1
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Li W, Guo L, Ding XL, Ding Y, Ji LN, Xia XH, Wang K. High-Throughput Single-Molecule Surface-Enhanced Raman Spectroscopic Profiling of Single-Amino Acid Substitutions in Peptides by a Gold Plasmonic Nanopore. ACS NANO 2024; 18:19200-19207. [PMID: 38996344 DOI: 10.1021/acsnano.4c04775] [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: 07/14/2024]
Abstract
Simultaneous detection and structural characterization of protein variants on a single platform are highly desirable but technically challenging. Herein, we present a single-molecule spectral system based on a gold plasmonic nanopore for analyzing two peptides and their single-point mutated variants. The gold plasmonic nanopore enabled the high-throughput acquisition of surface-enhanced Raman scattering (SERS) spectra at the single-molecule level by electrically driving analytes into hot spots. Furthermore, a statistical method based on Boolean operations was developed to extract prominent features from fluctuated single-molecule SERS spectra. The effects of the single-amino acid substitutions on both the intramolecular interactions and the peptide conformations were directly characterized by the nanopore system, and the results agreed with the predictions by AlphaFold2. This study highlights the mutual benefits of spectroscopy and nanopore technology, whereby the gold plasmonic nanopore offers a powerful tool for the structural analysis of single-molecule proteins.
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Affiliation(s)
- Wang Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Linru Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xin-Lei Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yanru Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Li-Na Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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2
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Morajkar RV, Fatrekar AP, Vernekar AA. Approach of a small protein to the biomimetic bis-(μ-oxo) dicopper active-site installed in MOF-808 pores with restricted access perturbs substrate selectivity of oxidase nanozyme. Chem Sci 2024; 15:10810-10822. [PMID: 39027301 PMCID: PMC11253172 DOI: 10.1039/d4sc02136c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/05/2024] [Indexed: 07/20/2024] Open
Abstract
Advances in nanozymes have taken shape over the past few years in several domains. However, persisting challenging limitations of selectivity, specificity, and efficiency necessitate careful attention to aid in the development of next-generation artificial enzymes. Despite nanozymes having significant therapeutic and biotechnological prospects, the multienzyme mimetic activities can compromise their intended applications. Furthermore, the lack of substrate selectivity can hamper crucial biological pathways. While working on addressing the challenges of nanozymes, in this work, we aim to highlight the interplay between the substrates and bis-(μ-oxo) dicopper active site-installed MOF-808 for selectively mimicking oxidase. This oxidase mimetic with a small pore-aperture (1.4 nm), similar to the opening of enzyme binding pockets, projects a tight control over the dynamics and the reactivity of substrates, making it distinct from the general oxidase nanozymes. Interestingly, the design and the well-regulated activity of this nanozyme effectively thwart DNA from approaching the active site, thereby preventing its oxidative damage. Crucially, we also show that despite these merits, the oxidase selectivity is compromised by small proteins such as cytochrome c (Cyt c), having dimensions larger than the pore aperture of MOF-808. This reaction lucidly produces water molecules as a result of four electron transfer to an oxygen molecule. Such unintended side reactivities warrant special attention as they can perturb redox processes and several cellular energy pathways. Through this study, we provide a close look at designing next-generation artificial enzymes that can address the complex challenges for their utility in advanced applications.
