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Wohlwend D, Mérono L, Bucka S, Ritter K, Jessen HJ, Friedrich T. Structures of 3-acetylpyridine adenine dinucleotide and ADP-ribose bound to the electron input module of respiratory complex I. Structure 2024:S0969-2126(24)00052-2. [PMID: 38503292 DOI: 10.1016/j.str.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/06/2024] [Accepted: 02/21/2024] [Indexed: 03/21/2024]
Abstract
Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is a major enzyme of energy metabolism that couples NADH oxidation and ubiquinone reduction with proton translocation. The NADH oxidation site features different enzymatic activities with various nucleotides. While the kinetics of these reactions are well described, only binding of NAD+ and NADH have been structurally characterized. Here, we report the structures of the electron input module of Aquifex aeolicus complex I with bound ADP-ribose and 3-acetylpyridine adenine dinucleotides at resolutions better than 2.0 Å. ADP-ribose acts as inhibitor by blocking the "ADP-handle" motif essential for nucleotide binding. The pyridine group of APADH is minimally offset from flavin, which could contribute to its poorer suitability as substrate. A comparison with other nucleotide co-structures surprisingly shows that the adenine ribose and the pyrophosphate moiety contribute most to nucleotide binding, thus all adenine dinucleotides share core binding modes to the unique Rossmann-fold in complex I.
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Affiliation(s)
- Daniel Wohlwend
- Institute of Biochemistry, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Luca Mérono
- Institute of Biochemistry, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Sarah Bucka
- Institute of Biochemistry, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Kevin Ritter
- Institute of Organic Chemistry, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Thorsten Friedrich
- Institute of Biochemistry, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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2
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Ilicic K, Dollinger G, Dombrowsky A, Greubel C, Girst S, Sammer M, Siebenwirth C, Schmid E, Friedrich T, Kundrát P, Friedland W, Scholz M, Combs SE, Schmid TE, Reindl J. Enhanced RBE of Particle Radiation Depends on Beam Size in the Micrometer Range. Radiat Res 2024; 201:140-149. [PMID: 38214379 DOI: 10.1667/rade-23-00217.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024]
Abstract
High-linear energy transfer (LET) radiation, such as heavy ions is associated with a higher relative biological effectiveness (RBE) than low-LET radiation, such as photons. Irradiation with low- and high-LET particles differ in the interaction with the cellular matter and therefore in the spatial dose distribution. When a single high-LET particle interacts with matter, it results in doses of up to thousands of gray (Gy) locally concentrated around the ion trajectory, whereas the mean dose averaged over the target, such as a cell nucleus is only in the range of a Gy. DNA damage therefore accumulates in this small volume. In contrast, up to hundreds of low-LET particle hits are required to achieve the same mean dose, resulting in a quasi-homogeneous damage distribution throughout the cell nucleus. In this study, we investigated the dependence of RBE from different spatial dose depositions using different focused beam spot sizes of proton radiation with respect to the induction of chromosome aberrations and clonogenic cell survival. Human-hamster hybrid (AL) as well as Chinese hamster ovary cells (CHO-K1) were irradiated with focused low LET protons of 20 MeV (LET = 2.6 keV/µm) beam energy with a mean dose of 1.7 Gy in a quadratic matrix pattern with point spacing of 5.4 × 5.4 µm2 and 117 protons per matrix point at the ion microbeam SNAKE using different beam spot sizes between 0.8 µm and 2.8 µm (full width at half maximum). The dose-response curves of X-ray reference radiation were used to determine the RBE after a 1.7 Gy dose of radiation. The RBE for the induction of dicentric chromosomes and cell inactivation was increased after irradiation with the smallest beam spot diameter (0.8 µm for chromosome aberration experiments and 1.0 µm for cell survival experiments) compared to homogeneous proton radiation but was still below the RBE of a corresponding high LET single ion hit. By increasing the spot size to 1.6-1.8 µm, the RBE decreased but was still higher than for homogeneously distributed protons. By further increasing the spot size to 2.7-2.8 µm, the RBE was no longer different from the homogeneous radiation. Our experiments demonstrate that varying spot size of low-LET radiation gradually modifies the RBE. This underlines that a substantial fraction of enhanced RBE originates from inhomogeneous energy concentrations on the µm scale (mean intertrack distances of low-LET particles below 0.1 µm) and quantifies the link between such energy concentration and RBE. The missing fraction of RBE enhancement when comparing with high-LET ions is attributed to the high inner track energy deposition on the nanometer scale. The results are compared with model results of PARTRAC and LEM for chromosomal aberration and cell survival, respectively, which suggest mechanistic interpretations of the observed radiation effects.
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Affiliation(s)
- K Ilicic
- Institute of Radiation Medicine (IRM), Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Radiation Oncology, School of Medicine, Technische Universität München, Germany
| | - G Dollinger
- Institute for Applied Physics and Measurement Technology, Universität der Bundeswehr München, Neubiberg, Germany
| | - A Dombrowsky
- Institute of Radiation Medicine (IRM), Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Radiation Oncology, School of Medicine, Technische Universität München, Germany
| | - C Greubel
- Institute for Applied Physics and Measurement Technology, Universität der Bundeswehr München, Neubiberg, Germany
| | - S Girst
- Institute for Applied Physics and Measurement Technology, Universität der Bundeswehr München, Neubiberg, Germany
| | - M Sammer
- Institute for Applied Physics and Measurement Technology, Universität der Bundeswehr München, Neubiberg, Germany
| | - C Siebenwirth
- Department of Radiation Oncology, School of Medicine, Technische Universität München, Germany
- Institute for Applied Physics and Measurement Technology, Universität der Bundeswehr München, Neubiberg, Germany
| | - E Schmid
- Department for Anatomy and Cell Biology, Ludwig-Maximilians Universität München, Germany
| | - T Friedrich
- GSI Helmholtz Center for Heavy Ion Research, Department of Biophysics, Darmstadt, Germany
| | - P Kundrát
- GSI Helmholtz Center for Heavy Ion Research, Department of Biophysics, Darmstadt, Germany
| | - W Friedland
- Institute of Radiation Medicine (IRM), Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - M Scholz
- GSI Helmholtz Center for Heavy Ion Research, Department of Biophysics, Darmstadt, Germany
| | - S E Combs
- Institute of Radiation Medicine (IRM), Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Radiation Oncology, School of Medicine, Technische Universität München, Germany
| | - T E Schmid
- Institute of Radiation Medicine (IRM), Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Radiation Oncology, School of Medicine, Technische Universität München, Germany
| | - J Reindl
- Institute for Applied Physics and Measurement Technology, Universität der Bundeswehr München, Neubiberg, Germany
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3
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Friedrich T, Pfuhl T, Scholz M. Spectral composition of secondary electrons based on the Kiefer-Straaten ion track structure model. Phys Med Biol 2024; 69:025013. [PMID: 38118162 DOI: 10.1088/1361-6560/ad1765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 12/20/2023] [Indexed: 12/22/2023]
Abstract
The major part of energy deposition of ionizing radiation is caused by secondary electrons, independent of the primary radiation type. However, their spatial concentration and their spectral properties strongly depend on the primary radiation type and finally determine the pattern of molecular damage e.g. to biological targets as the DNA, and thus the final effect of the radiation exposure. To describe the physical and to predict the biological consequences of charged ion irradiation, amorphous track structure approaches have proven to be pragmatic and helpful. There, the local dose deposition in the ion track is equated by considering the emission and slowing down of the secondary electrons from the primary particle track. In the present work we exploit the model of Kiefer and Straaten and derive the spectral composition of secondary electrons as function of the distance to the track center. The spectral composition indicates differences to spectra of low linear energy transfer (LET) photon radiation, which we confirm by a comparison with Monte Carlo studies. We demonstrate that the amorphous track structure approach provides a simple tool for evaluating the spectral electron properties within the track structure. Predictions of the LET of electrons across the track structure as well as the electronic dose build-up effect are derived. Implications for biological effects and corresponding predicting models based on amorphous track structure are discussed.
