health Organization (WHO) identified a new zoonotic virus, SARS-CoV-2, responsible for causing the COVID-19 (coronavirus disease 2019). Since then, there has been a collaborative trend between the scientific community and industry. Multidisciplinary research networks try to understand the whole SARS-CoV-2 pathophysiology and its relationship with the different grades of severity presented by COVID-19. The scientific community has gathered all the data in the quickly developed vaccines that offer a protective effect for all variants of the virus and promote new diagnostic alternatives able to have a high standard of efficiency, added to shorter response analysis time and portability. The industry enters in the context of accelerating the path taken by science until obtaining the final product. In this review, we show the principal diagnostic methods developed during the COVID-19 pandemic. However, when we observe the diagnostic tools section of an efficient infection outbreak containment report and the features required for such tools, we could observe a highlight of electrochemical biosensing platforms. Such devices present a high standard of analytical performance, are low-cost tools, easy to handle and interpret, and can be used in the most remote and low-resource regions. Therefore, probably, they are the ideal point-of-care diagnostic tools for pandemic scenarios.
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Affiliation(s)
- D. Campos-Ferreira
- Laboratório de Imunopatologia Keizo Asami – LIKA/ UFPE, Av. Prof. Moraes Rego, s/n, CEP: 506070-901 Recife, PE, Brazil,Corresponding author
| | - V. Visani
- Laboratório de Imunopatologia Keizo Asami – LIKA/ UFPE, Av. Prof. Moraes Rego, s/n, CEP: 506070-901 Recife, PE, Brazil
| | - C. Córdula
- Laboratório de Imunopatologia Keizo Asami – LIKA/ UFPE, Av. Prof. Moraes Rego, s/n, CEP: 506070-901 Recife, PE, Brazil
| | - G.A. Nascimento
- Laboratório de Imunopatologia Keizo Asami – LIKA/ UFPE, Av. Prof. Moraes Rego, s/n, CEP: 506070-901 Recife, PE, Brazil,Centro Acadêmico do Agreste - CAA/UFPE, Av. Marielle Franco, s/n - Km 59 - Bairro Nova Caruaru, CEP: 55.014-900 Caruaru, PE, Brazil
| | - L.M.L. Montenegro
- Fundação Oswaldo Cruz (Fiocruz), Centro de Pesquisas Instituto Aggeu Magalhães (IAM), Av. Professor Moraes Rego s/n, CEP: 50670-901 Recife, PE, Brazil
| | - H.C. Schindler
- Fundação Oswaldo Cruz (Fiocruz), Centro de Pesquisas Instituto Aggeu Magalhães (IAM), Av. Professor Moraes Rego s/n, CEP: 50670-901 Recife, PE, Brazil
| | - I.M.F. Cavalcanti
- Laboratório de Imunopatologia Keizo Asami – LIKA/ UFPE, Av. Prof. Moraes Rego, s/n, CEP: 506070-901 Recife, PE, Brazil,Centro Acadêmico de Vitória – CAV/UFPE, R. Alto do Reservatório, CEP: 55 612-440 Vitória de Santo Antão, PE, Brazil
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43
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Liu Y, Pan T, Wang K, Wang Y, Yan S, Wang L, Zhang S, Du X, Jia W, Zhang P, Chen H, Huang S. Allosteric Switching of Calmodulin in a
Mycobacterium smegmatis
porin A (MspA) Nanopore‐Trap. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Tiezheng Pan
- School of Life Sciences Northwestern Polytechnical University 710072 Xi'an China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Hong‐Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
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44
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Liu Y, Pan T, Wang K, Wang Y, Yan S, Wang L, Zhang S, Du X, Jia W, Zhang P, Chen HY, Huang S. Allosteric Switching of Calmodulin in a Mycobacterium smegmatis porin A (MspA) Nanopore-Trap. Angew Chem Int Ed Engl 2021; 60:23863-23870. [PMID: 34449124 DOI: 10.1002/anie.202110545] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/21/2021] [Indexed: 01/23/2023]
Abstract
Recent developments concerning large protein nanopores suggest a new approach to structure profiling of native folded proteins. In this work, the large vestibule of Mycobacterium smegmatis porin A (MspA) and calmodulin (CaM), a Ca2+ -binding protein, were used in the direct observation of the protein structure. Three conformers, including the Ca2+ -free, Ca2+ -bound, and target peptide-bound states of CaM, were unambiguously distinguished. A disease related mutant, CaM D129G was also discriminated by MspA, revealing how a single amino acid replacement can interfere with the Ca2+ -binding capacity of the whole protein. The binding capacity and aggregation effect of CaM induced by different ions (Mg2+ /Sr2+ /Ba2+ /Ca2+ /Pb2+ /Tb3+ ) were also investigated and the stability of MspA in extreme conditions was evaluated. This work demonstrates the most systematic single-molecule investigation of different allosteric conformers of CaM, acknowledging the high sensing resolution offered by the MspA nanopore trap.
