1
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Zhang Y, Hu C, Liu R, He S, Yang J, Yao W, Li Y, Guo X. Protein nanopore-based sensors for public health analyte detection. J Mater Chem B 2024; 12:9845-9862. [PMID: 39258387 DOI: 10.1039/d4tb01149j] [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: 09/12/2024]
Abstract
High-throughput and label-free protein nanopore-based sensors are extensively used in DNA sequencing, single-protein analysis, molecular sensing and chemical catalysis with single channel recording. These technologies show great potential for identifying various harmful substances linked to public health by addressing the limitations of current portability and the speed of existing techniques. In this review, we provide an overview of the fundamental principles of nanopore sensing, with a focus on chemical modification and genetic engineering strategies aimed at enhancing the detection sensitivity and identification accuracy of protein nanopores. The engineered protein nanopores enable direct sensing, while the introduction of aptamers and substrates enables indirect sensing, translating the physical structure and chemical properties of analytes into readable signals. These scientific discoveries and engineering efforts have provided new prospects for detecting and monitoring trace hazardous substances.
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Affiliation(s)
- Yanhua Zhang
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Chan Hu
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Ronghui Liu
- School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China.
| | - Shujun He
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Jie Yang
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Wen Yao
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Yi Li
- School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China.
| | - Xinrong Guo
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
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2
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Wiswedel R, Bui ATN, Kim J, Lee MK. Beta-Barrel Nanopores as Diagnostic Sensors: An Engineering Perspective. BIOSENSORS 2024; 14:345. [PMID: 39056622 PMCID: PMC11274599 DOI: 10.3390/bios14070345] [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: 05/30/2024] [Revised: 07/13/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024]
Abstract
Biological nanopores are ultrasensitive and highly attractive platforms for disease diagnostics, including the sequencing of viral and microbial genes and the detection of biomarkers and pathogens. To utilize biological nanopores as diagnostic sensors, they have been engineered through various methods resulting in the accurate and highly sensitive detection of biomarkers and disease-related biomolecules. Among diverse biological nanopores, the β-barrel-containing nanopores have advantages in nanopore engineering because of their robust structure, making them well-suited for modifications. In this review, we highlight the engineering approaches for β-barrel-containing nanopores used in single-molecule sensing for applications in early diagnosis and prognosis. In the highlighted studies, β-barrel nanopores can be modified by genetic mutation to change the structure; alter charge distributions; or add enzymes, aptamers, and protein probes to enhance sensitivity and accuracy. Furthermore, this review discusses challenges and future perspectives for advancing nanopore-based diagnostic sensors.
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Affiliation(s)
- Rani Wiswedel
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Anh Thi Ngoc Bui
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
| | - Jinhyung Kim
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Mi-Kyung Lee
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
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3
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Mayse LA, Movileanu L. Gating of β-Barrel Protein Pores, Porins, and Channels: An Old Problem with New Facets. Int J Mol Sci 2023; 24:12095. [PMID: 37569469 PMCID: PMC10418385 DOI: 10.3390/ijms241512095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
β barrels are ubiquitous proteins in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. These transmembrane proteins (TMPs) execute a wide variety of tasks. For example, they can serve as transporters, receptors, membrane-bound enzymes, as well as adhesion, structural, and signaling elements. In addition, multimeric β barrels are common structural scaffolds among many pore-forming toxins. Significant progress has been made in understanding the functional, structural, biochemical, and biophysical features of these robust and versatile proteins. One frequently encountered fundamental trait of all β barrels is their voltage-dependent gating. This process consists of reversible or permanent conformational transitions between a large-conductance, highly permeable open state and a low-conductance, solute-restrictive closed state. Several intrinsic molecular mechanisms and environmental factors modulate this universal property of β barrels. This review article outlines the typical signatures of voltage-dependent gating. Moreover, we discuss recent developments leading to a better qualitative understanding of the closure dynamics of these TMPs.
