51
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Quantum Dots and Gold Nanoparticles as Scaffolds for Enzymatic Enhancement: Recent Advances and the Influence of Nanoparticle Size. Catalysts 2020. [DOI: 10.3390/catal10010083] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Nanoparticle scaffolds can impart multiple benefits onto immobilized enzymes including enhanced stability, activity, and recoverability. The magnitude of these benefits is modulated by features inherent to the scaffold–enzyme conjugate, amongst which the size of the nanoscaffold itself can be critically important. In this review, we highlight the benefits of enzyme immobilization on nanoparticles and the factors affecting these benefits using quantum dots and gold nanoparticles as representative materials due to their maturity. We then review recent literature on the use of these scaffolds for enzyme immobilization and as a means to dissect the underlying mechanisms. Detailed analysis of the literature suggests that there is a “sweet-spot” for scaffold size and the ratio of immobilized enzyme to scaffold, with smaller scaffolds and lower enzyme:scaffold ratios generally providing higher enzymatic activities. We anticipate that ongoing studies of enzyme immobilization onto nanoscale scaffolds will continue to sharpen our understanding of what gives rise to beneficial characteristics and allow for the next important step, namely, that of translation to large-scale processes that exploit these properties.
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52
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Klein WP, Thomsen RP, Turner KB, Walper SA, Vranish J, Kjems J, Ancona MG, Medintz IL. Enhanced Catalysis from Multienzyme Cascades Assembled on a DNA Origami Triangle. ACS NANO 2019; 13:13677-13689. [PMID: 31751123 DOI: 10.1021/acsnano.9b05746] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Developing reliable methods of constructing cell-free multienzyme biocatalytic systems is a milestone goal of synthetic biology. It would enable overcoming the limitations of current cell-based systems, which suffer from the presence of competing pathways, toxicity, and inefficient access to extracellular reactants and removal of products. DNA nanostructures have been suggested as ideal scaffolds for assembling sequential enzymatic cascades in close enough proximity to potentially allow for exploiting of channeling effects; however, initial demonstrations have provided somewhat contradictory results toward confirming this phenomenon. In this work, a three-enzyme sequential cascade was realized by site-specifically immobilizing DNA-conjugated amylase, maltase, and glucokinase on a self-assembled DNA origami triangle. The kinetics of seven different enzyme configurations were evaluated experimentally and compared to simulations of optimized activity. A 30-fold increase in the pathway's kinetic activity was observed for enzymes assembled to the DNA. Detailed kinetic analysis suggests that this catalytic enhancement originated from increased enzyme stability and a localized DNA surface affinity or hydration layer effect and not from a directed enzyme-to-enzyme channeling mechanism. Nevertheless, the approach used to construct this pathway still shows promise toward improving other more elaborate multienzymatic cascades and could potentially allow for the custom synthesis of complex (bio)molecules that cannot be realized with conventional organic chemistry approaches.
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Affiliation(s)
- William P Klein
- National Research Council , Washington , D.C. 20001 , United States
| | - Rasmus P Thomsen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics , Aarhus University , 8000 Aarhus , Denmark
| | | | - Scott A Walper
- National Research Council , Washington , D.C. 20001 , United States
| | - James Vranish
- Ave Maria University , Ave Maria , Florida 34142 , United States
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics , Aarhus University , 8000 Aarhus , Denmark
| | | | - Igor L Medintz
- National Research Council , Washington , D.C. 20001 , United States
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53
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Zhang Y, Hess H. Inhibitors in Commercially Available 2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonate) Affect Enzymatic Assays. Anal Chem 2019; 92:1502-1510. [DOI: 10.1021/acs.analchem.9b04751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yifei Zhang
- Department of Biomedical Engineering, Columbia University, 351L Engineering Terrace, 1210 Amsterdam Avenue, New York, New York 10027, United States
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, 351L Engineering Terrace, 1210 Amsterdam Avenue, New York, New York 10027, United States
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54
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Cao Y, Li X, Xiong J, Wang L, Yan LT, Ge J. Investigating the origin of high efficiency in confined multienzyme catalysis. NANOSCALE 2019; 11:22108-22117. [PMID: 31720641 DOI: 10.1039/c9nr07381g] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biomimetic strategies have successfully been applied to confine multiple enzymes on scaffolds to obtain higher catalytic efficiency of enzyme cascades than freely distributed enzymes. However, the origin of high efficiency is poorly understood. We developed a coarse-grained, particle-based model to understand the origin of high efficiency. We found that a reaction intermediate is the key in affecting reaction kinetics. In the case of unstable intermediates, the confinement of multiple enzymes in clusters enhanced the catalytic efficiency and a shorter distance between enzymes resulted in a higher reaction rate and yield. This understanding was verified by co-encapsulating multiple enzymes in metal-organic framework (MOF) nanocrystals as artificially confined multienzyme complexes. The activity enhancement of multiple enzymes in MOFs depended on the distance between enzymes, when the decay of intermediates existed. The finding of this study is useful for designing in vitro synthetic biology systems based on artificial multienzyme complexes.