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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, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Tiezheng Pan
- School of Life Sciences, Northwestern Polytechnical University, 710072, Xi'an, China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
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45
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Wen C, Dematties D, Zhang SL. A Guide to Signal Processing Algorithms for Nanopore Sensors. ACS Sens 2021; 6:3536-3555. [PMID: 34601866 PMCID: PMC8546757 DOI: 10.1021/acssensors.1c01618] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/20/2021] [Indexed: 12/19/2022]
Abstract
Nanopore technology holds great promise for a wide range of applications such as biomedical sensing, chemical detection, desalination, and energy conversion. For sensing performed in electrolytes in particular, abundant information about the translocating analytes is hidden in the fluctuating monitoring ionic current contributed from interactions between the analytes and the nanopore. Such ionic currents are inevitably affected by noise; hence, signal processing is an inseparable component of sensing in order to identify the hidden features in the signals and to analyze them. This Guide starts from untangling the signal processing flow and categorizing the various algorithms developed to extracting the useful information. By sorting the algorithms under Machine Learning (ML)-based versus non-ML-based, their underlying architectures and properties are systematically evaluated. For each category, the development tactics and features of the algorithms with implementation examples are discussed by referring to their common signal processing flow graphically summarized in a chart and by highlighting their key issues tabulated for clear comparison. How to get started with building up an ML-based algorithm is subsequently presented. The specific properties of the ML-based algorithms are then discussed in terms of learning strategy, performance evaluation, experimental repeatability and reliability, data preparation, and data utilization strategy. This Guide is concluded by outlining strategies and considerations for prospect algorithms.
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Affiliation(s)
- Chenyu Wen
- Division
of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Dario Dematties
- Instituto
de Ciencias Humanas, Sociales y Ambientales, CONICET Mendoza Technological Scientific Center, Mendoza M5500, Argentina
| | - Shi-Li Zhang
- Division
of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, SE-751 03 Uppsala, Sweden
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46
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Abstract
This paper provides a perspective on potential applications of a new single-molecule technique, viz., the nanopore electro-osmotic trap (NEOtrap). This solid-state nanopore-based method uses locally induced electro-osmosis to form a hydrodynamic trap for single molecules. Ionic current recordings allow one to study an unlabeled protein or nanoparticle of arbitrary charge that can be held in the nanopore's most sensitive region for very long times. After motivating the need for improved single-molecule technologies, we sketch various possible technical extensions and combinations of the NEOtrap. We lay out diverse applications in biosensing, enzymology, protein folding, protein dynamics, fingerprinting of proteins, detecting post-translational modifications, and all that at the level of single proteins - illustrating the unique versatility and potential of the NEOtrap.
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Affiliation(s)
- Sonja Schmid
- Nanodynamics Lab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
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47
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Lucas FLR, Piso TRC, van der Heide NJ, Galenkamp NS, Hermans J, Wloka C, Maglia G. Automated Electrical Quantification of Vitamin B1 in a Bodily Fluid using an Engineered Nanopore Sensor. Angew Chem Int Ed Engl 2021; 60:22849-22855. [PMID: 34390104 PMCID: PMC8518494 DOI: 10.1002/anie.202107807] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/20/2021] [Indexed: 12/27/2022]
Abstract
The ability to measure the concentration of metabolites in biological samples is important, both in the clinic and for home diagnostics. Here we present a nanopore-based biosensor and automated data analysis for quantification of thiamine in urine in less than a minute, without the need for recalibration. For this we use the Cytolysin A nanopore and equip it with an engineered periplasmic thiamine binding protein (TbpA). To allow fast measurements we tuned the affinity of TbpA for thiamine by redesigning the π-π stacking interactions between the thiazole group of thiamine and TbpA. This substitution resulted furthermore in a marked difference between unbound and bound state, allowing the reliable discrimination of thiamine from its two phosphorylated forms by residual current only. Using an array of nanopores, this will allow the quantification within seconds, paving the way for next-generation single-molecule metabolite detection systems.
