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Yong Y, Ouyang P, Wu J, Liu Z. A Diffusion‐Reaction Model for One‐Pot Synthesis of Chemicals with Enzyme Cascades. ChemCatChem 2019. [DOI: 10.1002/cctc.201901161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- You Yong
- Key Lab of Industrial Biocatalysis Ministry of Education Department of Chemical EngineeringTsinghua University Beijing 100084 P. R. China
| | - Pingkai Ouyang
- Jiangsu National Synergistic Innovation Centre for Advanced Materials Nanjing 211800 P. R. China
| | - Jianzhong Wu
- Department of Chemical and Environmental EngineeringUniversity of California Riverside CA 92521 USA
| | - Zheng Liu
- Key Lab of Industrial Biocatalysis Ministry of Education Department of Chemical EngineeringTsinghua University Beijing 100084 P. R. China
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52
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Nahar S, Sokullu E, Gauthier MA. The phage display of Bacillus subtilis Lipase A significantly enhances catalytic activity due to altered nanoscale distribution in colloidal solution. Biotechnol Bioeng 2019; 117:868-872. [PMID: 31758554 DOI: 10.1002/bit.27229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/08/2019] [Accepted: 11/17/2019] [Indexed: 11/10/2022]
Abstract
Screening libraries of mutant proteins by phage display is now relatively common. However, one unknown factor is how the bacteriophage scaffold itself influences the properties of the displayed protein. This communication evaluates the effect of solution parameters on the catalytic activity of phage displayed Bacillus subtilis Lipase A (BSLA), compared to the free enzyme in solution. While the pH- and temperature-activity profiles of BSLA were not intrinsically affected by phage display, the nanoscale distribution of BSLA within the micellar assay buffer was. This lead to a pronounced increase of activity of phage-BSLA relative to the free enzyme, owing to the accumulation of phage-BSLA at the substrate-rich micelles. Considering this result obtained for BSLA, caution is warranted and similar effects should be considered when selecting other enzymes/proteins by phage display, as the activity of the displayed protein may differ from that of the free protein.
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Affiliation(s)
- Sharifun Nahar
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, Quebec, Canada
| | - Esen Sokullu
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, Quebec, Canada
| | - Marc A Gauthier
- Institut National de la Recherche Scientifique (INRS), EMT Research Center, Varennes, Quebec, Canada
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53
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Zhang G, Johnston T, Quin MB, Schmidt-Dannert C. Developing a Protein Scaffolding System for Rapid Enzyme Immobilization and Optimization of Enzyme Functions for Biocatalysis. ACS Synth Biol 2019; 8:1867-1876. [PMID: 31305981 DOI: 10.1021/acssynbio.9b00187] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Immobilization of enzymes is required for most biocatalytic processes, but chemistries used in enzyme immobilization are limited and can be challenging. Genetically encoded protein-based biomaterials could provide easy-to-use immobilization platforms for biocatalysts. We recently developed a self-assembling protein scaffold that covalently immobilized SpyTagged enzymes by engineering the bacterial microcompartment protein EutM from Salmonella enterica with a SpyCatcher domain. We also identified a range of EutM homologues as robust protein nanostructures with diverse architectures and electrostatic surface properties. In this work, we created a modular immobilization platform with tunable surface properties by developing a toolbox of self-assembling, robust EutM-SpyCatcher scaffolds. Using an alcohol dehydrogenase as model biocatalyst, we show that the scaffolds improve enzyme activity and stability. This work provides a modular, easy-to-use immobilization system that can be tailored for the optimal function of biocatalysts of interest.
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Affiliation(s)
- Guoqiang Zhang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Timothy Johnston
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Maureen B. Quin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota 55108, United States
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55
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Graphene oxide enabled long-term enzymatic transesterification in an anhydrous gas flux. Nat Commun 2019; 10:2684. [PMID: 31213607 PMCID: PMC6582274 DOI: 10.1038/s41467-019-10686-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/19/2019] [Indexed: 11/25/2022] Open
Abstract
Gas-phase enzymatic catalysis has been long pursued but not yet utilized in industrial processes due to many limitations. Herein, we report a hydroxyl-rich graphene oxide (GO) aerogel that can preserve the enzymatic activity and stability in an anhydrous gas flow by providing a water-like microenvironment. Lipase immobilized in the GO aerogel exhibits a 5 to 10-fold increase in apparent activity than the lyophilized lipase powder in transesterification of geraniol and vinyl acetate in the gas phase and maintains the initial activity for more than 500 h. The solid-state circular dichroism measurement confirms that the lipase keeps its native conformation in the aerogel, and the thermogravimetric analysis shows that water molecules essential for the lipase activity can be replaced by the hydroxyl groups at the GO surface. The versatility of this method is demonstrated for two other lipases with different structures, promising unprecedented applications of enzyme-GO aerogels to gas-phase enzymatic catalysis. Implementing enzymatic reactions in gas phase has several limitations. Here, the authors report on a method to overcome these using graphene oxide aerogels to immobilize lipase, improve stability/lifetime and investigate the mechanism for improved function.