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Affiliation(s)
- Yufei Cao
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
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55
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Ellis GA, Klein WP, Lasarte-Aragonés G, Thakur M, Walper SA, Medintz IL. Artificial Multienzyme Scaffolds: Pursuing in Vitro Substrate Channeling with an Overview of Current Progress. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02413] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, 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
- National Research Council, Washington, D.C. 20001, United States
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, 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
| | - 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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56
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Synthetic bionanotechnology: synthetic biology finds a toehold in nanotechnology. Emerg Top Life Sci 2019; 3:507-516. [PMID: 33523177 PMCID: PMC7288988 DOI: 10.1042/etls20190100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 12/23/2022]
Abstract
Enabled by its central role in the molecular networks that govern cell function, RNA has been widely used for constructing components used in biological circuits for synthetic biology. Nucleic acid nanotechnology, which exploits predictable nucleic acid interactions to implement programmable molecular systems, has seen remarkable advances in in vitro nanoscale self-assembly and molecular computation, enabling the production of complex nanostructures and DNA-based neural networks. Living cells genetically engineered to execute nucleic acid nanotechnology programs thus have outstanding potential to significantly extend the current limits of synthetic biology. This perspective discusses the recent developments and future challenges in the field of synthetic bionanotechnology. Thus far, researchers in this emerging area have implemented dozens of programmable RNA nanodevices that provide precise control over gene expression at the transcriptional and translational levels and through CRISPR/Cas effectors. Moreover, they have employed synthetic self-assembling RNA networks in engineered bacteria to carry out computations featuring up to a dozen inputs and to substantially enhance the rate of chemical synthesis. Continued advancement of the field will benefit from improved in vivo strategies for streamlining nucleic acid network synthesis and new approaches for enhancing network function. As the field matures and the complexity gap between in vitro and in vivo systems narrows, synthetic bionanotechnology promises to have diverse potential applications ranging from intracellular circuits that detect and treat disease to synthetic enzymatic pathways that efficiently produce novel drug molecules.
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57
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Jaekel A, Stegemann P, Saccà B. Manipulating Enzymes Properties with DNA Nanostructures. Molecules 2019; 24:molecules24203694. [PMID: 31615123 PMCID: PMC6832416 DOI: 10.3390/molecules24203694] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids and proteins are two major classes of biopolymers in living systems. Whereas nucleic acids are characterized by robust molecular recognition properties, essential for the reliable storage and transmission of the genetic information, the variability of structures displayed by proteins and their adaptability to the environment make them ideal functional materials. One of the major goals of DNA nanotechnology-and indeed its initial motivation-is to bridge these two worlds in a rational fashion. Combining the predictable base-pairing rule of DNA with chemical conjugation strategies and modern protein engineering methods has enabled the realization of complex DNA-protein architectures with programmable structural features and intriguing functionalities. In this review, we will focus on a special class of biohybrid structures, characterized by one or many enzyme molecules linked to a DNA scaffold with nanometer-scale precision. After an initial survey of the most important methods for coupling DNA oligomers to proteins, we will report the strategies adopted until now for organizing these conjugates in a predictable spatial arrangement. The major focus of this review will be on the consequences of such manipulations on the binding and kinetic properties of single enzymes and enzyme complexes: an interesting aspect of artificial DNA-enzyme hybrids, often reported in the literature, however, not yet entirely understood and whose full comprehension may open the way to new opportunities in protein science.
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Affiliation(s)
- Andreas Jaekel
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
| | - Pierre Stegemann
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
| | - Barbara Saccà
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
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58
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Breger JC, Oh E, Susumu K, Klein WP, Walper SA, Ancona MG, Medintz IL. Nanoparticle Size Influences Localized Enzymatic Enhancement—A Case Study with Phosphotriesterase. Bioconjug Chem 2019; 30:2060-2074. [DOI: 10.1021/acs.bioconjchem.9b00362] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- KeyW Corporation, Hanover, Maryland 21076, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- KeyW 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
- National Research Council, Washington, D.C. 20001, 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
| | - Mario G. Ancona
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, 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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59
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Liu Y, Hickey DP, Minteer SD, Dickson A, Calabrese Barton S. Markov-State Transition Path Analysis of Electrostatic Channeling. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2019; 123:15284-15292. [PMID: 31275507 PMCID: PMC6602406 DOI: 10.1021/acs.jpcc.9b02844] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/20/2019] [Indexed: 06/01/2023]
Abstract
Electrostatic channeling is a naturally occurring approach to control the flux of charged intermediates in catalytic cascades. Computational techniques have enabled quantitative understanding of such mechanisms, augmenting experimental approaches by modeling molecular interactions in atomic detail. In this work, we report the first utilization of a Markov-state model (MSM) to describe the surface diffusion of a reaction intermediate, glucose 6-phosphate, on an artificially modified cascade where hexokinase and glucose-6-phosphate dehydrogenase are covalently conjugated by a cationic oligopeptide bridge. Conformation space networks are used to represent intermediate transport on enzyme surfaces, along with committor probabilities that assess the desorption probability of the intermediate on each segment of the channeling pathway. For the region between the peptide bridge and downstream active site, the ionic strength dependence of desorption probability by MSM agreed well with that by transition state theory. A kinetic Monte Carlo model integrates parameters from different computational methods to evaluate the contribution of desorption during each step. The approach is validated by calculation of kinetic lag time, which agrees well with experimental results. These results further demonstrate the applicability of molecular simulations and advanced sampling techniques to the design of chemical networks.
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Affiliation(s)
- Yuanchao Liu
- Department
of Chemical Engineering and Materials Science and Department of
Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| | - David P. Hickey
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Shelley D. Minteer
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Alex Dickson
- Department
of Chemical Engineering and Materials Science and Department of
Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| | - Scott Calabrese Barton
- Department
of Chemical Engineering and Materials Science and Department of
Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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60
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Lim S, Jung GA, Glover DJ, Clark DS. Enhanced Enzyme Activity through Scaffolding on Customizable Self-Assembling Protein Filaments. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805558. [PMID: 30920729 DOI: 10.1002/smll.201805558] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/21/2019] [Indexed: 06/09/2023]
Abstract
Precisely organized enzyme complexes are often found in nature to support complex metabolic reactions in a highly efficient and specific manner. Scaffolding enzymes on artificial materials has thus gained attention as a promising biomimetic strategy to design biocatalytic systems with enhanced productivity. Herein, a versatile scaffolding platform that can immobilize enzymes on customizable nanofibers is reported. An ultrastable self-assembling filamentous protein, the gamma-prefoldin (γ-PFD), is genetically engineered to display an array of peptide tags, which can specifically and stably bind enzymes containing the counterpart domain through simple in vitro mixing. Successful immobilization of proteins along the filamentous template in tunable density is first verified using fluorescent proteins. Then, two different model enzymes, glucose oxidase and horseradish peroxidase, are used to demonstrate that scaffold attachment could enhance the intrinsic catalytic activity of the immobilized enzymes. Considering the previously reported ability of γ-PFD to bind and stabilize a broad range of proteins, the filament's interaction with the bound enzymes may have created a favorable microenvironment for catalysis. It is envisioned that the strategy described here may provide a generally applicable methodology for the scaffolded assembly of multienzymatic complexes for use in biocatalysis.