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Affiliation(s)
- Lauren A. Mayse
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244, USA;
- Department of Biomedical and Chemical Engineering, Syracuse University, 223 Link Hall, Syracuse, NY 13244, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244, USA;
- Department of Biomedical and Chemical Engineering, Syracuse University, 223 Link Hall, Syracuse, NY 13244, USA
- The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
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4
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Kim M, Foster JC, Moore MD, Chen M. Improving Single-Molecule Antibody Detection Selectivity through Optimization of Peptide Epitope Presentation in OmpG Nanopore. ACS Sens 2023. [PMID: 37379512 DOI: 10.1021/acssensors.3c00528] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Outer membrane protein G (OmpG) is a monomeric porin found in Escherichia coli, which possesses seven flexible loops. OmpG has been engineered as a nanopore sensor, where its loops can host affinity epitopes for selective detection of biological molecules. In this study, we investigated various loop positions to incorporate a FLAG peptide antigen epitope in the most flexible loop 6 and tested the efficacy and sensitivity of these nanopore constructs in antibody detection. We observed an OmpG construct containing inserted FLAG sequence, which exhibited strong interaction with anti-FLAG antibodies in flow cytometry; however, it could not translate molecule interactions into a readable signal in current recordings. Further optimization of the peptide presentation strategy by replacing specific sections of loop 6 sequences with the FLAG tag created a construct capable of generating unique and distinct signals when interacting with various monoclonal or polyclonal anti-FLAG clones IgG antibodies in the mixture. The peptide display scheme demonstrated in this study can be generalized for the engineering of OmpG sensors, which can be used for screening and validating positive clones during antibody development, as well as for real-time quality control of cell cultures in monoclonal antibody production.
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Affiliation(s)
- Minji Kim
- Department of Food Science, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Joshua C Foster
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Matthew D Moore
- Department of Food Science, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Min Chen
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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5
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Foster JC, Pham B, Pham R, Kim M, Moore MD, Chen M. An Engineered OmpG Nanopore with Displayed Peptide Motifs for Single-Molecule Multiplex Protein Detection. Angew Chem Int Ed Engl 2023; 62:e202214566. [PMID: 36457283 PMCID: PMC9898208 DOI: 10.1002/anie.202214566] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022]
Abstract
Molecular detection via nanopore, achieved by monitoring changes in ionic current arising from analyte interaction with the sensor pore, is a promising technology for multiplex sensing development. Outer Membrane Protein G (OmpG), a monomeric porin possessing seven functionalizable loops, has been reported as an effective sensing platform for selective protein detection. Using flow cytometry to screen unfavorable constructs, we identified two OmpG nanopores with unique peptide motifs displayed in either loop 3 or 6, which also exhibited distinct analyte signals in single-channel current recordings. We exploited these motif-displaying loops concurrently to facilitate single-molecule multiplex protein detection in a mixture. We additionally report a strategy to increase sensor sensitivity via avidity motif display. These sensing schemes may be expanded to more sophisticated designs utilizing additional loops to increase multiplicity and sensitivity.
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Affiliation(s)
- Joshua C Foster
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Bach Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Current address: Department of Chemistry, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Ryan Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Minji Kim
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Matthew D Moore
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Min Chen
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
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6
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Recent Advances in Aptamer‐Based Nanopore Sensing at Single‐Molecule Resolution. Chem Asian J 2022; 17:e202200364. [DOI: 10.1002/asia.202200364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/20/2022] [Indexed: 11/07/2022]
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7
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Hwang HJ, Kim JS, Lee J, Min JS, Jeong KB, Kim E, Lee MK, Chi SW. Single-Molecule Sensing of an Anticancer Therapeutic Protein-Protein Interaction Using the Chemically Modified OmpG Nanopore. Anal Chem 2022; 94:7449-7454. [PMID: 35583342 DOI: 10.1021/acs.analchem.1c04840] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nanopore sensors are a highly attractive platform for single-molecule sensing for sequencing, disease diagnostics, and drug screening. Outer membrane protein G (OmpG) nanopores have advantages for single-molecule sensing owing to their rigid monomeric structure, which comprises seven flexible loops, providing distinct gating patterns upon analyte binding. Blocking of the protein-protein interaction between B-cell lymphoma-extra-large (Bcl-xL) and the BH3 domain of Bcl-2 homologous antagonist/killer (Bak-BH3) has been reported as a promising strategy for anticancer therapy. Here, we characterized the interaction between Bcl-xL and Bak-BH3 as well as its inhibition by a small-molecule inhibitor using click chemistry-based Bak-BH3 peptide-conjugated OmpG nanopores. The binding of Bcl-xL to Bak-BH3 generated characteristic gating signals involving significant changes in the amplitudes of noise and gating parameters such as gating frequency, open probability, and durations of open and closed states. Notably, specific inhibition of Bcl-xL by the small-molecule antagonist, ABT-737, led to the recovery of the noise and gating parameters. Collectively, these results revealed that the chemically modified OmpG nanopore can serve as a valuable sensor platform for ultrasensitive, rapid, and single-molecule-based drug screening against protein-protein interactions, which are therapeutic targets for various diseases.