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56
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Patino T, Porchetta A, Jannasch A, Lladó A, Stumpp T, Schäffer E, Ricci F, Sánchez S. Self-Sensing Enzyme-Powered Micromotors Equipped with pH-Responsive DNA Nanoswitches. NANO LETTERS 2019; 19:3440-3447. [PMID: 30704240 DOI: 10.1021/acs.nanolett.8b04794] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Biocatalytic micro- and nanomotors have emerged as a new class of active matter self-propelled through enzymatic reactions. The incorporation of functional nanotools could enable the rational design of multifunctional micromotors for simultaneous real-time monitoring of their environment and activity. Herein, we report the combination of DNA nanotechnology and urease-powered micromotors as multifunctional tools able to swim, simultaneously sense the pH of their surrounding environment, and monitor their intrinsic activity. With this purpose, a FRET-labeled triplex DNA nanoswitch for pH sensing was immobilized onto the surface of mesoporous silica-based micromotors. During self-propulsion, urea decomposition and the subsequent release of ammonia led to a fast pH increase, which was detected by real-time monitoring of the FRET efficiency through confocal laser scanning microscopy at different time points (i.e., 30 s, 2 and 10 min). Furthermore, the analysis of speed, enzymatic activity, and propulsive force displayed a similar exponential decay, matching the trend observed for the FRET efficiency. These results illustrate the potential of using specific DNA nanoswitches not only for sensing the micromotors' surrounding microenvironment but also as an indicator of the micromotor activity status, which may aid to the understanding of their performance in different media and in different applications.
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Affiliation(s)
- Tania Patino
- Institute for Bioengineering of Catalonia (IBEC) , The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12 , Barcelona 08028 , Spain
| | - Alessandro Porchetta
- Department of Chemistry , University of Rome , Tor Vergata, Via della Ricerca Scientifica 1 , Rome 00133 , Italy
| | - Anita Jannasch
- Center for Plant Molecular Biology (ZMBP) , University of Tübingen , Auf der Morgenstelle 32 , Tübingen 72076 , Germany
| | - Anna Lladó
- Advanced Digital Microscopy , Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Barcelona 08010 , Spain
| | - Tom Stumpp
- Center for Plant Molecular Biology (ZMBP) , University of Tübingen , Auf der Morgenstelle 32 , Tübingen 72076 , Germany
| | - Erik Schäffer
- Center for Plant Molecular Biology (ZMBP) , University of Tübingen , Auf der Morgenstelle 32 , Tübingen 72076 , Germany
| | - Francesco Ricci
- Department of Chemistry , University of Rome , Tor Vergata, Via della Ricerca Scientifica 1 , Rome 00133 , Italy
| | - Samuel Sánchez
- Institute for Bioengineering of Catalonia (IBEC) , The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12 , Barcelona 08028 , Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) , Pg. Lluís Companys 23 , Barcelona 08010 , Spain
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57
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Abdallah W, Chirino V, Wheeldon I, Banta S. Catalysis of Thermostable Alcohol Dehydrogenase Improved by Engineering the Microenvironment through Fusion with Supercharged Proteins. Chembiochem 2019; 20:1827-1837. [PMID: 30859665 DOI: 10.1002/cbic.201900066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/09/2019] [Indexed: 11/09/2022]
Abstract
The enzymatic microenvironment can impact biocatalytic activity; however, these effects can be difficult to investigate as mutations and fusions can introduce multiple variables and overlapping effects. The fusion of a supercharged protein is a potentially facile means to alter the enzymatic microenvironment. We have investigated complexes made between a thermostable alcohol dehydrogenase (AdhD) and superfolding green fluorescent protein (sfGFP) mutants with extreme surface charges. Three charged sfGFP variants, -30, 0, and +36 were covalently attached to AdhD through the SpyCatcher/SpyTag system. Specific rates for the NAD+ -dependent oxidation of butane-2,3-diol were significantly increased in the -30 sfGFP complex, a mixed effect was seen for the 0 sfGFP complexes, and the rates were unaffected by +36 sfGFP complexation. Reactions performed at various pH values (7.8-9.8) and salt concentrations (7.75-500 mm) showed that there was a complex interplay between these effects that was consistent with fusion proteins affecting the local ionic strength, as opposed to the local pH. Steady-state kinetic analyses were performed with the -30 and 0 AdhD-sfGFP complexes. The overall catalytic efficiency was dependent on the charge of the fused sfGFP variant; the -30 sfGFP fusions exhibited the largest beneficial effects at pH 8.8. The impact of the fusions on the apparent ionic strength provides further insight into the effects of charged patches observed on metabolon-forming enzyme complexes.