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Affiliation(s)
- T Friedrich
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstraße 1, D-64291 Darmstadt, Germany
| | - T Pfuhl
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstraße 1, D-64291 Darmstadt, Germany
| | - M Scholz
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstraße 1, D-64291 Darmstadt, Germany
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4
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Fix I, Heidinger L, Friedrich T, Layer G. The Radical SAM Heme Synthase AhbD from Methanosarcina barkeri Contains Two Auxiliary [4Fe-4S] Clusters. Biomolecules 2023; 13:1268. [PMID: 37627333 PMCID: PMC10452713 DOI: 10.3390/biom13081268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/11/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
In archaea and sulfate-reducing bacteria, heme is synthesized via the siroheme-dependent pathway. The last step of this route is catalyzed by the Radical SAM enzyme AhbD and consists of the conversion of iron-coproporphyrin III into heme. AhbD belongs to the subfamily of Radical SAM enzymes containing a SPASM/Twitch domain carrying either one or two auxiliary iron-sulfur clusters in addition to the characteristic Radical SAM cluster. In previous studies, AhbD was reported to contain one auxiliary [4Fe-4S] cluster. In this study, the amino acid sequence motifs containing conserved cysteine residues in AhbD proteins from different archaea and sulfate-reducing bacteria were reanalyzed. Amino acid sequence alignments and computational structural models of AhbD suggested that a subset of AhbD proteins possesses the full SPASM motif and might contain two auxiliary iron-sulfur clusters (AuxI and AuxII). Therefore, the cluster content of AhbD from Methanosarcina barkeri was studied using enzyme variants lacking individual clusters. The purified enzymes were analyzed using UV/Visible absorption and EPR spectroscopy as well as iron/sulfide determinations showing that AhbD from M. barkeri contains two auxiliary [4Fe-4S] clusters. Heme synthase activity assays suggested that the AuxI cluster might be involved in binding the reaction intermediate and both clusters potentially participate in electron transfer.
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Affiliation(s)
- Isabelle Fix
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 19, 79104 Freiburg, Germany
| | - Lorenz Heidinger
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (L.H.); (T.F.)
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (L.H.); (T.F.)
| | - Gunhild Layer
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 19, 79104 Freiburg, Germany
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5
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Kägi J, Sloan W, Schimpf J, Nasiri HR, Lashley D, Friedrich T. Exploring ND-011992, a quinazoline-type inhibitor targeting quinone reductases and quinol oxidases. Sci Rep 2023; 13:12226. [PMID: 37507428 PMCID: PMC10382516 DOI: 10.1038/s41598-023-39430-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023] Open
Abstract
Bacterial energy metabolism has become a promising target for next-generation tuberculosis chemotherapy. One strategy to hamper ATP production is to inhibit the respiratory oxidases. The respiratory chain of Mycobacterium tuberculosis comprises a cytochrome bcc:aa3 and a cytochrome bd ubiquinol oxidase that require a combined approach to block their activity. A quinazoline-type compound called ND-011992 has previously been reported to ineffectively inhibit bd oxidases, but to act bactericidal in combination with inhibitors of cytochrome bcc:aa3 oxidase. Due to the structural similarity of ND-011992 to quinazoline-type inhibitors of respiratory complex I, we suspected that this compound is also capable of blocking other respiratory chain complexes. Here, we synthesized ND-011992 and a bromine derivative to study their effect on the respiratory chain complexes of Escherichia coli. And indeed, ND-011992 was found to inhibit respiratory complex I and bo3 oxidase in addition to bd-I and bd-II oxidases. The IC50 values are all in the low micromolar range, with inhibition of complex I providing the lowest value with an IC50 of 0.12 µM. Thus, ND-011992 acts on both, quinone reductases and quinol oxidases and could be very well suited to regulate the activity of the entire respiratory chain.
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Affiliation(s)
- Jan Kägi
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Willough Sloan
- Department of Chemistry, William & Mary, Williamsburg, VA, USA
| | - Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Hamid R Nasiri
- Department of Cellular Microbiology, University Hohenheim, Stuttgart, Germany
| | - Dana Lashley
- Department of Chemistry, William & Mary, Williamsburg, VA, USA.
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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Makarchuk I, Gerasimova T, Kägi J, Wohlwend D, Melin F, Friedrich T, Hellwig P. Mutating the environment of heme b 595 of E. coli cytochrome bd-I oxidase shifts its redox potential by 200 mV without inactivating the enzyme. Bioelectrochemistry 2023; 151:108379. [PMID: 36736178 DOI: 10.1016/j.bioelechem.2023.108379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/11/2023] [Accepted: 01/22/2023] [Indexed: 01/31/2023]
Abstract
Cytochrome bd-I catalyzes the reduction of oxygen to water with the aid of hemes b558, b595 and d. Here, effects of a mutation of E445, a ligand of heme b595 and of R448, hydrogen bonded to E445 are studied electrochemically in the E. coli enzyme. The equilibrium potential of the three hemes are shifted by up to 200 mV in these mutants. Strikingly the E445D and the R448N mutants show a turnover of 41 ± 2 % and 20 ± 4 %, respectively. Electrocatalytic studies confirm that the mutants react with oxygen and bind and release NO. These results point towards the ability of cytochrome bd to react even if the electron transfer is less favorable.
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Affiliation(s)
- Iryna Makarchuk
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Tatjana Gerasimova
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Jan Kägi
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Daniel Wohlwend
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Frédéric Melin
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Thorsten Friedrich
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany.
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7
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Strotmann L, Harter C, Gerasimova T, Ritter K, Jessen HJ, Wohlwend D, Friedrich T. H 2O 2 selectively damages the binuclear iron-sulfur cluster N1b of respiratory complex I. Sci Rep 2023; 13:7652. [PMID: 37169846 PMCID: PMC10175503 DOI: 10.1038/s41598-023-34821-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023] Open
Abstract
NADH:ubiquinone oxidoreductase, respiratory complex I, plays a major role in cellular energy metabolism by coupling electron transfer with proton translocation. Electron transfer is catalyzed by a flavin mononucleotide and a series of iron-sulfur (Fe/S) clusters. As a by-product of the reaction, the reduced flavin generates reactive oxygen species (ROS). It was suggested that the ROS generated by the respiratory chain in general could damage the Fe/S clusters of the complex. Here, we show that the binuclear Fe/S cluster N1b is specifically damaged by H2O2, however, only at high concentrations. But under the same conditions, the activity of the complex is hardly affected, since N1b can be easily bypassed during electron transfer.
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Affiliation(s)
- Lisa Strotmann
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Caroline Harter
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Tatjana Gerasimova
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Kevin Ritter
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Henning J Jessen
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany.
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8
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Makarchuk I, Kägi J, Gerasimova T, Wohlwend D, Friedrich T, Melin F, Hellwig P. pH-dependent kinetics of NO release from E. coli bd-I and bd-II oxidase reveals involvement of Asp/Glu58 B. Biochim Biophys Acta Bioenerg 2023; 1864:148952. [PMID: 36535430 DOI: 10.1016/j.bbabio.2022.148952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Escherichia coli contains two cytochrome bd oxidases, bd-I and bd-II. The structure of both enzymes is highly similar, but they exhibit subtle differences such as the accessibility of the active site through a putative proton channel. Here, we demonstrate that the duroquinol:dioxygen oxidoreductase activity of bd-I increased with alkaline pH, whereas bd-II showed a broad activity maximum around pH 7. Likewise, the pH dependence of NO release from the reduced active site, an essential property of bd oxidases, differed between the two oxidases as detected by UV/vis spectroscopy. Both findings may be attributed to differences in the proton channel leading to the active site heme d. The channel comprises a titratable residue (Asp58B in bd-I and Glu58B in bd-II). Conservative mutations at this position drastically altered NO release demonstrating its contribution to the process.
