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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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2
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Algov I, Alfonta L. Use of Protein Engineering to Elucidate Electron Transfer Pathways between Proteins and Electrodes. ACS MEASUREMENT SCIENCE AU 2022; 2:78-90. [PMID: 36785727 PMCID: PMC9836065 DOI: 10.1021/acsmeasuresciau.1c00038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Herein, we review protein engineering tools for electron transfer enhancement and investigation in bioelectrochemical systems. We present recent studies in the field while focusing on how electron transfer investigation and measurements were performed and discuss the use of protein engineering to interpret electron transfer mechanisms.
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Komatsu T, Hishii K, Kimura M, Amaya S, Sakamoto H, Takamura E, Satomura T, Suye SI. Highly Efficient Multi-Step Oxidation Bioanode Using Microfluidic Channels. Int J Mol Sci 2021; 22:ijms222413503. [PMID: 34948296 PMCID: PMC8703374 DOI: 10.3390/ijms222413503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/12/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
With the rapid decline of fossil fuels, various types of biofuel cells (BFCs) are being developed as an alternative energy source. BFCs based on multi-enzyme cascade reactions are utilized to extract more electrons from substrates. Thus, more power density is obtained from a single molucule of substrate. In the present study, a bioanode that could extract six electrons from a single molecule of L-proline via a three-enzyme cascade reaction was developed and investigated for its possible use in BFCs. These enzymes were immobilized on the electrode to ensure highly efficient electron transfer. Then, oriented immobilization of enzymes was achieved using two types of self-assembled monolayers (SAMs). In addition, a microfluidic system was incorporated to achieve efficient electron transfer. The microfluidic system, in which the electrodes were arranged in a tooth-shaped comb, allowed for substrates to be supplied continuously to the cascade, which resulted in smooth electron transfer. Finally, we developed a high-performance bioanode which resulted in the accumulation of higher current density compared to that of a gold disc electrode (205.8 μA cm−2: approximately 187 times higher). This presents an opportunity for using the bioanode to develop high-performance BFCs in the future.
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Affiliation(s)
- Tomohiro Komatsu
- Department of Advanced Interdisciplinary Science and Technology, Graduate School of Engineering, University of Fukui, Fukui 910-8507, Japan;
| | - Kazuki Hishii
- Department of Frontier Fiber Technology and Science, Graduate School of Engineering, University of Fukui, Fukui 910-8507, Japan; (K.H.); (M.K.); (E.T.); (S.-i.S.)
| | - Michiko Kimura
- Department of Frontier Fiber Technology and Science, Graduate School of Engineering, University of Fukui, Fukui 910-8507, Japan; (K.H.); (M.K.); (E.T.); (S.-i.S.)
| | - Satoshi Amaya
- Department of Mechanical Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan;
| | - Hiroaki Sakamoto
- Department of Frontier Fiber Technology and Science, Graduate School of Engineering, University of Fukui, Fukui 910-8507, Japan; (K.H.); (M.K.); (E.T.); (S.-i.S.)
- Correspondence:
| | - Eiichiro Takamura
- Department of Frontier Fiber Technology and Science, Graduate School of Engineering, University of Fukui, Fukui 910-8507, Japan; (K.H.); (M.K.); (E.T.); (S.-i.S.)
| | - Takenori Satomura
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui 910-8507, Japan;
| | - Shin-ichiro Suye
- Department of Frontier Fiber Technology and Science, Graduate School of Engineering, University of Fukui, Fukui 910-8507, Japan; (K.H.); (M.K.); (E.T.); (S.-i.S.)
