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Heme Reconstitution

Heme Reconstitution

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Heme reconstitution is a biochemical process involving the assembly of heme groups into apoproteins, restoring their functional capabilities. This process is crucial for studying hemoproteins' structure and function, as well as for understanding various biological mechanisms and diseases related to heme metabolism.
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Heme reconstitution is a biochemical process involving the assembly of heme groups into apoproteins, restoring their functional capabilities. This process is crucial for studying hemoproteins' structure and function, as well as for understanding various biological mechanisms and diseases related to heme metabolism.
Apoenzyme Reconstitution as a Chemical Tool for Structural Enzymology and Biotechnology
by Eduardo Torres

2024, Angewandte Chemie International Edition

Enzymes with artificial cofactors: Nondiffusible organic cofactors of enzymes can often be replaced by artifical analogues to generate semisynthetic enzymes (see scheme). This approach can be used to study structure–function relationships... more
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Apoenzyme Reconstitution as a Chemical Tool for Structural Enzymology and Biotechnology
by Eduardo Torres

2024, Angewandte Chemie International Edition

Enzymes with artificial cofactors: Nondiffusible organic cofactors of enzymes can often be replaced by artifical analogues to generate semisynthetic enzymes (see scheme). This approach can be used to study structure–function relationships... more
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Photocatalytic Hydrogen Production and Carbon Dioxide Reduction Catalyzed by an Artificial Cobalt Hemoprotein
by Rémy Ricoux

2023, International Journal of Molecular Sciences

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
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Apoenzyme Reconstitution as a Chemical Tool for Structural Enzymology and Biotechnology
by Eduardo Torres

