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Wang BP, Yin X, Huang MY, Li TY, Long XF, Li Y, Niu FX. A Self-Assembling γPFD-SpyCatcher Hydrogel Scaffold for the Coimmobilization of SpyTag-Enzymes to Facilitate the Catalysis of Regulated Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39194331 DOI: 10.1021/acs.jafc.4c03403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
In this study, a γPFD-SpyCatcher hydrogel scaffold with the capacity for spontaneous assembly was established. With a maximum loading capacity of a 1:1 molar ratio with SpyTag-enzymes, the immobilized proteins can not only rapidly provide pure enzymes but also exhibit improved thermal and pH stability. The results of the transmission electron microscopic analysis and the traits they present indicated that SpyCatcher promotes the aggregation of γPFD and the formation of hydrogels. In the cell-free pyruvate synthesis system, the γPFD-SpyCatcher coimmobilized SpyTag-hexokinase (HK), SpyTag-phosphofructokinase (PFK) and SpyTag-pyruvate kinase (PK) were employed, and the production of pyruvate increased by 43, 78 and 47% respectively. In in vitro experiments, the oxidative deamination activity of glutamate dehydrogenase (GDH) coimmobilized with γPFD-SpyCatcher was 38% higher than that of purified enzymes. These findings indicate that the γPFD-SpyCatcher-based hydrogels play an important role in breaking the barrier of regulatory enzymes and will provide more strategies for the development of synthetic biology.
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Affiliation(s)
- Bei-Ping Wang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Xue Yin
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Ming-Yue Huang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Tian-Yan Li
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Xiu-Feng Long
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Ya Li
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Fu-Xing Niu
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
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2
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Huang J, Jaekel A, van den Boom J, Podlesainski D, Elnaggar M, Heuer-Jungemann A, Kaiser M, Meyer H, Saccà B. A modular DNA origami nanocompartment for engineering a cell-free, protein unfolding and degradation pathway. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01738-7. [PMID: 39075293 DOI: 10.1038/s41565-024-01738-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 05/28/2024] [Indexed: 07/31/2024]
Abstract
Within the cell, chemical reactions are often confined and organized through a modular architecture. This facilitates the targeted localization of molecular species and their efficient translocation to subsequent sites. Here we present a cell-free nanoscale model that exploits compartmentalization strategies to carry out regulated protein unfolding and degradation. Our synthetic model comprises two connected DNA origami nanocompartments (each measuring 25 nm × 41 nm × 53 nm): one containing the protein unfolding machine, p97, and the other housing the protease chymotrypsin. We achieve the unidirectional immobilization of p97 within the first compartment, establishing a gateway mechanism that controls substrate recruitment, translocation and processing within the second compartment. Our data show that, whereas spatial confinement increases the rate of the individual reactions by up to tenfold, the physical connection of the compartmentalized enzymes into a chimera efficiently couples the two reactions and reduces off-target proteolysis by almost sixfold. Hence, our modular approach may serve as a blueprint for engineering artificial nanofactories with reshaped catalytic performance and functionalities beyond those observed in natural systems.
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Affiliation(s)
- J Huang
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, Essen, Germany
| | - A Jaekel
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, Essen, Germany
| | - J van den Boom
- Molecular Biology, ZMB, University of Duisburg-Essen, Essen, Germany
| | - D Podlesainski
- Chemical Biology, ZMB, University of Duisburg-Essen, Essen, Germany
| | - M Elnaggar
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - M Kaiser
- Chemical Biology, ZMB, University of Duisburg-Essen, Essen, Germany
| | - H Meyer
- Molecular Biology, ZMB, University of Duisburg-Essen, Essen, Germany.
| | - B Saccà
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, Essen, Germany.
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3
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Kröll S, Niemeyer CM. Nucleic Acid-based Enzyme Cascades-Current Trends and Future Perspectives. Angew Chem Int Ed Engl 2024; 63:e202314452. [PMID: 37870888 DOI: 10.1002/anie.202314452] [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: 09/26/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 10/24/2023]
Abstract
The natural micro- and nanoscale organization of biomacromolecules is a remarkable principle within living cells, allowing for the control of cellular functions by compartmentalization, dimensional diffusion and substrate channeling. In order to explore these biological mechanisms and harness their potential for applications such as sensing and catalysis, molecular scaffolding has emerged as a promising approach. In the case of synthetic enzyme cascades, developments in DNA nanotechnology have produced particularly powerful scaffolds whose addressability can be programmed with nanometer precision. In this minireview, we summarize recent developments in the field of biomimetic multicatalytic cascade reactions organized on DNA nanostructures. We emphasize the impact of the underlying design principles like DNA origami, efficient strategies for enzyme immobilization, as well as the importance of experimental design parameters and theoretical modeling. We show how DNA nanostructures have enabled a better understanding of diffusion and compartmentalization effects at the nanometer length scale, and discuss the challenges and future potential for commercial applications.
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Affiliation(s)
- Sandra Kröll
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1, Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1, Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany
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4
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Naveenkumar PM, Maheshwari H, Gundabala V, Mann S, Sharma KP. Patterning of Protein-Sequestered Liquid-Crystal Droplets Using Acoustic Wave Trapping. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:871-881. [PMID: 38131278 DOI: 10.1021/acs.langmuir.3c03031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Development of spatially organized structures and understanding their role in controlling kinetics of multistep chemical reactions are essential for the successful design of efficient systems and devices. While studies that showcase different types of methodologies for the spatial organization of various colloidal systems are known, design and development of well-defined hierarchical assemblies of liquid-crystal (LC) droplets and subsequent demonstration of biological reactions using such assemblies still remain elusive. Here, we show reversible and reconfigurable one-dimensional (1D) assemblies of protein-bioconjugate-sequestered monodisperse LC droplets by combining microfluidics with noninvasive acoustic wave trapping technology. Tunable spatial geometries and lattice dimensions can be achieved in an aqueous medium comprising ≈19 or 62 μm LC droplets. Different assemblies of a mixed population of larger and smaller droplets sequestered with glucose oxidase (GOx) and horseradish peroxidase (HRP), respectively, exhibit spatially localized enzyme kinetics with higher initial rates of reaction compared with GOx/HRP cascades implemented in the absence of an acoustic field. This can be attributed to the direct substrate transfer/channeling between the two complementary enzymes in close proximity. Therefore, our study provides an initial step toward the fabrication of LC-based devices for biosensing applications.
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Affiliation(s)
| | - Harsha Maheshwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Venkat Gundabala
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Stephen Mann
- Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, BS8 1TS Bristol, U.K
| | - Kamendra P Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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5
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Kröll S, Burgahn T, Rabe KS, Franzreb M, Niemeyer CM. Nano- and Microscale Confinements in DNA-Scaffolded Enzyme Cascade Reactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304578. [PMID: 37732702 DOI: 10.1002/smll.202304578] [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: 05/31/2023] [Revised: 08/24/2023] [Indexed: 09/22/2023]
Abstract
Artificial reconstruction of naturally evolved principles, such as compartmentalization and cascading of multienzyme complexes, offers enormous potential for the development of biocatalytic materials and processes. Due to their unique addressability at the nanoscale, DNA origami nanostructures (DON) have proven to be an exceptionally powerful tool for studying the fundamental processes in biocatalytic cascades. To systematically investigate the diffusion-reaction network of (co)substrate transfer in enzyme cascades, a model system of stereoselective ketoreductase (KRED) with cofactor regenerating enzyme is assembled in different spatial arrangements on DNA nanostructures and is located in the sphere of microbeads (MB) as a spatially confining nano- and microenvironment, respectively. The results, obtained through the use of highly sensitive analytical methods, Western blot-based quantification of the enzymes, and mass spectrometric (MS) product detection, along with theoretical modeling, provide strong evidence for the presence of two interacting compartments, the diffusion layers around the microbead and the DNA scaffold, which influence the catalytic efficiency of the cascade. It is shown that the microscale compartment exerts a strong influence on the productivity of the cascade, whereas the nanoscale arrangement of enzymes has no influence but can be modulated by the insertion of a diffusion barrier.