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4
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Abiological catalysis by myoglobin mutant with a genetically incorporated unnatural amino acid. Biochem J 2021; 478:1795-1808. [PMID: 33821889 PMCID: PMC10071548 DOI: 10.1042/bcj20210091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/13/2022]
Abstract
To inculcate biocatalytic activity in the oxygen-storage protein myoglobin (Mb), a genetically engineered myoglobin mutant H64DOPA (DOPA = L-3,4-dihydroxyphenylalanine) has been created. Incorporation of unnatural amino acids has already demonstrated their ability to accomplish many non-natural functions in proteins efficiently. Herein, the presence of redox-active DOPA residue in the active site of mutant Mb presumably stabilizes the compound I in the catalytic oxidation process by participating in an additional hydrogen bonding (H-bonding) as compared to the WT Mb. Specifically, a general acid-base catalytic pathway was achieved due to the availability of the hydroxyl moieties of DOPA. The reduction potential values of WT (E° = -260 mV) and mutant Mb (E° = -300 mV), w.r.t. Ag/AgCl reference electrode, in the presence of hydrogen peroxide, indicated an additional H-bonding in the mutant protein, which is responsible for the peroxidase activity of the mutant Mb. We observed that in the presence of 5 mM H2O2, H64DOPA Mb oxidizes thioanisole and benzaldehyde with a 10 and 54 folds higher rate, respectively, as opposed to WT Mb. Based on spectroscopic, kinetic, and electrochemical studies, we deduce that DOPA residue, when present within the distal pocket of mutant Mb, alone serves the role of His/Arg-pair of peroxidases.
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Encapsulation of Microorganisms, Enzymes, and Redox Mediators in Graphene Oxide and Reduced Graphene Oxide. Methods Enzymol 2019; 609:197-219. [PMID: 30244790 DOI: 10.1016/bs.mie.2018.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Graphene oxide (GO) and reduced graphene oxide (rGO) were demonstrated in the past decade as biocompatible carbon-based materials that could be efficiently used in bioelectrochemical systems (BESs). Specifically, for redox enzyme encapsulation in order to improve electron communication between enzymes and electrodes. The addition of GO to different solvents was shown to cause gelation while still allowing small molecule diffusion through its gel-like matrix. Taking the combination of these traits together, we decided to use GO hydrogels for the encapsulation of enzymes displayed on the surface of yeast in anodes of microbial fuel cells. During our studies we have followed the changes in the physical characteristics of GO upon encapsulation of yeast cells displaying glucose oxidase in the presence of glucose and noted that GO is being rapidly reduced to rGO as a function of glucose concentrations. GO reduction under these conditions served as a proof of electron communication between the surface-displayed enzymes and GO. Hence, we set out to study this phenomenon by the encapsulation of a purified glucose dehydrogenase (in the absence of microbial cells) in rGO where improved electron transfer to the electrode could be observed in the presence of phenothiazone. In this chapter, we describe how these systems were technically constructed and characterized and how a very affordable matrix such as GO could be used to electrically wire enzymes as a good replacement for expensive mediator containing redox active polymers commonly used in BESs.
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Yates NDJ, Fascione MA, Parkin A. Methodologies for "Wiring" Redox Proteins/Enzymes to Electrode Surfaces. Chemistry 2018; 24:12164-12182. [PMID: 29637638 PMCID: PMC6120495 DOI: 10.1002/chem.201800750] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Indexed: 12/22/2022]
Abstract
The immobilization of redox proteins or enzymes onto conductive surfaces has application in the analysis of biological processes, the fabrication of biosensors, and in the development of green technologies and biochemical synthetic approaches. This review evaluates the methods through which redox proteins can be attached to electrode surfaces in a "wired" configuration, that is, one that facilitates direct electron transfer. The feasibility of simple electroactive adsorption onto a range of electrode surfaces is illustrated, with a highlight on the recent advances that have been achieved in biotechnological device construction using carbon materials and metal oxides. The covalent crosslinking strategies commonly used for the modification and biofunctionalization of electrode surfaces are also evaluated. Recent innovations in harnessing chemical biology methods for electrically wiring redox biology to surfaces are emphasized.
