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Grempka A, Dziubak D, Puszko AK, Bachurska-Szpala P, Ivanov M, Vilarinho PM, Pulka-Ziach K, Sek S. Stimuli-Responsive Oligourea Molecular Films. ACS APPLIED MATERIALS & INTERFACES 2024; 16:31817-31825. [PMID: 38848259 PMCID: PMC11194770 DOI: 10.1021/acsami.4c04767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/10/2024] [Accepted: 05/31/2024] [Indexed: 06/09/2024]
Abstract
We have designed and synthesized a helical cysteamine-terminated oligourea foldamer composed of ten urea residues featuring side carboxyl and amine groups. The carboxyl group is located in proximity to the C-terminus of the oligourea and hence at the negative pole of the helix dipole. The amine group is located close to the N-terminus and hence at the positive pole of the helix dipole. Beyond the already remarkable dipole moment inherent in oligourea 2.5 helices, the incorporation of additional charges originating from the carboxylic and amine groups is supposed to impact the overall charge distribution along the molecule. These molecules were self-assembled into monolayers on a gold substrate, allowing us to investigate the influence of an electric field on these polar helices. By applying surface-enhanced infrared reflection-absorption spectroscopy, we proved that molecules within the monolayers tend to reorient themselves more vertically when a negative bias is applied to the surface. It was also found that surface-confined oligourea molecules affected by the external electric field tend to rearrange the electron density at urea groups, leading to the stabilization of the resonance structure with charge transfer character. The presence of the external electric field also affected the nanomechanical properties of the oligourea films, suggesting that molecules also tend to reorient in the ambient environment without an electrolyte solution. Under the same conditions, the helical oligourea displayed a robust piezoresponse, particularly noteworthy given the slender thickness of the monolayer, which measured approximately 1.2 nm. This observation demonstrates that thin molecular films composed of oligoureas may exhibit stimulus-responsive properties. This, in turn, may be used in nanotechnology systems as actuators or functional films, enabling precise control of their thickness in the range of even fractions of nanometers.
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Affiliation(s)
- Arkadiusz Grempka
- Biological
and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warsaw 02-089, Poland
| | - Damian Dziubak
- Biological
and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warsaw 02-089, Poland
| | - Anna K. Puszko
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | | | - Maxim Ivanov
- Department
of Materials and Ceramic Engineering & CICECO—Aveiro Institute
of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Paula M. Vilarinho
- Department
of Materials and Ceramic Engineering & CICECO—Aveiro Institute
of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | | | - Slawomir Sek
- Biological
and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, Warsaw 02-089, Poland
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2
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Abstract
Transmembrane proteins involved in metabolic redox reactions and photosynthesis catalyse a plethora of key energy-conversion processes and are thus of great interest for bioelectrocatalysis-based applications. The development of membrane protein modified electrodes has made it possible to efficiently exchange electrons between proteins and electrodes, allowing mechanistic studies and potentially applications in biofuels generation and energy conversion. Here, we summarise the most common electrode modification and their characterisation techniques for membrane proteins involved in biofuels conversion and semi-artificial photosynthesis. We discuss the challenges of applications of membrane protein modified electrodes for bioelectrocatalysis and comment on emerging methods and future directions, including recent advances in membrane protein reconstitution strategies and the development of microbial electrosynthesis and whole-cell semi-artificial photosynthesis.
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3
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Penkauskas T, Preta G. Biological applications of tethered bilayer lipid membranes. Biochimie 2019; 157:131-141. [DOI: 10.1016/j.biochi.2018.11.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022]
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4
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Kinetics of cytochrome c oxidase from R. sphaeroides initiated by direct electron transfer followed by tr-SEIRAS. Bioelectrochemistry 2016; 112:1-8. [PMID: 27398977 DOI: 10.1016/j.bioelechem.2016.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 06/18/2016] [Accepted: 06/24/2016] [Indexed: 11/20/2022]
Abstract
Time-resolved surface-enhanced IR-absorption spectroscopy (tr-SEIRAS) has been performed on cytochrome c oxidase from Rhodobacter sphaeroides. The enzyme was converted electrochemically into the fully reduced state. Thereafter, in the presence of oxygen, the potential was switched to open circuit potential (OCP). Under these conditions, the enzyme is free to undergo enzymatic oxidation in the absence of an external electric field. Tr-SEIRAS was performed using the step-scan technique, triggered by periodic potential pulses switching between - 800mV and OCP. Single bands were resolved in a broad band in the amide I region using phase sensitive detection. Amplitudes of these bands were analyzed as a function of time. Time constants in the ms time scale were considered in terms of conformational changes of the protein secondary structures associated with the enzymatic turnover of the protein.
