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Zheng Y, Chen J, Wang X, Xu D, Sun H, Huang Z, Wang P, Fang Y. Absorption-Based Rapid Acquisition of Single-Molecule Kinetics from Unstable Enzymes in Microdroplets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309463. [PMID: 38342668 DOI: 10.1002/smll.202309463] [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: 10/18/2023] [Revised: 01/30/2024] [Indexed: 02/13/2024]
Abstract
Single-molecule catalysis reflects the heterogeneity of each molecule, providing a unique insight into the complex catalytic mechanism through the statistics of stochastic individuals. However, the present study methods for single-molecule catalysis are either complicated or have low throughput, limiting their rapid acquisition of single-molecule reaction kinetics with statistical significance. Here, a label-free imaging method is developed for the study of single-molecule catalysis in microdroplets with high throughput based on the absorption of the reaction molecules. A wide distribution of the catalytic reaction rate constant value of 238-2026 molecules s-1 is observed from 68 single enzymes. Interestingly, an exponential decayed distribution of the enzyme activity can be clearly observed due to the rapid denaturation of the enzymes. The denaturation mechanism of the Horse Radish Peroxidase (HRP) enzyme is clarified. It is revealed that the denaturation of each enzyme goes through a gradual decay rather than a truncated turn-off process from a single molecule point of view. This absorption-based method can be applied to most of the catalytic reactions with high throughput, which offers an indispensable route for the rapid statistical analysis of various single-molecule catalytic reactions, making it particularly suitable for the acquisition of catalytic kinetics from highly unstable enzymes.
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Affiliation(s)
- Yuhao Zheng
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Jinghu Chen
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Xinyi Wang
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Dou Xu
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Hao Sun
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Zongxiong Huang
- National Textile and Garment Quality Supervision Testing Center, Fujian Fiber Inspection Center, Fuzhou, Fujian, 350026, China
| | - Pengcheng Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Yimin Fang
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
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Wan Y, Qiu Y, Zhou J, Liu J, Stuart MAC, Peng Y, Wang J. Stable and permeable polyion complex vesicles designed as enzymatic nanoreactors. SOFT MATTER 2024; 20:3499-3507. [PMID: 38595066 DOI: 10.1039/d4sm00216d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Polymeric vesicles are perspective vehicles for fabricating enzymatic nanoreactors towards diverse biomedical and catalytic applications, yet the design of stable and permeable vesicles remains challenging. Herein, we developed polyion complex (PIC) vesicles featuring high stability and a permeable membrane for adequate enzyme loading and activation. Our design relies on co-assembly of an anionic diblock copolymer (PSS96-b-PEO113) with cationic branched poly(ethylenimine) (PEI). The polymer combination endows strong electrostatic interaction between the PSS and PEI building blocks, so their assembly can be implemented at a high salt concentration (500 mM NaCl), under which the charge interaction of the enzyme-polymer is inhibited. This control realizes the successful and safe loading of enzymes associated with the formation of stable PIC vesicles with an intrinsic permeable membrane that is favourable for enhancing enzymatic activity. The control factors for vesicle formation and enzyme loading were investigated, and the general application of loading different enzymes for cascade reaction was validated as well. Our study reveals that proper design and combination of polyelectrolytes is a facile strategy for fabricating stable and permeable polymeric PIC vesicles, which exhibit clear advantages for loading and activating enzymes, consequently boosting their diverse applications as enzymatic nanoreactors.
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Affiliation(s)
- Yuting Wan
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China.
| | - Yuening Qiu
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China.
| | - Jin Zhou
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China.
| | - Jinbo Liu
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China.
| | - Martien A Cohen Stuart
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China.
| | - Yangfeng Peng
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China.
| | - Junyou Wang
- State-Key Laboratory of Chemical Engineering, and Shanghai Key Laboratory of Multiphase Materials Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China.
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Ghosh S, Baltussen MG, Ivanov NM, Haije R, Jakštaitė M, Zhou T, Huck WTS. Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems. Chem Rev 2024; 124:2553-2582. [PMID: 38476077 PMCID: PMC10941194 DOI: 10.1021/acs.chemrev.3c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.