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Affiliation(s)
- Walaa Abdallah
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, Room 801, New York, NY, 10027, USA
| | - Vanessa Chirino
- Department of Biochemistry, Barnard College, 3009 Broadway, New York, NY, 10027, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, Room 801, New York, NY, 10027, USA
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58
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Bilal M, Cui J, Iqbal HMN. Tailoring enzyme microenvironment: State-of-the-art strategy to fulfill the quest for efficient bio-catalysis. Int J Biol Macromol 2019; 130:186-196. [PMID: 30817963 DOI: 10.1016/j.ijbiomac.2019.02.141] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/15/2019] [Accepted: 02/23/2019] [Indexed: 02/08/2023]
Abstract
Enzymes as green industrial biocatalysts have become a powerful norm that offers several advantages over traditional catalytic agents with regard to process efficiency, reusability, sustainability, and overall cost-effective ratio. However, enzymes obtained from natural origins are often engineered/tailored since their native forms do not fulfill the acute need for the industrial application. Revolutionary developments in protein engineering provide excellent opportunities for designing and constructing novel industrial biocatalysts with improved functional properties including catalytic activity, stability, substrate specificity, and reaction product inhibition. Momentum in enzyme immobilization has enabled robustness and optimal functions in extreme industrial environments, such as high temperature or organic solvents. The emergence of multi-enzyme catalytic cascade based on a combination of biocatalysts presents multifarious opportunities in biosynthesis, biocatalysis, and biotransformation. This review focuses on the emerging and state-of-the-art enzyme engineering trends and approaches to constructing innovative nano- and microstructured biocatalysts with enhanced catalytic activity and stability features requisite for industrial exploitation. Continuous key developments in this direction together with protein engineering in unique ways might offer ever-increasing opportunities for future biocatalysis-based industrial bioprocesses.
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Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Jiandong Cui
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, No 29, 13th, Avenue, Tianjin Economic and Technological Development Area (TEDA), Tianjin 300457, China.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L. CP 64849, Mexico.
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59
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Tao W, Wang J, Parak WJ, Farokhzad OC, Shi J. Nanobuffering of pH-Responsive Polymers: A Known but Sometimes Overlooked Phenomenon and Its Biological Applications. ACS NANO 2019; 13:4876-4882. [PMID: 30985108 PMCID: PMC6748625 DOI: 10.1021/acsnano.9b01696] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
With recent advances in polymer chemistry, materials science, and nanotechnology, pH-responsive polymers have a significant impact in a number of diverse fields. Fundamental studies of these polymers are thus highly desirable as they may lead to new insights into the rational design of pH-responsive polymers with specific effects. In this Perspective, we focus on the nanobuffering of pH-responsive polymers (NBPRP). Although researchers have known of such buffering effects for more than a century, for example, in the context of the Henderson-Hasselbalch equation, modern synthesis and analysis routes now enable us to analyze these effects on the nanometer scale. In this way, the NBPRP phenomenon was explicitly defined and described by Gauthier and colleagues in the February issue of ACS Nano. Here, we highlight several potential areas in which the NBPRP could enable innovative classes of biological applications. We expect deeper mechanistic understanding of nanobuffering effects induced by pH-responsive polymers to have a significant impact on the future development and applications of these polymers.