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Affiliation(s)
- Rasmi V Morajkar
- Inorganic and Physical Chemistry Laboratory, CSIR-Central Leather Research Institute Chennai 600020 Tamil Nadu India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
| | - Adarsh P Fatrekar
- Inorganic and Physical Chemistry Laboratory, CSIR-Central Leather Research Institute Chennai 600020 Tamil Nadu India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
| | - Amit A Vernekar
- Inorganic and Physical Chemistry Laboratory, CSIR-Central Leather Research Institute Chennai 600020 Tamil Nadu India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
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3
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Ju H, Cheng L, Li M, Mei K, He S, Jia C, Guo X. Single-Molecule Electrical Profiling of Peptides and Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401877. [PMID: 38639403 PMCID: PMC11267281 DOI: 10.1002/advs.202401877] [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: 02/22/2024] [Revised: 04/03/2024] [Indexed: 04/20/2024]
Abstract
In recent decades, there has been a significant increase in the application of single-molecule electrical analysis platforms in studying proteins and peptides. These advanced analysis methods have the potential for deep investigation of enzymatic working mechanisms and accurate monitoring of dynamic changes in protein configurations, which are often challenging to achieve in ensemble measurements. In this work, the prominent research progress in peptide and protein-related studies are surveyed using electronic devices with single-molecule/single-event sensitivity, including single-molecule junctions, single-molecule field-effect transistors, and nanopores. In particular, the successful commercial application of nanopores in DNA sequencing has made it one of the most promising techniques in protein sequencing at the single-molecule level. From single peptides to protein complexes, the correlation between their electrical characteristics, structures, and biological functions is gradually being established. This enables to distinguish different molecular configurations of these biomacromolecules through real-time electrical monitoring of their life activities, significantly improving the understanding of the mechanisms underlying various life processes.
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Affiliation(s)
- Hongyu Ju
- School of Pharmaceutical Science and TechnologyTianjin UniversityTianjin300072P. R. China
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Li Cheng
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Mengmeng Li
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Kunrong Mei
- School of Pharmaceutical Science and TechnologyTianjin UniversityTianjin300072P. R. China
| | - Suhang He
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Chuancheng Jia
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Xuefeng Guo
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
- Beijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871P. R. China
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4
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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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5
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Yang CN, Liu W, Liu HT, Zhang JC, Yu RJ, Ying YL, Long YT. Electrochemical Visualization of Single-Molecule Thiol Substitution with Nanopore Measurement. ACS MEASUREMENT SCIENCE AU 2024; 4:76-80. [PMID: 38404487 PMCID: PMC10885329 DOI: 10.1021/acsmeasuresciau.3c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 02/27/2024]
Abstract
Reactions involving sulfhydryl groups play a critical role in maintaining the structure and function of proteins. However, traditional mechanistic studies have mainly focused on reaction rates and the efficiency in bulk solutions. Herein, we have designed a cysteine-mutated nanopore as a biological protein nanoreactor for electrochemical visualization of the thiol substitute reaction. Statistical analysis of characteristic current signals shows that the apparent reaction rate at the single-molecule level in this confined nanoreactor reached 1400 times higher than that observed in bulk solution. This substantial acceleration of thiol substitution reactions within the nanopore offers promising opportunities for advancing the design and optimization of micro/nanoreactors. Moreover, our results could shed light on the understanding of sulfhydryl reactions and the thiol-involved signal transduction mechanisms in biological systems.
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Affiliation(s)
- Chao-Nan Yang
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Wei Liu
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Hao-Tian Liu
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Ji-Chang Zhang
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Ru-Jia Yu
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
- Chemistry
and Biomedicine Innovation Center, Nanjing
University, Nanjing 210023, P.R. China
| | - Yi-Lun Ying
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
- Chemistry
and Biomedicine Innovation Center, Nanjing
University, Nanjing 210023, P.R. China
| | - Yi-Tao Long
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
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6
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Tripathi P, Mehrafrooz B, Aksimentiev A, Jackson SE, Gruebele M, Wanunu M. A Marcus-Type Inverted Region in the Translocation Kinetics of a Knotted Protein. J Phys Chem Lett 2023; 14:10719-10726. [PMID: 38009629 PMCID: PMC11176711 DOI: 10.1021/acs.jpclett.3c02183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Knotted proteins are rare but important species, yet how their complex topologies affect their physical properties is not fully understood. Here we combine single molecule nanopore experiments and all-atom MD simulations to study the electric-field-driven unfolding during the translocation through a model pore of individual protein knots important for methylating tRNA. One of these knots shows an unusual behavior that resembles the behavior of electrons hopping between two potential surfaces: as the electric potential driving the translocation reaction is increased, the rate eventually plateaus or slows back down in the "Marcus inverted regime". Our results shed light on the influence of topology in knotted proteins on their forced translocation through a pore connecting two electrostatic potential wells.