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Affiliation(s)
- Souvik Ghosh
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mathieu G. Baltussen
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Nikita M. Ivanov
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Rianne Haije
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Miglė Jakštaitė
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Tao Zhou
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and
Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Zhao Y, Huang Q, Li Q, Chen Z, Liu Y. Bidirectional Regulation of Intracellular Enzyme Activity Using Light-Driven Nano-Inhibitors. Angew Chem Int Ed Engl 2024; 63:e202318533. [PMID: 38196066 DOI: 10.1002/anie.202318533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/24/2023] [Accepted: 01/09/2024] [Indexed: 01/11/2024]
Abstract
Photochemical regulation provides precise control over enzyme activities with high spatiotemporal resolution. A promising approach involves anchoring "photoswitches" at enzyme active sites to modulate substrate recognition. However, current methods often require genetic mutations and irreversible enzyme modifications for the site-specific anchoring of "photoswitches", potentially compromising the enzyme activities. Herein, we present a pioneering reversible nano-inhibitor based on molecular imprinting technique for bidirectional regulation of intracellular enzyme activity. The nano-inhibitor employs a molecularly imprinted polymer nanoparticle as its body and azobenzene-modified inhibitors ("photoswitches") as the arms. By using a target enzyme as the molecular template, the nano-inhibitor acquires oriented binding sites on its surface, resulting in a high affinity for the target enzyme and non-covalently firm anchoring of the azobenzene-modified inhibitor to the enzyme active site. Harnessing the reversible isomerization of azobenzene units upon exposure to ultraviolet and visible light, the nano-inhibitor achieves bidirectional enzyme activity regulation by precisely docking and undocking inhibitor at the active site. Notably, this innovative approach enables the facile in situ regulation of intracellular endogenous enzymes, such as carbonic anhydrase. Our results represent a practical and versatile tool for precise enzyme activity regulation in complex intracellular environments.
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Affiliation(s)
- Yu Zhao
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Qingqing Huang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Qiushi Li
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Zihan Chen
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Yang Liu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
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Duru J, Rüfenacht A, Löhle J, Pozzi M, Forró C, Ledermann L, Bernardi A, Matter M, Renia A, Simona B, Tringides CM, Bernhard S, Ihle SJ, Hengsteler J, Maurer B, Zhang X, Nakatsuka N. Driving electrochemical reactions at the microscale using CMOS microelectrode arrays. LAB ON A CHIP 2023; 23:5047-5058. [PMID: 37916299 PMCID: PMC10661664 DOI: 10.1039/d3lc00630a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/25/2023] [Indexed: 11/03/2023]
Abstract
Precise control of pH values at electrode interfaces enables the systematic investigation of pH-dependent processes by electrochemical means. In this work, we employed high-density complementary metal-oxide-semiconductor (CMOS) microelectrode arrays (MEAs) as miniaturized systems to induce and confine electrochemical reactions in areas corresponding to the pitch of single electrodes (17.5 μm). First, we present a strategy for generating localized pH patterns on the surface of the CMOS MEA with unprecedented spatial resolution. Leveraging the versatile routing capabilities of the switch matrix beneath the CMOS MEA, we created arbitrary combinations of anodic and cathodic electrodes and hence pH patterns. Moreover, we utilized the system to produce polymeric surface patterns by additive and subtractive methods. For additive patterning, we controlled the in situ formation of polydopamine at the microelectrode surface through oxidation of free dopamine above a threshold pH > 8.5. For subtractive patterning, we removed cell-adhesive poly-L-lysine from the electrode surface and backfilled the voids with antifouling polymers. Such polymers were chosen to provide a proof-of-concept application of controlling neuronal growth via electrochemically-induced patterns on the CMOS MEA surface. Importantly, our platform is compatible with commercially available high-density MEAs and requires no custom equipment, rendering the findings generalizable and accessible.
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Affiliation(s)
- Jens Duru
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | - Arielle Rüfenacht
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | - Josephine Löhle
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | - Marcello Pozzi
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | - Csaba Forró
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | - Linus Ledermann
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | - Aeneas Bernardi
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | - Michael Matter
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | - André Renia
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | | | - Christina M Tringides
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | - Stéphane Bernhard
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland
| | - Stephan J Ihle
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | - Julian Hengsteler
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | - Benedikt Maurer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | - Xinyu Zhang
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland.
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Zhao Y, Gao S, Song D, Ye Z, Xu R, Luo Y, Xu Q. Lipidoid Artificial Compartments for Bidirectional Regulation of Enzyme Activity through Nanomechanical Action. J Am Chem Soc 2023; 145:551-559. [PMID: 36537880 DOI: 10.1021/jacs.2c11004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Photoresponsive inhibitor and noninhibitor systems have been developed to achieve on-demand enzyme activity control. However, inhibitors are only effective for a specific and narrow range of enzymes. Noninhibitor systems usually require mutation and modification of the enzymes, leading to irreversible loss of enzymatic activities. Inspired by biological membranes, we herein report a lipidoid-based artificial compartment composed of azobenzene (Azo) lipidoids and helper lipids, which can bidirectionally regulate the activity of the encapsulated enzymes by light. In this system, the reversible photoisomerization of Azo lipidoids triggered by UV/vis light creates a continuous rotation-inversion movement, thereby enhancing the permeability of the compartment membrane and allowing substrates to pass through. Moreover, the membrane can revert to its impermeable state when light is removed. Thus, enzyme activity can be switched on and off when encapsulating enzymes in the compartments. Importantly, since neither mutation nor modification is required, negligible loss of activity is observed for the encapsulated enzymes after repeated activation and inhibition. Furthermore, this approach provides a generic strategy for controlling multiple enzymes by forgoing the use of inhibitors and may broaden the applications of enzymes in biological mechanism research and precision medicine.
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Affiliation(s)
- Yu Zhao
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Shuliang Gao
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Donghui Song
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Zhongfeng Ye
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Ruijie Xu
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Ying Luo
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
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