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Affiliation(s)
- Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Junqing Wang
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wolfgang J. Parak
- Center for Hybrid Nanostructures (CHyN), Univeristät Hamburg, 22607 Hamburg, Germany
| | - Omid C. Farokhzad
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jinjun Shi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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60
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Affiliation(s)
- Ee Taek Hwang
- Center for Convergence Bioceramic Materials, Korea Institute of Ceramic Engineering & Technology, Cheongju-si, Chungcheongbuk-do 28160, Republic of Korea
| | - Seonbyul Lee
- Center for Convergence Bioceramic Materials, Korea Institute of Ceramic Engineering & Technology, Cheongju-si, Chungcheongbuk-do 28160, Republic of Korea
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61
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Anees P, Zhao Y, Greschner AA, Congdon TR, de Haan HW, Cottenye N, Gauthier MA. Evidence, Manipulation, and Termination of pH 'Nanobuffering' for Quantitative Homogenous Scavenging of Monoclonal Antibodies. ACS NANO 2019; 13:1019-1028. [PMID: 30588795 DOI: 10.1021/acsnano.8b07202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This study demonstrates that pH-responsive polymers have a very high buffering capacity in their immediate vicinity, a phenomenon termed "nanobuffering". This can be exploited to dissociate local nanoscale pH from bulk solution pH. Herein, a series of pH-responsive polymers were conjugated to Protein-A to rationally manipulate the latter's binding affinity toward antibodies via nanobuffering ( i. e., this interaction is pH dependent), independently of bulk solution pH. Moreover, the nanobuffering effect could be terminated using low concentrations of strong ion-pairing salts, to achieve quantitative release of the antibodies from the bioconjugate. These complementary discoveries are showcased in the context of the development of a homogeneous affinity precipitation agent ( i. e., a scavenger) for the purification of polyclonal immunoglobulin G and two monoclonal antibodies from cell culture supernatant. Indeed, while bulk solution pH was used to induce precipitation of the scavenger, maintaining local nanoscale pH via nanobuffering maximized binding interaction with the antibodies. A 2:1 binding stoichiometry was observed, which was similar to that observed for native protein. The scavenger could be recycled multiple times, and the purification protocol circumvented lengthy/tedious physical purification processes typically associated with mAb manufacturing. Overall, this study provides perspectives on the local nanoscale pH near pH-responsive polymers and establishes lines of thought for predictably manipulating or even terminating nanobuffering, to control the activity of proteins.
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Affiliation(s)
- Palapuravan Anees
- EMT Research Center , Institut National de la Recherche Scientifique (INRS) , Varennes , Quebec J3X 1S2 , Canada
| | - Yi Zhao
- EMT Research Center , Institut National de la Recherche Scientifique (INRS) , Varennes , Quebec J3X 1S2 , Canada
| | - Andrea A Greschner
- EMT Research Center , Institut National de la Recherche Scientifique (INRS) , Varennes , Quebec J3X 1S2 , Canada
| | - Thomas R Congdon
- EMT Research Center , Institut National de la Recherche Scientifique (INRS) , Varennes , Quebec J3X 1S2 , Canada
| | - Hendrick W de Haan
- Faculty of Science , University of Ontario Institute of Technology , Oshawa , Ontario L1H 7K4 , Canada
| | | | - Marc A Gauthier
- EMT Research Center , Institut National de la Recherche Scientifique (INRS) , Varennes , Quebec J3X 1S2 , Canada
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62
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Zhang C, Song W, Liu J, Chen X, Liu L. Production of enantiopure (R)- or (S)-2-hydroxy-4-(methylthio)butanoic acid by multi-enzyme cascades. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0244-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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63
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Zhang G, Schmidt-Dannert S, Quin MB, Schmidt-Dannert C. Protein-based scaffolds for enzyme immobilization. Methods Enzymol 2019; 617:323-362. [PMID: 30784408 DOI: 10.1016/bs.mie.2018.12.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Biocatalysis is emerging as an alternative approach to chemical synthesis of industrially relevant complex molecules. To obtain suitable yields of compounds in a cost-effective manner, biocatalytic reaction cascades must be efficient, robust, and self-sufficient. One approach is to immobilize biocatalysts on a solid support, stabilizing the enzymes and providing optimal microenvironments for reaction sequences. Protein-based scaffolds can be designed as immobilization platforms for biocatalysts, enabling the genetically encoded spatial organization of single enzymes and multistep enzyme cascades. Additionally, protein scaffolds are versatile, are easily adapted, and remain robust under different reaction conditions. In this chapter, we describe methods for the design and production of a self-assembling protein scaffold system for in vitro coimmobilization of biocatalytic cascade enzymes. We provide detailed methods for the characterization of the protein scaffolds, as well as approaches to load biocatalytic cargo enzymes and test activity of immobilized cascades. In addition, we also discuss methods for the development of a scaffold building block toolbox with different surface properties, which could be adapted for a diversity of biocatalysts requiring alternative microenvironments for function.