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Affiliation(s)
- Florian Leonardus Rudolfus Lucas
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Tjemme Rinze Cornelis Piso
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Nicole Stéphanie Galenkamp
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Jos Hermans
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713, AV, The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
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48
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Lucas FLR, Piso TRC, Heide NJ, Galenkamp NS, Hermans J, Wloka C, Maglia G. Automated Electrical Quantification of Vitamin B1 in a Bodily Fluid using an Engineered Nanopore Sensor. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Tjemme Rinze Cornelis Piso
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
| | - Nieck Jordy Heide
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
| | - Nicole Stéphanie Galenkamp
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
| | - Jos Hermans
- Analytical Biochemistry Department of Pharmacy University of Groningen Antonius Deusinglaan 1 Groningen 9713 AV The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
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49
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Abstract
Chemical reactions of single molecules, caused by rapid formation or breaking of chemical bonds, are difficult to observe even with state-of-the-art instruments. A biological nanopore can be engineered into a single molecule reactor, capable of detecting the binding of a monatomic ion or the transient appearance of chemical intermediates. Pore engineering of this type is however technically challenging, which has significantly restricted further development of this technique. We propose a versatile strategy, "programmable nano-reactors for stochastic sensing" (PNRSS), by which a variety of single molecule reactions of hydrogen peroxide, metal ions, ethylene glycol, glycerol, lactic acid, vitamins, catecholamines or nucleoside analogues can be observed directly. PNRSS presents a refined sensing resolution which can be further enhanced by an artificial intelligence algorithm. Remdesivir, a nucleoside analogue and an investigational anti-viral drug used to treat COVID-19, can be distinguished from its active triphosphate form by PNRSS, suggesting applications in pharmacokinetics or drug screening.
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50
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Bhatti H, Jawed R, Ali I, Iqbal K, Han Y, Lu Z, Liu Q. Recent advances in biological nanopores for nanopore sequencing, sensing and comparison of functional variations in MspA mutants. RSC Adv 2021; 11:28996-29014. [PMID: 35478559 PMCID: PMC9038099 DOI: 10.1039/d1ra02364k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/09/2021] [Indexed: 12/14/2022] Open
Abstract
Biological nanopores are revolutionizing human health by the great myriad of detection and diagnostic skills. Their nano-confined area and ingenious shape are suitable to investigate a diverse range of molecules that were difficult to identify with the previous techniques. Additionally, high throughput and label-free detection of target analytes instigated the exploration of new bacterial channel proteins such as Fragaceatoxin C (FraC), Cytolysin A (ClyA), Ferric hydroxamate uptake component A (FhuA) and Curli specific gene G (CsgG) along with the former ones, like α-hemolysin (αHL), Mycobacterium smegmatis porin A (MspA), aerolysin, bacteriophage phi 29 and Outer membrane porin G (OmpG). Herein, we discuss some well-known biological nanopores but emphasize on MspA and compare the effects of site-directed mutagenesis on the detection ability of its mutants in view of the surface charge distribution, voltage threshold and pore-analyte interaction. We also discuss illustrious and latest advances in biological nanopores for past 2-3 years due to limited space. Last but not the least, we elucidate our perspective for selecting a biological nanopore and propose some future directions to design a customized nanopore that would be suitable for DNA sequencing and sensing of other nontrivial molecules in question.
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Affiliation(s)
- Huma Bhatti
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Rohil Jawed
- School of Life Science and Technology, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China
| | - Irshad Ali
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Khurshid Iqbal
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Yan Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
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