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Affiliation(s)
- Samuel Lim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Gi Ahn Jung
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
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61
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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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62
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Li T, Li J, Pang Q, Ma L, Tong W, Gao C. Construction of Microreactors for Cascade Reaction and Their Potential Applications as Antibacterial Agents. ACS APPLIED MATERIALS & INTERFACES 2019; 11:6789-6795. [PMID: 30702277 DOI: 10.1021/acsami.8b20069] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Enzymatic cascade reactions in confined microenvironments play important roles in cellular chemical transformation. They also have important biotechnological and therapeutic applications. Here, enzymatic cascade microreactors (MRs) coupling glucose oxidase (GOx) and hemoglobin (Hb) (GOx-Hb MRs) were successfully fabricated by co-precipitation of GOx and Hb into a MnCO3 template, followed by the assembly of a multilayer film on a template surface, slight cross-linking, and final removal of MnCO3. In the presence of glucose with blood-relevant concentration, the GOx-Hb MRs exhibited a higher cascade reaction activity under mild acidic conditions than that under neutral conditions at physiological temperature. The GOx-Hb MRs effectively consumed glucose to generate HO· at pH = 5, which significantly inhibited bacterial growth and biofilm formation. This kind of enzymatic cascade microreactors might be useful for applications in biomedical fields.
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Affiliation(s)
- Tong Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Jiawei Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Qian Pang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Lie Ma
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Weijun Tong
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Changyou Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
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63
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Kuzmak A, Carmali S, von Lieres E, Russell AJ, Kondrat S. Can enzyme proximity accelerate cascade reactions? Sci Rep 2019; 9:455. [PMID: 30679600 PMCID: PMC6345930 DOI: 10.1038/s41598-018-37034-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/26/2018] [Indexed: 01/23/2023] Open
Abstract
The last decade has seen an exponential expansion of interest in conjugating multiple enzymes of cascades in close proximity to each other, with the overarching goal being to accelerate the overall reaction rate. However, some evidence has emerged that there is no effect of proximity channeling on the reaction velocity of the popular GOx-HRP cascade, particularly in the presence of a competing enzyme (catalase). Herein, we rationalize these experimental results quantitatively. We show that, in general, proximity channeling can enhance reaction velocity in the presence of competing enzymes, but in steady state a significant enhancement can only be achieved for diffusion-limited reactions or at high concentrations of competing enzymes. We provide simple equations to estimate the effect of channeling quantitatively and demonstrate that proximity can have a more pronounced effect under crowding conditions in vivo, particularly that crowding can enhance the overall rates of channeled cascade reactions.
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Affiliation(s)
- Andrij Kuzmak
- Department for Theoretical Physics, I. Franko National University of Lviv, Lviv, Ukraine
| | - Sheiliza Carmali
- Department of Chemistry, Aarhus University, 8000, Aarhus C, Denmark.,Center for Polymer-Based Protein Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA
| | - Eric von Lieres
- Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Alan J Russell
- Center for Polymer-Based Protein Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, 15213, USA.,Department of Chemical Engineering, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Svyatoslav Kondrat
- Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany. .,Department of Complex Systems, Institute of Physical Chemistry, Warsaw, Poland.
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64
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Cui C, Fang Y, Chen B, Tan T. Glucose oxidation performance is improved by the use of a supramolecular self-assembly of glucose oxidase and catalase. Catal Sci Technol 2019. [DOI: 10.1039/c8cy01945b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A multi-enzymes complex was assembled successfully via host/guest interactions, and it was used for rapid transformation of glucose.
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Affiliation(s)
- Caixia Cui
- National Energy R&D Center for Biorefinery
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
| | - Yunming Fang
- National Energy R&D Center for Biorefinery
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
| | - Biqiang Chen
- National Energy R&D Center for Biorefinery
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
| | - Tianwei Tan
- National Energy R&D Center for Biorefinery
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
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65
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Affiliation(s)
- Simona Ranallo
- Department of Chemical Sciences and Technologies , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
| | - Alessandro Porchetta
- Department of Chemical Sciences and Technologies , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
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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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Filipov Y, Zakharchenko A, Minko S, Katz E. Magneto‐Controlled Biocatalytic Cascades with Logically Processed Input Signals – Substrate Channeling versus Free Diffusion. Chemphyschem 2018; 19:3035-3043. [DOI: 10.1002/cphc.201800851] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Yaroslav Filipov
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699 USA
| | | | - Sergiy Minko
- Nanostructured Materials Lab University of Georgia Athens GA 30602 USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699 USA
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69
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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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70
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Chen H, Huang R, Kim EJ, Zhang YHPJ. Building a Thermostable Metabolon for Facilitating Coenzyme Transport and In Vitro Hydrogen Production at Elevated Temperature. CHEMSUSCHEM 2018; 11:3120-3130. [PMID: 30014617 DOI: 10.1002/cssc.201801141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/12/2018] [Indexed: 06/08/2023]
Abstract
To facilitate coenzyme transport and in vitro enzymatic hydrogen production, a multi-enzyme metabolon comprising a miniscaffoldin containing three cohesins, a dockerin-containing mutant dehydrogenase, a dockerin-containing diaphorase, and a Histidine-tagged (His-tagged) NiFe hydrogenase was constructed. As the NiFe hydrogenase has very complicated structure and cannot be fused directly with a dockerin, a bifunctional peptide was designed. The bifunctional peptide, in which one terminus contains a modified dockerin binding the cohesin of the miniscaffoldin and the other, after chemical modification, binds the His-tag of NiFe hydrogenase, enabled His-tagged proteins to be integrated into the cohesin-dockerin-based metabolon. The metabolon exhibited an initial reaction rate 4.5 times that of the enzyme cocktail at the same enzyme loading, which indicated enhanced coenzyme transport of the metabolon. However, this metabolon was unstable owing to the degradation of the miniscaffoldin at elevated temperature. Glutaraldehyde was used to cross-link the metabolon for locking its spatial organization. The cross-linked metabolon not only exhibited 2.5 times the reaction rate of the enzyme cocktail, but also retained its stability at 70 °C. The amount of hydrogen production catalyzed by the cross-linked metabolon was nearly twice that of the metabolon without glutaraldehyde cross-linking and four times that of the enzyme cocktail at 70 °C after 22 h of reaction.