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Affiliation(s)
- Iryna Makarchuk
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France
| | - Jan Kägi
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Tatjana Gerasimova
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Frédéric Melin
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France.
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9
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Friedrich T, Stengel A. Current state of phoenixin-the implications of the pleiotropic peptide in stress and its potential as a therapeutic target. Front Pharmacol 2023; 14:1076800. [PMID: 36860304 PMCID: PMC9968724 DOI: 10.3389/fphar.2023.1076800] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/04/2023] [Indexed: 02/15/2023] Open
Abstract
Phoenixin is a pleiotropic peptide, whose known functions have broadened significantly over the last decade. Initially first described as a reproductive peptide in 2013, phoenixin is now recognized as being implicated in hypertension, neuroinflammation, pruritus, food intake, anxiety as well as stress. Due to its wide field of involvement, an interaction with physiological as well as psychological control loops has been speculated. It has shown to be both able to actively reduce anxiety as well as being influenced by external stressors. Initial rodent models have shown that central administration of phoenixin alters the behavior of the subjects when confronted with stress-inducing situations, proposing an interaction with the perception and processing of stress and anxiety. Although the research on phoenixin is still in its infancy, there are several promising insights into its functionality, which might prove to be of value in the pharmacological treatment of several psychiatric and psychosomatic illnesses such as anorexia nervosa, post-traumatic stress disorder as well as the increasingly prevalent stress-related illnesses of burnout and depression. In this review, we aim to provide an overview of the current state of knowledge of phoenixin, its interactions with physiological processes as well as focus on the recent developments in stress response and the possible novel treatment options this might entail.
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Affiliation(s)
- T. Friedrich
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - A. Stengel
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany,Department of Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Tübingen, Germany,*Correspondence: A. Stengel,
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10
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Oppermann S, Seng K, Shweich L, Friedrich T. The gene order in the nuo-operon is not essential for the assembly of E. coli complex I. Biochim Biophys Acta Bioenerg 2022; 1863:148592. [PMID: 35863511 DOI: 10.1016/j.bbabio.2022.148592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/25/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Energy-converting NADH: ubiquinone oxidoreductase, respiratory complex I, plays an important role in cellular energy metabolism. Bacterial complex I is generally composed of 14 different subunits, seven of which are membranous and the other seven are globular proteins. They are encoded by the nuo-operon, whose gene order is strictly conserved in bacteria. The operon starts with nuoA encoding a membranous subunit followed by genes encoding globular subunits. To test the idea that NuoA acts as a seed to initiate the assembly of the complex in the membrane, we generated mutants that either lacked nuoA or contain nuoA at a different position within the operon. To enable the detection of putative assembly intermediates, the globular subunit NuoF and the membranous subunit NuoM were individually decorated with the fluorescent protein mCherry. Deletion of nuoA led to the assembly of an inactive complex in the membrane containing NuoF and NuoM. Re-arrangement of nuoA within the nuo-operon led to a slightly diminished amount of complex I in the membrane that was fully active. Thus, nuoA but not its distinct position in the operon is required for the assembly of E. coli complex I. Furthermore, we detected a previously unknown assembly intermediate in the membrane containing NuoM that is present in greater amounts than complex I.
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Affiliation(s)
- S Oppermann
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - K Seng
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - L Shweich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - T Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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11
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Kägi J, Makarchuk I, Wohlwend D, Melin F, Friedrich T, Hellwig P. E. coli cytochrome bd-I requires Asp58 in the CydB subunit for catalytic activity. FEBS Lett 2022; 596:2418-2424. [PMID: 36029102 DOI: 10.1002/1873-3468.14482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 11/07/2022]
Abstract
The reduction of oxygen to water is crucial to life and a central metabolic process. To fulfill this task, prokaryotes use among other enzymes cytochrome bd oxidases (Cyt bds) that also play an important role in bacterial virulence and antibiotic resistance. To fight microbial infections by pathogens, an in-depth understanding of the enzyme mechanism is required. Here, we combine bioinformatics, mutagenesis, enzyme kinetics and FTIR spectroscopy to demonstrate that proton delivery to the active site contributes to the rate limiting steps in Cyt bd-I and involves Asp58 of subunit CydB. Our findings reveal a previously unknown catalytic function of subunit CydB in the reaction of Cyt bd-I.
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Affiliation(s)
- Jan Kägi
- Institut für Biochemie, Albert-Ludwigs-Universität, Albertstr 21, 79104, Freiburg, Germany
| | - Iryna Makarchuk
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS 4, Rue Blaise Pascal, 67081, Strasbourg, France
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität, Albertstr 21, 79104, Freiburg, Germany
| | - Frédéric Melin
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS 4, Rue Blaise Pascal, 67081, Strasbourg, France
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität, Albertstr 21, 79104, Freiburg, Germany
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS 4, Rue Blaise Pascal, 67081, Strasbourg, France
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12
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Gagsteiger J, Jahn S, Heidinger L, Gericke L, Andexer JN, Friedrich T, Loenarz C, Layer G. A Cobalamin-Dependent Radical SAM Enzyme Catalyzes the Unique C α -Methylation of Glutamine in Methyl-Coenzyme M Reductase. Angew Chem Int Ed Engl 2022; 61:e202204198. [PMID: 35638156 PMCID: PMC9401015 DOI: 10.1002/anie.202204198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Indexed: 12/22/2022]
Abstract
Methyl‐coenzyme M reductase, which is responsible for the production of the greenhouse gas methane during biological methane formation, carries several unique posttranslational amino acid modifications, including a 2‐(S)‐methylglutamine. The enzyme responsible for the Cα‐methylation of this glutamine is not known. Herein, we identify and characterize a cobalamin‐dependent radical SAM enzyme as the glutamine C‐methyltransferase. The recombinant protein from Methanoculleus thermophilus binds cobalamin in a base‐off, His‐off conformation and contains a single [4Fe‐4S] cluster. The cobalamin cofactor cycles between the methyl‐cob(III)alamin, cob(II)alamin and cob(I)alamin states during catalysis and produces methylated substrate, 5′‐deoxyadenosine and S‐adenosyl‐l‐homocysteine in a 1 : 1 : 1 ratio. The newly identified glutamine C‐methyltransferase belongs to the class B radical SAM methyltransferases known to catalyze challenging methylation reactions of sp3‐hybridized carbon atoms.