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Affiliation(s)
- Prabhat Tripathi
- Department of Chemistry, Indian Institute of Technology (Banaras Hindu University), Varanasi, UP-221005, India
| | - Behzad Mehrafrooz
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL-61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL-61801, USA
| | - Sophie E. Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield `Road, Cambridge CB2 1EW, UK
| | - Martin Gruebele
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL-61801, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA-02115, USA
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7
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Shuto Y, Walinda E, Morimoto D, Sugase K. Conformational Fluctuations and Induced Orientation of a Protein, Its Solvation Shell, and Bulk Water in Weak Non-Unfolding External Electric Fields. J Phys Chem B 2023; 127:7417-7430. [PMID: 37587419 DOI: 10.1021/acs.jpcb.3c01683] [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: 08/18/2023]
Abstract
Extreme external electric fields have been reported to disrupt the tertiary structure of stably folded proteins; however, the effects of weaker electric fields on many biomolecules, especially net-uncharged proteins, and on the surrounding aqueous environment have been rarely discussed. To explore these effects at the atomic level, here, we have used molecular dynamics simulations to estimate rotational motion and induced structural fluctuations in the model protein ubiquitin and its hydration layer due to applied non-unfolding electrostatic fields. When exposed to weak electric fields of up to 0.2 V nm-1, ubiquitin displayed competition between internal structure-maintaining molecular interactions and the external orienting force, which disrupted the local structure in certain regions of the protein. Moreover, relative to hydration water, bulk water showed a greater tendency to align with the electric field, indicating that the presence of protein caused hydration water to acquire rotational mobility different from that in a pure-water system. The differential influence of the applied electric field on the hydration and bulk water surrounding ubiquitin will be common to almost all (nonmembrane) biomacromolecules. Our findings highlight the importance of local dipoles and their electric polarizability even in net-uncharged biomolecules.
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Affiliation(s)
- Yusuke Shuto
- Graduate School of Agriculture, Kyoto University, N346 Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kenji Sugase
- Graduate School of Agriculture, Kyoto University, N346 Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
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8
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Li W, Zhou J, Lan Q, Ding XL, Pan XT, Ahmed SA, Ji LN, Wang K, Xia XH. Single-Molecule Electrical and Spectroscopic Profiling Protein Allostery Using a Gold Plasmonic Nanopore. NANO LETTERS 2023; 23:2586-2592. [PMID: 36942994 DOI: 10.1021/acs.nanolett.2c04848] [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: 06/18/2023]
Abstract
Direct structural and dynamic characterization of protein conformers in solution is highly desirable but currently impractical. Herein, we developed a single molecule gold plasmonic nanopore system for observation of protein allostery, enabling us to monitor translocation dynamics and conformation transition of proteins by ion current detection and SERS spectrum measurement, respectively. Allosteric transition of calmodulin (CaM) was elaborately probed by the nanopore system. Two conformers of CaM were well-resolved at a single-molecule level using both the ion current blockage signal and the SERS spectra. The collected SERS spectra provided structural evidence to confirm the interaction between CaM and the gold plasmonic nanopore, which was responsible for the different translocation behaviors of the two conformers. SERS spectra revealed the amino acid residues involved in the conformational change of CaM upon calcium binding. The results demonstrated that the excellent spectral characterization furnishes a single-molecule nanopore technique with an advanced capability of direct structure analysis.