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Affiliation(s)
- Hui Chen
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia, 24061, USA
| | - Rui Huang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia, 24061, USA
| | - Eui-Jin Kim
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia, 24061, USA
| | - Yi-Heng P Job Zhang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia, 24061, USA
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
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71
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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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72
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Memon AH, Ding R, Yuan Q, Liang H, Wei Y. Coordination of GMP ligand with Cu to enhance the multiple enzymes stability and substrate specificity by co-immobilization process. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.04.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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73
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Engelen W, Wijnands SPW, Merkx M. Accelerating DNA-Based Computing on a Supramolecular Polymer. J Am Chem Soc 2018; 140:9758-9767. [PMID: 29989400 PMCID: PMC6077772 DOI: 10.1021/jacs.8b06146] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Dynamic
DNA-based circuits represent versatile systems to perform
complex computing operations at the molecular level. However, the
majority of DNA circuits relies on freely diffusing reactants, which
slows down their rate of operation substantially. Here we introduce
the use of DNA-functionalized benzene-1,3,5-tricarboxamide (BTA) supramolecular
polymers as dynamic scaffolds to template DNA-based molecular computing.
By selectively recruiting DNA circuit components to a supramolecular
BTA polymer functionalized with 10-nucleotide handle strands, the
kinetics of strand displacement and strand exchange reactions were
accelerated 100-fold. In addition, strand exchange reactions were
also favored thermodynamically by bivalent interactions between the
reaction product and the supramolecular polymer. The noncovalent assembly
of the supramolecular polymers enabled straightforward optimization
of the polymer composition to best suit various applications. The
ability of supramolecular BTA polymers to increase the efficiency
of DNA-based computing was demonstrated for three well-known and practically
important DNA-computing operations: multi-input AND gates, Catalytic
Hairpin Assembly and Hybridization Chain Reactions. This work thus
establishes supramolecular BTA polymers as an efficient platform for
DNA-based molecular operations, paving the way for the construction
of autonomous bionanomolecular systems that confine and combine molecular
sensing, computation, and actuation.
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Affiliation(s)
- Wouter Engelen
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands.,Laboratory of Chemical Biology, Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands
| | - Sjors P W Wijnands
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands
| | - Maarten Merkx
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands.,Laboratory of Chemical Biology, Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, Eindhoven 5600 MB , The Netherlands
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74
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Liu Y, Matanovic I, Hickey DP, Minteer SD, Atanassov P, Barton SC. Cascade Kinetics of an Artificial Metabolon by Molecular Dynamics and Kinetic Monte Carlo. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yuanchao Liu
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | - Ivana Matanovic
- Department of Chemical and Biological Engineering and Center for Micro-Engineered Materials, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - David P. Hickey
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Shelley D. Minteer
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Plamen Atanassov
- Department of Chemical and Biological Engineering and Center for Micro-Engineered Materials, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Scott Calabrese Barton
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
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75
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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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76
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Jakobson CM, Tullman-Ercek D, Mangan NM. Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory. Sci Rep 2018; 8:8196. [PMID: 29844460 PMCID: PMC5974357 DOI: 10.1038/s41598-018-26399-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/09/2018] [Indexed: 12/20/2022] Open
Abstract
Natural biochemical systems are ubiquitously organized both in space and time. Engineering the spatial organization of biochemistry has emerged as a key theme of synthetic biology, with numerous technologies promising improved biosynthetic pathway performance. One strategy, however, may produce disparate results for different biosynthetic pathways. We use a spatially resolved kinetic model to explore this fundamental design choice in systems and synthetic biology. We predict that two example biosynthetic pathways have distinct optimal organization strategies that vary based on pathway-dependent and cell-extrinsic factors. Moreover, we demonstrate that the optimal design varies as a function of kinetic and biophysical properties, as well as culture conditions. Our results suggest that organizing biosynthesis has the potential to substantially improve performance, but that choosing the appropriate strategy is key. The flexible design-space analysis we propose can be adapted to diverse biosynthetic pathways, and lays a foundation to rationally choose organization strategies for biosynthesis.
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Affiliation(s)
- Christopher M Jakobson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Niall M Mangan
- Department of Engineering Science and Applied Mathematics, Northwestern University, Evanston, IL, 60208, USA.
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77
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Zhao J, Wang S, Lu S, Bao X, Sun J, Yang X. An Enzyme Cascade-Triggered Fluorogenic and Chromogenic Reaction Applied in Enzyme Activity Assay and Immunoassay. Anal Chem 2018; 90:7754-7760. [DOI: 10.1021/acs.analchem.8b01845] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jiahui Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shasha Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xingfu Bao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jian Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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78
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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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79
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Earl E, Calabrese Barton S. Simulation of intermediate transport in nanoscale scaffolds for multistep catalytic reactions. Phys Chem Chem Phys 2018; 19:15463-15470. [PMID: 28580995 DOI: 10.1039/c7cp00239d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient catalytic cascades that involve several sequential reactions are found frequently in nature. The efficiency of multi-step biochemical pathways is enhanced by substrate channelling, wherein the product of one reaction is directed toward and acts as substrate to the next sequential reaction. Such mechanisms can partially overcome diffusion, which is often fast compared to reaction rates, and promotes loss of intermediates. Biochemical substrate channelling is achieved by the architecture and scaffolding of enzymes, and mimicking these natural structures could lead to innovative catalyst designs. We investigate the efficiency of two channelling approaches - electrostatic interactions and surface adsorption - through continuum modelling, to identify the limits of these modes and the extent to which they can interact. The model considers transport between two active sites where an intermediate is produced at the first active site and consumed at the second. The system includes mass transport through diffusion and migration, and reaction kinetics at the active sites. The effectiveness of this model is quantified by yield of the second reaction relative to the first. Channelling via proximity between active sites and via surface adsorption are found to be inefficient, requiring high values of the rate constant at the second active site to obtain significant yields. The introduction of electrostatic interactions, however, leads to yields of over 90% at much lower values of the rate constant.