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Affiliation(s)
- Sandra Kröll
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Teresa Burgahn
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Matthias Franzreb
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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6
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Wang X, Jiang Y, Liu H, Yuan H, Huang D, Wang T. Research progress of multi-enzyme complexes based on the design of scaffold protein. BIORESOUR BIOPROCESS 2023; 10:72. [PMID: 38647916 PMCID: PMC10992622 DOI: 10.1186/s40643-023-00695-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/04/2023] [Indexed: 04/25/2024] Open
Abstract
Multi-enzyme complexes designed based on scaffold proteins are a current topic in molecular enzyme engineering. They have been gradually applied to increase the production of enzyme cascades, thereby achieving effective biosynthetic pathways. This paper reviews the recent progress in the design strategy and application of multi-enzyme complexes. First, the metabolic channels in the multi-enzyme complex have been introduced, and the construction strategies of the multi-enzyme complex emerging in recent years have been summarized. Then, the discovered enzyme cascades related to scaffold proteins are discussed, emphasizing on the influence of the linker on the fusion enzyme (fusion protein) and its possible mechanism. This review is expected to provide a more theoretical basis for the modification of multi-enzyme complexes and broaden their applications in synthetic biology.
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Affiliation(s)
- Xiangyi Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Yi Jiang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Hongling Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Haibo Yuan
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Di Huang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Tengfei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China.
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China.
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7
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Wang Y, Douglas T. Tuning Multistep Biocatalysis through Enzyme and Cofactor Colocalization in Charged Porous Protein Macromolecular Frameworks. ACS APPLIED MATERIALS & INTERFACES 2023; 15:43621-43632. [PMID: 37695852 DOI: 10.1021/acsami.3c10340] [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: 09/13/2023]
Abstract
Spatial organization of biocatalytic activities is crucial to organisms to efficiently process complex metabolism. Inspired by this mechanism, artificial scaffold structures are designed to harbor functionally coupled biocatalysts, resulting in acellular materials that can complete multistep reactions at high efficiency and low cost. Substrate channeling is an approach for efficiency enhancement of multistep reactions, but fast diffusion of small molecule intermediates poses a major challenge to achieve channeling in vitro. Here, we explore how multistep biocatalysis is affected, and can be modulated, by cofactor-enzyme colocalization within a synthetic bioinspired material. In this material, a heterogeneous protein macromolecular framework (PMF) acts as a porous host matrix for colocalization of two coupled enzymes and their small molecule cofactor, nicotinamide adenine dinucleotide (NAD). After formation of the PMF from a higher order assembly of P22 virus-like particles (VLPs), the enzymes were partitioned into the PMF by covalent attachment and presentation on the VLP exterior. Using a collective property of the PMF (i.e., high density of negative charges in the PMF), NAD molecules were partitioned into the framework via electrostatic interactions after being conjugated to a polycationic species. This effectively controlled the localization and diffusion of NAD, resulting in substrate channeling between the enzymes. Changing ionic strength modulates the PMF-NAD interactions, tuning two properties that impact the multistep efficiency oppositely in response to ionic strength: cofactor partitioning (colocalization with the enzymes) and cofactor mobility (translocation between the enzymes). Within the range tested, we observed a maximum of 5-fold increase or 75% decrease in multistep efficiency as compared to free enzymes in solution, which suggest both the colocalization and the mobility are critical for the multistep efficiency. This work demonstrates utility of collective behaviors, exhibited by hierarchical bioassemblies, in the construction of functional materials for enzyme cascades, which possess properties such as tunable multistep biocatalysis.
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Affiliation(s)
- Yang Wang
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 E Kirkwood Avenue, Bloomington, Indiana 47405, United States
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8
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Tajwar MA, Cheng C, Qi L. Design of enzyme@metal organic framework composites with thermo-responsivity for colourimetric detection of glucose. NANOSCALE 2023; 15:14055-14060. [PMID: 37581282 DOI: 10.1039/d3nr03514j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Enzyme immobilization on metal-organic frameworks (MOFs) has interested researchers in recent decades due to the outstanding characteristics of MOFs. However, despite some enzyme@MOF composites exhibiting better tolerance, stability and catalysis than free enzymes, boosting the catalytic performance of stimuli-responsive polymer-grafted MOFs composites remains a challenging task. Herein, a glucose oxidase (GOx)-horseradish peroxidase (HRP)@MOF (UiO-66-NH2, U)@polymer composite with tunable catalytic ability was constructed by modification with thermo-responsive poly(N-isopropylacrylamide) (PN) via a surface-selective post-synthetic protocol. Temperature increases changed the PN-based soft armour from a "stretch" to a "coil" conformation on the MOF surface, resulting in the confinement effect and boosting the catalytic performance of the GOx-HRP@U@PN composites. Compared with its maximum catalytic reaction rate at 25 °C, the proposed composites showed 18-fold improvement in catalytic performance at 37 °C. Additionally, a colourimetric method for serum glucose analysis was developed using a GOx-HRP-based catalytic cascade reaction with a linear range from 0.1 to 2.0 mM and a low detection limit of 0.03 mM. Remarkably, the surface PN-shell-based soft armour proved to be the key factor for enhancing the catalytic performance of the as-designed composites. The co-immobilization of GOx-HRP onto the thermo-responsive U@PN surface provides a new approach for the development of highly sensitive colourimetric glucose sensing protocols.
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Affiliation(s)
- Muhammad Ali Tajwar
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Cheng Cheng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.
- College of Chemistry & Environmental Science, Hebei University, Baoding 071002, P. R. China
| | - Li Qi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
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Ledesma-Fernandez A, Velasco-Lozano S, Santiago-Arcos J, López-Gallego F, Cortajarena AL. Engineered repeat proteins as scaffolds to assemble multi-enzyme systems for efficient cell-free biosynthesis. Nat Commun 2023; 14:2587. [PMID: 37142589 PMCID: PMC10160029 DOI: 10.1038/s41467-023-38304-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/21/2023] [Indexed: 05/06/2023] Open
Abstract
Multi-enzymatic cascades with enzymes arranged in close-proximity through a protein scaffold can trigger a substrate channeling effect, allowing for efficient cofactor reuse with industrial potential. However, precise nanometric organization of enzymes challenges the design of scaffolds. In this study, we create a nanometrically organized multi-enzymatic system exploiting engineered Tetrapeptide Repeat Affinity Proteins (TRAPs) as scaffolding for biocatalysis. We genetically fuse TRAP domains and program them to selectively and orthogonally recognize peptide-tags fused to enzymes, which upon binding form spatially organized metabolomes. In addition, the scaffold encodes binding sites to selectively and reversibly sequester reaction intermediates like cofactors via electrostatic interactions, increasing their local concentration and, consequently, the catalytic efficiency. This concept is demonstrated for the biosynthesis of amino acids and amines using up to three enzymes. Scaffolded multi-enzyme systems present up to 5-fold higher specific productivity than the non-scaffolded ones. In-depth analysis suggests that channeling of NADH cofactor between the assembled enzymes enhances the overall cascade throughput and the product yield. Moreover, we immobilize this biomolecular scaffold on solid supports, creating reusable heterogeneous multi-functional biocatalysts for consecutive operational batch cycles. Our results demonstrate the potential of TRAP-scaffolding systems as spatial-organizing tools to increase the efficiency of cell-free biosynthetic pathways.
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Affiliation(s)
- Alba Ledesma-Fernandez
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Susana Velasco-Lozano
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
- Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH-CSIC), University of Zaragoza, C/ Pedro Cerbuna, 12, 50009, Zaragoza, Spain
- Aragonese Foundation for Research and Development (ARAID), Zaragoza, Spain
| | - Javier Santiago-Arcos
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Fernando López-Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain.
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain.
