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Khursandov J, Mashalov R, Makhkamov M, Turgunboev F, Sharipov A, Razzokov J. Exploring α-synuclein stability under the external electrostatic fields: Effect of repeat unit. J Struct Biol 2024; 216:108109. [PMID: 38964522 DOI: 10.1016/j.jsb.2024.108109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Parkinson's disease (PD) is a category of neurodegenerative disorders (ND) that currently lack comprehensive and definitive treatment strategies. The etiology of PD can be attributed to the presence and aggregation of a protein known as α-synuclein. Researchers have observed that the application of an external electrostatic field holds the potential to induce the separation of the fibrous structures into peptides. To comprehend this phenomenon, our investigation involved simulations conducted on the α-synuclein peptides through the application of Molecular Dynamics (MD) simulation techniques under the influence of a 0.1 V/nm electric field. The results obtained from the MD simulations revealed that in the presence of external electric field, the monomer and oligomeric forms of α-synuclein are experienced significant conformational changes which could prevent them from further aggregation. However, as the number of peptide units in the model system increases, forming trimers and tetramers, the stability against the electric field also increases. This enhanced stability in larger aggregates indicates a critical threshold in α-synuclein assembly where the electric field's effectiveness in disrupting the aggregation diminishes. Therefore, our findings suggest that early diagnosis and intervention could be crucial in preventing PD progression. When α-synuclein predominantly exists in its monomeric or dimeric form, applying even a lower electric field could effectively disrupt the initial aggregation process. Inhibition of α-synuclein fibril formation at early stages might serve as a viable solution to combat PD by halting the formation of more stable and pathogenic α-synuclein fibrils.
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Affiliation(s)
- Javokhir Khursandov
- Department of Physics, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan; Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Universitet 7, Tashkent 100174, Uzbekistan
| | - Rasulbek Mashalov
- Department of Physics, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan; Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Universitet 7, Tashkent 100174, Uzbekistan
| | - Mukhriddin Makhkamov
- Department of Chemistry, National University of Uzbekistan, Universitet 4, 100174 Tashkent, Uzbekistan; Department of Information Technologies, Tashkent International University of Education, Imom Bukhoriy 6, Tashkent 100207, Uzbekistan
| | - Farkhad Turgunboev
- Department of Physics, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan
| | - Avez Sharipov
- Depatment of Inorganic, Physical and Colloidal Chemistry, Tashkent Pharmaceutical Institute, Oybek Street 45, Tashkent 100015, Uzbekistan
| | - Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, Tashkent 100000, Uzbekistan; Department of Natural Sciences, Shakhrisabz State Pedagogical Institute, Shakhrisabz Street 10, Kashkadarya 181301, Uzbekistan; Department of Biotechnology, Tashkent State Technical University, Universitet 2, Tashkent 100095, Uzbekistan
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Bhattacharjee N, Alonso-Cotchico L, Lucas MF. Enzyme immobilization studied through molecular dynamic simulations. Front Bioeng Biotechnol 2023; 11:1200293. [PMID: 37362217 PMCID: PMC10285225 DOI: 10.3389/fbioe.2023.1200293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
In recent years, simulations have been used to great advantage to understand the structural and dynamic aspects of distinct enzyme immobilization strategies, as experimental techniques have limitations in establishing their impact at the molecular level. In this review, we discuss how molecular dynamic simulations have been employed to characterize the surface phenomenon in the enzyme immobilization procedure, in an attempt to decipher its impact on the enzyme features, such as activity and stability. In particular, computational studies on the immobilization of enzymes using i) nanoparticles, ii) self-assembled monolayers, iii) graphene and carbon nanotubes, and iv) other surfaces are covered. Importantly, this thorough literature survey reveals that, while simulations have been primarily performed to rationalize the molecular aspects of the immobilization event, their use to predict adequate protocols that can control its impact on the enzyme properties is, up to date, mostly missing.
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Hao H, Ruiz Pestana L, Qian J, Liu M, Xu Q, Head‐Gordon T. Chemical transformations and transport phenomena at interfaces. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hongxia Hao
- Kenneth S. Pitzer Theory Center and Department of Chemistry University of California Berkeley California USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
| | - Luis Ruiz Pestana
- Department of Civil and Architectural Engineering University of Miami Coral Gables Florida USA
| | - Jin Qian
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
| | - Meili Liu
- Department of Civil and Architectural Engineering University of Miami Coral Gables Florida USA
| | - Qiang Xu
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
| | - Teresa Head‐Gordon
- Kenneth S. Pitzer Theory Center and Department of Chemistry University of California Berkeley California USA
- Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley California USA
- Department of Bioengineering and Chemical and Biomolecular Engineering University of California Berkeley California USA
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Dahl PJ, Yi SM, Gu Y, Acharya A, Shipps C, Neu J, O’Brien JP, Morzan UN, Chaudhuri S, Guberman-Pfeffer MJ, Vu D, Yalcin SE, Batista VS, Malvankar NS. A 300-fold conductivity increase in microbial cytochrome nanowires due to temperature-induced restructuring of hydrogen bonding networks. SCIENCE ADVANCES 2022; 8:eabm7193. [PMID: 35544567 PMCID: PMC9094664 DOI: 10.1126/sciadv.abm7193] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/28/2022] [Indexed: 06/10/2023]
Abstract
Although proteins are considered as nonconductors that transfer electrons only up to 1 to 2 nanometers via tunneling, Geobacter sulfurreducens transports respiratory electrons over micrometers, to insoluble acceptors or syntrophic partner cells, via nanowires composed of polymerized cytochrome OmcS. However, the mechanism enabling this long-range conduction is unclear. Here, we demonstrate that individual nanowires exhibit theoretically predicted hopping conductance, at rate (>1010 s-1) comparable to synthetic molecular wires, with negligible carrier loss over micrometers. Unexpectedly, nanowires show a 300-fold increase in their intrinsic conductance upon cooling, which vanishes upon deuteration. Computations show that cooling causes a massive rearrangement of hydrogen bonding networks in nanowires. Cooling makes hemes more planar, as revealed by Raman spectroscopy and simulations, and lowers their reduction potential. We find that the protein surrounding the hemes acts as a temperature-sensitive switch that controls charge transport by sensing environmental perturbations. Rational engineering of heme environments could enable systematic tuning of extracellular respiration.