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Affiliation(s)
- Erica Earl
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA.
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80
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Wijnands SPW, Engelen W, Lafleur RPM, Meijer EW, Merkx M. Controlling protein activity by dynamic recruitment on a supramolecular polymer platform. Nat Commun 2018; 9:65. [PMID: 29302054 PMCID: PMC5754363 DOI: 10.1038/s41467-017-02559-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/08/2017] [Indexed: 12/20/2022] Open
Abstract
Nature uses dynamic molecular platforms for the recruitment of weakly associating proteins into higher-order assemblies to achieve spatiotemporal control of signal transduction. Nanostructures that emulate this dynamic behavior require features such as plasticity, specificity and reversibility. Here we introduce a synthetic protein recruitment platform that combines the dynamics of supramolecular polymers with the programmability offered by DNA-mediated protein recruitment. Assembly of benzene-1,3,5-tricarboxamide (BTA) derivatives functionalized with a 10-nucleotide receptor strand into µm-long supramolecular BTA polymers is remarkably robust, even with high contents of DNA-functionalized BTA monomers and associated proteins. Specific recruitment of DNA-conjugated proteins on the supramolecular polymer results in a 1000-fold increase in protein complex formation, while at the same time enabling their rapid exchange along the BTA polymer. Our results establish supramolecular BTA polymers as a generic protein recruitment platform and demonstrate how assembly of protein complexes along the supramolecular polymer allows efficient and dynamic control of protein activity. DNA-origami allows the precise recruitment of DNA-protein conjugates but lacks the dynamics found in natural protein assemblies. Here the authors present a synthetic polymer platform that combines the dynamics of supramolecular polymers with the programmability of DNA-mediated protein recruitment.
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Affiliation(s)
- Sjors P W Wijnands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - Wouter Engelen
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands.,Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - René P M Lafleur
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - E W Meijer
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands.
| | - Maarten Merkx
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands. .,Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands.
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81
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Yong Y, Su R, Liu X, Xu W, Zhang Y, Wang R, Ouyang P, Wu J, Ge J, Liu Z. Lectin corona enhances enzymatic catalysis on the surface of magnetic nanoparticles. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2017.09.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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82
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Rabe KS, Müller J, Skoupi M, Niemeyer CM. Cascades in Compartments: En Route to Machine-Assisted Biotechnology. Angew Chem Int Ed Engl 2017; 56:13574-13589. [DOI: 10.1002/anie.201703806] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Kersten S. Rabe
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Joachim Müller
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Marc Skoupi
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Christof M. Niemeyer
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
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83
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Rabe KS, Müller J, Skoupi M, Niemeyer CM. Kaskaden in Kompartimenten: auf dem Weg zu maschinengestützter Biotechnologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703806] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kersten S. Rabe
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
| | - Joachim Müller
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
| | - Marc Skoupi
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
| | - Christof M. Niemeyer
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
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84
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Lang X, Zhu L, Gao Y, Wheeldon I. Enhancing Enzyme Activity and Immobilization in Nanostructured Inorganic-Enzyme Complexes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:9073-9080. [PMID: 28813159 DOI: 10.1021/acs.langmuir.7b02004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding the chemical and physical interactions at the interface of protein surfaces and inorganic crystals has important implications in the advancement of immobilized enzyme catalysis. Recently, enzyme-inorganic hybrid complexes have been demonstrated as effective materials for enzyme immobilization. The precipitation of phosphate nanocrystals in the presence of enzymes creates enzyme-Cu3(PO4)2·3H2O particles with high surface-to-volume ratios, enhanced activity, and increased stability. Here, we begin to develop a mechanistic understanding of enzyme loading in such complexes. Using a series of enzymes including horseradish peroxidase (HRP), a thermostable alcohol dehydrogenase (AdhD), diaphorase, catalase, glucose oxidase (GOx), and the protein bovine serum albumin (BSA), we identified a correlation between particle synthesis temperature, overall enzyme charge, and enzyme loading. The model enzyme HRP has a high predicted pI of ∼7.5 and maintains an overall positive charge under the synthesis conditions, phosphate buffer pH 7.4. HRP loading in HRP-Cu3(PO4)2 complexes was enhanced by 4.2-fold when synthesis was carried out at 37 °C in comparison with synthesis at 4 °C. HRP loading was further enhanced with synthesis at pH 8.0, correlating with a decrease in overall enzyme charge. Proteins with lower predicted pI values and negative overall charge (AdhD, pI of 5.6; diaphorase, pI of 6.8; GOx, pI of 5.2; catalase, pI of 6.9; and, BSA, pI of 5.7) exhibited higher enzyme loadings with 4 °C synthesis, 2.7-, 2.6-, 2.5-, 1.8-, and 1.7-fold protein loading enhancements, respectively. Using HRP as a model system, we also demonstrate that activity increased concomitantly with enzyme loading, and that particle nanostructure was minimally affected by synthesis temperature. Combined, the results presented here demonstrate the control of enzyme loading in enzyme-inorganic particles opening up new possibilities in enzyme and multienzyme catalysis.