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Affiliation(s)
- Jana Gagsteiger
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany
| | - Sören Jahn
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Lorenz Heidinger
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Lukas Gericke
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Jennifer N Andexer
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Christoph Loenarz
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Gunhild Layer
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany
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13
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Wegner F, Schwenke H, von Gladiß A, Behrends A, Friedrich T, Lüdtke-Buzug K, Neumann A, Barkhausen J, Buzug MT, Bakenecker CA. Steuerung und Visualisierung eines endovaskulären Mikroroboters mittels Magnetic Particle Imaging. ROFO-FORTSCHR RONTG 2022. [DOI: 10.1055/s-0042-1749779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- F Wegner
- UKSH, Campus Lübeck, Klinik f. Radiologie u. Nuklearmedizin, Lübeck
| | - H Schwenke
- Institut für Neuroradiologie, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck
| | - A von Gladiß
- Institut für Computervisualistik, Universität Koblenz-Landau, Koblenz
| | - A Behrends
- Fraunhofer Einrichtung für Individualisierte und Zell-basierte Medizintechnik, Lübeck
| | - T Friedrich
- Fraunhofer Einrichtung für Individualisierte und Zell-basierte Medizintechnik, Lübeck
| | | | | | - J Barkhausen
- Klinik für Radiologie und Nuklearmedizin, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck
| | - M T Buzug
- Fraunhofer Einrichtung für Individualisierte und Zell-basierte Medizintechnik, Lübeck
| | - C A Bakenecker
- Fraunhofer Einrichtung für Individualisierte und Zell-basierte Medizintechnik, Lübeck
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14
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Grzyska U, Friedrich T, Haegele J, Buzug MT, Barkhausen J, Wegner F. Sicherheit eines neuen Stentdesigns hinsichtlich der Erwärmung in Magnetic Particle Imaging und Magnetresonanztomographie. ROFO-FORTSCHR RONTG 2022. [DOI: 10.1055/s-0042-1749780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- U Grzyska
- UKSH – Campus Lübeck, Klinik f. Radiologie u. Nuklearmedizin, Lübeck
| | - T Friedrich
- Fraunhofer Einrichtung für Individualisierte und Zell-basierte Medizintechnik, Lübeck
| | - J Haegele
- Zentrum für Radiologie und Nuklearmedizin Rheinland, Dormagen
| | - M T Buzug
- Fraunhofer Einrichtung für Individualisierte und Zell-basierte Medizintechnik, Lübeck
| | - J Barkhausen
- Klinik für Radiologie und Nuklearmedizin, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck
| | - F Wegner
- Klinik für Radiologie und Nuklearmedizin, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck
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15
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Gagsteiger J, Jahn S, Heidinger L, Gericke L, Andexer JN, Friedrich T, Loenarz C, Layer G. A Cobalamin‐Dependent Radical SAM Enzyme Catalyzes the Unique Cα‐Methylation of Glutamine in Methyl‐Coenzyme M Reductase. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jana Gagsteiger
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie GERMANY
| | - Sören Jahn
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie GERMANY
| | - Lorenz Heidinger
- Albert-Ludwigs-Universität Freiburg Institut für Biochemie GERMANY
| | - Lukas Gericke
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie GERMANY
| | - Jennifer N. Andexer
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie GERMANY
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Biochemie GERMANY
| | - Christoph Loenarz
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie GERMANY
| | - Gunhild Layer
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie Stefan-Meier-Str. 19 79104 Freiburg GERMANY
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16
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Friedrich T, Wohlwend D, Borisov VB. Recent Advances in Structural Studies of Cytochrome bd and Its Potential Application as a Drug Target. Int J Mol Sci 2022; 23:ijms23063166. [PMID: 35328590 PMCID: PMC8951039 DOI: 10.3390/ijms23063166] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 02/06/2023] Open
Abstract
Cytochrome bd is a triheme copper-free terminal oxidase in membrane respiratory chains of prokaryotes. This unique molecular machine couples electron transfer from quinol to O2 with the generation of a proton motive force without proton pumping. Apart from energy conservation, the bd enzyme plays an additional key role in the microbial cell, being involved in the response to different environmental stressors. Cytochrome bd promotes virulence in a number of pathogenic species that makes it a suitable molecular drug target candidate. This review focuses on recent advances in understanding the structure of cytochrome bd and the development of its selective inhibitors.
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Affiliation(s)
- Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, D-79104 Freiburg, Germany; (T.F.); (D.W.)
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, D-79104 Freiburg, Germany; (T.F.); (D.W.)
| | - Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
- Correspondence:
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17
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Hoeser F, Weiß M, Friedrich T. The clinically relevant triple mutation in the mtND1 gene inactivates Escherichia coli complex I. FEBS Lett 2022; 596:1124-1132. [PMID: 35234296 DOI: 10.1002/1873-3468.14325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/07/2022]
Abstract
NADH:ubiquinone oxidoreductase (respiratory complex I) plays a major role in cellular energy metabolism. Complex I deficiencies are the most common cause of mitochondrial dysfunction. Patients suffering from a variety of neurodegenerative diseases carry numerous mutations in the mitochondrially encoded subunits of the complex. The biochemical consequences of these mutations are largely unknown because these genes are difficult to access experimentally. Here, we use Escherichia coli as a model system to characterize the effect of a 7 bp inversion in mtND1 (m.3902-3908inv7) that results in a triple mutation. The triple mutant grew poorly but contained a normal amount of the stably assembled variant. The variant showed no enzymatic activity, which might contribute to the deleterious effect of the mutation in humans.
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Affiliation(s)
- Franziska Hoeser
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Maximilian Weiß
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
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18
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Van den Bergh B, Schramke H, Michiels JE, Kimkes TEP, Radzikowski JL, Schimpf J, Vedelaar SR, Burschel S, Dewachter L, Lončar N, Schmidt A, Meijer T, Fauvart M, Friedrich T, Michiels J, Heinemann M. Mutations in respiratory complex I promote antibiotic persistence through alterations in intracellular acidity and protein synthesis. Nat Commun 2022; 13:546. [PMID: 35087069 PMCID: PMC8795404 DOI: 10.1038/s41467-022-28141-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 01/04/2022] [Indexed: 11/28/2022] Open
Abstract
Antibiotic persistence describes the presence of phenotypic variants within an isogenic bacterial population that are transiently tolerant to antibiotic treatment. Perturbations of metabolic homeostasis can promote antibiotic persistence, but the precise mechanisms are not well understood. Here, we use laboratory evolution, population-wide sequencing and biochemical characterizations to identify mutations in respiratory complex I and discover how they promote persistence in Escherichia coli. We show that persistence-inducing perturbations of metabolic homeostasis are associated with cytoplasmic acidification. Such cytoplasmic acidification is further strengthened by compromised proton pumping in the complex I mutants. While RpoS regulon activation induces persistence in the wild type, the aggravated cytoplasmic acidification in the complex I mutants leads to increased persistence via global shutdown of protein synthesis. Thus, we propose that cytoplasmic acidification, amplified by a compromised complex I, can act as a signaling hub for perturbed metabolic homeostasis in antibiotic persisters.
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Affiliation(s)
- Bram Van den Bergh
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Hannah Schramke
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Joran Elie Michiels
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
| | - Tom E P Kimkes
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Jakub Leszek Radzikowski
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Johannes Schimpf
- Molecular Bioenergetics, Institute of Biochemistry, Albert-Ludwigs-University of Freiburg, Freiburg im Breisgau, Germany
| | - Silke R Vedelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Sabrina Burschel
- Molecular Bioenergetics, Institute of Biochemistry, Albert-Ludwigs-University of Freiburg, Freiburg im Breisgau, Germany
| | - Liselot Dewachter
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
| | - Nikola Lončar
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Tim Meijer
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Thorsten Friedrich
- Molecular Bioenergetics, Institute of Biochemistry, Albert-Ludwigs-University of Freiburg, Freiburg im Breisgau, Germany
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium.
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium.
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, The Netherlands.
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19
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Vranas M, Wohlwend D, Qiu D, Gerhardt S, Trncik C, Pervaiz M, Ritter K, Steimle S, Randazzo A, Einsle O, Günther S, Jessen HJ, Kotlyar A, Friedrich T. Structural Basis for Inhibition of ROS-Producing Respiratory Complex I by NADH-OH. Angew Chem Int Ed Engl 2021; 60:27277-27281. [PMID: 34612584 PMCID: PMC9299107 DOI: 10.1002/anie.202112165] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Indexed: 11/09/2022]
Abstract
NADH:ubiquinone oxidoreductase, respiratory complex I, plays a central role in cellular energy metabolism. As a major source of reactive oxygen species (ROS) it affects ageing and mitochondrial dysfunction. The novel inhibitor NADH-OH specifically blocks NADH oxidation and ROS production by complex I in nanomolar concentrations. Attempts to elucidate its structure by NMR spectroscopy have failed. Here, by using X-ray crystallographic analysis, we report the structure of NADH-OH bound in the active site of a soluble fragment of complex I at 2.0 Å resolution. We have identified key amino acid residues that are specific and essential for binding NADH-OH. Furthermore, the structure sheds light on the specificity of NADH-OH towards the unique Rossmann-fold of complex I and indicates a regulatory role in mitochondrial ROS generation. In addition, NADH-OH acts as a lead-structure for the synthesis of a novel class of ROS suppressors.