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Affiliation(s)
- Hye-Jin Hwang
- Disease Target Structure Research Center, Division of Biomedical Research, 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, KRIBB, Daejeon 34141, Republic of Korea
| | - Jeonghyun Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Jun Sik Min
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Ki-Baek Jeong
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon 34141, Republic of Korea
| | - Eunha Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, 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, 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
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8
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Abstract
SignificanceOuter membrane porins play a crucial role in processes as varied as energy production, photosynthesis, and nutrient transport. They act as the gatekeepers between a gram-negative bacterium and its environment. Understanding how these proteins fold and function is important in improving our understanding and control of these processes. Here we use single-molecule methods to help resolve the apparent differences between the fast folding expected on a molecular scale and the slow kinetics observed in ensemble measurements in the laboratory.
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9
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Imran A, Moyer BS, Wolfe AJ, Cosgrove MS, Makarov DE, Movileanu L. Interplay of Affinity and Surface Tethering in Protein Recognition. J Phys Chem Lett 2022; 13:4021-4028. [PMID: 35485934 PMCID: PMC9106920 DOI: 10.1021/acs.jpclett.2c00621] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/27/2022] [Indexed: 05/10/2023]
Abstract
Surface-tethered ligand-receptor complexes are key components in biological signaling and adhesion. They also find increasing utility in single-molecule assays and biotechnological applications. Here, we study the real-time binding kinetics between various surface-immobilized peptide ligands and their unrestrained receptors. A long peptide tether increases the association of ligand-receptor complexes, experimentally proving the fly casting mechanism where the disorder accelerates protein recognition. On the other hand, a short peptide tether enhances the complex dissociation. Notably, the rate constants measured for the same receptor, but under different spatial constraints, are strongly correlated to one another. Furthermore, this correlation can be used to predict how surface tethering on a ligand-receptor complex alters its binding kinetics. Our results have immediate implications in the broad areas of biomolecular recognition, intrinsically disordered proteins, and biosensor technology.
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Affiliation(s)
- Ali Imran
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Brandon S. Moyer
- Ichor
Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United
States
- Lewis
School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Aaron J. Wolfe
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor
Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United
States
- Lewis
School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
- Department
of Chemistry, State University of New York
College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
| | - Michael S. Cosgrove
- Department
of Biochemistry and Molecular Biology, State
University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving
Avenue, Syracuse, New York 13210, United States
| | - Dmitrii E. Makarov
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Oden
Institute
for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Liviu Movileanu
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United
States
- The BioInspired
Institute, Syracuse University, Syracuse, New York 13244, United States
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10
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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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11
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Modifying the pH sensitivity of OmpG nanopore for improved detection at acidic pH. Biophys J 2022; 121:731-741. [PMID: 35131293 PMCID: PMC8943698 DOI: 10.1016/j.bpj.2022.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 01/02/2022] [Accepted: 01/25/2022] [Indexed: 11/22/2022] Open
Abstract
The outer membrane protein G (OmpG) nanopore is a monomeric β-barrel channel consisting of seven flexible extracellular loops. Its most flexible loop, loop 6, can be used to host high-affinity binding ligands for the capture of protein analytes, which induces characteristic current patterns for protein identification. At acidic pH, the ability of OmpG to detect protein analytes is hampered by its tendency toward the closed state, which renders the nanopore unable to reveal current signal changes induced by bound analytes. In this work, critical residues that control the pH-dependent gating of loop 6 were identified, and an OmpG nanopore that can stay predominantly open at a broad range of pHs was created by mutating these pH-sensitive residues. A short single-stranded DNA was chemically tethered to the pH-insensitive OmpG to demonstrate the utility of the OmpG nanopore for sensing complementary DNA and a DNA binding protein at an acidic pH.
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12
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Kamiya K. Formation and function of OmpG or OmpA-incorporated liposomes using an in vitro translation system. Sci Rep 2022; 12:2376. [PMID: 35149747 PMCID: PMC8837779 DOI: 10.1038/s41598-022-06314-4] [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: 10/12/2021] [Accepted: 01/28/2022] [Indexed: 02/08/2023] Open
Abstract
Outer membrane proteins (OMPs), located on the outer membrane of gram-negative bacteria, have a β-strand structure and form nanopores, which allow passage of ions, sugars, and small molecules. Recently, OMPs have been used as sensing elements to detect biological molecules. OMPs are normally expressed and purified from Escherichia coli (E. coli). Although the cell-free synthesis of OMPs, such as OmpA and OmpG, is achieved in the presence of liposomes and periplasmic chaperones, the amount of OmpA and OmpG incorporated into the nano-sized liposomes is not clear. In this study, after in vitro translation, the incorporation of OmpG into purified nano-sized liposomes with various lipid compositions was investigated. Liposomes containing the synthesized OmpG were purified using a stepwise sucrose density gradient. We report that liposomes prepared with the E. coli lipid extract (PE/PG) had the highest amount of OmpG incorporated compared to liposomes with other lipid compositions, as detected by recording the current across the OmpG containing liposomes using the patch clamp technique. This study reveals some of the requirements for the insertion and refolding of OMPs synthesized by the in vitro translation system into lipid membranes, which plays a role in the biological sensing of various molecules.