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Liu M, Song Y, Zhang YHPJ, You C. Carrier-Free Immobilization of Multi-Enzyme Complex Facilitates In Vitro Synthetic Enzymatic Biosystem for Biomanufacturing. CHEMSUSCHEM 2023; 16:e202202153. [PMID: 36538347 DOI: 10.1002/cssc.202202153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/20/2022] [Indexed: 06/17/2023]
Abstract
A method is developed for carrier-free immobilization of multi-enzyme complexes with more than four enzymes by utilization of polypeptide interactions (SpyCatcher-SpyTag and dockerin-cohesin) and enzyme component self-oligomerization. Two pairs of scaffoldins with different arrangements of SpyCatcher-SpyTag and cohesins are prepared to recruit the four dockerin-containing cascade enzymes (i. e., alpha-glucan phosphorylase, phosphoglucomutase, inositol 1-phosphate synthase, and inositol 1-phosphatase) that can convert starch into inositol, forming multi-enzyme complexes. These self-assembled enzyme complexes show higher initial reaction rates than the four-enzyme cocktail. Moreover, water-insoluble self-assembled multi-enzyme complexes are observed, being the carrier-free immobilized multi-enzyme complex aggregates. These immobilized enzyme complexes can be recycled easily by simple centrifuging followed by resuspension for another round of reaction. Not only can these immobilized enzyme complexes be obtained by mixing the purified enzyme components, but also by the mixing of crude cell extracts. Therefore, the strategy for the carrier-free immobilization of enzyme complex sheds light on improving the catalytic capability of in vitro synthetic enzymatic biosystems.
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Affiliation(s)
- Miaomiao Liu
- Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230022, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Yunhong Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
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11
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Liu M, Wang Y, Jiang H, Han Y, Xia J. Synthetic Multienzyme Assemblies for Natural Product Biosynthesis. Chembiochem 2023; 24:e202200518. [PMID: 36625563 DOI: 10.1002/cbic.202200518] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
In nature, enzymes that catalyze sequential reactions are often assembled as clusters or complexes. The formation of multienzyme complexes, or metabolons, brings the enzyme active sites into proximity to promote intermediate transfer, decrease intermediate leakage, and streamline the metabolic flux towards the desired products. We and others have developed synthetic versions of metabolons through various strategies to enhance the catalytic rates for synthesizing valuable chemicals inside microbes. Synthetic multienzyme complexes range from static enzyme nanostructures to dynamic enzyme coacervates. Enzyme complexation optimizes the metabolic fluxes inside microbes, increases the product titer, and supplies the field with high-yield microbe strains that are amenable to large-scale fermentation. Enzyme complexes constructed inside microbial cells can be separated as independent entities and catalyze biosynthetic reactions ex vivo; such a feature gains these complexes another name, "synthetic organelles" - new subcellular entities with independent structures and functions. Still, the field is seeking new strategies to better balance dynamicity and confinement and to achieve finer control of local compartmentalization in the cells, as the natural multienzyme complexes do. Industrial applications of synthetic multienzyme complexes for the large-scale production of valuable chemicals are yet to be realized. This review focuses on synthetic multienzyme complexes that are constructed and function inside microbial cells.
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Affiliation(s)
- Min Liu
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yue Wang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hao Jiang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yongxu Han
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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12
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Huang J, Gambietz S, Saccà B. Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202253. [PMID: 35775957 DOI: 10.1002/smll.202202253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.
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Affiliation(s)
- Jing Huang
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Sabrina Gambietz
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Barbara Saccà
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
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13
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Santiago-Arcos J, Velasco-Lozano S, López-Gallego F. Multienzyme Coimmobilization on Triheterofunctional Supports. Biomacromolecules 2023; 24:929-942. [PMID: 36649203 PMCID: PMC10018741 DOI: 10.1021/acs.biomac.2c01364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Immobilized multienzyme systems are gaining momentum in applied biocatalysis; however, the coimmobilization of several enzymes on one carrier is still challenging. In this work, we exploited a heterofunctional support activated with three different chemical functionalities to immobilize a wide variety of different enzymes. This support is based on agarose microbeads activated with aldehyde, amino, and cobalt chelate moieties that allow a fast and irreversible immobilization of enzymes, enhancing the thermostability of most of the heterogeneous biocatalysts (up to 21-fold higher than the soluble one). Furthermore, this trifunctional support serves to efficiently coimmobilize a multienzyme system composed of an alcohol dehydrogenase, a reduced nicotinamide adenine dinucleotide (NADH) oxidase, and a catalase. The confined multienzymatic system demonstrates higher performance than its free counterpart, achieving a total turnover number (TTN) of 1 × 105 during five batch consecutive cycles. We envision this solid material as a platform for coimmobilizing multienzyme systems with enhanced properties to catalyze stepwise biotransformations.
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Affiliation(s)
- Javier Santiago-Arcos
- Heterogeneous Biocatalysis Laboratory, CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009 Donostia, Spain
| | - Susana Velasco-Lozano
- Heterogeneous Biocatalysis Laboratory, CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009 Donostia, Spain.,Instituto de Síntesis Química y Catálisis Homogénea (ISQCH-CSIC), Universidad de Zaragoza, C/ Pedro Cerbuna, 12, 50009 Zaragoza, Spain.,Aragonese Foundation for Research and Development (ARAID), 50018 Zaragoza, Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Laboratory, CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009 Donostia, Spain.,IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
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14
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Braz JF, Dencheva NV, Malfois M, Denchev ZZ. Synthesis of Novel Polymer-Assisted Organic-Inorganic Hybrid Nanoflowers and Their Application in Cascade Biocatalysis. Molecules 2023; 28:molecules28020839. [PMID: 36677897 PMCID: PMC9864776 DOI: 10.3390/molecules28020839] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
This study reports on the synthesis of novel bienzyme polymer-assisted nanoflower complexes (PANF), their morphological and structural characterization, and their effectiveness as cascade biocatalysts. First, highly porous polyamide 6 microparticles (PA6 MP) are synthesized by activated anionic polymerization in solution. Second, the PA6 MP are used as carriers for hybrid bienzyme assemblies comprising glucose oxidase (GOx) and horseradish peroxidase (HRP). Thus, four PANF complexes with different co-localization and compartmentalization of the two enzymes are prepared. In samples NF GH/PA and NF GH@PA, both enzymes are localized within the same hybrid flowerlike organic-inorganic nanostructures (NF), the difference being in the way the PA6 MP are assembled with NF. In samples NF G/PAiH and NF G@PAiH, only GOx is located in the NF, while HRP is preliminary immobilized on PA6 MP. The morphology and the structure of the four PANF complexes have been studied by microscopy, spectroscopy, and synchrotron X-ray techniques. The catalytic activity of the four PANF was assessed by a two-step cascade reaction of glucose oxidation. The PANF complexes are up to 2-3 times more active than the free GOx/HRP dyad. They also display enhanced kinetic parameters, superior thermal stability in the 40-60 °C range, optimum performance at pH 4-6, and excellent storage stability. All PANF complexes are active for up to 6 consecutive operational cycles.
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Affiliation(s)
- Joana F. Braz
- IPC—Institute for Polymers and Composites, University of Minho, 4800-056 Guimarães, Portugal
| | - Nadya V. Dencheva
- IPC—Institute for Polymers and Composites, University of Minho, 4800-056 Guimarães, Portugal
- Correspondence: (N.V.D.); (Z.Z.D.)
| | - Marc Malfois
- ALBA Synchrotron Facility, Cerdanyola del Valés, 0890 Barcelona, Spain
| | - Zlatan Z. Denchev
- IPC—Institute for Polymers and Composites, University of Minho, 4800-056 Guimarães, Portugal
- Correspondence: (N.V.D.); (Z.Z.D.)