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Affiliation(s)
- Xuye Lang
- Department of Chemical and Environmental Engineering, University of California , Riverside 92521, United States
| | - Lingling Zhu
- School of Materials Science and Engineering, Zhengzhou University , Zhengzhou 450001 China
| | - Yingning Gao
- Department of Chemical and Environmental Engineering, University of California , Riverside 92521, United States
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California , Riverside 92521, United States
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85
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Malanoski AP, Breger JC, Brown CW, Deschamps JR, Susumu K, Oh E, Anderson GP, Walper SA, Medintz IL. Kinetic enhancement in high-activity enzyme complexes attached to nanoparticles. NANOSCALE HORIZONS 2017; 2:241-252. [PMID: 32260679 DOI: 10.1039/c7nh00052a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Accumulating studies by many groups have found consistent enhancement in a wide variety of enzyme activities when they are displayed around nanoparticles. However, the underlying mechanism(s) that give rise to this phenomenon are still largely unknown. Herein, we develop a detailed reaction scheme that considers many of the various possible interactions between a substrate and a given enzyme-nanoparticle bioconjugate. The properties and some functional predictions that emanate from the reaction scheme were then tested using a model system where the homotetrameric beta-galactosidase enzyme complex was assembled with luminescent semiconductor nanocrystalline quantum dots displayed around its periphery. This type of assembly occurs as the ∼465 kDa enzyme complex is significantly larger than the 4.2 nm diameter green emitting quantum dots utilized. This unique architecture, in conjunction with the fact that this enzyme functions at or near the diffusion limit, provided a unique opportunity to selectively probe certain aspects of enzyme enhancement when attached to a nanoparticle with minimal potential perturbations to the native enzyme structure. Experimental assays were conducted where both free enzymes and quantum dot-decorated enzymes were compared directly in side-by-side samples and included formats where the kinetic processes were challenged with increasing viscosity and competitive inhibitors. The results strongly suggest that it is possible for there to be significant enhancements in an enzyme's catalytic rate or kcat after attachment to a nanoparticle even when it is apparently diffusion limited without requiring any gross changes to the enzyme's structure. A discussion of how this reaction scheme and model can be applied to other systems is provided.
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Affiliation(s)
- Anthony P Malanoski
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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86
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Lin JL, Zhu J, Wheeldon I. Synthetic Protein Scaffolds for Biosynthetic Pathway Colocalization on Lipid Droplet Membranes. ACS Synth Biol 2017; 6:1534-1544. [PMID: 28497697 DOI: 10.1021/acssynbio.7b00041] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Eukaryotic biochemistry is organized throughout the cell in and on membrane-bound organelles. When engineering metabolic pathways this organization is often lost, resulting in flux imbalance and a loss of kinetic advantages from enzyme colocalization and substrate channeling. Here, we develop a protein-based scaffold for colocalizing multienzyme pathways on the membranes of intracellular lipid droplets. Scaffolds based on the plant lipid droplet protein oleosin and cohesin-dockerin interaction pairs recruited upstream enzymes in yeast ester biosynthesis to the native localization of the terminal reaction step, alcohol-O-acetyltransferase (Atf1). The native localization is necessary for high activity and pathway assembly in close proximity to Atf1 increased pathway flux. Screening a library of scaffold variants further showed that pathway structure can alter catalysis and revealed an optimized scaffold and pathway expression levels that produced ethyl acetate at a rate nearly 2-fold greater than unstructured pathways. This strategy should prove useful in spatially organizing other metabolic pathways with key lipid droplet-localized and membrane-bound reaction steps.
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Affiliation(s)
- Jyun-Liang Lin
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Jie Zhu
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Ian Wheeldon
- Department of Chemical and
Environmental Engineering, University of California, Riverside, California 92521, United States
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87
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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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88
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Wang SZ, Zhang YH, Ren H, Wang YL, Jiang W, Fang BS. Strategies and perspectives of assembling multi-enzyme systems. Crit Rev Biotechnol 2017; 37:1024-1037. [PMID: 28423958 DOI: 10.1080/07388551.2017.1303803] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Multi-enzyme complexes have the potential to achieve high catalytic efficiency for sequence reactions due to their advantages in eliminating product inhibition, facilitating intermediate transfer and in situ regenerating cofactors. Constructing functional multi-enzyme systems to mimic natural multi-enzyme complexes is of great interest for multi-enzymatic biosynthesis and cell-free synthetic biotransformation, but with many challenges. Currently, various assembly strategies have been developed based on the interaction of biomacromolecules such as DNA, peptide and scaffolding protein. On the other hand, chemical-induced assembly is based on the affinity of enzymes with small molecules including inhibitors, cofactors and metal ions has the advantage of simplicity, site-to-site oriented structure control and economy. This review summarizes advances and progresses employing these strategies. Furthermore, challenges and perspectives in designing multi-enzyme systems are highlighted.
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Affiliation(s)
- Shi-Zhen Wang
- a Department of Chemical and Biochemical Engineering , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , China.,b The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University , Xiamen , China.,c State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University , Xiamen , China
| | - Yong-Hui Zhang
- a Department of Chemical and Biochemical Engineering , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , China
| | - Hong Ren
- a Department of Chemical and Biochemical Engineering , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , China
| | - Ya-Li Wang
- a Department of Chemical and Biochemical Engineering , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , China
| | - Wei Jiang
- a Department of Chemical and Biochemical Engineering , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , China
| | - Bai-Shan Fang
- a Department of Chemical and Biochemical Engineering , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , China.,b The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University , Xiamen , China.,d The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University , Xiamen , China
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89
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Vranish JN, Ancona MG, Oh E, Susumu K, Medintz IL. Enhancing coupled enzymatic activity by conjugating one enzyme to a nanoparticle. NANOSCALE 2017; 9:5172-5187. [PMID: 28393943 DOI: 10.1039/c7nr00200a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Enzymes have long been a prime research target for the commercial production of commodity and specialty chemicals, design of sensing devices, and the development of therapeutics and new chemical processes. Industrial applications for enzymes can potentially be enhanced by enzyme immobilization which often allows for increased enzyme stability, facile product purification, and minimized substrate diffusion times in multienzymatic cascades, but this is usually at the cost of a significant decrease in catalytic rates. Recently, enzyme immobilization has been advanced by the discovery that nanoparticle surfaces are frequently able to enhance the activity of the bound enzyme. Here we extend this observation to a multienzymatic coupled system using semiconductor quantum dots (QDs) as a model nanoparticle material and the prototypical enzyme pair of glucose oxidase (GOX) and horseradish peroxidase (HRP). We first demonstrate that HRP binding to QDs has a significant beneficial effect on enzymatic activity, producing a >2-fold improvement in kcat. We argue that this enhancement is due to affinity of the QD surface for the substrate. Furthermore, we demonstrate that when the ratio of GOX to HRP is adjusted to allow HRP to be the rate-limiting step of the pathway, the QD-induced rate enhancement of HRP can be maintained in a multi-enzyme cascade. Kinetic analysis shows that the underlying processes can be simulated numerically and provide insight into the governing mechanisms. The potential of nanoparticle-based catalytic enhancement is then discussed in the context of multienzyme cascades and synthetic biology.