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Affiliation(s)
- Peter J. Dahl
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Sophia M. Yi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Yangqi Gu
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Atanu Acharya
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Catharine Shipps
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Jens Neu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - J. Patrick O’Brien
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Uriel N. Morzan
- Department of Chemistry, Yale University, New Haven, CT, USA
| | | | - Matthew J. Guberman-Pfeffer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Dennis Vu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Sibel Ebru Yalcin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | | | - Nikhil S. Malvankar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
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5
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Sarhangi SM, Matyushov DV. Anomalously Small Reorganization Energy of the Half Redox Reaction of Azurin. J Phys Chem B 2022; 126:3000-3011. [DOI: 10.1021/acs.jpcb.2c00338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Setare M. Sarhangi
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, United States
| | - Dmitry V. Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, United States
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Goto T, Ogami S, Yoshimume K, Yumoto I. Differences in Bioenergetic Metabolism of Obligately Alkaliphilic Bacillaceae Under High pH Depend on the Aeration Conditions. Front Microbiol 2022; 13:842785. [PMID: 35401478 PMCID: PMC8992544 DOI: 10.3389/fmicb.2022.842785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/22/2022] [Indexed: 11/26/2022] Open
Abstract
Alkaliphilic Bacillaceae appear to produce ATP based on the H+-based chemiosmotic theory. However, the bulk-based chemiosmotic theory cannot explain the ATP production in alkaliphilic bacteria because the H+ concentration required for driving ATP synthesis through the ATPase does not occur under the alkaline conditions. Alkaliphilic bacteria produce ATP in an H+-diluted environment by retaining scarce H+ extruded by the respiratory chain on the outer surface of the membrane and increasing the potential of the H+ for ATP production on the outer surface of the membrane using specific mechanisms of ATP production. Under high-aeration conditions, the high ΔΨ (ca. -170 mV) of the obligate alkaliphilic Evansella clarkii retains H+ at the outer surface of the membrane and increases the intensity of the protonmotive force (Δp) per H+ across the membrane. One of the reasons for the production of high ΔΨ is the Donnan potential, which arises owing to the induction of impermeable negative charges in the cytoplasm. The intensity of the potential is further enhanced in the alkaliphiles compared with neutralophiles because of the higher intracellular pH (ca. pH 8.1). However, the high ΔΨ observed under high-aeration conditions decreased (∼ -140 mV) under low-aeration conditions. E. clarkii produced 2.5–6.3-fold higher membrane bound cytochrome c in the content of the cell extract under low-aeration conditions than under high-aeration conditions. The predominant membrane-bound cytochrome c in the outer surface of the membrane possesses an extra Asn-rich segment between the membrane anchor and the main body of protein. This structure may influence the formation of an H+-bond network that accumulates H+ on the outer surface of the membrane. Following accumulation of the H+-bond network producing cytochrome c, E. clarkii constructs an H+ capacitor to overcome the energy limitation of low aeration at high pH conditions. E. clarkii produces more ATP than other neutralophilic bacteria by enhancing the efficacy per H+ in ATP synthesis. In low H+ environments, E. clarkii utilizes H+ efficiently by taking advantage of its high ΔΨ under high-aeration conditions, whereas under low-aeration conditions E. clarkii uses cytochrome c bound on its outer surface of the membrane as an H+ capacitor.
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Affiliation(s)
- Toshitaka Goto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Shinichi Ogami
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kazuaki Yoshimume
- College of Industrial Technology, Nihon University, Narashino, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
- *Correspondence: Isao Yumoto,
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7
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Wang W, Zhang H, Jiang J, He Y, He J, Liu J, Yu K, Liu Q, Qiao L. Thin interfacial film spontaneously produces hydrogen peroxide: mechanism and application for perfluorooctanoic acid degradation. NEW J CHEM 2022. [DOI: 10.1039/d1nj04791d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have unambiguously demonstrated spontaneous formation of hydrogen peroxide (H2O2) in thin film formats by evaporating almost all the water and its effective for perfluorooctanoic acid (PFOA) degradation without catalysts.
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Affiliation(s)
- Wenxin Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
| | - Hong Zhang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
| | - Jie Jiang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
| | - Yuwei He
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
| | - Jing He
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
| | - Junyu Liu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
| | - Kai Yu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
| | - Qianhui Liu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
| | - Lina Qiao
- Marine College, Shandong University (Weihai), Weihai, Shandong 264209, China
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8
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Zhang Q, Shao D, Xu P, Jiang Z. Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different Frequencies. Polymers (Basel) 2021; 14:polym14010123. [PMID: 35012145 PMCID: PMC8747415 DOI: 10.3390/polym14010123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 12/21/2022] Open
Abstract
The effect of pulsed and oscillating electric fields with different frequencies on the conformational properties of all-α proteins was investigated by molecular dynamics simulations. The root mean square deviation, the root mean square fluctuation, the dipole moment distribution, and the secondary structure analysis were used to assess the protein samples’ structural characteristics. In the simulation, we found that the higher frequency of the electric field influences the rapid response to the secondary structural transitions. However, the conformational changes measured by RMSD are diminished by applying the electrical field with a higher frequency. During the dipole moment analysis, we found that the magnitude and frequency of the dipole moment was directly related to the strength and frequency of the external electric field. In terms of the type of electric fields, we found that the average values of RMSD and RMSF of whole molecular protein are larger when the protein is exposed in the pulsed electric field. Concerning the typical sample 1BBL, the secondary structure analysis showed that two alpha-helix segments both transit to turns or random coils almost simultaneously when it is exposed in a pulsed electric field. Meanwhile, two segments present the different characteristic times when the transition occurs in the condition of an oscillating electric field. This study also demonstrated that the protein with fewer charged residues or more residues in forming α-helical structures display the higher conformational stability. These conclusions, achieved using MD simulations, provide a theoretical understanding of the effect of the frequency and expression form of external electric fields on the conformational changes of the all-α proteins with charged residues and the guidance for anticipative applications.
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Komorek P, Jachimska B, Brand I. Adsorption of lysozyme on gold surfaces in the presence of an external electric potential. Bioelectrochemistry 2021; 142:107946. [PMID: 34507162 DOI: 10.1016/j.bioelechem.2021.107946] [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: 05/27/2021] [Revised: 07/30/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
Adsorbed protein films consist of essential building blocks of many biotechnological and biomedical devices. The electrostatic potential may significantly modulate the protein behaviour on surfaces, affecting their structure and biological activity. In this study, lysozyme was used to investigate the effects of applied electric potentials on adsorption and the protein structure. The pH and the surface charge determine the amount and secondary structure of adsorbed lysozyme on a gold surface. In-situ measurements using polarization modulation infrared reflection absorption spectroscopy indicated that the concentration of both the adsorbed anions and the lysozyme led to conformational changes in the protein film, which was demonstrated by a greater amount of aggregated β-sheets in films fabricated at net positive charges of the Au electrode (Eads > Epzc). The changes in secondary structure involved two parallel processes. One comprised changes in the hydration/hydrogen-bond network at helices, leading to diverse helical structures: α-, 310- and/or π-helices. In the second process β-turns, β-sheets, and random coils displayed an ability to form aggregated β-sheet structures. The study illuminates the understanding of electrical potential-dependent changes involved in the protein misfolding process.
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Affiliation(s)
- Paulina Komorek
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland
| | - Barbara Jachimska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Cracow, Poland.
| | - Izabella Brand
- Department of Chemistry, University of Oldenburg, 26111 Oldenburg, Germany.