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Affiliation(s)
- Wang Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Juan Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qing Lan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xin-Lei Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiao-Tong Pan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Saud Asif Ahmed
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Li-Na Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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9
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Zhou J, Lan Q, Li W, Ji LN, Wang K, Xia XH. Single Molecule Protein Segments Sequencing by a Plasmonic Nanopore. NANO LETTERS 2023; 23:2800-2807. [PMID: 36927001 DOI: 10.1021/acs.nanolett.3c00086] [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: 06/18/2023]
Abstract
Obtaining sequential and conformational information on proteins is vital to understand their functions. Although the nanopore-based electrical detection can sense single molecule (SM) protein and distinguish among different amino acids, this approach still faces difficulties in slowing down protein translocation and improving ionic current signal-to-noise ratio. Here, we observe the unfolding and multistep sequential translocation of SM cytochrome c (cyt c) through a surface enhanced Raman scattering (SERS) active conical gold nanopore. High bias voltage unfolds SM protein causing more exposure of amino acid residues to the nanopore, which slows down the protein translocation. Specific SERS traces of different SM cyt c segments are then recorded sequentially when they pass through the hotspot inside the gold nanopore. This study shows that the combination of SM SERS with a nanopore can provide a direct insight into protein segments and expedite the development of nanopore toward SM protein sequencing.
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Affiliation(s)
- Juan Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qing Lan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wang Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Li-Na Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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10
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Maffeo C, Quednau L, Wilson J, Aksimentiev A. DNA double helix, a tiny electromotor. NATURE NANOTECHNOLOGY 2023; 18:238-242. [PMID: 36564521 DOI: 10.1038/s41565-022-01285-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
Flowing fluid past chiral objects has been used for centuries to power rotary motion in man-made machines. By contrast, rotary motion in nanoscale biological or chemical systems is produced by biasing Brownian motion through cyclic chemical reactions. Here we show that a chiral biological molecule, a DNA or RNA duplex rotates unidirectionally at billions of revolutions per minute when an electric field is applied along the duplex, with the rotation direction being determined by the chirality of the duplex. The rotation is found to be powered by the drag force of the electro-osmotic flow, realizing the operating principle of a macroscopic turbine at the nanoscale. The resulting torques are sufficient to power rotation of nanoscale beads and rods, offering an engineering principle for constructing nanoscale systems powered by electric field.
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lauren Quednau
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - James Wilson
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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11
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Threading single proteins through pores to compare their energy landscapes. Proc Natl Acad Sci U S A 2022; 119:e2202779119. [PMID: 36122213 PMCID: PMC9522335 DOI: 10.1073/pnas.2202779119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Protein function correlates with its structural dynamics. While theoretical approaches to studying protein energy landscapes are well developed, experimental methods that enable probing these landscapes of proteins remain challenging. We used solid-state nanopores to study the translocation behavior of three mutants of a helix bundle protein and quantified the number of energetically accessible conformational states for each mutant. We found that a slower-folding mutant with access to more conformational states translocates faster than a faster-folding mutant with a smaller number of accessible states, suggesting that ease of folding and ease of translocation are at odds in this case. Translocation of proteins is correlated with structural fluctuations that access conformational states higher in free energy than the folded state. We use electric fields at the solid-state nanopore to control the relative free energy and occupancy of different protein conformational states at the single-molecule level. The change in occupancy of different protein conformations as a function of electric field gives rise to shifts in the measured distributions of ionic current blockades and residence times. We probe the statistics of the ionic current blockades and residence times for three mutants of the λ-repressor family in order to determine the number of accessible conformational states of each mutant and evaluate the ruggedness of their free energy landscapes. Translocation becomes faster at higher electric fields when additional flexible conformations are available for threading through the pore. At the same time, folding rates are not correlated with ease of translocation; a slow-folding mutant with a low-lying intermediate state translocates faster than a faster-folding two-state mutant. Such behavior allows us to distinguish among protein mutants by selecting for the degree of current blockade and residence time at the pore. Based on these findings, we present a simple free energy model that explains the complementary relationship between folding equilibrium constants and translocation rates.