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5
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Naumann RLC, Geiss AF, Steininger C, Knoll W. Biomimetic Membranes for Multi-Redox Center Proteins. Int J Mol Sci 2016; 17:330. [PMID: 26950120 PMCID: PMC4813192 DOI: 10.3390/ijms17030330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 11/27/2015] [Accepted: 02/17/2016] [Indexed: 11/22/2022] Open
Abstract
His-tag technology was applied for biosensing purposes involving multi-redox center proteins (MRPs). An overview is presented on various surfaces ranging from flat to spherical and modified with linker molecules with nitrile-tri-acetic acid (NTA) terminal groups to bind his-tagged proteins in a strict orientation. The bound proteins are submitted to in situ dialysis in the presence of lipid micelles to form a so-called protein-tethered bilayer lipid membrane (ptBLM). MRPs, such as the cytochrome c oxidase (CcO) from R. sphaeroides and P. denitrificans, as well as photosynthetic reactions centers (RCs) from R. sphaeroides, were thus investigated. Electrochemical and surface-sensitive optical techniques, such as surface plasmon resonance, surface plasmon-enhanced fluorescence, surface-enhanced infrared absorption spectroscopy (SEIRAS) and surface-enhanced resonance Raman spectroscopy (SERRS), were employed in the case of the ptBLM structure on flat surfaces. Spherical particles ranging from µm size agarose gel beads to nm size nanoparticles modified in a similar fashion were called proteo-lipobeads (PLBs). The particles were investigated by laser-scanning confocal fluorescence microscopy (LSM) and UV/Vis spectroscopy. Electron and proton transfer through the proteins were demonstrated to take place, which was strongly affected by the membrane potential. MRPs can thus be used for biosensing purposes under quasi-physiological conditions.
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Affiliation(s)
- Renate L C Naumann
- Austrian Institute of Technology GmbH, AIT, Donau-City-Str. 1, 1220 Vienna, Austria.
| | - Andreas F Geiss
- Austrian Institute of Technology GmbH, AIT, Donau-City-Str. 1, 1220 Vienna, Austria.
| | - Christoph Steininger
- Austrian Institute of Technology GmbH, AIT, Donau-City-Str. 1, 1220 Vienna, Austria.
| | - Wolfgang Knoll
- Austrian Institute of Technology GmbH, AIT, Donau-City-Str. 1, 1220 Vienna, Austria.
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6
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Mid-infrared spectroscopy for protein analysis: potential and challenges. Anal Bioanal Chem 2016; 408:2875-89. [PMID: 26879650 DOI: 10.1007/s00216-016-9375-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/22/2016] [Accepted: 01/28/2016] [Indexed: 12/11/2022]
Abstract
Mid-infrared (MIR) spectroscopy investigates the interaction of MIR photons with both organic and inorganic molecules via the excitation of vibrational and rotational modes, providing inherent molecular selectivity. In general, infrared (IR) spectroscopy is particularly sensitive to protein structure and structural changes via vibrational resonances originating from the polypeptide backbone or side chains; hence information on the secondary structure of proteins can be obtained in a label-free fashion. In this review, the challenges for IR spectroscopy for protein analysis are discussed as are the potential and limitations of different IR spectroscopic techniques enabling protein analysis. In particular, the amide I spectral range has been widely used to study protein secondary structure, conformational changes, protein aggregation, protein adsorption, and the formation of amyloid fibrils. In addition to representative examples of the potential of IR spectroscopy in various fields related to protein analysis, the potential of protein analysis taking advantage of miniaturized MIR systems, including waveguide-enhanced MIR sensors, is detailed.
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7
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Time-resolved surface-enhanced IR-absorption spectroscopy of direct electron transfer to cytochrome c oxidase from R. sphaeroides. Biophys J 2014; 105:2706-13. [PMID: 24359742 DOI: 10.1016/j.bpj.2013.10.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 10/07/2013] [Accepted: 10/10/2013] [Indexed: 11/20/2022] Open
Abstract
Time-resolved surface-enhanced IR-absorption spectroscopy triggered by electrochemical modulation has been performed on cytochrome c oxidase from Rhodobacter sphaeroides. Single bands isolated from a broad band in the amide I region using phase-sensitive detection were attributed to different redox centers. Their absorbances changing on the millisecond timescale could be fitted to a model based on protonation-dependent chemical reaction kinetics established previously. Substantial conformational changes of secondary structures coupled to redox transitions were revealed.