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15
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Armstrong FA, Cheng B, Herold RA, Megarity CF, Siritanaratkul B. From Protein Film Electrochemistry to Nanoconfined Enzyme Cascades and the Electrochemical Leaf. Chem Rev 2022; 123:5421-5458. [PMID: 36573907 PMCID: PMC10176485 DOI: 10.1021/acs.chemrev.2c00397] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein film electrochemistry (PFE) has given unrivalled insight into the properties of redox proteins and many electron-transferring enzymes, allowing investigations of otherwise ill-defined or intractable topics such as unstable Fe-S centers and the catalytic bias of enzymes. Many enzymes have been established to be reversible electrocatalysts when attached to an electrode, and further investigations have revealed how unusual dependences of catalytic rates on electrode potential have stark similarities with electronics. A special case, the reversible electrochemistry of a photosynthetic enzyme, ferredoxin-NADP+ reductase (FNR), loaded at very high concentrations in the 3D nanopores of a conducting metal oxide layer, is leading to a new technology that brings PFE to myriad enzymes of other classes, the activities of which become controlled by the primary electron exchange. This extension is possible because FNR-based recycling of NADP(H) can be coupled to a dehydrogenase, and thence to other enzymes linked in tandem by the tight channelling of cofactors and intermediates within the nanopores of the material. The earlier interpretations of catalytic wave-shapes and various analogies with electronics are thus extended to initiate a field perhaps aptly named "cascade-tronics", in which the flow of reactions along an enzyme cascade is monitored and controlled through an electrochemical analyzer. Unlike in photosynthesis where FNR transduces electron transfer and hydride transfer through the unidirectional recycling of NADPH, the "electrochemical leaf" (e-Leaf) can be used to drive reactions in both oxidizing and reducing directions. The e-Leaf offers a natural way to study how enzymes are affected by nanoconfinement and crowding, mimicking the physical conditions under which enzyme cascades operate in living cells. The reactions of the trapped enzymes, often at very high local concentration, are thus studied electrochemically, exploiting the potential domain to control rates and direction and the current-rate analogy to derive kinetic data. Localized NADP(H) recycling is very efficient, resulting in very high cofactor turnover numbers and new opportunities for controlling and exploiting biocatalysis.
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Affiliation(s)
- Fraser A. Armstrong
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Beichen Cheng
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Ryan A. Herold
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Clare F. Megarity
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Bhavin Siritanaratkul
- Stephenson Institute for Renewable Energy and the Department of Chemistry, University of Liverpool, Liverpool L69 7ZF, United Kingdom
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16
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Ye Q, Jin X, Gao H, Wei N. Site-Specific and Tunable Co-immobilization of Proteins onto Magnetic Nanoparticles via Spy Chemistry. ACS APPLIED BIO MATERIALS 2022; 5:5665-5674. [PMID: 36194637 DOI: 10.1021/acsabm.2c00709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Co-immobilization of multiple proteins onto one nanosupport has large potential in mimicking natural multiprotein complexes and constructing efficient cascade biocatalytic systems. However, control of different proteins regarding their spatial arrangement and loading ratio remains a big challenge, and protein co-immobilization often requires the use of purified proteins. Herein, built upon our recently designed SpyTag-functionalized magnetic nanoparticles (MNPs), we established a modular MNP platform for site-specific, tunable, and cost-effective protein co-immobilization. SpyCatcher-fused enhanced green fluorescent protein (i.e., EGFP-SpyCatcher) and mCherry red fluorescent protein (i.e., RFP-SpyCatcher) were designed and conjugated on MNPs, and the immobilized proteins showed 3-7-fold enhancement in storage stability and greatly improved stability against the freeze-thaw process compared to free proteins. The protein-conjugated MNPs also retained desirable colloidal stability and magnetic responsiveness, enabling facile proteins' recovery. Also, one-pot co-immobilization of the two proteins could be fine-tuned with their feed ratios. In addition, MNPs could selectively and efficiently co-immobilize both SpyCatcher-fused proteins from combined cell lysates without purification, offering a convenient and cost-effective approach for multiprotein immobilization. This MNP platform provides a facile and efficient tool to construct bionano hybrid materials (i.e., protein-based MNPs) and multiprotein systems for a variety of industrial and green chemistry applications.
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Affiliation(s)
- Quanhui Ye
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, 205 N. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Xiuyu Jin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Haifeng Gao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Na Wei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, 205 N. Mathews Avenue, Urbana, Illinois 61801, United States
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17
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Nucleic acid-based scaffold systems and application in enzyme cascade catalysis. Appl Microbiol Biotechnol 2022; 107:9-23. [DOI: 10.1007/s00253-022-12315-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022]
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18
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Biosynthesis of alkanes/alkenes from fatty acids or derivatives (triacylglycerols or fatty aldehydes). Biotechnol Adv 2022; 61:108045. [DOI: 10.1016/j.biotechadv.2022.108045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022]
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19
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Majikes JM, Liddle JA. Synthesizing the biochemical and semiconductor worlds: the future of nucleic acid nanotechnology. NANOSCALE 2022; 14:15586-15595. [PMID: 36268635 PMCID: PMC10949957 DOI: 10.1039/d2nr04040a] [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] [Indexed: 06/16/2023]
Abstract
Since its inception nearly 40 years ago [Kallenbach, et al., Nature, 1983, 305, 829; N. C. Seeman, J. Theoretical Biology, 1982, 99, 237], Nucleic Acid Nanotechnology (NAN) has matured and is beginning to find commercial applications. For the last 20 years, it has been suggested that NAN might be an effective replacement for parts of the semiconductor lithography or protein engineering workflows. However, in that time, these incumbent technologies have made significant advances, and our understanding of NAN's strengths and weaknesses has progressed, suggesting that the greatest opportunities in fact lie elsewhere. Given the commitment of resources necessary to bring new technologies to the market and the desire to use those resources as wisely as possible, we conduct a critical examination of where NAN may benefit from, and provide benefit to, adjacent technologies and compete least with market incumbents. While the accuracy of our conclusions may be limited by our ability to extrapolate from the current state of NAN to its future commercial success, we conclude that the next promising direction is to create a bridge between biology and semiconductor technology. We also hope to stimulate a robust conversation around this technology's capabilities with the goal of building consensus on those research and development efforts that would advance NAN to the greatest effect in real-world applications.
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Affiliation(s)
- Jacob M Majikes
- Physical Measurement Laboratory, National Institute Standards and Technology, 100 Bureau drive, Gaithersburg, MD, 20878, USA.
| | - J Alexander Liddle
- Physical Measurement Laboratory, National Institute Standards and Technology, 100 Bureau drive, Gaithersburg, MD, 20878, USA.
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20
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Lin P, Yang H, Nakata E, Morii T. Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold. Molecules 2022; 27:molecules27196309. [PMID: 36234845 PMCID: PMC9572797 DOI: 10.3390/molecules27196309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Cells have developed intelligent systems to implement the complex and efficient enzyme cascade reactions via the strategies of organelles, bacterial microcompartments and enzyme complexes. The scaffolds such as the membrane or protein in the cell are believed to assist the co-localization of enzymes and enhance the enzymatic reactions. Inspired by nature, enzymes have been located on a wide variety of carriers, among which DNA scaffolds attract great interest for their programmability and addressability. Integrating these properties with the versatile DNA–protein conjugation methods enables the spatial arrangement of enzymes on the DNA scaffold with precise control over the interenzyme distance and enzyme stoichiometry. In this review, we survey the reactions of a single type of enzyme on the DNA scaffold and discuss the proposed mechanisms for the catalytic enhancement of DNA-scaffolded enzymes. We also review the current progress of enzyme cascade reactions on the DNA scaffold and discuss the factors enhancing the enzyme cascade reaction efficiency. This review highlights the mechanistic aspects for the modulation of enzymatic reactions on the DNA scaffold.
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21
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Xiong Y, Tsitkov S, Hess H, Gang O, Zhang Y. Microscale Colocalization of Cascade Enzymes Yields Activity Enhancement. ACS NANO 2022; 16:10383-10391. [PMID: 35549238 DOI: 10.1021/acsnano.2c00475] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Colocalization of cascade enzymes is broadly discussed as a phenomenon that can boost the cascade reaction throughput, although a direct experimental verification is often challenging. This is mainly due to difficulties in establishing proper size regimes and in the analytical quantification of colocalization effect with adequate experimental systems and simulations. In this study, by taking advantage of reversible DNA-directed colocalization of enzymes on microspheres, we established a cascade system that can be used to directly evaluate the colocalization effect with exactly the same experimental settings except for the state of enzyme dispersion. In the regime of highly dilute microspheres of particular sizes, the colocalized cascade shows enhanced activity compared with the freely diffusing cascade, as evidenced by a shortened lag phase in the time-course production. Reaction-diffusion modeling reveals that the enhancement can be ascribed to the initial accumulation of intermediate substrate around the colocalized enzymes and is found to be carrier-size-dependent. This work demonstrates the dependence of the colocalization effect of enzyme cascades on an interplay of nano- and microscales, lending theoretical support to the rational design of highly efficient multienzyme catalysts.