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Affiliation(s)
- Marta Vranas
- Institute of Biochemistry, University of Freiburg, 79104, Freiburg, Germany.,Magellan Biologics & Consulting, 4200-135, Porto, Portugal
| | - Daniel Wohlwend
- Institute of Biochemistry, University of Freiburg, 79104, Freiburg, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, 79104, Freiburg, Germany
| | - Stefan Gerhardt
- Institute of Biochemistry, University of Freiburg, 79104, Freiburg, Germany
| | - Christian Trncik
- Institute of Biochemistry, University of Freiburg, 79104, Freiburg, Germany
| | - Mehrosh Pervaiz
- Institute of Pharmazeutical Sciences, University of Freiburg, Germany
| | - Kevin Ritter
- Institute of Organic Chemistry, University of Freiburg, 79104, Freiburg, Germany
| | - Stefan Steimle
- Institute of Biochemistry, University of Freiburg, 79104, Freiburg, Germany.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples, 80131, Napoli, Italy
| | - Oliver Einsle
- Institute of Biochemistry, University of Freiburg, 79104, Freiburg, Germany
| | - Stefan Günther
- Institute of Pharmazeutical Sciences, University of Freiburg, Germany
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, 79104, Freiburg, Germany
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Thorsten Friedrich
- Institute of Biochemistry, University of Freiburg, 79104, Freiburg, Germany
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20
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Vranas M, Wohlwend D, Qiu D, Gerhardt S, Trncik C, Pervaiz M, Ritter K, Steimle S, Randazzo A, Einsle O, Günther S, Jessen HJ, Kotlyar A, Friedrich T. Structural Basis for Inhibition of ROS‐Producing Respiratory Complex I by NADH‐OH. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202112165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marta Vranas
- Institute of Biochemistry University of Freiburg 79104 Freiburg Germany
- Magellan Biologics & Consulting 4200-135 Porto Portugal
| | - Daniel Wohlwend
- Institute of Biochemistry University of Freiburg 79104 Freiburg Germany
| | - Danye Qiu
- Institute of Organic Chemistry University of Freiburg 79104 Freiburg Germany
| | - Stefan Gerhardt
- Institute of Biochemistry University of Freiburg 79104 Freiburg Germany
| | - Christian Trncik
- Institute of Biochemistry University of Freiburg 79104 Freiburg Germany
| | - Mehrosh Pervaiz
- Institute of Pharmazeutical Sciences University of Freiburg Germany
| | - Kevin Ritter
- Institute of Organic Chemistry University of Freiburg 79104 Freiburg Germany
| | - Stefan Steimle
- Institute of Biochemistry University of Freiburg 79104 Freiburg Germany
- Department of Biochemistry and Biophysics University of Pennsylvania Philadelphia PA 19104 USA
| | | | - Oliver Einsle
- Institute of Biochemistry University of Freiburg 79104 Freiburg Germany
| | - Stefan Günther
- Institute of Pharmazeutical Sciences University of Freiburg Germany
| | - Henning J. Jessen
- Institute of Organic Chemistry University of Freiburg 79104 Freiburg Germany
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology Tel Aviv University 69978 Tel Aviv Israel
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21
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Abstract
Ethylbenzene dehydrogenase (EbDH), the initial enzyme of anaerobic ethylbenzene degradation from the beta-proteobacterium Aromatoleum aromaticum, is a soluble periplasmic molybdenum enzyme consisting of three subunits. It contains a Mo-bis-molybdopterin guanine dinucleotide (Mo-bis-MGD) cofactor and an 4Fe-4S cluster (FS0) in the α-subunit, three 4Fe-4S clusters (FS1 to FS3) and a 3Fe-4S cluster (FS4) in the β-subunit and a heme b cofactor in the γ-subunit. Ethylbenzene is hydroxylated by a water molecule in an oxygen-independent manner at the Mo-bis-MGD cofactor, which is reduced from the MoVI to the MoIV state in two subsequent one-electron steps. The electrons are then transferred via the Fe-S clusters to the heme b cofactor. In this report, we determine the midpoint redox potentials of the Mo-bis-MGD cofactor and FS1-FS4 by EPR spectroscopy, and that of the heme b cofactor by electrochemically induced redox difference spectroscopy. We obtained relatively high values of > 250 mV both for the MoVI-MoV redox couple and the heme b cofactor, whereas FS2 is only reduced at a very low redox potential, causing magnetic coupling with the neighboring FS1 and FS3. We compare the results with the data on related enzymes and interpret their significance for the function of EbDH.
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Affiliation(s)
- Corina Hagel
- Labor für Mikrobielle Biochemie and Synmikro Zentrum für Synthetische Mikrobiologie, Philipps Universität Marburg, 35043, Marburg, Germany
| | - Bärbel Blaum
- Institut für Biochemie, Albert-Ludwigs Universität, Albertstr. 21, 79104, Freiburg im Breisgau, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs Universität, Albertstr. 21, 79104, Freiburg im Breisgau, Germany.
| | - Johann Heider
- Labor für Mikrobielle Biochemie and Synmikro Zentrum für Synthetische Mikrobiologie, Philipps Universität Marburg, 35043, Marburg, Germany.
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22
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Schimpf J, Oppermann S, Gerasimova T, Santos Seica AF, Hellwig P, Grishkovskaya I, Wohlwend D, Haselbach D, Friedrich T. Structure of the peripheral arm of a minimalistic respiratory complex I. Structure 2021; 30:80-94.e4. [PMID: 34562374 DOI: 10.1016/j.str.2021.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/09/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Respiratory complex I drives proton translocation across energy-transducing membranes by NADH oxidation coupled with (ubi)quinone reduction. In humans, its dysfunction is associated with neurodegenerative diseases. The Escherichia coli complex represents the structural minimal form of an energy-converting NADH:ubiquinone oxidoreductase. Here, we report the structure of the peripheral arm of the E. coli complex I consisting of six subunits, the FMN cofactor, and nine iron-sulfur clusters at 2.7 Å resolution obtained by cryo electron microscopy. While the cofactors are in equivalent positions as in the complex from other species, individual subunits are adapted to the absence of supernumerary proteins to guarantee structural stability. The catalytically important subunits NuoC and D are fused resulting in a specific architecture of functional importance. Striking features of the E. coli complex are scrutinized by mutagenesis and biochemical characterization of the variants. Moreover, the arrangement of the subunits sheds light on the unknown assembly of the complex.
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Affiliation(s)
- Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Sabrina Oppermann
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Tatjana Gerasimova
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, 4 Rue Blaise Pascal, 67081 Strasbourg, France
| | - Ana Filipa Santos Seica
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, 4 Rue Blaise Pascal, 67081 Strasbourg, France
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, 4 Rue Blaise Pascal, 67081 Strasbourg, France; University of Strasbourg, Institute for Advanced Studies (USIAS), 5 Allée du Général Rouvillois, 67083 Strasbourg, France
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany.
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Hartel C, Nasonova E, Ritter S, Friedrich T. Alpha-Particle Exposure Induces Mainly Unstable Complex Chromosome Aberrations which do not Contribute to Radiation-Associated Cytogenetic Risk. Radiat Res 2021; 196:561-573. [PMID: 34411274 DOI: 10.1667/rade-21-00116.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/06/2021] [Indexed: 11/03/2022]
Abstract
The mechanism underlying the carcinogenic potential of α radiation is not fully understood, considering that cell inactivation (e.g., mitotic cell death) as a main consequence of exposure efficiently counteracts the spreading of heritable DNA damage. The aim of this study is to improve our understanding of the effectiveness of α particles in inducing different types of chromosomal aberrations, to determine the respective values of the relative biological effectiveness (RBE) and to interpret the results with respect to exposure risk. Human peripheral blood lymphocytes (PBLs) from a single donor were exposed ex vivo to doses of 0-6 Gy X rays or 0-2 Gy α particles. Cells were harvested at two different times after irradiation to account for the mitotic delay of heavily damaged cells, which is known to occur after exposure to high-LET radiation (including α particles). Analysis of the kinetics of cells reaching first or second (and higher) mitosis after irradiation and aberration data obtained by the multiplex fluorescence in situ hybridization (mFISH) technique are used to determine of the cytogenetic risk, i.e., the probability for transmissible aberrations in surviving lymphocytes. The analysis shows that the cytogenetic risk after α exposure is lower than after X rays. This indicates that the actually observed higher carcinogenic effect of α radiation is likely to stem from small scale mutations that are induced effectively by high-LET radiation but cannot be resolved by mFISH analysis.