2023, Angewandte Chemie International Edition

Chemie Christof M. Niemeyer studied chemistry at the University of Marburg and received his PhD at the MPI für Kohlenforschung (Mülheim/Ruhr) with M. T. Reetz. After postdoctoral work at the Center for Advanced Biotechnology in Boston... more
Figure 1. a) Schematic illustration of apoenzyme reconstitution. Extrac- tion of the native cofactor (green) leads to the formation of an apoenzyme which can be subsequently reconstituted with an artificial cofactor (blue). b) Comparison of three different heme enzyme struc- tures, with the heme cofactor indicated in red. The heme in Mb is positioned close to the surface of the protein, while in P450,,,, the reaction pocket is buried deeply in the tertiary structure of the protein. HRP is an example of a partially buried heme which can still be chemically removed. Note that these differences in the protein shell and the positioning of the cofactor account for the differences in the ease of cofactor extraction and reconstitution. Many proteins contain a nondiffusible cofactor, often termed a prosthetic group, which is a nonpeptidic molecular moiety bound in the active site of the protein. Such a cofactor is required for the protein to conduct its function, such as the binding of substrates and other reaction partners as well as for the catalytic conversion. Prominent examples of prosthetic groups are porphyrin and flavin derivatives,"! which are often involved in electron-transfer reactions. These derivatives can often be removed from the enzyme by chemical methods or biological manipulation, modified, and reinserted to obtain 1. Introduction
The cofactor flavin adenine dinucleotide (FAD, 1) is a prosthetic group and cofactor found in numerous enzymes. It is involved in one and two electron transfer reactions in a 2. Flavin Adenine Dinucleotide (FAD) Reconstitution In the past 30 years the reconstitution of, in particular, flavo and heme enzymes has been harnessed to enable electrical communication between enzymes and electrodes. This has allowed the elucidation of catalytic mechanisms as well as protein-protein and protein-ligand recognition pro- cesses, and the creation of novel biomaterials. From a synthetic chemistry and biocatalysis point of view, there is great interest in the design of novel, semisynthetic metal- loenzymes which possess high selectivity and reactivity under mild conditions. Exciting progress has been made so that these semisynthetic metalloenzymes mimic their native counterparts. For example, heme enzymes with their metal- containing porphyrin cofactors are excellent scaffolds for the introduction of novel functions through reconstitution with artificial cofactors. This Review article presents an overview of the current state-of-the art of the reconstitution method as a tool to elucidate structure—activity relationships of enzymes and also to design novel biosensors and biomaterials.
Figure 4. The structures of five known covalent linkages between FAD and protein.” R: ribityl-5’-diphosphoadenosine.
Figure 3. Four groups of FAD proteins based on the sequence— structure relationship. A) Glutathione reductase type; B) ferredoxin reductase type; C) p-cresol methylhydroxylase type; D) pyruvate ox- idase type. Adapted from Ref. [7]. Figure 2. Structure of FAD and its a) elongated and b) bent butterfly conformation present in flavoenzymes.
Figure 5. Artificial FAD cofactors used in reconstitution studies. FAD derivatives 4-7 were used for the reconstitution of pCMH and the investigation of its activity. R: ribityl-5’-diphosphoadenosine. The activity of pCMH increased with the redox potential (4—7).°7! Reconstitution of apoflavoproteins with native,°°") arti- ficial," or isotopically enriched"! flavins has been used for investigating the flavoprotein structure as well as mechanisms during redox catalysis. Recently, for example, the enzyme UDP-Galp mutase, which is involved in the synthesis of galactofuranose, was reconstituted with 1- and 5-deazaflavin derivatives (2 and 7, respectively, in Figure 5), thereby
Figure 20. Top: Preparation of artificial metalloenzymes by reconstitu- tion of apoMb with Mn- or Cr-containing salophen. Bottom: molecular models of the active centers of the native (left) and artificial Mb (right). Adapted from Ref. [191].
Figure G. Reconstitution of apoGOx with ferrocene-modified FAD. The enzyme was subsequently adsorbed on gold electrodes. Adapted from Ref. [39]. The gray bar represents the gold electrode.
Figure 7. a) Preparation of GOx-modified electrodes using Au nanoparticles as electrochemical relays. 1) Reconstitution of apoGOx with the FAL modified nanoparticles and subsequent binding to the electrode. II) Binding of the FAD-modified Au nanoparticle and subsequent in situ reconstitution. Adapted and reprinted with permission from Ref. [57]. Copyright 2003 Science/AAAS. b) Reconstitution of apoGOx on gold electrodes containing single-walled carbon nanotubes (SWCNT) modified with FAD using 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC). The AFM image of the electrode coverage is shown at the bottom. Adapted from Ref. [59].
Figure 9. a) Modification of heme propionate groups and the reconsti- tution of apoMb to rMb25. b) Structure of the reconstituted rMb25 prepared by Hayashi et al."?5! c) An increased activity towards guiacol oxidation was observed with this modified protein (@) relative to native Mb (oc); vo: initial rate. Adapted and reprinted with permission from Ref. [125]. Copyright 1999 American Chemical Society. Hayashi et al. reported that the chemical modification of heme propionate chains with eight carboxy groups (25; Figure 9) led to alterations in both the substrate specificity and reactivity of Mb, despite the fact that the UV/Vis, CD, and NMR spectra of the modified rMb25 (r: reconstituted) were comparable to those of native Mb." Tt was also
Figure 10. Mb reconstituted with heme containing a phenylboronic acid moiety to enable binding of monosaccharides.!"*7