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10
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Rodríguez-Maciá P, Breuer N, DeBeer S, Birrell JA. Insight into the Redox Behavior of the [4Fe–4S] Subcluster in [FeFe] Hydrogenases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02771] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Patricia Rodríguez-Maciá
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, Mülheim an der Ruhr 45470, Germany
| | - Nina Breuer
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, Mülheim an der Ruhr 45470, Germany
| | - Serena DeBeer
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, Mülheim an der Ruhr 45470, Germany
| | - James A. Birrell
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, Mülheim an der Ruhr 45470, Germany
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11
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Effect of Electrostatic Field Strength on Bioelectrochemical Nitrogen Removal from Nitrogen-Rich Wastewater. ENERGIES 2020. [DOI: 10.3390/en13123218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The effect of electrostatic fields on the bioelectrochemical removal of ammonium and nitrite from nitrogen-rich wastewater was investigated at strengths ranging from 0.2 to 0.67 V/cm in bioelectrochemical anaerobic batch reactors. The electrostatic field enriched the bulk solution with electroactive bacteria, including ammonium oxidizing exoelectrogens (AOE) and denitritating electrotrophs (DNE). The electroactive bacteria removed ammonium and nitrite simultaneously with alkalinity consumption through biological direct interspecies electron transfer (DIET) in the bulk solution. However, the total nitrogen (ammonium and nitrite) removal rate increased from 106.1 to 166.3 mg N/g volatile suspended solids (VSS).d as the electrostatic field strength increased from 0.2 to 0.67 V/cm. In the cyclic voltammogram, the redox peaks corresponding to the activities of AOE and DNE increased as the strength of the electrostatic field increased. Based on the microbial taxonomic profiling, the dominant genera involved in the bioelectrochemical nitrogen removal were identified as Pseudomonas, Petrimonas, DQ677001_g, Thiopseudomonas, Lentimicrobium, and Porphyromonadaceae_uc. This suggests that the electrostatic field of 0.67 V/cm significantly improves the bioelectrochemical nitrogen removal by enriching the bulk solution with AOE and DNE and promoting the biological DIET between them.
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12
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Rauly D, Vindret M, Chamberod E, Martins JMF, Xavier P. Distribution of AC Electric Field-Induced Transmembrane Voltage in Escherichia coli Cell Wall Layers. Bioelectromagnetics 2020; 41:279-288. [PMID: 32207548 DOI: 10.1002/bem.22261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/14/2020] [Indexed: 11/11/2022]
Abstract
On the basis of Gram-negative bacterium Escherichia coli models previously published in the literature, the transmembrane voltage induced by the application of an alternating current (AC) electric field on a bacterial suspension is calculated using COMSOL Multiphysics software, in the range 1-20 MHz, for longitudinal and transverse field orientations. The voltages developed on each of the three layers of the cell wall are then calculated using an electrical equivalent circuit. This study shows that the overall voltage on the cell wall, whose order of magnitude is a few tens of µV, is mainly distributed on inner and outer layers, while a near-zero voltage is found on the periplasm, due to its much higher electrical conductivity compared with the other layers. Although the outer membrane electrical conductivity taken in the model is a thousand times higher than that of the inner membrane, the voltage there is about half of that on the inner membrane, due to capacitive effects. It follows that the expression of protein complexes anchored in the inner membrane could potentially be disrupted, inducing in particular a possible perturbation of biological processes related to cellular respiration and proton cycle, and leading to growth inhibition as a consequence. Protein complexes anchored in the outer membrane or constituting a bridge between the three layers of the cell wall, such as some porins, may also undergo the same action, which would add another growth inhibition factor, as a result of deficiency in porin filtration function when the external environment contains biocides. Bioelectromagnetics. 2020;41:279-288 © 2020 Bioelectromagnetics Society.
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Affiliation(s)
- Dominique Rauly
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, Grenoble INP, IMEP-LAHC, 38000, Grenoble, France
| | - Médéric Vindret
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, Grenoble INP, IMEP-LAHC, 38000, Grenoble, France
| | | | - Jean M F Martins
- Univ. Grenoble Alpes, Inst. Geosci Environ. IGE HyDRIMZ, CNRS, Grenoble INP, IRD, UGA CS 40700, Grenoble, France
| | - Pascal Xavier
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, Grenoble INP, IMEP-LAHC, 38000, Grenoble, France
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13
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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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14
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Pradhan B, Engelhard C, Van Mulken S, Miao X, Canters GW, Orrit M. Single electron transfer events and dynamical heterogeneity in the small protein azurin from Pseudomonas aeruginosa. Chem Sci 2019; 11:763-771. [PMID: 34123050 PMCID: PMC8146731 DOI: 10.1039/c9sc05405g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/25/2019] [Indexed: 01/07/2023] Open
Abstract
Monitoring the fluorescence of single-dye-labeled azurin molecules, we observed the reaction of azurin with hexacyanoferrate under controlled redox potential yielding data on the timing of individual (forward and backward) electron transfer (ET) events. Change-point analysis of the time traces demonstrates significant fluctuations of ET rates and of mid-point potential E 0. These fluctuations are a signature of dynamical heterogeneity, here observed on a 14 kDa protein, the smallest to date. By correlating changes in forward and backward reaction rates we found that 6% of the observed change events could be explained by a change in midpoint potential, while for 25% a change of the donor-acceptor coupling could explain the data. The remaining 69% are driven by variations in complex association constants or structural changes that cause forward and back ET rates to vary independently. Thus, the observed spread in individual ET rates could be related in a unique way to variations in molecular parameters. The relevance for the understanding of metabolic processes is briefly discussed.
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Affiliation(s)
- Biswajit Pradhan
- Huygens-Kamerlingh Onnes Laboratory, Leiden University 2300 RA Leiden Netherlands
| | | | | | - Xueyan Miao
- School of Public Health, Guilin Medical University 541004 Guilin China
| | - Gerard W Canters
- Huygens-Kamerlingh Onnes Laboratory, Leiden University 2300 RA Leiden Netherlands
| | - Michel Orrit
- Huygens-Kamerlingh Onnes Laboratory, Leiden University 2300 RA Leiden Netherlands
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Abstract
Water is considered to be a stable and relatively inert molecule in bulk solution. We report an exceptional behavior of water: Water molecules are spontaneously oxidized to form hydrogen peroxide near the water−air interface of micron-sized water droplets. This process does not require any chemical reagent, catalyst, applied electric potential, or radiation. Only pure water in the form of microdroplets in air is necessary for the appearance of hydrogen peroxide. We suggest that this discovery opens various innovative opportunities including green and inexpensive production of hydrogen peroxide, green chemical synthesis, safe cleaning, and food processing. We show H2O2 is spontaneously produced from pure water by atomizing bulk water into microdroplets (1 μm to 20 µm in diameter). Production of H2O2, as assayed by H2O2-sensitve fluorescence dye peroxyfluor-1, increased with decreasing microdroplet size. Cleavage of 4-carboxyphenylboronic acid and conversion of phenylboronic acid to phenols in microdroplets further confirmed the generation of H2O2. The generated H2O2 concentration was ∼30 µM (∼1 part per million) as determined by titration with potassium titanium oxalate. Changing the spray gas to O2 or bubbling O2 decreased the yield of H2O2 in microdroplets, indicating that pure water microdroplets directly generate H2O2 without help from O2 either in air surrounding the droplet or dissolved in water. We consider various possible mechanisms for H2O2 formation and report a number of different experiments exploring this issue. We suggest that hydroxyl radical (OH) recombination is the most likely source, in which OH is generated by loss of an electron from OH− at or near the surface of the water microdroplet. This catalyst-free and voltage-free H2O2 production method provides innovative opportunities for green production of hydrogen peroxide.