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Affiliation(s)
- C Hartel
- GSI Helmholtz Centre for Heavy Ion Research, Department of Biophysics, Darmstadt, Germany
| | - E Nasonova
- GSI Helmholtz Centre for Heavy Ion Research, Department of Biophysics, Darmstadt, Germany.,Joint Institute for Nuclear Research, Laboratory of Radiation Biology, Dubna, Russia
| | - S Ritter
- GSI Helmholtz Centre for Heavy Ion Research, Department of Biophysics, Darmstadt, Germany
| | - T Friedrich
- GSI Helmholtz Centre for Heavy Ion Research, Department of Biophysics, Darmstadt, Germany
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24
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Nuber F, Mérono L, Oppermann S, Schimpf J, Wohlwend D, Friedrich T. A Quinol Anion as Catalytic Intermediate Coupling Proton Translocation With Electron Transfer in E. coli Respiratory Complex I. Front Chem 2021; 9:672969. [PMID: 34026733 PMCID: PMC8138167 DOI: 10.3389/fchem.2021.672969] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/09/2021] [Indexed: 11/18/2022] Open
Abstract
Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, plays a major role in cellular energy metabolism. It couples NADH oxidation and quinone reduction with the translocation of protons across the membrane, thus contributing to the protonmotive force. Complex I has an overall L-shaped structure with a peripheral arm catalyzing electron transfer and a membrane arm engaged in proton translocation. Although both reactions are arranged spatially separated, they are tightly coupled by a mechanism that is not fully understood. Using redox-difference UV-vis spectroscopy, an unknown redox component was identified in Escherichia coli complex I as reported earlier. A comparison of its spectrum with those obtained for different quinone species indicates features of a quinol anion. The re-oxidation kinetics of the quinol anion intermediate is significantly slower in the D213GH variant that was previously shown to operate with disturbed quinone chemistry. Addition of the quinone-site inhibitor piericidin A led to strongly decreased absorption peaks in the difference spectrum. A hypothesis for a mechanism of proton-coupled electron transfer with the quinol anion as catalytically important intermediate in complex I is discussed.
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Affiliation(s)
- Franziska Nuber
- Institut für Biochemie, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Luca Mérono
- Institut für Biochemie, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Sabrina Oppermann
- Institut für Biochemie, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität, Freiburg, Germany
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25
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Nikolaev A, Safarian S, Thesseling A, Wohlwend D, Friedrich T, Michel H, Kusumoto T, Sakamoto J, Melin F, Hellwig P. Electrocatalytic evidence of the diversity of the oxygen reaction in the bacterial bd oxidase from different organisms. Biochim Biophys Acta Bioenerg 2021; 1862:148436. [PMID: 33940039 DOI: 10.1016/j.bbabio.2021.148436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 11/30/2022]
Abstract
Cytochrome bd oxidase is a bacterial terminal oxygen reductase that was suggested to enable adaptation to different environments and to confer resistance to stress conditions. An electrocatalytic study of the cyt bd oxidases from Escherichia coli, Corynebacterium glutamicum and Geobacillus thermodenitrificans gives evidence for a different reactivity towards oxygen. An inversion of the redox potential values of the three hemes is found when comparing the enzymes from different bacteria. This inversion can be correlated with different protonated glutamic acids as evidenced by reaction induced FTIR spectroscopy. The influence of the microenvironment of the hemes on the reactivity towards oxygen is discussed.
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Affiliation(s)
- Anton Nikolaev
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg - CNRS 4, rue Blaise Pascal, 67081 Strasborg, France
| | - Schara Safarian
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | | | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Hartmut Michel
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Tomoichirou Kusumoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Fukuoka, Japan
| | - Junshi Sakamoto
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Fukuoka, Japan
| | - Frederic Melin
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg - CNRS 4, rue Blaise Pascal, 67081 Strasborg, France.
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg - CNRS 4, rue Blaise Pascal, 67081 Strasborg, France; USIAS, University of Strasbourg Institute for Advanced Studies, Strasbourg, France.
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26
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Olerinyova A, Sonn-Segev A, Gault J, Eichmann C, Schimpf J, Kopf AH, Rudden LSP, Ashkinadze D, Bomba R, Frey L, Greenwald J, Degiacomi MT, Steinhilper R, Killian JA, Friedrich T, Riek R, Struwe WB, Kukura P. Mass Photometry of Membrane Proteins. Chem 2021; 7:224-236. [PMID: 33511302 PMCID: PMC7815066 DOI: 10.1016/j.chempr.2020.11.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/20/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023]
Abstract
Integral membrane proteins (IMPs) are biologically highly significant but challenging to study because they require maintaining a cellular lipid-like environment. Here, we explore the application of mass photometry (MP) to IMPs and membrane-mimetic systems at the single-particle level. We apply MP to amphipathic vehicles, such as detergents and amphipols, as well as to lipid and native nanodiscs, characterizing the particle size, sample purity, and heterogeneity. Using methods established for cryogenic electron microscopy, we eliminate detergent background, enabling high-resolution studies of membrane-protein structure and interactions. We find evidence that, when extracted from native membranes using native styrene-maleic acid nanodiscs, the potassium channel KcsA is present as a dimer of tetramers—in contrast to results obtained using detergent purification. Finally, using lipid nanodiscs, we show that MP can help distinguish between functional and non-functional nanodisc assemblies, as well as determine the critical factors for lipid nanodisc formation. We introduce a label-free, single molecule approach for membrane-protein characterization Mass photometry quantifies membrane proteins in different membrane-mimetic systems MP reveals carrier and protein heterogeneity It helps distinguish different functional states of membrane proteins
Membrane proteins are some of the most important biological molecules, carrying out vital functions and being frequent drug targets. Yet, preferring lipid environments and so requiring solubilization, they are challenging to study. Here, we show that mass photometry can characterize the heterogeneity of membrane proteins and the carriers in which they are solubilized. It can also distinguish different functional states of membrane proteins. Our approach thus opens the door to more comprehensive studies of function, structure, and interaction of these critical proteins in their native membrane environment at the single-molecule level.
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Affiliation(s)
- Anna Olerinyova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Adar Sonn-Segev
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Joseph Gault
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Cédric Eichmann
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität, Alberstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Adrian H Kopf
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Lucas S P Rudden
- Department of Physics, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Dzmitry Ashkinadze
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Radoslaw Bomba
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Lukas Frey
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Matteo T Degiacomi
- Department of Physics, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Ralf Steinhilper
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - J Antoinette Killian
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität, Alberstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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27
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Schalla MA, Goebel-Stengel M, Friedrich T, Kühne SG, Kobelt P, Rose M, Stengel A. Restraint stress affects circulating NUCB2/nesfatin-1 and phoenixin levels in male rats. Psychoneuroendocrinology 2020; 122:104906. [PMID: 33059202 DOI: 10.1016/j.psyneuen.2020.104906] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 12/27/2022]
Abstract
The two peptides phoenixin and nesfatin-1 are colocalized in hypothalamic nuclei involved in the mediation of food intake and behavior. Phoenixin stimulates food intake and is anxiolytic, while nesfatin-1 is an anorexigenic peptide shown to increase anxiety and anhedonia. Interestingly, central activation of both peptides can be stimulated by restraint stress giving rise to a role in the mediation of stress. Thus, the aim of the study was to test whether also peripheral circulating levels of NUCB2/nesfatin-1 and phoenixin are altered by restraint stress. Male ad libitum fed Sprague Dawley rats equipped with a chronic intravenous catheter were subjected to restraint stress and plasma levels of NUCB2/nesfatin-1, phoenixin and cortisol were measured over a period of 240 min and compared to levels of freely moving rats. Peripheral cortisol levels were significantly increased in restrained rats at 30, 60, 120 and 240 min compared to controls (p < 0.05). In contrast, restraint stress decreased plasma phoenixin levels at 15 min compared to unstressed conditions (0.8-fold, p < 0.05). Circulating NUCB2/nesfatin-1 levels were increased only at 240 min in restrained rats compared to those in unstressed controls (1.3-fold, p < 0.05). In addition, circulating NUCB2/nesfatin-1 levels correlated positively with phoenixin levels (r = 0.378, p < 0.001), while neither phoenixin nor nesfatin-1 were associated with cortisol levels (r = 0.0275, and r=-0.143, p> 0.05). These data suggest that both peptides, NUCB2/nesfatin-1 and phoenixin, are affected by restraint stress, although less pronounced than circulating cortisol.