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8
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Frontiers of two-dimensional correlation spectroscopy. Part 2. Perturbation methods, fields of applications, and types of analytical probes. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.01.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Volpati D, Aoki PHB, Alessio P, Pavinatto FJ, Miranda PB, Constantino CJL, Oliveira ON. Vibrational spectroscopy for probing molecular-level interactions in organic films mimicking biointerfaces. Adv Colloid Interface Sci 2014; 207:199-215. [PMID: 24530000 DOI: 10.1016/j.cis.2014.01.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/28/2013] [Accepted: 01/13/2014] [Indexed: 01/26/2023]
Abstract
Investigation into nanostructured organic films has served many purposes, including the design of functionalized surfaces that may be applied in biomedical devices and tissue engineering and for studying physiological processes depending on the interaction with cell membranes. Of particular relevance are Langmuir monolayers, Langmuir-Blodgett (LB) and layer-by-layer (LbL) films used to simulate biological interfaces. In this review, we shall focus on the use of vibrational spectroscopy methods to probe molecular-level interactions at biomimetic interfaces, with special emphasis on three surface-specific techniques, namely sum frequency generation (SFG), polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS) and surface-enhanced Raman scattering (SERS). The two types of systems selected for exemplifying the potential of the methods are the cell membrane models and the functionalized surfaces with biomolecules. Examples will be given on how SFG and PM-IRRAS can be combined to determine the effects from biomolecules on cell membrane models, which include determination of the orientation and preservation of secondary structure. Crucial information for the action of biomolecules on model membranes has also been obtained with PM-IRRAS, as is the case of chitosan removing proteins from the membrane. SERS will be shown as promising for enabling detection limits down to the single-molecule level. The strengths and limitations of these methods will also be discussed, in addition to the prospects for the near future.
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Affiliation(s)
- Diogo Volpati
- São Carlos Institute of Physics, University of São Paulo, CP 369, São Carlos, SP 13560-970, Brazil
| | - Pedro H B Aoki
- Faculty of Science and Technology, UNESP, Presidente Prudente, CEP 19060-900 SP,Brazil
| | - Priscila Alessio
- Faculty of Science and Technology, UNESP, Presidente Prudente, CEP 19060-900 SP,Brazil
| | - Felippe J Pavinatto
- São Carlos Institute of Physics, University of São Paulo, CP 369, São Carlos, SP 13560-970, Brazil
| | - Paulo B Miranda
- São Carlos Institute of Physics, University of São Paulo, CP 369, São Carlos, SP 13560-970, Brazil
| | | | - Osvaldo N Oliveira
- São Carlos Institute of Physics, University of São Paulo, CP 369, São Carlos, SP 13560-970, Brazil.
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10
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Zou C, Larisika M, Nagy G, Srajer J, Oostenbrink C, Chen X, Knoll W, Liedberg B, Nowak C. Two-dimensional heterospectral correlation analysis of the redox-induced conformational transition in cytochrome c using surface-enhanced Raman and infrared absorption spectroscopies on a two-layer gold surface. J Phys Chem B 2013; 117:9606-14. [PMID: 23930980 PMCID: PMC3753128 DOI: 10.1021/jp404573q] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
heme protein cytochrome c adsorbed to a two-layer
gold surface modified with a self-assembled monolayer of 2-mercaptoethanol
was analyzed using a two-dimensional (2D) heterospectral correlation
analysis that combined surface-enhanced infrared absorption spectroscopy
(SEIRAS) and surface-enhanced Raman spectroscopy (SERS). Stepwise
increasing electric potentials were applied to alter the redox state
of the protein and to induce conformational changes within the protein
backbone. We demonstrate herein that 2D heterospectral correlation
analysis is a particularly suitable and useful technique for the study
of heme-containing proteins as the two spectroscopies address different
portions of the protein. Thus, by correlating SERS and SEIRAS data
in a 2D plot, we can obtain a deeper understanding of the conformational
changes occurring at the redox center and in the supporting protein
backbone during the electron transfer process. The correlation analyses
are complemented by molecular dynamics calculations to explore the
intramolecular interactions.
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Affiliation(s)
- Changji Zou
- School of Materials Science and Engineering, Nanyang Technological University, Singapore
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11
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Srajer J, Schwaighofe A, Hildenbrandt DM, Kibrom A, Naumann RL. A Kinetic Model of Proton Transport in a Multi-Redox Centre Protein: Cytochrome c Oxidase. PROGRESS IN REACTION KINETICS AND MECHANISM 2013. [DOI: 10.3184/146867812x13558465325118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We use chemical reaction kinetics to explore the stepwise electron and proton transfer reactions of cytochrome c oxidase (C cO) from R. sphaeroides. Proton transport coupled to electron transport (ET) is investigated in terms of a sequence of protonation-dependent second-order redox reactions. Thereby, we assume fixed rather than shifting dissociation constants of the redox sites. Proton transport can thus be simulated particularly when separate proton uptake and release sites are assumed rather than the same proton pump site for every ET step. In order to test these assumptions, we make use of a model system introduced earlier, which allows us to study direct ET of redox enzymes by electrochemistry. A four-electron transfer model of C cO had been developed before, according to which electrons are transferred from the electrode to CuA. Thereafter, electrons are transferred along the sequence heme a, heme a3 and CuB. In the present investigation, we consider protonation equilibria of the oxidised and reduced species for each of the four centres. Moreover, we add oxygen/H2O as the terminal (fifth) redox couple including protonation of reduced oxygen to water. Finally we arrive at a kinetic model comprising five protonation-dependent redox couples. The results from the simulations are compared with experimental data obtained in the absence and presence of oxygen. As a result, we can show that proton transport can be modelled in terms of protonation-dependent redox kinetics.