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16
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Samajdar RN, Kumar C, Viswanath P, Bhattacharyya AJ. Studying Hemoglobin and a Bare Metal–Porphyrin Complex Immobilized on Functionalized Silicon Surfaces Using Synchrotron X-ray Reflectivity. J Phys Chem B 2019; 123:7492-7503. [DOI: 10.1021/acs.jpcb.9b03085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Rudra N. Samajdar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Chandan Kumar
- Center for Nano and Soft Matter Science, Bengaluru 560013, India
| | - P. Viswanath
- Center for Nano and Soft Matter Science, Bengaluru 560013, India
| | - Aninda J. Bhattacharyya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, India
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17
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Jiang Z, You L, Dou W, Sun T, Xu P. Effects of an Electric Field on the Conformational Transition of the Protein: A Molecular Dynamics Simulation Study. Polymers (Basel) 2019; 11:polym11020282. [PMID: 30960266 PMCID: PMC6419079 DOI: 10.3390/polym11020282] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 12/30/2022] Open
Abstract
The effect of the electric field on the conformational properties of the protein 1BBL was investigated by molecular dynamics simulations. Our simulation results clearly capture the structural transitions of the protein sample from helix to turn or random coil conformation induced by the increasing strength of the electric field. During our analysis, we found that the conformational stability is weakened, and the protein sample is stretched as an unfolded structure when it was exposed in a sufficiently high electric field. The characteristic time when the jump occurs in the time evolution curves of root mean square deviation (RMSD) and radius of gyration Rg decreases with increasing electric strength, which demonstrates the rapidly conformational transition that occurs. The number of intra-protein hydrogen bonds, which is the key factor for stabilizing the protein structure, is related to the overall size of the protein. The value of the dipole moment and characteristic time are both influenced by the strength, but are independent of the direction of the external field. The protein sample becomes rotated with the electric field direction. These conclusions provide a theoretical realization of understanding the protein conformational transition in an electric field and the guidance for anticipative applications.
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Affiliation(s)
- Zhouting Jiang
- Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China.
| | - Le You
- Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China.
| | - Wenhui Dou
- Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China.
| | - Tingting Sun
- Department of Physics, Zhejiang University of Science and Technology, No. 318 Liuhe Road, Hangzhou 310023, China.
| | - Peng Xu
- Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, China.
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18
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Matsuno T, Goto T, Ogami S, Morimoto H, Yamazaki K, Inoue N, Matsuyama H, Yoshimune K, Yumoto I. Formation of Proton Motive Force Under Low-Aeration Alkaline Conditions in Alkaliphilic Bacteria. Front Microbiol 2018; 9:2331. [PMID: 30333809 PMCID: PMC6176047 DOI: 10.3389/fmicb.2018.02331] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/11/2018] [Indexed: 11/22/2022] Open
Abstract
In Mitchell’s chemiosmotic theory, a proton (H+) motive force across the membrane (Δp), generated by the respiratory chain, drives F1Fo-ATPase for ATP production in various organisms. The bulk-base chemiosmotic theory cannot account for ATP production in alkaliphilic bacteria. However, alkaliphiles thrive in environments with a H+ concentrations that are one-thousandth (ca. pH 10) the concentration required by neutralophiles. This situation is similar to the production of electricity by hydroelectric turbines under conditions of very limited water. Alkaliphiles manage their metabolism via various strategies involving the cell wall structure, solute transport systems and molecular mechanisms on the outer surface membrane. Our experimental results indicate that efficient ATP production in alkaliphilic Bacillus spp. is attributable to a high membrane electrical potential (ΔΨ) generated for an attractive force for H+ on the outer surface membrane. In addition, the enhanced F1Fo-ATPase driving force per H+ is derived from the high ΔΨ. However, it is difficult to explain the reasons for high ΔΨ formation based on the respiratory rate. The Donnan effect (which is observed when charged particles that are unable to pass through a semipermeable membrane create an uneven electrical charge) likely contributes to the formation of the high ΔΨ because the intracellular negative ion capacities of alkaliphiles are much higher than those of neutralophiles. There are several variations in the adaptation to alkaline environments by bacteria. However, it could be difficult to utilize high ΔΨ in the low aeration condition due to the low activity of respiration. To explain the efficient ATP production occurring in H+-less and air-limited environments in alkaliphilic bacteria, we propose a cytochrome c-associated “H+ capacitor mechanism” as an alkaline adaptation strategy. As an outer surface protein, cytochrome c-550 from Bacillusclarkii possesses an extra Asn-rich segment between the region anchored to the membrane and the main body of the cytochrome c. This structure may contribute to the formation of the proton-binding network to transfer H+ at the outer surface membrane in obligate alkaliphiles. The H+ capacitor mechanism is further enhanced under low-aeration conditions in both alkaliphilic Bacillus spp. and the Gram-negative alkaliphile Pseudomonas alcaliphila.
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Affiliation(s)
- Toshihide Matsuno
- Department of Chemistry and Biology, National Institute of Technology, Fukui College, Sabae, Japan
| | - Toshitaka Goto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Shinichi Ogami
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hajime Morimoto
- Department of Chemistry and Biology, National Institute of Technology, Fukui College, Sabae, Japan.,Department of Bioscience and Technology, School of Biological Sciences and Engineering, Tokai University, Sapporo, Japan
| | - Koji Yamazaki
- Division of Marine Life Science, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | | | - Hidetoshi Matsuyama
- Department of Bioscience and Technology, School of Biological Sciences and Engineering, Tokai University, Sapporo, Japan
| | - Kazuaki Yoshimune
- College of Industrial Technology, Nihon University, Narashino, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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19
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Abstract
Redox enzymes, which catalyze reactions involving electron transfers in living organisms, are very promising components of biotechnological devices, and can be envisioned for sensing applications as well as for energy conversion. In this context, one of the most significant challenges is to achieve efficient direct electron transfer by tunneling between enzymes and conductive surfaces. Based on various examples of bioelectrochemical studies described in the recent literature, this review discusses the issue of enzyme immobilization at planar electrode interfaces. The fundamental importance of controlling enzyme orientation, how to obtain such orientation, and how it can be verified experimentally or by modeling are the three main directions explored. Since redox enzymes are sizable proteins with anisotropic properties, achieving their functional immobilization requires a specific and controlled orientation on the electrode surface. All the factors influenced by this orientation are described, ranging from electronic conductivity to efficiency of substrate supply. The specificities of the enzymatic molecule, surface properties, and dipole moment, which in turn influence the orientation, are introduced. Various ways of ensuring functional immobilization through tuning of both the enzyme and the electrode surface are then described. Finally, the review deals with analytical techniques that have enabled characterization and quantification of successful achievement of the desired orientation. The rich contributions of electrochemistry, spectroscopy (especially infrared spectroscopy), modeling, and microscopy are featured, along with their limitations.