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Affiliation(s)
- Koki Kamiya
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan.
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13
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Chen H, Lin Y, Long YT, Minteer SD, Ying YL. Nanopore-based measurement of the interaction of P450cam monooxygenase and putidaredoxin at the single-molecule level. Faraday Discuss 2021; 233:295-302. [PMID: 34889330 DOI: 10.1039/d1fd00042j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein-protein interactions occur in a wide range of biological processes and are of great significance to life function. Characterization of transient protein-protein interactions remains a significant barrier to our understanding of cellular processes. Nanopores provide unique nanoscale environments that accommodate single molecules from the surrounding bulk solution. This method permits label-free sensing at the single-molecule level with extremely high sensitivity. Herein, the interaction between a single P450cam monooxygenase and its redox partner putidaredoxin (Pdx) was monitored via transient ionic current by using functionalized glass nanopores. Results show that the volume of P450cam determines the blockage current while the interactions between the P450cam and Pdx give a long blockage duration. Our glass nanopore sensor with adjustable diameter could be applied for real-time sensing of protein-protein interactions between individual proteins with a wide range of molecular weight.
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Affiliation(s)
- Hui Chen
- Department of Chemistry, University of Utah, USA.
| | - Yao Lin
- Department of Chemistry, University of Utah, USA. .,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | | | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China. .,Chemistry and Biomedicine Innovation Center, Nanjing University, China
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14
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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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15
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Robertson JW, Ghimire M, Reiner JE. Nanopore sensing: A physical-chemical approach. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183644. [PMID: 33989531 PMCID: PMC9793329 DOI: 10.1016/j.bbamem.2021.183644] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/30/2022]
Abstract
Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.
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Affiliation(s)
- Joseph W.F. Robertson
- Biophysical and Biomedical Measurement Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg MD. 20899, correspondence to:
| | - Madhav Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, VA
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA
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16
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Sen P, Hoi H, Gupta M. Low Noise Hybrid Nanopore with Engineered OmpG and Bilayer MoS 2. ACS APPLIED BIO MATERIALS 2021; 4:5416-5424. [DOI: 10.1021/acsabm.1c00095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Payel Sen
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton Alberta, Canada
| | - Hiofan Hoi
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton Alberta, Canada
| | - Manisha Gupta
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton Alberta, Canada
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17
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Fujinami Tanimoto IM, Cressiot B, Jarroux N, Roman J, Patriarche G, Le Pioufle B, Pelta J, Bacri L. Selective target protein detection using a decorated nanopore into a microfluidic device. Biosens Bioelectron 2021; 183:113195. [PMID: 33857755 DOI: 10.1016/j.bios.2021.113195] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 10/21/2022]
Abstract
Solid-state nanopores provide a powerful tool to electrically analyze nanoparticles and biomolecules at single-molecule resolution. These biosensors need to have a controlled surface to provide information about the analyte. Specific detection remains limited due to nonspecific interactions between the molecules and the nanopore. Here, a polymer surface modification to passivate the membrane is performed. This functionalization improves nanopore stability and ionic conduction. Moreover, one can control the nanopore diameter and the specific interactions between protein and pore surface. The effect of ionic strength and pH are probed. Which enables control of the electroosmotic driving force and dynamics. Furthermore, a study of polymer chain structure and permeability in the pore are carried out. The nanopore chip is integrated into a microfluidic device to ease its handling. Finally, a discussion of an ionic conductance model through a permeable crown along the nanopore surface is elucidated. The proof of concept is demonstrated by the capture of free streptavidin by the biotins grafted into the nanopore. In the future, this approach could be used for virus diagnostic, nanoparticle or biomarker sensing.