“igure 11. Modified heme cofactors and applications of the respective reconstituted enzymes; bpy: 2,2’-bipyridin The photoactivation of heme enzymes has been a subject of intensive research because it could provide not only temporal control over the activation of the enzyme but it could also eliminate the need for oxidative activators (such as scopic methods. For example, cobalt-porphyrin analogues, which are readily obtained by the complexation of Co salts, such as CoCl, or Co(OAc),, with the porphyrin ligand, have been used for the reconstitution of Mb and Hb,!4""“4] HRP! and P450cam.'*! Cobalt species are versatile probes for electron paramagnetic resonance (EPR) spectroscopy, and such studies enabled detailed investigation of the binding of molecular oxygen and other substrates to the artificial cofactor. In addition, Co and Mn derivatives were utilized to obtain reconstituted myoglobin, which was then exten- sively investigated by electrochemical means to explore applications in biosensing,!4°'"7 3.3.1. Design of Photoactive Centers The replacement of the native heme cofactor with an artificial derivative containing non-native functional groups opens up the way to generate novel enzymes with altered, enhanced, and even entirely new functions. An overview of representative modifications reported so far and their effects on the activity of the reconstituted enzymes is given in Figure 11. In this section, we will discuss selected examples of such artificial heme enzymes and their applications.
Figure 12. a) Electron abstraction from rMb27, which was reconstituted with photoactivatable 27. Inset: species that take part in the reaction. b) Photochemical production of the dioxygen complex oxy-Mb from tMb27; on/off: on and off switching of the visible light. oxy-Mb is only produced on irradiation. Adapted and reprinted from Refs. [148, 150]. Copyright 1993-1999 American Chemical Society. H,O, for peroxidases or NAD(P)H for oxygenases). To achieve this challenging goal the native enzymes need to be modified with photoactive groups, which can harvest light, harness the energy for redox reactions, and transfer generated electrons to the heme metal center. The native heme cofactor containing two carboxylic acid groups is an excellent starting point for a range of modifications by using site-selective and relatively simple chemical procedures. Much of the seminal work concerning the introduction of photoactivatable groups into myoglobin by reconstitution with artificial cofactors was carried out by the research groups of Hayashi and Shinkai. For example, Hamachi et al. synthesised heme derivative 27 (Figure 11), bearing a photosensitive tris(2,2’-bipyridyl)ru- thenium(II) {Ru(bpy)3}?* moiety. Complex 27 can be acti- vated effectively by visible light''*! and it was used for the reconstitution of apoMb to yield rMb27 (Figure 12). The
Figure 13. Preparation of photoactivable Mb, which is capable of hydrogenating acetylene.!*4l Another effective route to the design of photoactivatable biocatalysts by modification of heme with photoactive moieties was developed by Willner et al.“ They replaced the native iron-containing heme of Mb with Co" porphyrin 29, and the respective reconstituted Mb was chemically modified with eosine isothiocyanate to yield Eo,MbCo" (rMb29; Figures 11 and 13). This system was activated by irradiation in
Figure 14. In situ reconstitution of apoHRP on gold electrodes to which heme cofactor was bound through amide coupling by using 1- ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC). In a related approach, Zimmermann etal. used self- assembled monolayers containing linkers to immobilize heme on gold electrodes and to produce active enzyme electrodes by in situ reconstitution of apoHRP (Figure 14). In this
Figure 15. Reconstituted Mb bearing a cytochrome c receptor and the formation of a protein-protein complex with cytochrome c. Adapted from Ref. [163].
Figure 16. a) Giant amphiphiles prepared by reconstitution of apoHR (HRP is shown in gray); b) the vesicular aggregates formed. Adapted from Ref. [168].
Figure 17. Supramolecular polymers obtained by heme reconstitution of mutant cytochrome bs¢.. Adapted and reprinted with permission from Ref. [174]. Copyright 2007 American Chemical Society.
Figure 18. a) Reconstitution of DNA-modified heme into apoMb and apoHRP and b) the subsequent use of DNA to immobilize the enzymes on surfaces. Adapted from Ref. [186]. c) Generation of an array of DNA-HRP conjugates on a Au microelectrode using rHRP35a (I) or in situ reconstitution of apoHRP (II). The microelectrode chip containing four gold electrodes is also shown. Adapted from Ref. [187].
Figure 19. Preparation of rMb36 by reconstitution of apoMb with iron porphycene 36 as an abiotic cofactor. rMb36 has a blue color and displays strongly increased oxygen affinity."
Figure 21. The structure of cofactor PQQ (left) and PQQ-containing enzyme glucose dehydrogenase (right). In the enzyme structure, PQQ is shown as a black framework and the Ca?* ions necessary for PQQ coordination are depicted as gray spheres.
Figure 22. Immobilization of apoGDH onto the PQQ-modified gold nanoparticles attached to a gold electrode. Adapted and reprinted with permission from Ref. [206]. Copyright 2005 American Chemical Society. communication is possible due to the insulating protein shell. This problem was later circumvented by the employment of more efficient linker systems. For example, electrically contacted GDH enzyme electrodes were successfully con- structed by the reconstitution of apoGDH on PQOQ-function- alized polyaniline films.°°! In this approach, PQQ was coupled to a polyaniline/polyacrylic acid composite film deposited on a gold electrode through amide coupling. Such electrodes were used for the in situ reconstitution of apoGDH to yield sensors capable of detecting the biolectrocatalyzed oxidation of glucose. This system was later improved by using gold-nanoparticle relays (Figure 22) similar to those used for
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Apoenzyme Reconstitution as a Chemical Tool for Structural Enzymology and Biotechnology
by EDUARDO TORRES