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20
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Kielb P, Utesch T, Kozuch J, Jeoung JH, Dobbek H, Mroginski MA, Hildebrandt P, Weidinger I. Switchable Redox Chemistry of the Hexameric Tyrosine-Coordinated Heme Protein. J Phys Chem B 2017; 121:3955-3964. [DOI: 10.1021/acs.jpcb.7b01286] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patrycja Kielb
- Institut
für Chemie, Sekr. PC14, Technische Universität Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Tillmann Utesch
- Institut
für Chemie, Sekr. PC14, Technische Universität Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Jacek Kozuch
- Institut
für Chemie, Sekr. PC14, Technische Universität Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany
- Department
of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Jae-Hun Jeoung
- Institute
of Biology, Humboldt Universität Berlin, Philippstrasse
13, D-10115 Berlin, Germany
| | - Holger Dobbek
- Institute
of Biology, Humboldt Universität Berlin, Philippstrasse
13, D-10115 Berlin, Germany
| | - Maria Andrea Mroginski
- Institut
für Chemie, Sekr. PC14, Technische Universität Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Institut
für Chemie, Sekr. PC14, Technische Universität Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Inez Weidinger
- Department
of Chemistry and Food Chemistry, Technische Universität Dresden, Zellescher Weg 19, D-01069 Dresden, Germany
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21
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Gunawan CA, Nam EV, Marquis CP, Gooding JJ, Thordarson P, Zhao C. Scanning Electrochemical Microscopy of Cytochrome
c
Peroxidase through the Orientation‐Controlled Immobilisation of Cytochrome
c. ChemElectroChem 2016. [DOI: 10.1002/celc.201600195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Ekaterina V. Nam
- School of Chemistry The University of New South Wales Sydney 2052 Australia
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, School of Chemistry The University of New South Wales Sydney 2052 Australia
| | - Christopher P. Marquis
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney 2052 Australia
| | - J. Justin Gooding
- School of Chemistry The University of New South Wales Sydney 2052 Australia
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, School of Chemistry The University of New South Wales Sydney 2052 Australia
| | - Pall Thordarson
- School of Chemistry The University of New South Wales Sydney 2052 Australia
- The Australian Centre for Nanomedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, School of Chemistry The University of New South Wales Sydney 2052 Australia
| | - Chuan Zhao
- School of Chemistry The University of New South Wales Sydney 2052 Australia
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22
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Salewski J, Batista AP, Sena FV, Millo D, Zebger I, Pereira MM, Hildebrandt P. Substrate-Protein Interactions of Type II NADH:Quinone Oxidoreductase from Escherichia coli. Biochemistry 2016; 55:2722-34. [PMID: 27109164 DOI: 10.1021/acs.biochem.6b00070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Type II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins involved in respiratory chains and responsible for the maintenance of NADH/NAD(+) balance in cells. NDH-2s are the only enzymes with NADH dehydrogenase activity present in the respiratory chain of many pathogens, and thus, they were proposed as suitable targets for antimicrobial therapies. In addition, NDH-2s were also considered key players for the treatment of complex I-related neurodegenerative disorders. In this work, we explored substrate-protein interaction in NDH-2 from Escherichia coli (EcNDH-2) combining surface-enhanced infrared absorption spectroscopic studies with electrochemical experiments, fluorescence spectroscopy assays, and quantum chemical calculations. Because of the specific stabilization of substrate complexes of EcNDH-2 immobilized on electrodes, it was possible to demonstrate the presence of two distinct substrate binding sites for NADH and the quinone and to identify a bound semiprotonated quinol as a catalytic intermediate.
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Affiliation(s)
- Johannes Salewski
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Ana P Batista
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa , Av. da República EAN, P-2780-157 Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa , Av. da República EAN, P-2780-157 Oeiras, Portugal
| | - Diego Millo
- Biomolecular Spectroscopy/LaserLaB Amsterdam, Vrije Universiteit Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Ingo Zebger
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa , Av. da República EAN, P-2780-157 Oeiras, Portugal
| | - Peter Hildebrandt
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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23
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Zhu G, Chen G, Yu R, Li H, Wang C. Enhanced simultaneous nitrification/denitrification in the biocathode of a microbial fuel cell fed with cyanobacteria solution. Process Biochem 2016. [DOI: 10.1016/j.procbio.2015.11.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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24
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Yoon HJ, Liao KC, Lockett MR, Kwok SW, Baghbanzadeh M, Whitesides GM. Rectification in Tunneling Junctions: 2,2′-Bipyridyl-Terminated n-Alkanethiolates. J Am Chem Soc 2014; 136:17155-62. [DOI: 10.1021/ja509110a] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Hyo Jae Yoon
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Department
of Chemistry, Korea University, Seoul 136-701, Korea
| | - Kung-Ching Liao
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Matthew R. Lockett
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Sen Wai Kwok
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Mostafa Baghbanzadeh
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - George M. Whitesides
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, 60 Oxford Street, Cambridge, Massachusetts 02138, United States
- Kavli Institute for Bionano Science & Technology, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138, United States
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25
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Barba FJ, Grimi N, Vorobiev E. New Approaches for the Use of Non-conventional Cell Disruption Technologies to Extract Potential Food Additives and Nutraceuticals from Microalgae. FOOD ENGINEERING REVIEWS 2014. [DOI: 10.1007/s12393-014-9095-6] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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26
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Effects of external electric fields on lysozyme adsorption by molecular dynamics simulations. Biophys Chem 2013; 179:26-34. [DOI: 10.1016/j.bpc.2013.05.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 04/28/2013] [Accepted: 05/01/2013] [Indexed: 11/23/2022]
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27
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Ly HK, Utesch T, Díaz-Moreno I, García-Heredia JM, De La Rosa MÁ, Hildebrandt P. Perturbation of the Redox Site Structure of Cytochrome c Variants upon Tyrosine Nitration. J Phys Chem B 2012; 116:5694-702. [DOI: 10.1021/jp302301m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- H. Khoa Ly
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße
des 17 Juni 135, D-10623 Berlin, Germany
| | - Tillmann Utesch
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße
des 17 Juni 135, D-10623 Berlin, Germany
| | - Irene Díaz-Moreno
- Instituto de Bioquímica
Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevialla-CSIC, Avda Americo Vespucio 49, Sevilla
41092, Spain
| | - José M. García-Heredia
- Instituto de Bioquímica
Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevialla-CSIC, Avda Americo Vespucio 49, Sevilla
41092, Spain
| | - Miguel Ángel De La Rosa
- Instituto de Bioquímica
Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevialla-CSIC, Avda Americo Vespucio 49, Sevilla
41092, Spain
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße
des 17 Juni 135, D-10623 Berlin, Germany
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28
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Sezer M, Millo D, Weidinger IM, Zebger I, Hildebrandt P. Analyzing the catalytic processes of immobilized redox enzymes by vibrational spectroscopies. IUBMB Life 2012; 64:455-64. [PMID: 22535701 DOI: 10.1002/iub.1020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 02/12/2012] [Indexed: 11/10/2022]
Abstract
Analyzing the structure and function of redox enzymes attached to electrodes is a central challenge in many fields of fundamental and applied life science. Electrochemical techniques such as cyclic voltammetry which are routinely used do not provide insight into the molecular structure and reaction mechanisms of the immobilized proteins. Surface-enhanced infrared absorption (SEIRA) and surface-enhanced resonance Raman (SERR) spectroscopy may fill this gap, if nanostructured Au or Ag are used as conductive support materials. In this account, we will first outline the principles of the methodology including a description of the most important strategies for biocompatible protein immobilization. Subsequently, we will critically review SERR and SEIRA spectroscopic approaches to characterize the protein and active site structure of the immobilized enzymes. Special emphasis is laid on the combination of surface-enhanced vibrational spectroscopies with electrochemical methods to analyze equilibria and dynamics of the interfacial redox processes. Finally, we will assess the potential of SERR and SEIRA spectroscopy for in situ investigations on the basis of the first promising studies on human sulfite oxidase and hydrogenases under turnover conditions.