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Affiliation(s)
- Izadora Mayumi Fujinami Tanimoto
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025, Evry-Courcouronnes, France; Université Paris-Saclay, ENS Paris-Saclay, CNRS, LuMIn, Institut d'Alembert, 91190, Gif-sur-Yvette, France
| | | | - Nathalie Jarroux
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025, Evry-Courcouronnes, France
| | - Jean Roman
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, LuMIn, Institut d'Alembert, 91190, Gif-sur-Yvette, France
| | - Gilles Patriarche
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120, Palaiseau, France
| | - Bruno Le Pioufle
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, LuMIn, Institut d'Alembert, 91190, Gif-sur-Yvette, France.
| | - Juan Pelta
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025, Evry-Courcouronnes, France.
| | - Laurent Bacri
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025, Evry-Courcouronnes, France.
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18
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Diederichs T, Tampé R. Membrane-Suspended Nanopores in Microchip Arrays for Stochastic Transport Recording and Sensing. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.703673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The transport of nutrients, xenobiotics, and signaling molecules across biological membranes is essential for life. As gatekeepers of cells, membrane proteins and nanopores are key targets in pharmaceutical research and industry. Multiple techniques help in elucidating, utilizing, or mimicking the function of biological membrane-embedded nanodevices. In particular, the use of DNA origami to construct simple nanopores based on the predictable folding of nucleotides provides a promising direction for innovative sensing and sequencing approaches. Knowledge of translocation characteristics is crucial to link structural design with function. Here, we summarize recent developments and compare features of membrane-embedded nanopores with solid-state analogues. We also describe how their translocation properties are characterized by microchip systems. The recently developed silicon chips, comprising solid-state nanopores of 80 nm connecting femtoliter cavities in combination with vesicle spreading and formation of nanopore-suspended membranes, will pave the way to characterize translocation properties of nanopores and membrane proteins in high-throughput and at single-transporter resolution.
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19
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Fahie MA, Candido J, Andree G, Chen M. Tuning Protein Discrimination Through Altering the Sampling Interface Formed between the Analyte and the OmpG Nanopore. ACS Sens 2021; 6:1286-1294. [PMID: 33599487 DOI: 10.1021/acssensors.0c02580] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nanopore sensors capable of distinguishing homologous protein analytes are highly desirable tools for proteomics research and disease diagnostics. Recently, an engineered outer membrane protein G (OmpG) nanopore with a high-affinity ligand attached to a gating loop 6 showed specificity for distinguishing homologous proteins in complex mixtures. Here, we report the development of OmpG nanopores with the other six loops used as the anchoring point to host an affinity ligand for protein sensing. We investigated how the analyte binding to the affinity ligand located at different loops affects the detection sensitivity, selectivity, and specificity. Our results reveal that analytes weakly attracted to the OmpG nanopore surface are only detectable when the ligand is tethered to loop 6. In contrast, protein analytes that form a strong interaction with the OmpG surface via electrostatic attractions are distinguishable by all seven OmpG nanopore constructs. In addition, the same analyte can generate distinct binding signals with different OmpG nanopore constructs. The ability to exploit all seven OmpG loops will aid the design of a new generation of OmpG sensors with increased sensitivity, selectivity, and specificity for biomarker sensing.
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Affiliation(s)
- Monifa A. Fahie
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Jonathan Candido
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Gisele Andree
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Min Chen
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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20
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Larimi MG, Ha JH, Loh SN, Movileanu L. Insertion state of modular protein nanopores into a membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183570. [PMID: 33529578 DOI: 10.1016/j.bbamem.2021.183570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/06/2021] [Accepted: 01/13/2021] [Indexed: 01/04/2023]
Abstract
In the past decade, significant progress has been made in the development of new protein nanopores. Despite these advancements, there is a pressing need for the creation of nanopores equipped with relatively large functional groups for the sampling of biomolecular events on their extramembranous side. Here, we designed, produced, and analyzed protein nanopores encompassing a robust truncation of a monomeric β-barrel membrane protein. An exogenous stably folded protein was anchored within the aqueous phase via a flexible peptide tether of varying length. We have extensively examined the pore-forming properties of these modular protein nanopores using protein engineering and single-molecule electrophysiology. This study revealed distinctions in the nanopore conductance and current fluctuations that arose from tethering the exogenous protein to either the N terminus or the C terminus. Remarkably, these nanopores insert into a planar lipid membrane with one specific conductance among a set of three substate conductance values. Moreover, we demonstrate that the occurrence probabilities of these insertion substates depend on the length of the peptide tether, the orientation of the exogenous protein with respect to the nanopore opening, and the molecular mass of tethered protein. In addition, the three conductance values remain unaltered by major changes in the composition of modular nanopores. The outcomes of this work serve as a platform for further developments in areas of protein engineering of transmembrane pores and biosensor technology.