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Affiliation(s)
- Guoqiang Zhang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN, United States
| | - Sarah Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN, United States
| | - Maureen B Quin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN, United States.
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN, United States.
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64
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Huang J, Zhuang W, Ge L, Wang K, Wang Z, Niu H, Wu J, Zhu C, Chen Y, Ying H. Improving biocatalytic microenvironment with biocompatible ε-poly-l-lysine for one step gluconic acid production in low pH enzymatic systems. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.10.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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65
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Benson KR, Gorecki J, Nikiforov A, Tsui W, Kasi RM, Kumar CV. Cytochrome c–poly(acrylic acid) conjugates with improved peroxidase turnover number. Org Biomol Chem 2019; 17:4043-4048. [DOI: 10.1039/c9ob00541b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cytochrome c–poly(acrylic acid) conjugates with 34-fold enhanced peroxidase activity due to acidification of enzyme microenvironment and suppression of wasteful intermediates.
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Affiliation(s)
- K. R. Benson
- Department of Chemistry
- University of Connecticut
- Storrs
- USA
| | - J. Gorecki
- Department of Chemistry
- University of Connecticut
- Storrs
- USA
| | - A. Nikiforov
- Department of Chemistry
- University of Connecticut
- Storrs
- USA
| | - W. Tsui
- Department of Chemistry
- University of Connecticut
- Storrs
- USA
| | - R. M. Kasi
- Department of Chemistry
- University of Connecticut
- Storrs
- USA
- Institute of Materials Science
| | - C. V. Kumar
- Department of Chemistry
- University of Connecticut
- Storrs
- USA
- Institute of Materials Science
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66
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Vogele K, List J, Simmel FC, Pirzer T. Enhanced Efficiency of an Enzyme Cascade on DNA-Activated Silica Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14780-14786. [PMID: 30462511 DOI: 10.1021/acs.langmuir.8b01770] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In nature, compartmentalized and spatially organized enzyme cascades are utilized to increase the efficiency of enzymatic reactions. From a technologically relevant perspective, synthetic enzyme systems have to be optimized with emphasis on enzyme activity, productivity, scalability, and ease of use. But the underlying principles and relevant parameters that lead to an enhancement of the activity of enzyme cascades through spatial organization are still under debate. Here, we report on the 10-fold activity enhancement of the GOx-HRP enzyme cascade for the oxidation of luminol, when the enzymes are colocalized on micron-scaled solid scaffolds. Both enzymes were initially assembled and concentrated on DNA origami rectangles and finally further concentrated on the surface of silica particles. We show that each particular component of the designed system contributes to the activity enhancement. Furthermore, we measured an influence of the silica particle length scale on the total productivity by a factor of 5-10, but to a lesser extent on the maximum enzyme activity. Our findings demonstrate that micrometer-sized scaffolds can be used to enhance the efficiency of enzyme-cascades by at least a magnitude and that solid-phase scaffolds enable scalability for technological applications.