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90
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Velasco-Lozano S, López-Gallego F. Wiring step-wise reactions with immobilized multi-enzyme systems. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1310208] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Group, CIC biomaGUNE, Donostia, Spain
- Basque Foundation for Science, IKERBASQUE, Bilbao, Spain
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91
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Liu Y, Hickey DP, Guo JY, Earl E, Abdellaoui S, Milton RD, Sigman MS, Minteer SD, Calabrese Barton S. Substrate Channeling in an Artificial Metabolon: A Molecular Dynamics Blueprint for an Experimental Peptide Bridge. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03440] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuanchao Liu
- Department
of Chemical Engineering and Materials Science, Michigan State University, East
Lansing, Michigan 48824, United States
| | - David P. Hickey
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jing-Yao Guo
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Erica Earl
- Department
of Chemical Engineering and Materials Science, Michigan State University, East
Lansing, Michigan 48824, United States
| | - Sofiene Abdellaoui
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ross D. Milton
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Matthew S. Sigman
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Shelley D. Minteer
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Scott Calabrese Barton
- Department
of Chemical Engineering and Materials Science, Michigan State University, East
Lansing, Michigan 48824, United States
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92
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Zhang Y, Wang Q, Hess H. Increasing Enzyme Cascade Throughput by pH-Engineering the Microenvironment of Individual Enzymes. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03431] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Yifei Zhang
- Department
of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Qin Wang
- Department
of Biomedical Engineering, Tsinghua University, Beijing 100084, China
| | - Henry Hess
- Department
of Biomedical Engineering, Columbia University, New York, New York 10027, United States
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93
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Tippmann S, Anfelt J, David F, Rand JM, Siewers V, Uhlén M, Nielsen J, Hudson EP. Affibody Scaffolds Improve Sesquiterpene Production in Saccharomyces cerevisiae. ACS Synth Biol 2017; 6:19-28. [PMID: 27560952 DOI: 10.1021/acssynbio.6b00109] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Enzyme fusions have been widely used as a tool in metabolic engineering to increase pathway efficiency by reducing substrate loss and accumulation of toxic intermediates. Alternatively, enzymes can be colocalized through attachment to a synthetic scaffold via noncovalent interactions. Here we describe the use of affibodies for enzyme tagging and scaffolding. The scaffolding is based on the recognition of affibodies to their anti-idiotypic partners in vivo, and was first employed for colocalization of farnesyl diphosphate synthase and farnesene synthase in S. cerevisiae. Different parameters were modulated to improve the system, and the enzyme:scaffold ratio was most critical for its functionality. Ultimately, the yield of farnesene on glucose YSFar could be improved by 135% in fed-batch cultivations using a 2-site affibody scaffold. The scaffolding strategy was then extended to a three-enzyme polyhydroxybutyrate (PHB) pathway, heterologously expressed in E. coli. Within a narrow range of enzyme and scaffold induction, the affibody tagging and scaffolding increased PHB production 7-fold. This work demonstrates how the versatile affibody can be used for metabolic engineering purposes.
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Affiliation(s)
- Stefan Tippmann
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Josefine Anfelt
- Division
of Proteomics and Nanobiotechnology, School of Biotechnology, Royal Institute of Technology (KTH), Science for Life Laboratory, SE171 21 Stockholm, Sweden
| | - Florian David
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Jacqueline M. Rand
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Verena Siewers
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
| | - Mathias Uhlén
- Division
of Proteomics and Nanobiotechnology, School of Biotechnology, Royal Institute of Technology (KTH), Science for Life Laboratory, SE171 21 Stockholm, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2970 Hørsholm, Denmark
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2970 Hørsholm, Denmark
| | - Elton P. Hudson
- Division
of Proteomics and Nanobiotechnology, School of Biotechnology, Royal Institute of Technology (KTH), Science for Life Laboratory, SE171 21 Stockholm, Sweden
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94
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Quin MB, Wallin KK, Zhang G, Schmidt-Dannert C. Spatial organization of multi-enzyme biocatalytic cascades. Org Biomol Chem 2017; 15:4260-4271. [DOI: 10.1039/c7ob00391a] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multi-enzyme cascades provide a wealth of valuable chemicals. Efficiency of reaction schemes can be improved by spatial organization of biocatalysts. This review will highlight various methods of spatial organization of biocatalysts: fusion, immobilization, scaffolding and encapsulation.