2023, Angewandte Chemie International Edition

Chemie Christof M. Niemeyer studied chemistry at the University of Marburg and received his PhD at the MPI für Kohlenforschung (Mülheim/Ruhr) with M. T. Reetz. After postdoctoral work at the Center for Advanced Biotechnology in Boston... more
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Apoenzyme Reconstitution as a Chemical Tool for Structural Enzymology and Biotechnology
by Eduardo Torres

2023, Angewandte Chemie International Edition

Chemie Christof M. Niemeyer studied chemistry at the University of Marburg and received his PhD at the MPI für Kohlenforschung (Mülheim/Ruhr) with M. T. Reetz. After postdoctoral work at the Center for Advanced Biotechnology in Boston... more
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Apoenzyme Reconstitution as a Chemical Tool for Structural Enzymology and Biotechnology
by Kuo Chi-Hsien

2021, Angewandte Chemie International Edition

Chemie Christof M. Niemeyer studied chemistry at the University of Marburg and received his PhD at the MPI für Kohlenforschung (Mülheim/Ruhr) with M. T. Reetz. After postdoctoral work at the Center for Advanced Biotechnology in Boston... more
Figure 1. a) Schematic illustration of apoenzyme reconstitution. Extrac- tion of the native cofactor (green) leads to the formation of an apoenzyme which can be subsequently reconstituted with an artificial cofactor (blue). b) Comparison of three different heme enzyme struc- tures, with the heme cofactor indicated in red. The heme in Mb is positioned close to the surface of the protein, while in P450,,,, the reaction pocket is buried deeply in the tertiary structure of the protein. HRP is an example of a partially buried heme which can still be chemically removed. Note that these differences in the protein shell and the positioning of the cofactor account for the differences in the ease of cofactor extraction and reconstitution. Many proteins contain a nondiffusible cofactor, often termed a prosthetic group, which is a nonpeptidic molecular moiety bound in the active site of the protein. Such a cofactor is required for the protein to conduct its function, such as the binding of substrates and other reaction partners as well as for the catalytic conversion. Prominent examples of prosthetic groups are porphyrin and flavin derivatives,"! which are often involved in electron-transfer reactions. These derivatives can often be removed from the enzyme by chemical methods or biological manipulation, modified, and reinserted to obtain 1. Introduction
The cofactor flavin adenine dinucleotide (FAD, 1) is a prosthetic group and cofactor found in numerous enzymes. It is involved in one and two electron transfer reactions in a 2. Flavin Adenine Dinucleotide (FAD) Reconstitution In the past 30 years the reconstitution of, in particular, flavo and heme enzymes has been harnessed to enable electrical communication between enzymes and electrodes. This has allowed the elucidation of catalytic mechanisms as well as protein-protein and protein-ligand recognition pro- cesses, and the creation of novel biomaterials. From a synthetic chemistry and biocatalysis point of view, there is great interest in the design of novel, semisynthetic metal- loenzymes which possess high selectivity and reactivity under mild conditions. Exciting progress has been made so that these semisynthetic metalloenzymes mimic their native counterparts. For example, heme enzymes with their metal- containing porphyrin cofactors are excellent scaffolds for the introduction of novel functions through reconstitution with artificial cofactors. This Review article presents an overview of the current state-of-the art of the reconstitution method as a tool to elucidate structure—activity relationships of enzymes and also to design novel biosensors and biomaterials.
Figure 4. The structures of five known covalent linkages between FAD and protein.” R: ribityl-5’-diphosphoadenosine.
Figure 3. Four groups of FAD proteins based on the sequence— structure relationship. A) Glutathione reductase type; B) ferredoxin reductase type; C) p-cresol methylhydroxylase type; D) pyruvate ox- idase type. Adapted from Ref. [7]. Figure 2. Structure of FAD and its a) elongated and b) bent butterfly conformation present in flavoenzymes.