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Affiliation(s)
| | | | - Alison Parkin
- Department of ChemistryUniversity of YorkHeslington RoadYorkYO10 5DDUK
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Improved rate of substrate oxidation catalyzed by genetically-engineered myoglobin. Arch Biochem Biophys 2018; 639:44-51. [DOI: 10.1016/j.abb.2017.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/13/2017] [Accepted: 12/19/2017] [Indexed: 12/13/2022]
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8
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Deac AR, Muresan LM, Cotet LC, Baia L, Turdean GL. Hybrid composite material based on graphene and polyhemin for electrochemical detection of hydrogen peroxide. J Electroanal Chem (Lausanne) 2017. [DOI: 10.1016/j.jelechem.2017.08.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Shen M, Rusling J, Dixit CK. Site-selective orientated immobilization of antibodies and conjugates for immunodiagnostics development. Methods 2017; 116:95-111. [PMID: 27876681 PMCID: PMC5374010 DOI: 10.1016/j.ymeth.2016.11.010] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 01/11/2023] Open
Abstract
Immobilized antibody systems are the key to develop efficient diagnostics and separations tools. In the last decade, developments in the field of biomolecular engineering and crosslinker chemistry have greatly influenced the development of this field. With all these new approaches at our disposal, several new immobilization methods have been created to address the main challenges associated with immobilized antibodies. Few of these challenges that we have discussed in this review are mainly associated to the site-specific immobilization, appropriate orientation, and activity retention. We have discussed the effect of antibody immobilization approaches on the parameters on the performance of an immunoassay.
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Affiliation(s)
- Min Shen
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060
| | - James Rusling
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269-3136
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut 060
- School of Chemistry, National University of Ireland at Galway, Galway, Ireland
| | - Chandra K Dixit
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060
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Exploiting multi-function Metal-Organic Framework nanocomposite Ag@Zn-TSA as highly efficient immobilization matrixes for sensitive electrochemical biosensing. Anal Chim Acta 2016; 934:203-11. [DOI: 10.1016/j.aca.2016.05.040] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/18/2016] [Accepted: 05/23/2016] [Indexed: 11/19/2022]
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Peng L, Utesch T, Yarman A, Jeoung JH, Steinborn S, Dobbek H, Mroginski MA, Tanne J, Wollenberger U, Scheller FW. Surface-Tuned Electron Transfer and Electrocatalysis of Hexameric Tyrosine-Coordinated Heme Protein. Chemistry 2015; 21:7596-602. [DOI: 10.1002/chem.201405932] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Indexed: 11/11/2022]
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12
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Construction of a biocathode using the multicopper oxidase from the hyperthermophilic archaeon, Pyrobaculum aerophilum: towards a long-life biobattery. Biotechnol Lett 2015; 37:1399-404. [PMID: 25808819 DOI: 10.1007/s10529-015-1819-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/17/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVES The life of biobatteries remains an issue due to loss of enzyme activity over time. In this study, we sought to develop a biobattery with a long life using a hyperthermophilic enzyme. RESULTS We hypothesized that use of such hyperthermophilic enzymes would allow for the biofuel cells to have a long battery life. Using pyrroloquinoline quinone-glucose dehydrogenase and the multicopper oxidase from Pyrobaculum aerophilum, we constructed an anode and cathode. The maximum output was 11 μW at 0.2 V, and the stability of the both electrode was maintained at 70 % after 14 days. CONCLUSION The biofuel cells that use hyperthermophilic enzymes may prolong their life.
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Li M, Dong S, Li N, Tang H, Zheng J. Magnetic Fe3O4 carbon aerogel and ionic liquid composite films as an electrochemical interface for accelerated electrochemistry of glucose oxidase and myoglobin. RSC Adv 2015. [DOI: 10.1039/c4ra13400a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synthesized magnetic ferroferric oxide carbon aerogel (Fe3O4-CA) was characterized by scanning electron microscope (SEM), atomic force microscopy (AFM) and N2 adsorption–desorption isotherm measurements.
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Affiliation(s)
- Miao Li
- College of Sciences
- Xi′an University of Architecture and Technology
- Xi′an
- China
| | - Sheying Dong
- College of Sciences
- Xi′an University of Architecture and Technology
- Xi′an
- China
| | - Nan Li
- Xi′an Chuanglian Huate Surface Treatment Tech. Co. Ltd
- Xi′an 710055
- China
| | - Hongsheng Tang
- Institute of Analytical Science
- Shaanxi Provincial Key Laboratory of Electroanalytical Chemistry
- Northwest University
- Xi’an 710069
- China
| | - Jianbin Zheng
- Institute of Analytical Science
- Shaanxi Provincial Key Laboratory of Electroanalytical Chemistry
- Northwest University
- Xi’an 710069
- China
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