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Affiliation(s)
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY 13210, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA; Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY 13244, USA.
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21
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Pham B, Chisholm CM, Foster J, Friis E, Fahie MA, Chen M. A pH-independent quiet OmpG pore with enhanced electrostatic repulsion among the extracellular loops. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183485. [PMID: 33058855 DOI: 10.1016/j.bbamem.2020.183485] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/22/2020] [Indexed: 11/16/2022]
Abstract
Membrane protein pores have emerged as powerful nanopore sensors for single-molecule detection. OmpG, a monomeric nanopore, is comprised of fourteen β-strands connected by seven flexible extracellular loops. The OmpG nanopore exhibits pH-dependent gating as revealed by planar lipid bilayer studies. Current evidence strongly suggests that the dynamic movement of loop 6 is responsible for the gating mechanism. In this work, we have shown that enhancing the electrostatic repulsion forces between extracellular loops suppressed the pH-dependent gating. Our mutant containing additional negative charges in loop 6 and loop 1 exhibited minimal spontaneous gating and reduced sensitivity to pH changes compared to the wild type OmpG. These results provide new evidence to support the mechanism of OmpG gating controlled by the complex electrostatic network around the gating loop 6. The pH-independent quiet OmpG pores could potentially be used as a sensing platform that operates at a broad range of pH conditions.
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Affiliation(s)
- Bach Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - Christina M Chisholm
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - Joshua Foster
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - Emily Friis
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - Monifa A Fahie
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - Min Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, United States; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, United States.
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22
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Mutter NL, Huang G, van der Heide NJ, Lucas FLR, Galenkamp NS, Maglia G, Wloka C. Preparation of Fragaceatoxin C (FraC) Nanopores. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2020; 2186:3-10. [PMID: 32918725 DOI: 10.1007/978-1-0716-0806-7_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological nanopores are an emerging class of biosensors with high-end precision owing to their reproducible fabrication at the nanometer scale. Most notably, nanopore-based DNA sequencing applications are currently being commercialized, while nanopore-based proteomics may become a reality in the near future.Although membrane proteins often prove to be difficult to purify, we describe a straightforward protocol for the preparation of Fragaceatoxin C (FraC) nanopores, which may have applications for DNA analysis and nanopore-based proteomics. Recombinantly expressed FraC nanopores are purified via two rounds of Ni-NTA affinity chromatography before and after oligomerization on sphingomyelin-containing liposomes. Starting from a plasmid vector containing the FraC gene, our method allows the production of purified nanopores within a week. Afterward, the FraC nanopores can be stored at +4 °C for several months, or frozen.
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Affiliation(s)
- Natalie Lisa Mutter
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Gang Huang
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | | | - Nicole Stéphanie Galenkamp
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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23
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Zernia S, van der Heide NJ, Galenkamp NS, Gouridis G, Maglia G. Current Blockades of Proteins inside Nanopores for Real-Time Metabolome Analysis. ACS NANO 2020; 14:2296-2307. [PMID: 32003969 PMCID: PMC7045694 DOI: 10.1021/acsnano.9b09434] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/31/2020] [Indexed: 05/14/2023]
Abstract
Biological nanopores are emerging as powerful and low-cost sensors for real-time analysis of biological samples. Proteins can be incorporated inside the nanopore, and ligand binding to the protein adaptor yields changes in nanopore conductance. In order to understand the origin of these conductance changes and develop sensors for detecting metabolites, we tested the signal originating from 13 different protein adaptors. We found that the quality of the protein signal depended on both the size and charge of the protein. The engineering of a dipole within the surface of the adaptor reduced the current noise by slowing the protein dynamics within the nanopore. Further, the charge of the ligand and the induced conformational changes of the adaptor defined the conductance changes upon metabolite binding, suggesting that the protein resides in an electrokinetic minimum within the nanopore, the position of which is altered by the ligand. These results represent an important step toward understanding the dynamics of the electrophoretic trapping of proteins inside nanopores and will allow developing next-generation sensors for metabolome analysis.