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Affiliation(s)
- M A Schalla
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - M Goebel-Stengel
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; Department of Internal Medicine, HELIOS Kliniken GmbH, Rottweil, Germany; Department of Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Tübingen, Germany
| | - T Friedrich
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - S G Kühne
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - P Kobelt
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - M Rose
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, USA
| | - A Stengel
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; Department of Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Tübingen, Germany.
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28
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Oppermann S, Höfflin S, Friedrich T. ErpA is important but not essential for the Fe/S cluster biogenesis of Escherichia coli NADH:ubiquinone oxidoreductase (complex I). Biochim Biophys Acta Bioenerg 2020; 1861:148286. [PMID: 32777304 DOI: 10.1016/j.bbabio.2020.148286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/13/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
Energy converting NADH:ubiquinone oxidoreductase, complex I, is the first enzyme of respiratory chains in most eukaryotes and many bacteria. The complex comprises a peripheral arm catalyzing electron transfer and a membrane arm involved in proton-translocation. In Escherichia coli, the peripheral arm features a non-covalently bound flavin mononucleotide and nine iron-sulfur (Fe/S)-clusters. Very little is known about the incorporation of the Fe/S-clusters into the E. coli complex I. ErpA, an A-type carrier protein is discussed to act as a Fe/S-cluster carrier protein. To contribute to the understanding of ErpA for the assembly of E. coli complex I, we analyzed an erpA knock-out strain. Deletion of erpA decreased the complex I content in cytoplasmic membranes to approximately one third and the NADH oxidase activity to one fifth. EPR spectroscopy showed the presence of all Fe/S-clusters of the complex in the membrane but only in minor quantities. Sucrose gradient centrifugation and native PAGE revealed the presence of a marginal amount of a stable and fully assembled complex extractable from the membrane. Thus, ErpA is not essential for the assembly of complex I but its absence leads to a strong decrease of a functional complex in the cytoplasmic membrane due to a major lack of all EPR-detectable Fe/S-clusters.
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Affiliation(s)
- Sabrina Oppermann
- Albert-Ludwigs-Universität, Institut für Biochemie, Albertstr. 21, D-79104 Freiburg, Germany
| | - Simon Höfflin
- Albert-Ludwigs-Universität, Institut für Biochemie, Albertstr. 21, D-79104 Freiburg, Germany
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität, Institut für Biochemie, Albertstr. 21, D-79104 Freiburg, Germany.
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29
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Schalla MA, Kühne SG, Friedrich T, Kobelt P, Goebel-Stengel M, Long M, Rivalan M, Winter Y, Mori M, Rose M, Stengel A. Central blockage of nesfatin-1 has anxiolytic effects but does not prevent corticotropin-releasing factor-induced anxiety in male rats. Biochem Biophys Res Commun 2020; 529:773-777. [DOI: 10.1016/j.bbrc.2020.05.163] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/21/2020] [Indexed: 11/24/2022]
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30
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Abstract
![]()
The respiratory complex I transduces
redox energy into an electrochemical
proton gradient in aerobic respiratory chains, powering energy-requiring
processes in the cell. However, despite recently resolved molecular
structures, the mechanism of this gigantic enzyme remains poorly understood.
By combining large-scale quantum and classical simulations with site-directed
mutagenesis and biophysical experiments, we show here how the conformational
state of buried ion-pairs and water molecules control the protonation
dynamics in the membrane domain of complex I and establish evolutionary
conserved long-range coupling elements. We suggest that an electrostatic
wave propagates in forward and reverse directions across the 200 Å
long membrane domain during enzyme turnover, without significant dissipation
of energy. Our findings demonstrate molecular principles that enable
efficient long-range proton–electron coupling (PCET) and how
perturbation of this PCET machinery may lead to development of mitochondrial
disease.
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Affiliation(s)
- Max E Mühlbauer
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
| | - Franziska Nuber
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Andrea Di Luca
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748 Garching, Germany
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31
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Nikolaev A, Makarchuk I, Thesseling A, Hoeser J, Friedrich T, Melin F, Hellwig P. Stabilization of the Highly Hydrophobic Membrane Protein, Cytochrome bd Oxidase, on Metallic Surfaces for Direct Electrochemical Studies. Molecules 2020; 25:molecules25143240. [PMID: 32708635 PMCID: PMC7397230 DOI: 10.3390/molecules25143240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 11/23/2022] Open
Abstract
The cytochrome bd oxidase catalyzes the reduction of oxygen to water in bacteria and it is thus an interesting target for electrocatalytic studies and biosensor applications. The bd oxidase is completely embedded in the phospholipid membrane. In this study, the variation of the surface charge of thiol-modified gold nanoparticles, the length of the thiols and the other crucial parameters including optimal phospholipid content and type, have been performed, giving insight into the role of these factors for the optimal interaction and direct electron transfer of an integral membrane protein. Importantly, all three tested factors, the lipid type, the electrode surface charge and the thiol length mutually influenced the stability of films of the cytochrome bd oxidase. The best electrocatalytic responses were obtained on the neutral gold surface when the negatively charged phosphatidylglycerol (PG) was used and on the charged gold surface when the zwitterionic phosphatidylethanolamine (PE) was used. The advantages of the covalent binding of the membrane protein to the electrode surface over the non-covalent binding are also discussed.
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Affiliation(s)
- Anton Nikolaev
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, CNRS, 67081 Strasbourg, France; (A.N.); (I.M.)
| | - Iryna Makarchuk
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, CNRS, 67081 Strasbourg, France; (A.N.); (I.M.)
| | - Alexander Thesseling
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany; (A.T.); (J.H.); (T.F.)
| | - Jo Hoeser
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany; (A.T.); (J.H.); (T.F.)
| | - Thorsten Friedrich
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany; (A.T.); (J.H.); (T.F.)
| | - Frédéric Melin
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, CNRS, 67081 Strasbourg, France; (A.N.); (I.M.)
- Correspondence: (F.M.); (P.H.)
| | - Petra Hellwig
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, CNRS, 67081 Strasbourg, France; (A.N.); (I.M.)
- Correspondence: (F.M.); (P.H.)