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12
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Liu Y, Zhang S, Wang Y, Wang L, Cao Z, Sun W, Fan P, Zhang P, Chen HY, Huang S. Nanopore Identification of Alditol Epimers and Their Application in Rapid Analysis of Alditol-Containing Drinks and Healthcare Products. J Am Chem Soc 2022; 144:13717-13728. [PMID: 35867993 DOI: 10.1021/jacs.2c04595] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alditols, which have a sweet taste but produce much lower calories than natural sugars, are widely used as artificial sweeteners. Alditols are the reduced forms of monosaccharide aldoses, and different alditols are diastereomers or epimers of each other and direct and rapid identification by conventional methods is difficult. Nanopores, which are emerging single-molecule sensors with exceptional resolution when engineered appropriately, are useful for the recognition of diastereomers and epimers. In this work, direct distinguishing of alditols corresponding to all 15 monosaccharide aldoses was achieved by a boronic acid-appended hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore (MspA-PBA). Thirteen alditols including glycerol, erythritol, threitol, adonitol, arabitol, xylitol, mannitol, sorbitol, allitol, dulcitol, iditol, talitol, and gulitol (l-sorbitol) could be fully distinguished, and their sensing features constitute a complete nanopore alditol database. To automate event classification, a custom machine-learning algorithm was developed and delivered a 99.9% validation accuracy. This strategy was also used to identify alditol components in commercially available "zero-sugar" drinks and healthcare products, suggesting their use in rapid and sensitive quality control for the food and medical industry.
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Affiliation(s)
- Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zhenyuan Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Wen Sun
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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13
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Tripathi P, Firouzbakht A, Gruebele M, Wanunu M. Direct Observation of Single-Protein Transition State Passage by Nanopore Ionic Current Jumps. J Phys Chem Lett 2022; 13:5918-5924. [PMID: 35731125 DOI: 10.1021/acs.jpclett.2c01009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Conformational transitions of proteins are governed by chemical kinetics, often toggled by passage through an activated state separating two conformational ensembles. The passage time of a protein through the activated state can be too fast to be detected by single-molecule experiments without the aid of viscogenic agents. Here, we use high-bandwidth nanopore measurements to resolve microsecond-duration transitions that occur between conformational states of individual protein molecules partly blocking pore current. We measure the transition state passage time between folded and unfolded states of a two-state λ6-85 mutant and between metastable intermediates and the unfolded state of the multistate folder cytochrome c. Consistent with the principle of microscopic reversibility, the transition state passage time is the same for the forward and backward reactions. A passage time distribution whose tail is broader than a single exponential observed in cytochrome c suggests a multidimensional energy landscape for this protein.
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Affiliation(s)
- Prabhat Tripathi
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | | | | | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
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14
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Tan X, Lv C, Chen H. Advances of nanopore-based sensing techniques for contaminants evaluation of food and agricultural products. Crit Rev Food Sci Nutr 2022; 63:10866-10879. [PMID: 35687354 DOI: 10.1080/10408398.2022.2085238] [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] [Indexed: 11/03/2022]
Abstract
Food safety assurance systems are becoming more stringent in response to the growing food safety problems. Rapid, sensitive, and reliable detection technology is a prerequisite for the establishment of food safety assurance systems. Nanopore technology has been taken as one of the emerging technology capable of dealing with the detection of harmful contaminants as efficiently as possible due to the advantage of label-free, high-throughput, amplification-free, and rapid detection features. Start with the history of nanopore techniques, this review introduced the underlying knowledge of detection mechanism of nanopore-based sensing techniques. Meanwhile, sensing interfaces for the construction of nanopore sensors are comprehensively summarized. Moreover, this review covers the current advances of nanopore techniques in the application of food safety screening. Currently, the establishment of nanopore sensing devices is mainly based on the blocking current phenomenon. Sensing interfaces including biological nanopores, solid-state nanopores, DNA origami, and de novo designed nanopores can be used in the manufacture of sensing devices. Food harmful substances, including heavy metals, veterinary drugs, pesticide residues, food toxins, and other harmful substances can be quickly determined by nanopore-based sensors. Moreover, the combination of nanopore techniques with advanced materials has become one of the most effective methods to improve sensing properties.