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Affiliation(s)
- Sarah Zernia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Nieck Jordy van der Heide
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Nicole Stéphanie Galenkamp
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Giorgos Gouridis
- Rega
Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, Box 1037, 3000 Leuven, Belgium
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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24
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Wu X, Li M, Ying Y, Long Y. The Effects of Tetramethylammonium Cation on Oligonucleotide Analysis with Aerolysin Nanopore. ChemElectroChem 2019. [DOI: 10.1002/celc.201901376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Xue‐Yuan Wu
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Meng‐Yin Li
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Yi‐Lun Ying
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
- School of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P. R. China 163 Xianlin Road, Qixia District, Nanjing, Jiangsu Province
| | - Yi‐Tao Long
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
- School of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P. R. China 163 Xianlin Road, Qixia District, Nanjing, Jiangsu Province
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25
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Ying YL, Long YT. Nanopore-Based Single-Biomolecule Interfaces: From Information to Knowledge. J Am Chem Soc 2019; 141:15720-15729. [DOI: 10.1021/jacs.8b11970] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- 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
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, 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
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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26
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Pham B, Eron SJ, Hill ME, Li X, Fahie MA, Hardy JA, Chen M. A Nanopore Approach for Analysis of Caspase-7 Activity in Cell Lysates. Biophys J 2019; 117:844-855. [PMID: 31427065 PMCID: PMC6731459 DOI: 10.1016/j.bpj.2019.07.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 07/02/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022] Open
Abstract
Caspases are an important protease family that coordinate inflammation and programmed cell death. Two closely related caspases, caspase-3 and caspase-7, exhibit largely overlapping substrate specificities. Assessing their proteolytic activities individually has therefore proven extremely challenging. Here, we constructed an outer membrane protein G (OmpG) nanopore with a caspase substrate sequence DEVDG grafted into one of the OmpG loops. Cleavage of the substrate sequence in the nanopore by caspase-7 generated a characteristic signal in the current recording of the OmpG nanopore that allowed the determination of the activity of caspase-7 in Escherichia coli cell lysates. Our approach may provide a framework for the activity-based profiling of proteases that share highly similar substrate specificity spectrums.
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Affiliation(s)
- Bach Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Scott J Eron
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Maureen E Hill
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Xin Li
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Monifa A Fahie
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Jeanne A Hardy
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Min Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts.
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27
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Schmitt C, Bafna JA, Schmid B, Klingl S, Baier S, Hemmis B, Wagner R, Winterhalter M, Voll LM. Manipulation of charge distribution in the arginine and glutamate clusters of the OmpG pore alters sugar specificity and ion selectivity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183021. [PMID: 31306626 DOI: 10.1016/j.bbamem.2019.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 07/02/2019] [Accepted: 07/09/2019] [Indexed: 01/08/2023]
Abstract
OmpG is a general diffusion pore in the E. coli outer membrane with a molecular architecture comprising a 14-stranded β-barrel scaffold and unique structural features. In contrast to other non-specific porins, OmpG lacks a central constriction zone and has an exceptionally wide pore diameter of about 13 Å. The equatorial plane of OmpG harbors an annulus of four alternating basic and acidic patches whose function is only poorly characterized. We have investigated the role of charge distribution for ion selectivity and sugar transport with the help of OmpG variants mutated in the annulus. Substituting the glutamate residues of the annulus for histidines or alanines led to a strong reduction in cation selectivity. Replacement of the glutamates in the annulus by histidine residues also disfavored the passage of pentoses and hexoses relative to disaccharides. Our results demonstrate that despite the wide pore diameter, an annulus only consisting of two opposing basic patches confers reduced cation and monosaccharide transport compared to OmpG wild type. Furthermore, randomization of charged residues in the annulus had the potential to abolish pH-dependency of sugar transport. Our results indicate that E15, E31, R92, R111 and R211 in the annulus form electrostatic interactions with R228, E229 and D232 in loop L6 that influence pH-dependency of sugar transport.
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Affiliation(s)
- Christine Schmitt
- Division of Biochemistry and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany; Department Biology, Division of Plant Physiology, Philipps-University Marburg, D-35043 Marburg, Germany.
| | - Jayesh Arun Bafna
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719 Bremen, Germany.
| | - Benedikt Schmid
- Division of Biotechnology and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany.
| | - Stefan Klingl
- Division of Biotechnology and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany.
| | - Steffen Baier
- Division of Biochemistry and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany
| | - Birgit Hemmis
- Department of Biology and Chemistry, University of Osnabrück, D-49069 Osnabrück, Germany
| | - Richard Wagner
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719 Bremen, Germany; Department of Biology and Chemistry, University of Osnabrück, D-49069 Osnabrück, Germany.
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719 Bremen, Germany.
| | - Lars M Voll
- Division of Biochemistry and Applied Protein Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058 Erlangen, Germany; Department Biology, Division of Plant Physiology, Philipps-University Marburg, D-35043 Marburg, Germany.