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Affiliation(s)
- Murat Sezer
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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29
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Simulation of multihaem cytochromes. FEBS Lett 2011; 586:510-8. [DOI: 10.1016/j.febslet.2011.10.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 11/19/2022]
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30
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Salverda J, Patil A, Mizzon G, Kuznetsova S, Zauner G, Akkilic N, Canters G, Davis J, Heering H, Aartsma T. Fluorescent Cyclic Voltammetry of Immobilized Azurin: Direct Observation of Thermodynamic and Kinetic Heterogeneity. Angew Chem Int Ed Engl 2010; 49:5776-9. [DOI: 10.1002/anie.201001298] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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Salverda J, Patil A, Mizzon G, Kuznetsova S, Zauner G, Akkilic N, Canters G, Davis J, Heering H, Aartsma T. Fluorescent Cyclic Voltammetry of Immobilized Azurin: Direct Observation of Thermodynamic and Kinetic Heterogeneity. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001298] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Martins G, Rodrigues L, Cunha FM, Matos D, Hildebrandt P, Murgida DH, Pereira IAC, Todorovic S. Substrate Binding to a Nitrite Reductase Induces a Spin Transition. J Phys Chem B 2010; 114:5563-6. [DOI: 10.1021/jp9118502] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gabriel Martins
- Instituto de Tecnologia Química e Biologica, Universidade Nova de Lisboa, Av Republica (EAN), 2780-157 Oeiras, Portugal, Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany, and Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA Buenos Aires, Argentina
| | - Luisa Rodrigues
- Instituto de Tecnologia Química e Biologica, Universidade Nova de Lisboa, Av Republica (EAN), 2780-157 Oeiras, Portugal, Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany, and Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA Buenos Aires, Argentina
| | - Filipa M. Cunha
- Instituto de Tecnologia Química e Biologica, Universidade Nova de Lisboa, Av Republica (EAN), 2780-157 Oeiras, Portugal, Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany, and Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA Buenos Aires, Argentina
| | - Daniela Matos
- Instituto de Tecnologia Química e Biologica, Universidade Nova de Lisboa, Av Republica (EAN), 2780-157 Oeiras, Portugal, Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany, and Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA Buenos Aires, Argentina
| | - Peter Hildebrandt
- Instituto de Tecnologia Química e Biologica, Universidade Nova de Lisboa, Av Republica (EAN), 2780-157 Oeiras, Portugal, Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany, and Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA Buenos Aires, Argentina
| | - Daniel H. Murgida
- Instituto de Tecnologia Química e Biologica, Universidade Nova de Lisboa, Av Republica (EAN), 2780-157 Oeiras, Portugal, Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany, and Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA Buenos Aires, Argentina
| | - Inês A. C. Pereira
- Instituto de Tecnologia Química e Biologica, Universidade Nova de Lisboa, Av Republica (EAN), 2780-157 Oeiras, Portugal, Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany, and Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA Buenos Aires, Argentina
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biologica, Universidade Nova de Lisboa, Av Republica (EAN), 2780-157 Oeiras, Portugal, Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany, and Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, C1428EHA Buenos Aires, Argentina
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Balland V, Lecomte S, Limoges B. Characterization of the electron transfer of a ferrocene redox probe and a histidine-tagged hemoprotein specifically bound to a nitrilotriacetic-terminated self-assembled monolayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:6532-6542. [PMID: 19419181 DOI: 10.1021/la900062y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report the selective, controlled binding of a model redox probe, 1,1'-bis(N-imidazolylmethyl)ferrocene (Fc-Im2), and a small redox hemoprotein, histidine-tagged recombinant human neuroglobin (hNb), at the surface of metal electrodes (gold and SER-active silver) modified by a self-assembled monolayer (SAM) of a nitrilotriacetic (NTA)-terminated thiol. The resulting SAMs were characterized by cyclic voltammetry and surface-enhanced resonance Raman (SERR) spectroscopy coupled to electrochemistry. Once specifically bounded to the Ni(II)-NTA-modified gold electrode, nearly ideal cyclic voltammetric behavior with relatively fast electron-transfer (ET) communication through the SAM was determined for the Fc-Im2 redox probe. However, no direct electron transfer could be evidenced for the hNb redox protein under the same conditions. This outcome was different from the result obtained during SERR experiments coupled to electrochemistry in which a direct electrochemical conversion of hNb immobilized on a Ni(II)-NTA-modified SER-active Ag electrode was observed. The SERR spectra of the immobilized hNb was the same as the resonance Raman spectra of the protein in homogeneous solution, allowing us to conclude that the native structure of hNb was retained upon immobilization and that the direct ET was not the result of some partial or complete protein denaturation. The long-range ET rate constant (kET) through the SAM was determined by time-resolved SERR spectroscopy. A value of kET=0.12 s(-1) was obtained, which is within the predicted range of a fully nonadiabatic ET through a SAM thickness of approximately 26 A and close to the values previously determined for analogous small redox proteins at similar long-range ET distances. A SERR spectroelectrochemical titration of the immobilized hNb was also carried out, showing both an apparent standard potential (E0') negatively shifted by 100 mV compared with hNb in solution and a gentle slope in the titration curve. These results suggest a range of chemical environments in the surroundings of the redox protein and a variety of interactions with the NTA-terminated SAM. The influence of protein immobilization on E0' is discussed together with the long-range ET rate constant and molecular orientation of the surface-immobilized hNb.
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Affiliation(s)
- Véronique Balland
- Laboratoire d'Electrochimie Moléculaire, Université Paris Diderot, UMR CNRS 7591, Paris Cedex 13, France.
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34
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Microbial denitrification by immobilized bacteria Pseudomonas denitrificans stimulated by constant electric field. Biochem Eng J 2009. [DOI: 10.1016/j.bej.2008.12.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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35
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Todorovic S, Verissimo A, Wisitruangsakul N, Zebger I, Hildebrandt P, Pereira MM, Teixeira M, Murgida DH. SERR-spectroelectrochemical study of a cbb3 oxygen reductase in a biomimetic construct. J Phys Chem B 2009; 112:16952-9. [PMID: 19053671 DOI: 10.1021/jp807862m] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cbb3 oxygen reductase from Bradyrhizobium japonicum was immobilized on nanostructured silver electrodes by anchoring the enzyme via a His-tag to a Ni-NTA coating, followed by reconstitution of a lipid bilayer. The immobilized enzyme retains the native structure and catalytic activity as judged by in situ surface-enhanced vibrational spectroscopy and cyclic voltammetry, respectively. Spectroelectrochemical titrations followed by SERR spectroscopy of the integral enzyme and its monohemic (fixO) and dihemic subunits (fixP), allowed the determination of the reduction potentials for the different heme c groups. Both in the isolated subunits and in the integral enzyme the Met/His-coordinated hemes from the two subunits present identical reduction potentials of 180 mV, whereas for the bis-His heme from fixP the value is ca. 400 mV. The determination of reduction potentials of the individual hemes c reported in this work provides the basis for further exploring the mechanism of electroprotonic energy transduction of this complex enzyme.
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Affiliation(s)
- Smilja Todorovic
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, EAN, 2780-157 Oeiras, Portugal.