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Affiliation(s)
- Kilian Vogele
- Physics of Synthetic Biological Systems - E14, Physics Department and ZNN , Technische Universität München , Am Coulombwall 4a , 85748 Garching , Germany
| | - Jonathan List
- Physics of Synthetic Biological Systems - E14, Physics Department and ZNN , Technische Universität München , Am Coulombwall 4a , 85748 Garching , Germany
| | - Friedrich C Simmel
- Physics of Synthetic Biological Systems - E14, Physics Department and ZNN , Technische Universität München , Am Coulombwall 4a , 85748 Garching , Germany
- Nanosystems Initiative Munich , Schellingstraße 4 , 80539 Munich , Germany
| | - Tobias Pirzer
- Physics of Synthetic Biological Systems - E14, Physics Department and ZNN , Technische Universität München , Am Coulombwall 4a , 85748 Garching , Germany
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67
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Wang Z, Wang J, Chen G, Xu W, Fu Z, Jiang G, Wu J, Liu Z. Polyelectrolytes Tailored Enzyme Cascades with Enhanced Stability and Activity for One‐pot Synthesis. ChemCatChem 2018. [DOI: 10.1002/cctc.201801532] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Zheyu Wang
- Department of Chemical Engineering Tsinghua University Beijing 100084 P.R. China
| | - Junqian Wang
- Department of Chemical Engineering Tsinghua University Beijing 100084 P.R. China
| | - Gong Chen
- Department of Chemical Engineering Tsinghua University Beijing 100084 P.R. China
| | - Weina Xu
- Department of Chemical Engineering Tsinghua University Beijing 100084 P.R. China
| | - Zhongwang Fu
- Department of Chemical Engineering Tsinghua University Beijing 100084 P.R. China
| | - Guoqiang Jiang
- Department of Chemical Engineering Tsinghua University Beijing 100084 P.R. China
| | - Jianzhong Wu
- Department of Chemical and Environmental Engineering University of California, Riverside Riverside CA 92521 USA
| | - Zheng Liu
- Department of Chemical Engineering Tsinghua University Beijing 100084 P.R. China
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68
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Tsitkov S, Pesenti T, Palacci H, Blanchet J, Hess H. Queueing Theory-Based Perspective of the Kinetics of “Channeled” Enzyme Cascade Reactions. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02760] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stanislav Tsitkov
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Theo Pesenti
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
- École Supérieure de Physique et de Chimie Industrielles (ESPCI), Paris, 75231 Cedex 05, France
| | - Henri Palacci
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Jose Blanchet
- Management Science and Engineering, Stanford University, Palo Alto, California 94305, United States
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
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69
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Vranish JN, Ancona MG, Oh E, Susumu K, Lasarte Aragonés G, Breger JC, Walper SA, Medintz IL. Enhancing Coupled Enzymatic Activity by Colocalization on Nanoparticle Surfaces: Kinetic Evidence for Directed Channeling of Intermediates. ACS NANO 2018; 12:7911-7926. [PMID: 30044604 DOI: 10.1021/acsnano.8b02334] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Multistep enzymatic cascades are becoming more prevalent in industrial settings as engineers strive to synthesize complex products and pharmaceuticals in economical, environmentally friendly ways. Previous work has shown that immobilizing enzymes on nanoparticles can enhance their activity significantly due to localized interfacial effects, and this enhancement remains in place even when that enzyme's activity is coupled to another enzyme that is still freely diffusing. Here, we investigate the effects of displaying two enzymes with coupled catalytic activity directly on the same nanoparticle surface. For this, the well-characterized enzymes pyruvate kinase (PykA) and lactate dehydrogenase (LDH) were utilized as a model system; they jointly convert phosphoenolpyruvate to lactate in two sequential steps as part of downstream glycolysis. The enzymes were expressed with terminal polyhistidine tags to facilitate their conjugation to semiconductor quantum dots (QDs) which were used here as prototypical nanoparticles. Characterization of enzyme coassembly to two different sized QDs showed a propensity to cross-link into nanoclusters consisting of primarily dimers and some trimers. Individual and joint enzyme activity in this format was extensively investigated in direct comparison to control samples lacking the QD scaffolds. We found that QD association enhances LDH activity by >50-fold and its total turnover by at least 41-fold, and that this high activation appears to be largely due to stabilization of its quarternary structure. When both enzymes are simultaneously bound to the QD surfaces, their colocalization leads to >100-fold improvements in the overall rates of coupled activity. Experimental results in conjunction with detailed kinetic simulations provide evidence that this significant improvement in coupled activity is partially attributable to a combination of enhanced enzymatic activity and stabilization of LDH. More importantly, experiments aimed at disrupting channeled processes and further kinetic modeling suggest that the bulk of the performance enhancement arises from intermediary "channeling" between the QD-colocalized enzymes. A full understanding of the underlying processes that give rise to such enhancements from coupled enzymatic activity on nanoparticle scaffolds can provide design criteria for improved biocatalytic applications.