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Affiliation(s)
- Xiaoyi Tan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Hai Chen
- College of Food Science, Southwest University, Chongqing, China
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15
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Cardoch S, Timneanu N, Caleman C, Scheicher RH. Distinguishing between Similar Miniproteins with Single-Molecule Nanopore Sensing: A Computational Study. ACS NANOSCIENCE AU 2022; 2:119-127. [PMID: 37101662 PMCID: PMC10125149 DOI: 10.1021/acsnanoscienceau.1c00022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A nanopore is a tool in single-molecule sensing biotechnology that offers label-free identification with high throughput. Nanopores have been successfully applied to sequence DNA and show potential in the study of proteins. Nevertheless, the task remains challenging due to the large variability in size, charges, and folds of proteins. Miniproteins have a small number of residues, limited secondary structure, and stable tertiary structure, which can offer a systematic way to reduce complexity. In this computational work, we theoretically evaluated sensing two miniproteins found in the human body using a silicon nitride nanopore. We employed molecular dynamics methods to compute occupied-pore ionic current magnitudes and electronic structure calculations to obtain interaction strengths between pore wall and miniprotein. From the interaction strength, we derived dwell times using a mix of combinatorics and numerical solutions. This latter approach circumvents typical computational demands needed to simulate translocation events using molecular dynamics. We focused on two miniproteins potentially difficult to distinguish owing to their isotropic geometry, similar number of residues, and overall comparable structure. We found that the occupied-pore current magnitudes not to vary significantly, but their dwell times differ by 1 order of magnitude. Together, these results suggest a successful identification protocol for similar miniproteins.
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Affiliation(s)
- Sebastian Cardoch
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Ralph H. Scheicher
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
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16
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Liu W, Yang ZL, Yang CN, Ying YL, Long YT. Profiling single-molecule reaction kinetics under nanopore confinement. Chem Sci 2022; 13:4109-4114. [PMID: 35440975 PMCID: PMC8985585 DOI: 10.1039/d1sc06837g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/13/2022] [Indexed: 02/02/2023] Open
Abstract
The study of a single-molecule reaction under nanoconfinement is beneficial for understanding the reactive intermediates and reaction pathways. However, the kinetics model of the single-molecule reaction under confinement remains elusive. Herein we engineered an aerolysin nanopore reactor to elaborate the single-molecule reaction kinetics under nanoconfinement. By identifying the bond-forming and non-bond-forming events directly, a four-state kinetics model is proposed for the first time. Our results demonstrated that the single-molecule reaction kinetics inside a nanopore depends on the frequency of individual reactants captured and the fraction of effective collision inside the nanopore confined space. This insight will guide the design of confined nanopore reactors for resolving the single-molecule chemistry, and shed light on the mechanistic understanding of dynamic covalent chemistry inside confined systems such as supramolecular cages, coordination cages, and micelles. A four-state kinetics model is proposed to reveal the kinetics of a single-molecule reaction under nanopore confinement.![]()
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Zhong-Lin Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Chao-Nan Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China .,Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210023 P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
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17
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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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18
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Wan Y, Zong C, Li X, Wang A, Li Y, Yang T, Bao Q, Dubow M, Yang M, Rodrigo LA, Mao C. New Insights for Biosensing: Lessons from Microbial Defense Systems. Chem Rev 2022; 122:8126-8180. [PMID: 35234463 DOI: 10.1021/acs.chemrev.1c01063] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR-Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR-Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties. We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.