Figure 5. Artificial FAD cofactors used in reconstitution studies. FAD derivatives 4-7 were used for the reconstitution of pCMH and the investigation of its activity. R: ribityl-5’-diphosphoadenosine. The activity of pCMH increased with the redox potential (4—7).°7! Reconstitution of apoflavoproteins with native,°°") arti- ficial," or isotopically enriched"! flavins has been used for investigating the flavoprotein structure as well as mechanisms during redox catalysis. Recently, for example, the enzyme UDP-Galp mutase, which is involved in the synthesis of galactofuranose, was reconstituted with 1- and 5-deazaflavin derivatives (2 and 7, respectively, in Figure 5), thereby
Figure G. Reconstitution of apoGOx with ferrocene-modified FAD. The enzyme was subsequently adsorbed on gold electrodes. Adapted from Ref. [39]. The gray bar represents the gold electrode.
Figure 7. a) Preparation of GOx-modified electrodes using Au nanoparticles as electrochemical relays. 1) Reconstitution of apoGOx with the FAL modified nanoparticles and subsequent binding to the electrode. II) Binding of the FAD-modified Au nanoparticle and subsequent in situ reconstitution. Adapted and reprinted with permission from Ref. [57]. Copyright 2003 Science/AAAS. b) Reconstitution of apoGOx on gold electrodes containing single-walled carbon nanotubes (SWCNT) modified with FAD using 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC). The AFM image of the electrode coverage is shown at the bottom. Adapted from Ref. [59].
Figure 9. a) Modification of heme propionate groups and the reconsti- tution of apoMb to rMb25. b) Structure of the reconstituted rMb25 prepared by Hayashi et al."?5! c) An increased activity towards guiacol oxidation was observed with this modified protein (@) relative to native Mb (oc); vo: initial rate. Adapted and reprinted with permission from Ref. [125]. Copyright 1999 American Chemical Society. Hayashi et al. reported that the chemical modification of heme propionate chains with eight carboxy groups (25; Figure 9) led to alterations in both the substrate specificity and reactivity of Mb, despite the fact that the UV/Vis, CD, and NMR spectra of the modified rMb25 (r: reconstituted) were comparable to those of native Mb." Tt was also
Figure 10. Mb reconstituted with heme containing a phenylboronic acid moiety to enable binding of monosaccharides.!"*7
“igure 11. Modified heme cofactors and applications of the respective reconstituted enzymes; bpy: 2,2’-bipyridin The photoactivation of heme enzymes has been a subject of intensive research because it could provide not only temporal control over the activation of the enzyme but it could also eliminate the need for oxidative activators (such as scopic methods. For example, cobalt-porphyrin analogues, which are readily obtained by the complexation of Co salts, such as CoCl, or Co(OAc),, with the porphyrin ligand, have been used for the reconstitution of Mb and Hb,!4""“4] HRP! and P450cam.'*! Cobalt species are versatile probes for electron paramagnetic resonance (EPR) spectroscopy, and such studies enabled detailed investigation of the binding of molecular oxygen and other substrates to the artificial cofactor. In addition, Co and Mn derivatives were utilized to obtain reconstituted myoglobin, which was then exten- sively investigated by electrochemical means to explore applications in biosensing,!4°'"7 3.3.1. Design of Photoactive Centers The replacement of the native heme cofactor with an artificial derivative containing non-native functional groups opens up the way to generate novel enzymes with altered, enhanced, and even entirely new functions. An overview of representative modifications reported so far and their effects on the activity of the reconstituted enzymes is given in Figure 11. In this section, we will discuss selected examples of such artificial heme enzymes and their applications.
Figure 12. a) Electron abstraction from rMb27, which was reconstituted with photoactivatable 27. Inset: species that take part in the reaction. b) Photochemical production of the dioxygen complex oxy-Mb from tMb27; on/off: on and off switching of the visible light. oxy-Mb is only produced on irradiation. Adapted and reprinted from Refs. [148, 150]. Copyright 1993-1999 American Chemical Society. H,O, for peroxidases or NAD(P)H for oxygenases). To achieve this challenging goal the native enzymes need to be modified with photoactive groups, which can harvest light, harness the energy for redox reactions, and transfer generated electrons to the heme metal center. The native heme cofactor containing two carboxylic acid groups is an excellent starting point for a range of modifications by using site-selective and relatively simple chemical procedures. Much of the seminal work concerning the introduction of photoactivatable groups into myoglobin by reconstitution with artificial cofactors was carried out by the research groups of Hayashi and Shinkai. For example, Hamachi et al. synthesised heme derivative 27 (Figure 11), bearing a photosensitive tris(2,2’-bipyridyl)ru- thenium(II) {Ru(bpy)3}?* moiety. Complex 27 can be acti- vated effectively by visible light''*! and it was used for the reconstitution of apoMb to yield rMb27 (Figure 12). The