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Affiliation(s)
- James Nicholas Vranish
- National Research Council , Washington , DC 20001 , United States
- Department of Chemistry and Physics , Ave Maria University , Ave Maria , Florida 34142 , United States
| | | | - Eunkeu Oh
- KeyW Corporation , Hanover , Maryland 21076 , United States
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70
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Lancaster L, Abdallah W, Banta S, Wheeldon I. Engineering enzyme microenvironments for enhanced biocatalysis. Chem Soc Rev 2018; 47:5177-5186. [PMID: 29796541 DOI: 10.1039/c8cs00085a] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein engineering provides a means to alter protein structure leading to new functions. Much work has focused on the engineering of enzyme active sites to enhance catalytic activity, however there is an increasing trend towards engineering other aspects of biocatalysts as these efforts can also lead to useful improvements. This tutorial discusses recent advances in engineering an enzyme's local chemical and physical environment, with the goal of enhancing enzyme reaction kinetics, substrate selectivity, and activity in harsh conditions (e.g., low or high pH). By introducing stimuli-responsiveness to these enzyme modifications, dynamic control of activity also becomes possible. These new biomolecular and protein engineering techniques are separate and independent from traditional active site engineering and can therefore be applied synergistically to create new biocatalyst technologies with novel functions.
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Affiliation(s)
- Louis Lancaster
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA.
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71
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Wang H, Zhao Z, Liu Y, Shao C, Bian F, Zhao Y. Biomimetic enzyme cascade reaction system in microfluidic electrospray microcapsules. SCIENCE ADVANCES 2018; 4:eaat2816. [PMID: 29922720 PMCID: PMC6003728 DOI: 10.1126/sciadv.aat2816] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/09/2018] [Indexed: 05/20/2023]
Abstract
Mimicking subcellular compartments containing enzymes in organisms is considered a promising approach to substitute for missing or lost cellular functions. Inspired by the multicompartment structures of cellular architectures, we present a novel multienzyme system based on hollow hydrogel microcapsules with flexible enzymatic inverse opal particles. Benefiting from the precise operation capability of the microfluidic electrospray and the remarkable structural color marks in the inverse opal particles, we developed a multienzyme system with controllable number, type, and spatial arrangement of the encapsulated enzymes. The hydrogel shells also could improve enzyme stability against proteolysis in the system. The multienzyme system containing alcohol oxidase and catalase could act as a cascade biocatalyst and reduce alcohol levels in media, providing an alternative antidote and prophylactic for alcohol intoxication. These features indicated that our strategy provides an ideal enzyme cascade reaction system for complex biocatalysis and biomimetic functions of some organelles or organs.
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72
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Goh K, Li H, Lam K. Urease catalytic behaviors induced by both urea and salt concentrations in ion-exchange hydrogels as dialysis membranes. REACT FUNCT POLYM 2018. [DOI: 10.1016/j.reactfunctpolym.2018.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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73
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Sweetlove LJ, Fernie AR. The role of dynamic enzyme assemblies and substrate channelling in metabolic regulation. Nat Commun 2018; 9:2136. [PMID: 29849027 PMCID: PMC5976638 DOI: 10.1038/s41467-018-04543-8] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 05/08/2018] [Indexed: 11/08/2022] Open
Abstract
Transient physical association between enzymes appears to be a cardinal feature of metabolic systems, yet the purpose of this metabolic organisation remains enigmatic. It is generally assumed that substrate channelling occurs in these complexes. However, there is a lack of information concerning the mechanisms and extent of substrate channelling and confusion regarding the consequences of substrate channelling. In this review, we outline recent advances in the structural characterisation of enzyme assemblies and integrate this with new insights from reaction-diffusion modelling and synthetic biology to clarify the mechanistic and functional significance of the phenomenon.
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Affiliation(s)
- Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany.
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74
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Zhu Q, Zhuang W, Chen Y, Wang Z, Villacorta Hernandez B, Wu J, Yang P, Liu D, Zhu C, Ying H, Zhu Z. Nano-Biocatalysts of Cyt c@ZIF-8/GO Composites with High Recyclability via a de Novo Approach. ACS APPLIED MATERIALS & INTERFACES 2018; 10:16066-16076. [PMID: 29687711 DOI: 10.1021/acsami.8b00072] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To improve the stability and recyclability of enzymes immobilized on metal-organic frameworks (MOFs), graphene oxide (GO) with surface oxygen-rich functional groups was selected to form ZIF-8/GO nanocomposites with the zeolitic imidazolate framework (ZIF-8) for cytochrome c (Cyt c) immobilization. It was found that the functional groups on the GO surface were involved in the growth of ZIF-8 without affecting the crystal structure but their particle size was reduced to about 200 nm. The storage stability and resistance to organic solvents of Cyt c were obviously improved after the immobilization on the ZIF-8/GO nanocomposite. On one hand, compared with Cyt c@ZIF-8 and Cyt c@GO with 30 and 60% protein leakage, Cyt c@ZIF-8/GO displayed little protein leakage after 60 h of storage. On the other hand, Cyt c@ZIF-8/GO retained a residual activity of approximately 100% after being stored in ethanol and acetone for 2 h, whereas the free enzyme, Cyt c@ZIF-8, and Cyt c@GO retained only about 10, 50, and 40%, respectively. In addition, the Cyt c@ZIF-8/GO nanocomposites can be utilized up to four cycles with virtually no loss of activity and may be further applied on H2O2 biosensing systems. The synergistic effect between MOFs and GO in ZIF-8/GO nanocomposites provides infinite possibilities as immobilized enzyme carriers.