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Affiliation(s)
- Yan Xiong
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Stanislav Tsitkov
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yifei Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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22
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Cui S, Ge J. Diffusion process in enzyme—metal hybrid catalysts. Front Chem Sci Eng 2022. [DOI: 10.1007/s11705-022-2144-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Chu X, Shi Q. Versatile magnetic nanoparticles for spatially organized assemblies of enzyme cascades: a comprehensive investigation of catalytic performance. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xinshuang Chu
- Department of Biochemical Engineering School of Chemical Engineering and Technology, Tianjin University Tianjin 300350 China
| | - Qinghong Shi
- Department of Biochemical Engineering School of Chemical Engineering and Technology, Tianjin University Tianjin 300350 China
- Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University Tianjin 300350 China
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24
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Kahn J, Xiong Y, Huang J, Gang O. Cascaded Enzyme Reactions over a Three-Dimensional, Wireframe DNA Origami Scaffold. JACS AU 2022; 2:357-366. [PMID: 35252986 PMCID: PMC8889550 DOI: 10.1021/jacsau.1c00387] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Indexed: 05/31/2023]
Abstract
DNA nanotechnology has increasingly been used as a platform to scaffold enzymes based on its unmatched ability to structure enzymes in a desired format. The capability to organize enzymes has taken many forms from more traditional 2D pairings on individual scaffolds to recent works introducing enzyme organizations in 3D lattices. As the ability to define nanoscale structure has grown, it is critical to fully deconstruct the impact of enzyme organization at the single-scaffold level. Here, we present an open, three-dimensional (3D) DNA wireframe octahedron which is used to create a library of spatially arranged organizations of glucose oxidase and horseradish peroxidase. We explore the contribution of enzyme spacing, arrangement, and location on the 3D scaffold to cascade activity. The experiments provide insight into enzyme scaffold design, including the insignificance of scaffold sequence makeup on activity, an increase in activity at small enzyme spacings of <10 nm, and activity changes that arise from discontinuities in scaffold architecture. Most notably, the experiments allow us to determine that enzyme colocalization itself on the DNA scaffold dominates over any specific enzyme arrangement.
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Affiliation(s)
- Jason
S. Kahn
- Center
for Functional Nanomaterials, Brookhaven
National Laboratory, Upton, New York 11973, United States
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Yan Xiong
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - James Huang
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Oleg Gang
- Center
for Functional Nanomaterials, Brookhaven
National Laboratory, Upton, New York 11973, United States
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department
of Applied Physics and Applied Mathematics, Columbia University, New York New York 10027, United States
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25
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Liu S, Xiang K, Wang C, Zhang Y, Fan GC, Wang W, Han H. DNA Nanotweezers for Biosensing Applications: Recent Advances and Future Prospects. ACS Sens 2022; 7:3-20. [PMID: 34989231 DOI: 10.1021/acssensors.1c01647] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA nanotweezers (DTs) are reversible DNA nanodevices that can optionally switch between opened and closed states. Due to their excellent flexibility and high programmability, they have been recognized as a promising platform for constructing a diversity of biosensors and logic gates, as well as a versatile tool for molecular biology studies. In this review, we provide an overview of biosensing applications using DTs. First, the design and working principle of DTs are introduced. Next, the signal producing principles of DTs are summarized. Furthermore, biosensing applications of DTs for varying targets and purposes, both in buffers and complex biological environments, are highlighted. Finally, we provide potential opportunities and challenges for the further development of DTs.
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Affiliation(s)
- Shanshan Liu
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Kaikai Xiang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Chunyan Wang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Yutian Zhang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Gao-Chao Fan
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, Shandong, People’s Republic of China
| | - Wenjing Wang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, People’s Republic of China
| | - Heyou Han
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
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26
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Kosinski R, Perez JM, Schöneweiß EC, Ruiz-Blanco YB, Ponzo I, Bravo-Rodriguez K, Erkelenz M, Schlücker S, Uhlenbrock G, Sanchez-Garcia E, Saccà B. The role of DNA nanostructures in the catalytic properties of an allosterically regulated protease. SCIENCE ADVANCES 2022; 8:eabk0425. [PMID: 34985948 PMCID: PMC8730604 DOI: 10.1126/sciadv.abk0425] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/10/2021] [Indexed: 06/04/2023]
Abstract
DNA-scaffolded enzymes typically show altered kinetic properties; however, the mechanism behind this phenomenon is still poorly understood. We address this question using thrombin, a model of allosterically regulated serine proteases, encaged into DNA origami cavities with distinct structural and electrostatic features. We compare the hydrolysis of substrates that differ only in their net charge due to a terminal residue far from the cleavage site and presumably involved in the allosteric activation of thrombin. Our data show that the reaction rate is affected by DNA/substrate electrostatic interactions, proportionally to the degree of DNA/enzyme tethering. For substrates of opposite net charge, this leads to an inversion of the catalytic response of the DNA-scaffolded thrombin when compared to its freely diffusing counterpart. Hence, by altering the electrostatic environment nearby the encaged enzyme, DNA nanostructures interfere with charge-dependent mechanisms of enzyme-substrate recognition and may offer an alternative tool to regulate allosteric processes through spatial confinement.
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Affiliation(s)
- Richard Kosinski
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Joel Mieres Perez
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Elisa-C. Schöneweiß
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Irene Ponzo
- Dynamic Biosensors GmbH, 82152 Martinsried, Germany
| | | | - Michael Erkelenz
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sebastian Schlücker
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Elsa Sanchez-Garcia
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Barbara Saccà
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
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27
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Kondrat S, von Lieres E. Mechanisms and Effects of Substrate Channelling in Enzymatic Cascades. Methods Mol Biol 2022; 2487:27-50. [PMID: 35687228 DOI: 10.1007/978-1-0716-2269-8_3] [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: 06/15/2023]
Abstract
Substrate or metabolite channelling is a transfer of intermediates produced by one enzyme to the sequential enzyme of a reaction cascade or metabolic pathway, without releasing them entirely into bulk. Despite an enormous effort and more than three decades of research, substrate channelling remains the subject of continuing debates and active investigation. Herein, we review the benefits and mechanisms of substrate channelling in vivo and in vitro. We discuss critically the effects that substrate channelling can have on enzymatic cascades, including speeding up or slowing down reaction cascades and protecting intermediates from sequestration and enzymes' surroundings from toxic or otherwise detrimental intermediates. We also discuss how macromolecular crowding affects substrate channelling and point out the galore of open questions.
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Affiliation(s)
- Svyatoslav Kondrat
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
- Max-Planck-Institut für Intelligente Systeme, Stuttgart, Germany.