Figure 13. Preparation of photoactivable Mb, which is capable of hydrogenating acetylene.!*4l Another effective route to the design of photoactivatable biocatalysts by modification of heme with photoactive moieties was developed by Willner et al.“ They replaced the native iron-containing heme of Mb with Co" porphyrin 29, and the respective reconstituted Mb was chemically modified with eosine isothiocyanate to yield Eo,MbCo" (rMb29; Figures 11 and 13). This system was activated by irradiation in
Figure 14. In situ reconstitution of apoHRP on gold electrodes to which heme cofactor was bound through amide coupling by using 1- ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC). In a related approach, Zimmermann etal. used self- assembled monolayers containing linkers to immobilize heme on gold electrodes and to produce active enzyme electrodes by in situ reconstitution of apoHRP (Figure 14). In this
Figure 15. Reconstituted Mb bearing a cytochrome c receptor and the formation of a protein-protein complex with cytochrome c. Adapted from Ref. [163].
Figure 16. a) Giant amphiphiles prepared by reconstitution of apoHR (HRP is shown in gray); b) the vesicular aggregates formed. Adapted from Ref. [168].
Figure 17. Supramolecular polymers obtained by heme reconstitution of mutant cytochrome bs¢.. Adapted and reprinted with permission from Ref. [174]. Copyright 2007 American Chemical Society.
Figure 18. a) Reconstitution of DNA-modified heme into apoMb and apoHRP and b) the subsequent use of DNA to immobilize the enzymes on surfaces. Adapted from Ref. [186]. c) Generation of an array of DNA-HRP conjugates on a Au microelectrode using rHRP35a (I) or in situ reconstitution of apoHRP (II). The microelectrode chip containing four gold electrodes is also shown. Adapted from Ref. [187].
Figure 19. Preparation of rMb36 by reconstitution of apoMb with iron porphycene 36 as an abiotic cofactor. rMb36 has a blue color and displays strongly increased oxygen affinity."
Figure 20. Top: Preparation of artificial metalloenzymes by reconstitu- tion of apoMb with Mn- or Cr-containing salophen. Bottom: molecular models of the active centers of the native (left) and artificial Mb (right). Adapted from Ref. [191].
Figure 21. The structure of cofactor PQQ (left) and PQQ-containing enzyme glucose dehydrogenase (right). In the enzyme structure, PQQ is shown as a black framework and the Ca?* ions necessary for PQQ coordination are depicted as gray spheres.
Figure 22. Immobilization of apoGDH onto the PQQ-modified gold nanoparticles attached to a gold electrode. Adapted and reprinted with permission from Ref. [206]. Copyright 2005 American Chemical Society. communication is possible due to the insulating protein shell. This problem was later circumvented by the employment of more efficient linker systems. For example, electrically contacted GDH enzyme electrodes were successfully con- structed by the reconstitution of apoGDH on PQOQ-function- alized polyaniline films.°°! In this approach, PQQ was coupled to a polyaniline/polyacrylic acid composite film deposited on a gold electrode through amide coupling. Such electrodes were used for the in situ reconstitution of apoGDH to yield sensors capable of detecting the biolectrocatalyzed oxidation of glucose. This system was later improved by using gold-nanoparticle relays (Figure 22) similar to those used for
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Biomolecule-assisted Natural Computing Approaches for Simple Polynomial Algebra Over Fields
by Tomonori Kawano

2016

Biocomputing is a recently growing and highly interdisciplinary field of research that investigates models and computational techniques inspired by biology and related sciences. Here, cyclic behavior (redox cycling) of purified... more
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