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Affiliation(s)
- M. B. Quin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - K. K. Wallin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - G. Zhang
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - C. Schmidt-Dannert
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
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95
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Zhang Y, Tsitkov S, Hess H. Proximity does not contribute to activity enhancement in the glucose oxidase-horseradish peroxidase cascade. Nat Commun 2016; 7:13982. [PMID: 28004753 PMCID: PMC5196434 DOI: 10.1038/ncomms13982] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/14/2016] [Indexed: 12/23/2022] Open
Abstract
A proximity effect has been invoked to explain the enhanced activity of enzyme cascades on DNA scaffolds. Using the cascade reaction carried out by glucose oxidase and horseradish peroxidase as a model system, here we study the kinetics of the cascade reaction when the enzymes are free in solution, when they are conjugated to each other and when a competing enzyme is present. No proximity effect is found, which is in agreement with models predicting that the rapidly diffusing hydrogen peroxide intermediate is well mixed. We suggest that the reason for the activity enhancement of enzymes localized by DNA scaffolds is that the pH near the surface of the negatively charged DNA nanostructures is lower than that in the bulk solution, creating a more optimal pH environment for the anchored enzymes. Our findings challenge the notion of a proximity effect and provide new insights into the role of DNA scaffolds.
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Affiliation(s)
- Yifei Zhang
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, USA
| | - Stanislav Tsitkov
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, USA
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, USA
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96
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Lim SI, Yang B, Jung Y, Cha J, Cho J, Choi ES, Kim YH, Kwon I. Controlled Orientation of Active Sites in a Nanostructured Multienzyme Complex. Sci Rep 2016; 6:39587. [PMID: 28004799 PMCID: PMC5177890 DOI: 10.1038/srep39587] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 11/24/2016] [Indexed: 01/17/2023] Open
Abstract
Multistep cascade reactions in nature maximize reaction efficiency by co-assembling related enzymes. Such organization facilitates the processing of intermediates by downstream enzymes. Previously, the studies on multienzyme nanocomplexes assembled on DNA scaffolds demonstrated that closer interenzyme distance enhances the overall reaction efficiency. However, it remains unknown how the active site orientation controlled at nanoscale can have an effect on multienzyme reaction. Here, we show that controlled alignment of active sites promotes the multienzyme reaction efficiency. By genetic incorporation of a non-natural amino acid and two compatible bioorthogonal chemistries, we conjugated mannitol dehydrogenase to formate dehydrogenase with the defined active site arrangement with the residue-level accuracy. The study revealed that the multienzyme complex with the active sites directed towards each other exhibits four-fold higher relative efficiency enhancement in the cascade reaction and produces 60% more D-mannitol than the other complex with active sites directed away from each other.
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Affiliation(s)
- Sung In Lim
- Department of Chemical Engineering, University of Virginia, VA 22904, United States
| | - Byungseop Yang
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Younghan Jung
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Jaehyun Cha
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Jinhwan Cho
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Eun-Sil Choi
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea.,Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Inchan Kwon
- Department of Chemical Engineering, University of Virginia, VA 22904, United States.,School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
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97
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Roberts CC, Chang CEA. Modeling of enhanced catalysis in multienzyme nanostructures: effect of molecular scaffolds, spatial organization, and concentration. J Chem Theory Comput 2016; 11:286-92. [PMID: 26574226 DOI: 10.1021/ct5007482] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Colocalized multistep enzymatic reaction pathways within biological catabolic and metabolic processes occur with high yield and specificity. Spatial organization on membranes or surfaces may be associated with increased efficiency of intermediate substrate transfer. Using a new Brownian dynamics package, GeomBD, we explored the geometric features of a surface-anchored enzyme system by parallel coarse-grained Brownian dynamics simulations of substrate diffusion over microsecond (μs) to millisecond (ms) time scales. We focused on a recently developed glucose oxidase (GOx), horseradish peroxidase (HRP), and DNA origami-scaffold enzyme system, where the H2O2 substrate of HRP is produced by GOx. The results revealed and explained a significant advantage in catalytic enhancement by optimizing interenzyme distance and orientation in the presence of the scaffold model. The planar scaffold colocalized the enzymes and provided a diffusive barrier that enhanced substrate transfer probability, becoming more relevant with increasing interenzyme distance. The results highlight the importance of protein geometry in the proper assessment of distance and orientation dependence on the probability of substrate transfer. They shed light on strategies for engineering multienzyme complexes and further investigation of enhanced catalytic efficiency for substrate diffusion between membrane-anchoring proteins.
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Affiliation(s)
- Christopher C Roberts
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | - Chia-en A Chang
- Department of Chemistry, University of California , Riverside, California 92521, United States
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98
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Cox AJ, Bengtson HN, Gerasimova YV, Rohde KH, Kolpashchikov DM. DNA Antenna Tile-Associated Deoxyribozyme Sensor with Improved Sensitivity. Chembiochem 2016; 17:2038-2041. [PMID: 27620365 DOI: 10.1002/cbic.201600438] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Indexed: 12/17/2022]
Abstract
Some natural enzymes increase the rate of diffusion-limited reactions by facilitating substrate flow to their active sites. Inspired by this natural phenomenon, we developed a strategy for efficient substrate delivery to a deoxyribozyme (DZ) catalytic sensor. This resulted in a three- to fourfold increase in sensitivity and up to a ninefold improvement in the detection limit. The reported strategy can be used to enhance catalytic efficiency of diffusion-limited enzymes and to improve sensitivity of enzyme-based biosensors.
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Affiliation(s)
- Amanda J Cox
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA
| | - Hillary N Bengtson
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA
| | - Yulia V Gerasimova
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816-2366, USA
| | - Kyle H Rohde
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816-2366, USA. .,Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA. .,National Center for Forensic Science, University of Central Florida, 12354 Research Pkwy. Suite 225, Orlando, FL, 32826, USA.
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99
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Cui C, Chen H, Chen B, Tan T. Genipin Cross-Linked Glucose Oxidase and Catalase Multi-enzyme for Gluconic Acid Synthesis. Appl Biochem Biotechnol 2016; 181:526-535. [DOI: 10.1007/s12010-016-2228-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/26/2016] [Indexed: 12/12/2022]
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100
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Chado GR, Stoykovich MP, Kaar JL. Role of Dimension and Spatial Arrangement on the Activity of Biocatalytic Cascade Reactions on Scaffolds. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01302] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Garrett R. Chado
- Department of Chemical and
Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Mark P. Stoykovich
- Department of Chemical and
Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Joel L. Kaar
- Department of Chemical and
Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
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