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Affiliation(s)
- Yi Wan
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Chengli Zong
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, 1700 Fourth Street, Byers Hall 303C, San Francisco, California 94158, United States
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Yan Li
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Tao Yang
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Qing Bao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Michael Dubow
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, CEA, Université Paris-Saclay, Campus C.N.R.S, Bâtiment 12, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Mingying Yang
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Ledesma-Amaro Rodrigo
- Imperial College Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States.,School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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19
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Bandara YMNDY, Farajpour N, Freedman KJ. Nanopore Current Enhancements Lack Protein Charge Dependence and Elucidate Maximum Unfolding at Protein's Isoelectric Point. J Am Chem Soc 2022; 144:3063-3073. [PMID: 35143193 DOI: 10.1021/jacs.1c11540] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein sequencing, as well as protein fingerprinting, has gained tremendous attention in the electrical sensing realm of solid-state nanopores and is challenging due to fast translocations and the use of high molar electrolytes. Despite providing an appreciable signal-to-noise ratio, high electrolyte concentrations can have adverse effects on the native protein structure. Herein, we present a thorough investigation of low electrolyte sensing conditions across a broad pH and voltage range generating conductive pulses (CPs) irrespective of protein net charge. We used Cas9 as the model protein and demonstrated that unfolding is noncooperative, represented by the gradual elongation or stretching of the protein, and sensitive to both the applied voltage and pH (i.e., charge state). The magnitude of unfolding and the isoelectric point (pI) of Cas9 was found to be correlated and a critical factor in our experiments. Electroosmotic flow (EOF) was always aligned with the transit direction, whereas electrophoretic force (EPF) was either reinforcing (pH < pI) or opposing (pH > pI) the protein's movement, which led to slower translocations at higher pH values. Further exploration of higher pH values led to slowing down of protein with > 30% of the population being slower than 0.5 ms. Our results would be critical for protein sensing at very low electrolytes and to retard their translocation speed without resorting to high-bandwidth equipment.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Bioengineering, University of California, Riverside, 900 University Ave., Riverside, California 92521, United States
| | - Nasim Farajpour
- Department of Bioengineering, University of California, Riverside, 900 University Ave., Riverside, California 92521, United States
| | - Kevin J Freedman
- Department of Bioengineering, University of California, Riverside, 900 University Ave., Riverside, California 92521, United States
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20
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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: 26] [Impact Index Per Article: 13.0] [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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21
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Iizuka R, Yamazaki H, Uemura S. Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies. Biophys Physicobiol 2022; 19:e190032. [DOI: 10.2142/biophysico.bppb-v19.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/26/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Ryo Iizuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Hirohito Yamazaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
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22
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Abstract
[Figure: see text].
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Affiliation(s)
- Filip Bošković
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
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23
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Chen X, Zhang Y, Arora P, Guan X. Nanopore Stochastic Sensing Based on Non-covalent Interactions. Anal Chem 2021; 93:10974-10981. [PMID: 34319076 DOI: 10.1021/acs.analchem.1c02102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A variety of species could be detected by using nanopores engineered with various recognition sites based upon non-covalent interactions, including electrostatic, aromatic, and hydrophobic interactions. The existence of these engineered non-covalent bonding sites was supported by the single-channel recording technique. The advantage of the non-covalent interaction-based sensing strategy was that the recognition site of the engineered nanopore was not specific for a particular molecule but instead selective for a class of species (e.g., cationic, anionic, aromatic, and hydrophobic). Since different species produce current modulations with quite different signatures represented by amplitude, residence time, and even characteristic voltage-dependence curve, the non-covalent interaction-based nanopore sensor could not only differentiate individual molecules in the same category but also enable differentiation between species with similar structures or molecular weights. Hence, our developed non-covalent interaction-based nanopore sensing strategy may find useful application in the detection of molecules of medical and/or environmental importance.
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Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
| | - Pearl Arora
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
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