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36
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El Ichi S, Marzouki MN, Korri-Youssoufi H. Direct monitoring of pollutants based on an electrochemical biosensor with novel peroxidase (POX1B). Biosens Bioelectron 2009; 24:3084-90. [PMID: 19423328 DOI: 10.1016/j.bios.2009.03.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 03/13/2009] [Accepted: 03/25/2009] [Indexed: 10/20/2022]
Abstract
A biosensor for the monitoring of phenolic compounds based on a new protein named POX(1B) purified from garlic which demonstrates similar biochemical properties to peroxidase is investigated. The enzyme was immobilized into chitosan microspheres with covalent link. The properties of the biosensor were analyzed with Fourier transform-infrared spectroscopy (FT-IR), scanning electron microscopy (SEM) and cyclic voltammetry (CV). FT-IR demonstrates the covalent attachment of POX(1B) into chitosan and SEM shows high dispersion of the POX(1B) into the chitosan microspheres. The redox potential of POX(1B) in chitosan is 147 mV vs. SCE, which is much higher than reported works using HRP, demonstrating excellent direct electrochemical behaviour of the POX(1B). The electrocatalytic activity of the obtained biosensor towards chlorophenols derivatives in a large range from 10 pM to 10 microM was demonstrated. The mediator free POX(1B)-based biosensor exhibited high sensitivity towards 2,6-dichlorophenol, 4-chlorophenol and pentachlorophenol. A detection limit of 1 pM in the case of 4-chlorophenol was demonstrated with kinetic constant K(m,app) of 0.42 microM with high rapidity of electrochemical response of the biosensor of 1 s.
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Affiliation(s)
- Sarra El Ichi
- Equipe de Chimie Bioorganique et Bioinorganique, Institut de Chimie Moléculaire et Matériaux d'Orsay, Université Paris-sud, 91405 Orsay, France
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37
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Ogami S, Hijikata S, Tsukahara T, Mie Y, Matsuno T, Morita N, Hara I, Yamazaki K, Inoue N, Yokota A, Hoshino T, Yoshimune K, Yumoto I. A novel membrane-anchored cytochrome c-550 of alkaliphilic Bacillus clarkii K24-1U: expression, molecular features and properties of redox potential. Extremophiles 2009; 13:491-504. [PMID: 19266156 DOI: 10.1007/s00792-009-0234-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 02/11/2009] [Indexed: 10/21/2022]
Abstract
A membrane-anchored cytochrome c-550, which is highly expressed in obligately alkaliphilic Bacillus clarkii K24-1U, was purified and characterized. The protein contained a conspicuous sequence of Gly(22)-Asn(34), in comparison with the other Bacillus small cytochromes c. Analytical data indicated that the original and lipase-treated intermediate forms of cytochrome c-550 bind to fatty acids of C(15), C(16) and C(17) chain lengths and C(15) chain length, respectively, and it was considered that these fatty acids are bound to glycerol-Cys(18). Since there was a possibility that the presence of a diacylglycerol anchor contributed to the formation of dimeric states of this protein (20 and 17 kDa in SDS-PAGE), a C18M (Cys(18) --> Met)-cytochrome c-550 was constructed. The molecular mass of the C18M-cytochrome c-550 was determined as 15 and 10 kDa in SDS-PAGE and 23 kDa in blue native PAGE. The C18M-cytochrome c-550 bound with or without Triton X-100 formed a tetramer as the original cytochrome c-550 bound with Triton X-100, as determined by gel filtration. The midpoint redox potential of cytochrome c-550 as determined by redox titration was +83 mV, while that determined by cyclic voltammetric measurement was +7 mV. The above results indicate that cytochrome c-550 is a novel cytochrome c.
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Affiliation(s)
- Shinichi Ogami
- Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517, Japan
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38
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Zuo P, Albrecht T, Barker PD, Murgida DH, Hildebrandt P. Interfacial redox processes of cytochrome b562. Phys Chem Chem Phys 2009; 11:7430-6. [DOI: 10.1039/b904926f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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39
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Léger C, Bertrand P. Direct Electrochemistry of Redox Enzymes as a Tool for Mechanistic Studies. Chem Rev 2008; 108:2379-438. [DOI: 10.1021/cr0680742] [Citation(s) in RCA: 594] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Basova LV, Tiktopulo EI, Kutyshenko VP, Mauk AG, Bychkova VE. Phospholipid membranes affect tertiary structure of the soluble cytochrome b5 heme-binding domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:1015-26. [PMID: 18275841 DOI: 10.1016/j.bbamem.2007.12.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Revised: 12/21/2007] [Accepted: 12/28/2007] [Indexed: 11/30/2022]
Abstract
The influence of charged phospholipid membranes on the conformational state of the water-soluble fragment of cytochrome b5 has been investigated by a variety of techniques at neutral pH. The results of this work provide the first evidence that aqueous solutions with high phospholipid/protein molar ratios (pH 7.2) induce the cytochrome to undergo a structural transition from the native conformation to an intermediate state with molten-globule like properties that occur in the presence of an artificial membrane surface and that leads to binding of the protein to the membrane. At other phospholipid/protein ratios, equilibrium was observed between cytochrome free in solution and cytochrome bound to the surface of vesicles. Inhibition of protein binding to the vesicles with increasing ionic strength indicated for the most part an electrostatic contribution to the stability of cytochrome b5-vesicle interactions at pH 7.2. The possible physiological role of membrane-induced conformational change in the structure of cytochrome b5 upon the interaction with its redox partners is discussed.
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Affiliation(s)
- Liana V Basova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia
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41
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Murgida DH, Hildebrandt P. Disentangling interfacial redox processes of proteins by SERR spectroscopy. Chem Soc Rev 2008; 37:937-45. [DOI: 10.1039/b705976k] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Bonifacio A, Millo D, Keizers PHJ, Boegschoten R, Commandeur JNM, Vermeulen NPE, Gooijer C, van der Zwan G. Active-site structure, binding and redox activity of the heme-thiolate enzyme CYP2D6 immobilized on coated Ag electrodes: a surface-enhanced resonance Raman scattering study. J Biol Inorg Chem 2008; 13:85-96. [PMID: 17899220 PMCID: PMC2099460 DOI: 10.1007/s00775-007-0303-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 09/08/2007] [Indexed: 11/28/2022]
Abstract
Surface-enhance resonance Raman scattering spectra of the heme-thiolate enzyme cytochrome P450 2D6 (CYP2D6) adsorbed on Ag electrodes coated with 11-mercaptoundecanoic acid (MUA) were obtained in various experimental conditions. An analysis of these spectra, and a comparison between them and the RR spectra of CYP2D6 in solution, indicated that the enzyme's active site retained its nature of six-coordinated low-spin heme upon immobilization. Moreover, the spectral changes detected in the presence of dextromethorphan (a CYP2D6 substrate) and imidazole (an exogenous heme axial ligand) indicated that the immobilized enzyme also preserved its ability to reversibly bind a substrate and form a heme-imidazole complex. The reversibility of these processes could be easily verified by flowing alternately solutions of the various compounds and the buffer through a home-built spectroelectrochemical flow cell which contained a sample of immobilized protein, without the need to disassemble the cell between consecutive spectral data acquisitions. Despite immobilized CYP2D6 being effectively reduced by a sodium dithionite solution, electrochemical reduction via the Ag electrode was not able to completely reduce the enzyme, and led to its extensive inactivation. This behavior indicated that although the enzyme's ability to exchange electrons is not altered by immobilization per se, MUA-coated electrodes are not suited to perform direct electrochemistry of CYP2D6.