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Affiliation(s)
- Johannes Srajer
- Austrian Institute of Technology GmbH, AIT, Donau-City Str. 1, 1220 Vienna, Austria
- CEST Center of Electrochemical Surface Technology, Viktor-Kaplan-Strasse 2, 2700 Wiener Neustadt, Austria
| | - Andreas Schwaighofe
- Austrian Institute of Technology GmbH, AIT, Donau-City Str. 1, 1220 Vienna, Austria
| | | | - Asmorom Kibrom
- Austrian Institute of Technology GmbH, AIT, Donau-City Str. 1, 1220 Vienna, Austria
| | - Renate L.C. Naumann
- Austrian Institute of Technology GmbH, AIT, Donau-City Str. 1, 1220 Vienna, Austria
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12
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Buhrow L, Ferguson-Miller S, Kuhn LA. From static structure to living protein: computational analysis of cytochrome c oxidase main-chain flexibility. Biophys J 2012; 102:2158-66. [PMID: 22824280 DOI: 10.1016/j.bpj.2012.03.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 02/23/2012] [Accepted: 03/12/2012] [Indexed: 10/28/2022] Open
Abstract
Crystallographic structure and deuterium accessibility comparisons of CcO in different redox states have suggested conformational changes of mechanistic significance. To predict the intrinsic flexibility and low energy motions in CcO, this work has analyzed available high-resolution crystallographic structures with ProFlex and elNémo computational methods. The results identify flexible regions and potential conformational changes in CcO that correlate well with published structural and biochemical data and provide mechanistic insights. CcO is predicted to undergo rotational motions on the interior and exterior of the membrane, driven by transmembrane helical tilting and bending, coupled with rocking of the β-sheet domain. Consequently, the proton K-pathway becomes sufficiently flexible for internal water molecules to alternately occupy upper and lower parts of the pathway, associated with conserved Thr-359 and Lys-362 residues. The D-pathway helices are found to be relatively rigid, with a highly flexible entrance region involving the subunit I C-terminus, potentially regulating the uptake of protons. Constriction and dilation of hydrophobic channels in RsCcO suggest regulation of the oxygen supply to the binuclear center. This analysis points to coupled conformational changes in CcO and their potential to influence both proton and oxygen access.
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Affiliation(s)
- Leann Buhrow
- Cell and Molecular Biology Program, Michigan State University, East Lansing, MI, USA
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13
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Jackman JA, Knoll W, Cho NJ. Biotechnology Applications of Tethered Lipid Bilayer Membranes. MATERIALS 2012. [PMCID: PMC5449075 DOI: 10.3390/ma5122637] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Joshua A. Jackman
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; E-Mail:
- Centre for Biomimetic Sensor Science, 50 Nanyang Drive, Singapore 637553, Singapore; E-Mail:
| | - Wolfgang Knoll
- Centre for Biomimetic Sensor Science, 50 Nanyang Drive, Singapore 637553, Singapore; E-Mail:
- Austrian Institute of Technology (AIT) GmbH, Donau-City Str.1, Vienna 1220, Austria
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; E-Mail:
- Centre for Biomimetic Sensor Science, 50 Nanyang Drive, Singapore 637553, Singapore; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +65-6790-4925; Fax: +65-6790-9081
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14
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WANG LX, JIANG XE. Bioanalytical Applications of Surface-enhanced Infrared Absorption Spectroscopy. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2012. [DOI: 10.1016/s1872-2040(11)60556-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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15
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Ash PA, Vincent KA. Spectroscopic analysis of immobilised redox enzymes under direct electrochemical control. Chem Commun (Camb) 2011; 48:1400-9. [PMID: 22057715 DOI: 10.1039/c1cc15871f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article reviews recent developments in spectroscopic analysis of electrode-immobilised enzymes under direct, unmediated electrochemical control. These methods unite the suite of spectroscopic methods available for characterisation of structural, electronic and coordination changes in proteins with the exquisite control over complex redox enzymes that can be achieved in protein film electrochemistry in which immobilised protein molecules exchange electrons directly with an electrode. This combination is particularly powerful in studies of highly active enzymes where redox states can be controlled even under fast electrocatalytic turnover. We examine examples in which UV-visible, IR, Raman and MCD spectroscopy have been combined with direct electrochemistry to probe redox-dependent chemistry, and consider future opportunities for 'direct' spectroelectrochemistry of immobilised enzymes.
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Affiliation(s)
- Philip A Ash
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
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