- IV. Institut für Theoretische Physik, Universität Stuttgart, Stuttgart, Germany.
| | - Eric von Lieres
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
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Jolly BJ, Co NH, Davis AR, Diaconescu PL, Liu C. A generalized kinetic model for compartmentalization of organometallic catalysis. Chem Sci 2022; 13:1101-1110. [PMID: 35211276 PMCID: PMC8790775 DOI: 10.1039/d1sc04983f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/21/2021] [Indexed: 11/21/2022] Open
Abstract
Compartmentalization is an attractive approach to enhance catalytic activity by retaining reactive intermediates and mitigating deactivating pathways. Such a concept has been well explored in biochemical and more recently, organometallic catalysis to ensure high reaction turnovers with minimal side reactions. However, the scarcity of theoretical frameworks towards confined organometallic chemistry impedes broader utility for the implementation of compartmentalization. Herein, we report a general kinetic model and offer design guidance for a compartmentalized organometallic catalytic cycle. In comparison to a non-compartmentalized catalysis, compartmentalization is quantitatively shown to prevent the unwanted intermediate deactivation, boost the corresponding reaction efficiency (γ), and subsequently increase catalytic turnover frequency (TOF). The key parameter in the model is the volumetric diffusive conductance (FV) that describes catalysts' diffusion propensity across a compartment's boundary. Optimal values of FV for a specific organometallic chemistry are needed to achieve maximal values of γ and TOF. As illustrated in specific reaction examples, our model suggests that a tailored compartment design, including the use of nanomaterials, is needed to suit a specific organometallic catalytic cycle. This work provides justification and design principles for further exploration into compartmentalizing organometallics to enhance catalytic performance. The conclusions from this work are generally applicable to other catalytic systems that need proper design guidance in confinement and compartmentalization. Compartmentalization is an attractive approach to enhance catalytic activity by retaining reactive intermediates and mitigating deactivating pathways.![]()
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Affiliation(s)
- Brandon J. Jolly
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Nathalie H. Co
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Ashton R. Davis
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Paula L. Diaconescu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Chong Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA 90095, USA
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29
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Lin P, Dinh H, Nakata E, Morii T. Conditional dependence of enzyme cascade reaction efficiency on the inter-enzyme distance. Chem Commun (Camb) 2021; 57:11197-11200. [PMID: 34622899 DOI: 10.1039/d1cc04162b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A dual-enzyme cascade, xylitol dehydrogenase and xylulose kinase, derived from the xylose metabolic pathway, was constructed on a three-dimensional DNA scaffold which exhibited a dynamic shape transition from an open state to a closed hexagonal prism. Evaluation of the cascade reaction efficiencies in the open and closed states revealed little to no inter-enzyme distance dependence, presumably due to the far larger catalytic constant of the downstream enzyme. The inter-enzyme distance was not the dominant factor for cascade efficiency when the kinetic parameters of the cascade enzymes were imbalanced with the highly efficient downstream enzyme.
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Affiliation(s)
- Peng Lin
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
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30
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Abdallah W, Hong X, Banta S, Wheeldon I. Microenvironmental effects can masquerade as substrate channelling in cascade biocatalysis. Curr Opin Biotechnol 2021; 73:233-239. [PMID: 34521036 DOI: 10.1016/j.copbio.2021.08.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022]
Abstract
Natural cascades frequently use spatial organization to introduce beneficial substrate channeling mechanisms, a strategy that has been widely mimicked in many engineered multienzyme cascades with enhanced catalysis. Enabled by new molecular scaffolds it is now possible to test the effects of spatial organization on cascade kinetics; however, these scaffolds can also alter the microenvironment experienced by the assembled enzymes. We know from decades of enzyme immobilization research that the microenvironment affects enzymatic activity, thus complicating kinetic analysis. Here, we review these effects and discuss examples that exploit the microenvironment to improve single enzyme and cascade catalysis. In doing so, we highlight the challenges in ascribing kinetic enhancements directly to substrate channeling without first determining the effects of the microenvironment.
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Affiliation(s)
- Walaa Abdallah
- Chemical Engineering, Manhattan College, Bronx, 10463 NY, USA.
| | - Xiao Hong
- Biochemistry, University of California-Riverside, Riverside, 92521 CA, USA
| | - Scott Banta
- Chemical Engineering, Columbia University, NY, 10027 NY, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California-Riverside, Riverside, 92521 CA, USA.
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31
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Zhang YQ, Feng TT, Cao YF, Zhang XY, Wang T, Huanca Nina MR, Wang LC, Yu HL, Xu JH, Ge J, Bai YP. Confining Enzyme Clusters in Bacteriophage P22 Enhances Cofactor Recycling and Stereoselectivity for Chiral Alcohol Synthesis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02221] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yan-Qing Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Tao-Tao Feng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Yu-Fei Cao
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xiao-Yan Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Tao Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Mario Roque Huanca Nina
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Li-Cheng Wang
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Jun Ge
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Yun-Peng Bai
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
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32
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Xu R, Wang Y, Huang H, Jin X, Li J, Du G, Kang Z. Closed-Loop System Driven by ADP Phosphorylation from Pyrophosphate Affords Equimolar Transformation of ATP to 3′-Phosphoadenosine-5′-phosphosulfate. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ruirui Xu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yang Wang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Hao Huang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xuerong Jin
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhen Kang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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33
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Xie Y, Calabrese Barton S. Infrequent metadynamics study of rare-event electrostatic channeling. Phys Chem Chem Phys 2021; 23:13381-13388. [PMID: 34105559 DOI: 10.1039/d1cp01304a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The efficiency of cascade reactions, which consist of multiple chemical transformations that occur in a single pot without purification steps, is limited by the transport efficiency of intermediates between adjacent steps. Electrostatic channeling is a proven strategy for intermediate transfer in natural chemical cascades, but implementation into artificial cascades remains a challenge. Here, we combine infrequent metadynamics (InMetaD), umbrella sampling (US), and kinetic Monte Carlo (KMC) models to computationally study the transfer mechanism of glucose-6-phosphate (G6P) on a poly-arginine peptide bridging hexokinase (HK) and glucose-6-dehydrogenase (G6PDH). Transport of G6P by hopping in the presence of poly-arginine peptides is shown to be a rare event, and InMetaD is used to compute the hopping activation energy. US simulations capture the configurational change in the desorption process and enable the determination of the desorption energy. Parameterized by these results, a KMC model is used to estimate transport efficiency for the bridged enzyme complex. Results are compared to a similar complex using a poly-lysine bridge, using kinetic lag time as a metric. Even at a high ionic strength of 120 mM, poly-arginine peptides may be capable of more efficient transport as compared to poly-lysine, with a predicted lag time of 6 seconds for poly-arginine, compared to a previously reported lag time of 59 seconds for poly-lysine. This work indicates that poly-arginine peptides may be an improved bridge structure for electrostatic channeling of anionic intermediates.
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Affiliation(s)
- Yan Xie
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA.
| | - Scott Calabrese Barton
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA.
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Lee YS, Lim K, Minteer SD. Cascaded Biocatalysis and Bioelectrocatalysis: Overview and Recent Advances. Annu Rev Phys Chem 2021; 72:467-488. [DOI: 10.1146/annurev-physchem-090519-050109] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Enzyme cascades are plentiful in nature, but they also have potential in artificial applications due to the possibility of using the target substrate in biofuel cells, electrosynthesis, and biosensors. Cascade reactions from enzymes or hybrid bioorganic catalyst systems exhibit extended substrate range, reaction depth, and increased overall performance. This review addresses the strategies of cascade biocatalysis and bioelectrocatalysis for ( a) CO2 fixation, ( b) high value-added product formation, ( c) sustainable energy sources via deep oxidation, and ( d) cascaded electrochemical enzymatic biosensors. These recent updates in the field provide fundamental concepts, designs of artificial electrocatalytic oxidation-reduction pathways (using a flexible setup involving organic catalysts and engineered enzymes), and advances in hybrid cascaded sensors for sensitive analyte detection.
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Affiliation(s)
- Yoo Seok Lee
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Koun Lim
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Shelley D. Minteer
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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35
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Abstract
Enzymatic cascade reactions, where a substrate is converted into a product in several steps, play a critical role in many biological systems. The enzymes in such reactions are often clustered inside intracellular compartments. To understand the effect of localization, we develop a theory for cascade reactions converting substrates into intermediates and then into products when the enzymes are localized in clusters. The theory shows that the kinetic scheme that describes the reaction with dispersed enzymes changes as a result of clustering. A new reaction channel, in which the substrate is directly converted into product, appears with a diffusion-influenced rate that is expressed in terms of enzyme catalytic efficiencies, diffusion coefficient, and cluster size. This rate is proportional to the cluster channeling probability, which is the probability that an intermediate is converted into product within the cluster in which the intermediate was formed. Simple analytic formulas allow one to quantify how enzyme clustering can affect product formation and regulate the direction of metabolic reaction flux in biological and synthetic systems. The rate of the substrate conversion decreases whereas the cluster channeling probability increases as the number of enzyme molecules in a cluster increases. The interplay between these factors leads to an optimal number of enzyme molecules that maximizes the clustering efficiency.