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Affiliation(s)
| | - Wei Zhuang
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing Tech University , No. 5 Xinmofan Road , Nanjing 210009 , China
- School of Chemical Engineering , The University of Queensland , St. Lucia , Queensland 4072 , Australia
| | - Yong Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing Tech University , No. 5 Xinmofan Road , Nanjing 210009 , China
| | - Zhanke Wang
- School of Chemical Engineering , The University of Queensland , St. Lucia , Queensland 4072 , Australia
| | | | - Jinglan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing Tech University , No. 5 Xinmofan Road , Nanjing 210009 , China
| | - Pengpeng Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing Tech University , No. 5 Xinmofan Road , Nanjing 210009 , China
| | - Dong Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing Tech University , No. 5 Xinmofan Road , Nanjing 210009 , China
| | - Chenjie Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing Tech University , No. 5 Xinmofan Road , Nanjing 210009 , China
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering , Nanjing Tech University , No. 5 Xinmofan Road , Nanjing 210009 , China
| | - Zhonghua Zhu
- School of Chemical Engineering , The University of Queensland , St. Lucia , Queensland 4072 , Australia
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75
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Zhang Y, Tsitkov S, Hess H. Complex dynamics in a two-enzyme reaction network with substrate competition. Nat Catal 2018. [DOI: 10.1038/s41929-018-0053-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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76
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Chado GR, Holland EN, Tice AK, Stoykovich MP, Kaar JL. Modification of Lipase with Poly(4-acryloylmorpholine) Enhances Solubility and Transesterification Activity in Anhydrous Ionic Liquids. Biomacromolecules 2018. [DOI: 10.1021/acs.biomac.8b00176] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Garrett R. Chado
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Elijah N. Holland
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Andrew K. Tice
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Mark P. Stoykovich
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Joel L. Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
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77
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Vranish JN, Ancona MG, Walper SA, Medintz IL. Pursuing the Promise of Enzymatic Enhancement with Nanoparticle Assemblies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:2901-2925. [PMID: 29115133 DOI: 10.1021/acs.langmuir.7b02588] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The growing emphasis on green chemistry, renewable resources, synthetic biology, regio-/stereospecific chemical transformations, and nanotechnology for providing new biological products and therapeutics is reinvigorating research into enzymatic catalysis. Although the promise is profound, many complex issues remain to be addressed before this effort will have a significant impact. Prime among these is to combat the degradation of enzymes frequently seen in ex vivo formats following immobilization to stabilize the enzymes for long-term application and to find ways of enhancing their activity. One promising avenue for progress on these issues is via nanoparticle (NP) display, which has been found in a number of cases to enhance enzyme activity while also improving long-term stability. In this feature article, we discuss the phenomenon of enhanced enzymatic activity at NP interfaces with an emphasis on our own work in this area. Important factors such as NP surface chemistry, bioconjugation approaches, and assay formats are first discussed because they can critically affect the observed enhancement. Examples are given of improved performance for enzymes such as phosphotriesterase, alkaline phosphatase, trypsin, horseradish peroxidase, and β-galactosidase and in configurations with either the enzyme or the substrate attached to the NP. The putative mechanisms that give rise to the performance boost are discussed along with how detailed kinetic modeling can contribute to their understanding. Given the importance of biosensing, we also highlight how this configuration is already making a significant contribution to NP-based enzymatic sensors. Finally, a perspective is provided on how this field may develop and how NP-based enzymatic enhancement can be extended to coupled systems and multienzyme cascades.
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78
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Affiliation(s)
- Yifei Zhang
- 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
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