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28
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Wilson J, Sarthak K, Si W, Gao L, Aksimentiev A. Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model. ACS Sens 2019; 4:634-644. [PMID: 30821441 DOI: 10.1021/acssensors.8b01375] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nanopore sensing has emerged as a versatile approach to detection and identification of biomolecules. Presently, researchers rely on experience and intuition for choosing or modifying the nanopores to detect a target analyte. The field would greatly benefit from a computational method that could relate the atomic-scale geometry of the nanopores and analytes to the blockade nanopore currents they produce. Existing computational methods are either computationally too expensive to be used routinely in experimental laboratories or not sensitive enough to account for the atomic structure of the pore and the analytes. Here, we demonstrate a robust and inexpensive computational approach-the steric exclusion model (SEM) of nanopore conductance-that is orders of magnitude more efficient than all-atom MD and yet is sensitive enough to account for the atomic structure of the nanopore and the analyte. The method combines the computational efficiency of a finite element solver with the atomic precision of a nanopore conductance map to yield unprecedented speed and accuracy of ionic current prediction. We validate our SEM approach through comparison with the current blockades computed using the all-atom molecular dynamics method for a range of proteins confined to a solid-state nanopore, biological channels embedded in a lipid bilayer membranes, and blockade currents produced by DNA homopolymers in MspA. We illustrate potential applications of SEM by computing blockade currents produced by nucleosome proteins in a solid-state nanopore, individual amino acids in MspA, and by testing the effect of point mutations on amino acid distinguishability. We expect our SEM approach to become an integral part of future development of the nanopore sensing field.
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Affiliation(s)
| | | | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing, 210096, China
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29
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Neves MMPDS, Martín-Yerga D. Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging. BIOSENSORS 2018; 8:E100. [PMID: 30373209 PMCID: PMC6316691 DOI: 10.3390/bios8040100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 01/01/2023]
Abstract
Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.
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Affiliation(s)
| | - Daniel Martín-Yerga
- Department of Chemical Engineering, KTH Royal Institute of Technology, 100-44 Stockholm, Sweden.
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30
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Perez-Rathke A, Fahie MA, Chisholm C, Liang J, Chen M. Mechanism of OmpG pH-Dependent Gating from Loop Ensemble and Single Channel Studies. J Am Chem Soc 2018; 140:1105-1115. [PMID: 29262680 DOI: 10.1021/jacs.7b11979] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Outer membrane protein G (OmpG) from Escherichia coli has exhibited pH-dependent gating that can be employed by bacteria to alter the permeability of their outer membranes in response to environmental changes. We developed a computational model, Protein Topology of Zoetic Loops (Pretzel), to investigate the roles of OmpG extracellular loops implicated in gating. The key interactions predicted by our model were verified by single-channel recording data. Our results indicate that the gating equilibrium is primarily controlled by an electrostatic interaction network formed between the gating loop and charged residues in the lumen. The results shed light on the mechanism of OmpG gating and will provide a fundamental basis for the engineering of OmpG as a nanopore sensor. Our computational Pretzel model could be applied to other outer membrane proteins that contain intricate dynamic loops that are functionally important.
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Affiliation(s)
- Alan Perez-Rathke
- Department of Bioengineering, University of Illinois at Chicago , Chicago, Illinois 60607, United States
| | | | | | - Jie Liang
- Department of Bioengineering, University of Illinois at Chicago , Chicago, Illinois 60607, United States
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31
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Mádai E, Matejczyk B, Dallos A, Valiskó M, Boda D. Controlling ion transport through nanopores: modeling transistor behavior. Phys Chem Chem Phys 2018; 20:24156-24167. [DOI: 10.1039/c8cp03918f] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present a modeling study of a nanopore-based transistor computed by a mean-field continuum theory (Poisson–Nernst–Planck, PNP) and a hybrid method including particle simulation (Local Equilibrium Monte Carlo, LEMC) that is able to take ionic correlations into account including the finite size of ions.
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Affiliation(s)
- Eszter Mádai
- Department of Physical Chemistry
- University of Pannonia
- H-8201 Veszprém
- Hungary
| | | | - András Dallos
- Department of Physical Chemistry
- University of Pannonia
- H-8201 Veszprém
- Hungary
| | - Mónika Valiskó
- Department of Physical Chemistry
- University of Pannonia
- H-8201 Veszprém
- Hungary
| | - Dezső Boda
- Department of Physical Chemistry
- University of Pannonia
- H-8201 Veszprém
- Hungary
- Institute of Advanced Studies Köszeg (iASK)
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Affiliation(s)
- Wenqing Shi
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alicia K. Friedman
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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