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Affiliation(s)
- Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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36
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Dubey NC, Tripathi BP. Nature Inspired Multienzyme Immobilization: Strategies and Concepts. ACS APPLIED BIO MATERIALS 2021; 4:1077-1114. [PMID: 35014469 DOI: 10.1021/acsabm.0c01293] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In a biological system, the spatiotemporal arrangement of enzymes in a dense cellular milieu, subcellular compartments, membrane-associated enzyme complexes on cell surfaces, scaffold-organized proteins, protein clusters, and modular enzymes have presented many paradigms for possible multienzyme immobilization designs that were adapted artificially. In metabolic channeling, the catalytic sites of participating enzymes are close enough to channelize the transient compound, creating a high local concentration of the metabolite and minimizing the interference of a competing pathway for the same precursor. Over the years, these phenomena had motivated researchers to make their immobilization approach naturally realistic by generating multienzyme fusion, cluster formation via affinity domain-ligand binding, cross-linking, conjugation on/in the biomolecular scaffold of the protein and nucleic acids, and self-assembly of amphiphilic molecules. This review begins with the discussion of substrate channeling strategies and recent empirical efforts to build it synthetically. After that, an elaborate discussion covering prevalent concepts related to the enhancement of immobilized enzymes' catalytic performance is presented. Further, the central part of the review summarizes the progress in nature motivated multienzyme assembly over the past decade. In this section, special attention has been rendered by classifying the nature-inspired strategies into three main categories: (i) multienzyme/domain complex mimic (scaffold-free), (ii) immobilization on the biomolecular scaffold, and (iii) compartmentalization. In particular, a detailed overview is correlated to the natural counterpart with advances made in the field. We have then discussed the beneficial account of coassembly of multienzymes and provided a synopsis of the essential parameters in the rational coimmobilization design.
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Affiliation(s)
- Nidhi C Dubey
- Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Bijay P Tripathi
- Department of Materials Science and Engineering, Indian institute of Technology Delhi, New Delhi 110016, India
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37
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Díaz SA, Choo P, Oh E, Susumu K, Klein WP, Walper SA, Hastman DA, Odom TW, Medintz IL. Gold Nanoparticle Templating Increases the Catalytic Rate of an Amylase, Maltase, and Glucokinase Multienzyme Cascade through Substrate Channeling Independent of Surface Curvature. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03602] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, United States
| | - Priscilla Choo
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- Jacobs Corporation, Hanover, Maryland 21076, United States
| | - William P. Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, United States
| | - David A. Hastman
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, United States
- Fischell Department of Bioengineering, University of Maryland College Park, College Park, Maryland 20742, United States
| | - Teri W. Odom
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375, United States
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38
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Sasaki K, Furusawa H, Nagamine K, Tokito S. Constructive Optimization of a Multienzymatic Film Based on a Cascade Reaction for Electrochemical Biosensors. ACS OMEGA 2020; 5:32844-32851. [PMID: 33376922 PMCID: PMC7758940 DOI: 10.1021/acsomega.0c05521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
The application of a multienzyme cascade reaction in electrochemical biosensors has the advantage of expanding the target substrates in addition to selectivity combining multiple enzymes on an electrode. However, the multienzyme system has the drawback of inefficient substance conversion because of the time-consuming passing of intermediates between the enzymes and/or diffusional loss of the intermediates. In this study, the optimal construction of a multienzymatic film in an ammonia detection sensor was investigated using a cascade reaction of l-glutamate oxidase and l-glutamate dehydrogenase as a model sensor. Three enzymatic films were prepared: (1) a mixed film designed to have a short diffusional distance between closely located enzymes, (2) a normal-sequential layered film arranged for the correct reaction pathway, and (3) a reverse-sequential layered film as a negative control. This was followed by comparison of the conversion efficiency of ammonia to hydrogen peroxide using time-dependent potentiometric measurements of a Prussian blue electrode determining the hydrogen peroxide amount. The results indicate that the conversion efficiency of the normal-sequential layered film was the highest among the three enzymatic films. The quantitative evaluation of the intermediate conversion efficiency of the cascade reaction showed that compared to the mixed film (34%), a higher conversion efficiency of 92% was obtained in the first enzymatic reaction step. These findings will promote the use of multienzymatic cascade reaction systems not only in biosensors and bioreactors but also in various industrial fields.
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Affiliation(s)
- Kai Sasaki
- Graduate
School of Organic Materials Science, Yamagata
University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
- Innovative
Flex Course for Frontier Organic Material Systems (iFront), Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Hiroyuki Furusawa
- Innovative
Flex Course for Frontier Organic Material Systems (iFront), Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
- Institute
for the Promotion of General Graduate Education (IPGE), Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
- Research
Center for Organic Electronics (ROEL), Yamagata
University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Kuniaki Nagamine
- Graduate
School of Organic Materials Science, Yamagata
University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
- Research
Center for Organic Electronics (ROEL), Yamagata
University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Shizuo Tokito
- Graduate
School of Organic Materials Science, Yamagata
University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
- Research
Center for Organic Electronics (ROEL), Yamagata
University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
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Natinsky BS, Jolly BJ, Dumas DM, Liu C. Efficacy analysis of compartmentalization for ambient CH 4 activation mediated by a Rh II metalloradical in a nanowire array electrode. Chem Sci 2020; 12:1818-1825. [PMID: 34163945 PMCID: PMC8179293 DOI: 10.1039/d0sc05700b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Compartmentalization is a viable approach for ensuring the turnover of a solution cascade reaction with ephemeral intermediates, which may otherwise deactivate in the bulk solution. In biochemistry or enzyme-relevant cascade reactions, extensive models have been constructed to quantitatively analyze the efficacy of compartmentalization. Nonetheless, the application of compartmentalization and its quantitative analysis in non-biochemical reactions is seldom performed, leaving much uncertainty about whether compartmentalization remains effective for non-biochemical reactions, such as organometallic, cascade reactions. Here, we report our exemplary efficacy analysis of compartmentalization in our previously reported cascade reaction for ambient CH4-to-CH3OH conversion, mediated by an O2-deactivated RhII metalloradical with O2 as the terminal oxidant in a Si nanowire array electrode. We experimentally identified and quantified the key reaction intermediates, including the RhII metalloradical and reactive oxygen species (ROS) from O2. Based on such findings, we experimentally determined that the nanowire array enables about 81% of the generated ephemeral intermediate RhII metalloradical in air, to be utilized towards CH3OH formation, which is 0% in a homogeneous solution. Such an experimentally determined value was satisfactorily consistent with the results from our semi-quantitative kinetic model. The consistency suggests that the reported CH4-to-CH3OH conversion surprisingly possesses minimal unforeseen side reactions, and is favorably efficient as a compartmentalized cascade reaction. Our quantitative evaluation of the reaction efficacy offers design insights and caveats into application of nanomaterials to achieve spatially controlled organometallic cascade reactions. We integrated theory with experiment to evaluate the catalytic cycle of seemingly incompatible steps enabled by nanowire array for CH4-to-CH3OH conversion, and determined the array’s efficacy in the context of microscopic compartmentalization.![]()
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Affiliation(s)
- Benjamin S Natinsky
- Department of Chemistry and Biochemistry, University of California Los Angeles California 90095 USA
| | - Brandon J Jolly
- Department of Chemistry and Biochemistry, University of California Los Angeles California 90095 USA
| | - David M Dumas
- Department of Chemistry and Biochemistry, University of California Los Angeles California 90095 USA
| | - Chong Liu
- Department of Chemistry and Biochemistry, University of California Los Angeles California 90095 USA .,California NanoSystems Institute (CNSI), University of California Los Angeles CA 90095 USA
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40
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Xiong Y, Huang J, Wang ST, Zafar S, Gang O. Local Environment Affects the Activity of Enzymes on a 3D Molecular Scaffold. ACS NANO 2020; 14:14646-14654. [PMID: 32880434 DOI: 10.1021/acsnano.0c03962] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The ability to coordinate and confine enzymes presents an opportunity to affect their performance and to create chemically active materials. Recent studies show that polymers and biopolymers can be used to scaffold enzymes, and that can lead to the modulated biocatalytic efficiency. Here, we investigated the role of microenvironments on enzyme activity using a well-defined molecular scaffold. An enzyme, glucose oxidase (GOx), was positioned at different locations of a three-dimensional (3D) octahedral DNA scaffold (OS), allowing the enzyme's polyanionic environments to be altered. Using electrical sensing, based on a bipolar junction transistor, we measured directly and in real-time the enzyme's proton generation at these different microenvironments. We found a 200% enhancement of immobilized enzyme over free GOx and about a 30% increase in catalytic rates when the enzyme was moved on the same molecular scaffold to a microenvironment with a higher local concentration of polyanions, which suggests a role of local pH on the enzymatic activity.