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Affiliation(s)
- Alois Bonifacio
- Analytical Chemistry and Applied Spectroscopy, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Diego Millo
- Analytical Chemistry and Applied Spectroscopy, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Peter H. J. Keizers
- Molecular Toxicology, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Roald Boegschoten
- Mechanical Workshop, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Jan N. M. Commandeur
- Molecular Toxicology, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Nico P. E. Vermeulen
- Molecular Toxicology, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Cees Gooijer
- Analytical Chemistry and Applied Spectroscopy, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Gert van der Zwan
- Analytical Chemistry and Applied Spectroscopy, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
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43
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Electrochemical Behavior of Redox Proteins Immobilized on Nafion-Riboflavin Modified Gold Electrode. B KOREAN CHEM SOC 2007. [DOI: 10.5012/bkcs.2007.28.12.2266] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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44
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Tourmaline ceramic balls stimulate growth and metabolism of three fermentation microorganisms. World J Microbiol Biotechnol 2007. [DOI: 10.1007/s11274-007-9529-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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45
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Yu Q, Golden G. Probing the protein orientation on charged self-assembled monolayers on gold nanohole arrays by SERS. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:8659-62. [PMID: 17629308 DOI: 10.1021/la7007073] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In this work, surface-enhanced Raman scattering (SERS) was applied to probe the orientation of cytochrome c (Cyt-c) on gold nanohole arrays functionalized with self-assembled monolayers (SAMs) of alkane thiols with positively (-NH2) and negatively (-COOH) charged terminal groups. Square grid gold nanohole arrays with a nanohole diameter of 270 nm and a grating of 350 nm were fabricated by electron beam lithography (EBL) and were used as the SERS substrates. The SERS intensities of the nontotally symmetric mode (B(1g) mode nu(11)) and the totally symmetric mode (A(1g) mode nu(4)) and their ratios were used to determine the orientation of Cyt-c on surfaces. The results indicate that the heme group is close and perpendicular to the negatively charged surface but is far from and oriented at an angle to the positively charged surface. Cyt-c has a random or more flat orientation on the bare Au nanoholes surface.
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Affiliation(s)
- Qiuming Yu
- Department of Chemical Engineering, Center for Nanotechnology, University of Washington, Seattle, Washington 98195, USA.
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46
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Paquete CM, Turner DL, Louro RO, Xavier AV, Catarino T. Thermodynamic and kinetic characterisation of individual haems in multicentre cytochromes c3. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:1169-79. [PMID: 17692816 DOI: 10.1016/j.bbabio.2007.06.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 06/25/2007] [Indexed: 11/27/2022]
Abstract
The characterisation of individual centres in multihaem proteins is difficult due to the similarities in the redox and spectroscopic properties of the centres. NMR has been used successfully to distinguish redox centres and allow the determination of the microscopic thermodynamic parameters in several multihaem cytochromes c(3) isolated from different sulphate-reducing bacteria. In this article we show that it is also possible to discriminate the kinetic properties of individual centres in multihaem proteins, if the complete microscopic thermodynamic characterisation is available and the system displays fast intramolecular equilibration in the time scale of the kinetic experiment. The deconvolution of the kinetic traces using a model of thermodynamic control provides a reference rate constant for each haem that does not depend on driving force and can be related to structural factors. The thermodynamic characterisation of three tetrahaem cytochromes and their kinetics of reduction by sodium dithionite are reported in this paper. Thermodynamic and kinetic data were fitted simultaneously to a model to obtain microscopic reduction potentials, haem-haem and haem-proton interacting potentials, and reference rate constants for the haems. The kinetic information obtained for these cytochromes and recently published data for other multihaem cytochromes is discussed with respect to the structural factors that determine the reference rates. The accessibility for the reducing agent seems to play an important role in controlling the kinetic rates, although is clearly not the only factor.
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Affiliation(s)
- Catarina M Paquete
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6, Apt. 127, 2780-156 Oeiras, Portugal
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47
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Bonifacio A, Keizers PHJ, Vermeulen NPE, Commandeur JNM, Gooijer C, van der Zwan G. Surface-enhanced resonance Raman scattering of cytochrome P450-2D6 on coated silver hydrosols. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:1860-6. [PMID: 17279667 DOI: 10.1021/la062525w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Surface-enhanced resonance Raman scattering (SERRS) from dilute solutions (down to nanomolar concentrations) of human mono-oxygenase CYP2D6 is observed using aqueous dispersions of Ag nanoparticles (hydrosol) coated with self-assembled monolayers (SAMs) of mercaptoalkanoic acids of two different lengths. From a direct comparison with its resonance Raman spectrum in solution, CYP2D6 appears to fully retain its native structure upon adsorption on coated hydrosol through electrostatic interaction, while a structural change in the active site is observed when uncoated citrate-reduced hydrosol is used. Using SERRS on these biocompatible coated hydrosols, the effects of dextromethorphan on the enzyme's active site can be observed, demonstrating that CYP2D6 ability of binding substrates is preserved. Moreover, by tuning the wavelength of the exciting laser away from the main absorption band of the heme, the vibrational bands of the SAM coating are observed and analyzed to see how the presence of the protein affects the SAM structure.
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Affiliation(s)
- Alois Bonifacio
- Laser Centre/Analytical Chemistry and Applied Spectroscopy, and LACDR/Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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48
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De Biase PM, Doctorovich F, Murgida DH, Estrin DA. Electric field effects on the reactivity of heme model systems. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2006.11.104] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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49
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Gomes I, Di RE, Pereira PM, Pereira IAC, Saraiva LM, Penadés S, Franco R. Spectroelectrochemistry of type II cytochrome c3 on a glycosylated self-assembled monolayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:9809-11. [PMID: 17106964 DOI: 10.1021/la061392b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A modified silver electrode was prepared by the self-assembly of a thiol-derivatized neoglycoconjugate, forming a 2D surface with maltose functionality. This self-assembled-monolayer-modified electrode was utilized for adsorption and spectroelectrochemical studies of tetraheme-containing type II cytochrome c3. The glycosylated surface allowed for the determination of the hemes' redox potentials and demonstrated enhanced spectroelectrochemical performance, in comparison to the widely used self-assembled monolayer of 11-mercapto-undecanoic acid.
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Affiliation(s)
- Inês Gomes
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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50
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Louro RO. Proton thrusters: overview of the structural and functional features of soluble tetrahaem cytochromes c 3. J Biol Inorg Chem 2006; 12:1-10. [PMID: 16964504 DOI: 10.1007/s00775-006-0165-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2006] [Accepted: 08/21/2006] [Indexed: 10/24/2022]
Abstract
Tetrahaem cytochromes c (3) from sulfate-reducing bacteria have revealed exquisite complexity in their ligand binding properties and they couple the cooperative binding of two electrons with the binding of protons. In this review, the molecular mechanisms for these cooperative effects are described, and the functional consequences of these cooperativities are discussed in the context of the general mechanisms of biological energy transduction and the specific physiological metabolism of Desulfovibrio.
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Affiliation(s)
- Ricardo O Louro
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.
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