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Affiliation(s)
- Yan Xiong
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - James Huang
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
| | - Shih-Ting Wang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Sufi Zafar
- IBM T.J. Watson Research Center, Yorktown Heights, New York 10589, United States
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
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41
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42
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Borowicz P, Chan H, Hauge A, Spurkland A. Adaptor proteins: Flexible and dynamic modulators of immune cell signalling. Scand J Immunol 2020; 92:e12951. [DOI: 10.1111/sji.12951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Paweł Borowicz
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Hanna Chan
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Anette Hauge
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Anne Spurkland
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
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Zhang L, Manley OM, Ma D, Yin Y, Makris TM, Wang Q. Enhanced P450 fatty acid decarboxylase catalysis by glucose oxidase coupling and co-assembly for biofuel generation. BIORESOURCE TECHNOLOGY 2020; 311:123538. [PMID: 32485602 DOI: 10.1016/j.biortech.2020.123538] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Cytochrome P450 OleT is a fatty acid decarboxylase that uses hydrogen peroxide (H2O2) to catalyze the production of terminal alkenes, which are industrially important chemicals with biofuel and synthetic applications. Despite its requirement for large turnover levels, high concentrations of H2O2 may cause heme group degradation, diminishing enzymatic activity and limiting broad application for synthesis. Here, we report an artificial enzyme cascade composed of glucose oxidase (GOx) and OleTSA from Staphylococcus aureus for efficient terminal alkene production. By adjusting the ratio of GOx to OleTSA, the GOx-based tandem catalysis shows significantly improved product yield compared to the H2O2 injection method. Moreover, the co-assembly of the GOx/OleTSA enzymes with a polymer, forming polymer-dual enzymes nanoparticles, displays improved activity compared to the free enzyme. This dual strategy provides a simple and efficient system to transform a naturally abundant feedstock to industrially important chemicals.
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Affiliation(s)
- Libo Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Olivia M Manley
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Dumei Ma
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA; Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| | - Yingwu Yin
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| | - Thomas M Makris
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA.
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Rossetti M, Bertucci A, Patiño T, Baranda L, Porchetta A. Programming DNA-Based Systems through Effective Molarity Enforced by Biomolecular Confinement. Chemistry 2020; 26:9826-9834. [PMID: 32428310 DOI: 10.1002/chem.202001660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/12/2020] [Indexed: 12/12/2022]
Abstract
The fundamental concept of effective molarity is observed in a variety of biological processes, such as protein compartmentalization within organelles, membrane localization and signaling paths. To control molecular encountering and promote effective interactions, nature places biomolecules in specific sites inside the cell in order to generate a high, localized concentration different from the bulk concentration. Inspired by this mechanism, scientists have artificially recreated in the lab the same strategy to actuate and control artificial DNA-based functional systems. Here, it is discussed how harnessing effective molarity has led to the development of a number of proximity-induced strategies, with applications ranging from DNA-templated organic chemistry and catalysis, to biosensing and protein-supported DNA assembly.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Bertucci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Tania Patiño
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Lorena Baranda
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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Zhang S, Li X, Yuan Q, Secundo F, Li Y, Liang H. Step-wise immobilization of multi-enzymes by zirconium-based coordination polymer in situ self-assembly and specific absorption. J Inorg Biochem 2020; 208:111093. [DOI: 10.1016/j.jinorgbio.2020.111093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 10/24/2022]
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Li X, Cao X, Xiong J, Ge J. Enzyme-Metal Hybrid Catalysts for Chemoenzymatic Reactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1902751. [PMID: 31468669 DOI: 10.1002/smll.201902751] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/10/2019] [Indexed: 05/21/2023]
Abstract
Enzyme-metal hybrid catalysts (EMHCs), which combine enzymatic and metal catalysis, provide tremendous possibilities for new chemoenzymatic cascade reactions. Here, an overview of the representative achievements in the design of EMHCs and their applications in chemoenzymatic cascade reactions are presented. The preparation of hybrid catalysts is classified into two categories: coimmobilized enzyme-metal heterogeneous catalysts and carrier-free enzyme-metal bioconjugates. Examples of one-pot chemoenzymatic cascade processes catalyzed by the hybrid catalysts are then provided as potential applications. Finally, the limitations and future perspectives of EMHCs are discussed.
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Affiliation(s)
- Xiaoyang Li
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xun Cao
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Jiarong Xiong
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Jun Ge
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
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Vázquez-González M, Wang C, Willner I. Biocatalytic cascades operating on macromolecular scaffolds and in confined environments. Nat Catal 2020. [DOI: 10.1038/s41929-020-0433-1] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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McConnell SA, Cannon KA, Morgan C, McAllister R, Amer BR, Clubb RT, Yeates TO. Designed Protein Cages as Scaffolds for Building Multienzyme Materials. ACS Synth Biol 2020; 9:381-391. [PMID: 31922719 DOI: 10.1021/acssynbio.9b00407] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The functions of enzymes can be strongly affected by their higher-order spatial arrangements. In this study we combine multiple new technologies-designer protein cages and sortase-based enzymatic attachments between proteins-as a novel platform for organizing multiple enzymes (of one or more types) in specified configurations. As a scaffold we employ a previously characterized 24-subunit designed protein cage whose termini are outwardly exposed for attachment. As a first-use case, we test the attachment of two cellulase enzymes known to act synergistically in cellulose degradation. We show that, after endowing the termini of the cage subunits with a short "sort-tag" sequence (LPXTG) and the opposing termini of the cellulase enzymes with a short polyglycine sequence tag, addition of sortase covalently attaches the enzymes to the cage with good reactivity and high copy number. The doubly modified cages show enhanced activity in a cellulose degradation assay compared to enzymes in solution, and compared to a combination of singly modified cages. These new engineering strategies could be broadly useful in the development of enzymatic material and synthetic biology applications.
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Affiliation(s)
- Scott A. McConnell
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Kevin A. Cannon
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Christian Morgan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095, United States
| | - Rachel McAllister
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Brendan R. Amer
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Robert T. Clubb
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Todd O. Yeates
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
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Magneto-controlled enzyme reactions. Methods Enzymol 2020. [PMID: 31931981 DOI: 10.1016/bs.mie.2019.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Various approaches to magneto-controlled biocatalytic enzyme reactions are discussed with specific example systems. Magnetic nano- and micro-size particles functionalized with enzymes or cofactors/electron transfer mediators have been used to translocate the components of the biocatalytic processes and to activate/inhibit their reactions. Magneto-induced deposition of the functionalized particles on an electrode surface resulted in activation of bioelectrocatalytic reactions. On the other hand, magneto-induced removal of the particles from the electrode surface resulted in the inhibition of the electrochemical reactions. Aggregation/disaggregation of enzyme-modified magnetic nanoparticles resulted in different mechanisms of biocatalytic cascades, changing them reversibly between substrate diffusion and substrate channeling processes. Magnetohydrodynamic activation of bioelectrocatalytic processes allowed enhancement of a biofuel cell operation. Overall, a large variety of possible magneto-controlled enzyme reactions is briefly discussed, particularly emphasizing their applications in different bioelectronic systems.
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