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Kuhns M, Schuchmann V, Schmidt S, Friedrich T, Wiechmann A, Müller V. The Rnf complex from the acetogenic bacterium Acetobacterium woodii: Purification and characterization of RnfC and RnfB. Biochim Biophys Acta Bioenerg 2020; 1861:148263. [PMID: 32663477 DOI: 10.1016/j.bbabio.2020.148263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 02/09/2023]
Abstract
rnf genes are widespread in anaerobic bacteria and hypothesized to encode a respiratory enzyme that couples exergonic reduction of NAD with reduced ferredoxin as a reductant to vectorial ion (Na+, H+) translocation across the cytoplasmic membrane. However, despite its importance for the physiology of these bacteria, little is known about the subunit composition and the function of subunits. Here, we have purified the entire Rnf complex from the acetogen Acetobacterium woodii or after its production in Escherichia coli. These studies revealed covalently bound flavin in RnfB and RnfD. Unfortunately, the complex did not catalyze electron transfer from reduced ferredoxin to NAD. We, therefore, concentrated on the two cytosolic subunits RnfC and RnfB. RnfC was produced in E. coli, purified and shown to have 8.3 mol iron and 8.6 mol sulfur per mol of the subunit, consistent with the presence of two [4Fe-4S] centers, which were verified by EPR analysis. Flavins could not be detected, but RnfC catalyzed NADH-dependent FMN reduction. These data confirm RnfC as NADH-binding subunit and FMN as an intermediate in the electron transport chain. RnfB could only be produced as a fusion to the maltose-binding protein. It contained 25 mol iron and 26 mol sulfur, consistent with the predicted six [4Fe4S] centers. The FeS centers in RnfB were reduced with reduced ferredoxin as reductant. These data are consistent with RnfB as the ferredoxin-binding subunit of the complex.
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Affiliation(s)
- Martin Kuhns
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Verena Schuchmann
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Silke Schmidt
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Thorsten Friedrich
- Institute of Biochemistry, Albert-Ludwigs-University Freiburg, Alberstr. 21, 79104 Freiburg, Germany
| | - Anja Wiechmann
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.
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Bittner T, Wittwer C, Hauke S, Wohlwend D, Mundinger S, Dutta AK, Bezold D, Dürr T, Friedrich T, Schultz C, Jessen HJ. Photolysis of Caged Inositol Pyrophosphate InsP 8 Directly Modulates Intracellular Ca 2+ Oscillations and Controls C2AB Domain Localization. J Am Chem Soc 2020; 142:10606-10611. [PMID: 32459478 DOI: 10.1021/jacs.0c01697] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inositol pyrophosphates constitute a family of hyperphosphorylated signaling molecules involved in the regulation of glucose uptake and insulin sensitivity. While our understanding of the biological roles of inositol heptaphosphates (PP-InsP5) has greatly improved, the functions of the inositol octaphosphates ((PP)2-InsP4) have remained unclear. Here we present the synthesis of two enantiomeric cell-permeant and photocaged (PP)2-InsP4 derivatives and apply them to study the functions in living β-cells. Photorelease of the naturally occurring isomer 1,5-(PP)2-InsP4 led to an immediate and concentration-dependent reduction of intracellular calcium oscillations, while other caged inositol pyrophosphates (3,5-(PP)2-InsP4, 5-PP-InsP5, 1-PP-InsP5, 3-PP-InsP5) showed no immediate effect. Furthermore, uncaging of 1,5-(PP)2-InsP4 but not 3,5-(PP)2-InsP4 induced translocation of the C2AB domain of granuphilin from the plasma membrane to the cytosol. Granuphilin is involved in membrane docking of secretory vesicles. This suggests that 1,5-(PP)2-InsP4 impacts β-cell activity by regulating granule localization and/or priming and calcium signaling in concert.
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Affiliation(s)
- Tamara Bittner
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Christopher Wittwer
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Sebastian Hauke
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniel Wohlwend
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Stephan Mundinger
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Amit K Dutta
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Dominik Bezold
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Tobias Dürr
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Thorsten Friedrich
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany
| | - Carsten Schultz
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Department of Chemical Physiology and Biochemistry, Oregon Health & Science University (OHSU), Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
| | - Henning J Jessen
- Department of Chemistry and Pharmacy, Albert-Ludwigs University Freiburg, Albertstrasse 21, 79104 Freiburg i.B., Germany.,CIBSS-Centre for Integrative Biological Signalling Studies, 79104 Freiburg i.B., Germany.,Freiburg Research Institute for Advanced Studies (FRIAS), Albert-Ludwigs University Freiburg, Albertstrasse 19, 79104 Freiburg i.B., Germany
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Friedrich T, Schalla MA, Lommel R, Goebel-Stengel M, Kobelt P, Rose M, Stengel A. Restraint stress increases the expression of phoenixin immunoreactivity in rat brain nuclei. Brain Res 2020; 1743:146904. [PMID: 32474019 DOI: 10.1016/j.brainres.2020.146904] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/01/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022]
Abstract
Phoenixin is a recently discovered peptide, which has been associated with reproduction, anxiety and food intake. Based on a considerable co-localization it has been linked to nesfatin-1, with a possible antagonistic mode of action. Since nesfatin-1 is known to play a role in anxiety and the response to stress, this study aims to investigate the effects of a well-established psychological stress model, restraint stress, on phoenixin-expressing brain nuclei and phoenixin expression in rats. Male Sprague-Dawley rats were subjected to restraint stress (n = 8) or left undisturbed (control, n = 6) and the brains processed for c-Fos- and phoenixin immunohistochemistry. The number of c-Fos expressing cells was counted and phoenixin expression assessed semiquantitatively. Restraint stress significantly increased c-Fos expression in the dorsal motor nucleus of vagus nerve (DMN, 52-fold, p < 0.001), raphe pallidus (RPa, 15-fold, p < 0.001), medial part of the nucleus of the solitary tract (mNTS, 16-fold, p < 0.001), central amygdaloid nucleus, medial division (CeM, 9-fold, p = 0.01), supraoptic nucleus (SON, 9-fold, p < 0.001) and the arcuate nucleus (Arc, 2.5-fold, p < 0.03) compared to control animals. Also phoenixin expression significantly increased in the DMN (17-fold, p < 0.001), RPa (2-fold, p < 0.001) and mNTS (1.6-fold, p < 0.001) with positive correlations between c-Fos and phoenixin (r = 0.74-0.85; p < 0.01) in these nuclei. This pattern of activation suggests an involvement of phoenixin in response to restraint stress. Whether phoenixin mediates stress effects or is activated in a counterbalancing fashion will have to be further investigated.
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Affiliation(s)
- T Friedrich
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charite - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - M A Schalla
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charite - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - R Lommel
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charite - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - M Goebel-Stengel
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charite - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; Department of Internal Medicine, Helios Kliniken GmbH, Rottweil, Germany; Department of Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Tübingen, Germany
| | - P Kobelt
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charite - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - M Rose
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charite - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - A Stengel
- Charité Center for Internal Medicine and Dermatology, Department for Psychosomatic Medicine, Charite - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany; Department of Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Tübingen, Germany.
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Skorupa P, Lindenstrauß U, Burschel S, Blumenscheit C, Friedrich T, Pinske C. The N-terminal domains of the paralogous HycE and NuoCD govern assembly of the respective formate hydrogenlyase and NADH dehydrogenase complexes. FEBS Open Bio 2020; 10:371-385. [PMID: 31925988 PMCID: PMC7050243 DOI: 10.1002/2211-5463.12787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/17/2019] [Accepted: 01/08/2020] [Indexed: 11/23/2022] Open
Abstract
Formate hydrogenlyase (FHL) is the main hydrogen-producing enzyme complex in enterobacteria. It converts formate to CO2 and H2 via a formate dehydrogenase and a [NiFe]-hydrogenase. FHL and complex I are evolutionarily related and share a common core architecture. However, complex I catalyses the fundamentally different electron transfer from NADH to quinone and pumps protons. The catalytic FHL subunit, HycE, resembles NuoCD of Escherichia coli complex I; a fusion of NuoC and NuoD present in other organisms. The C-terminal domain of HycE harbours the [NiFe]-active site and is similar to other hydrogenases, while this domain in NuoCD is involved in quinone binding. The N-terminal domains of these proteins do not bind cofactors and are not involved in electron transfer. As these N-terminal domains are separate proteins in some organisms, we removed them in E. coli and observed that both FHL and complex I activities were essentially absent. This was due to either a disturbed assembly or to complex instability. Replacing the N-terminal domain of HycE with a 180 amino acid E. coli NuoC protein fusion did not restore activity, indicating that the domains have complex-specific functions. A FHL complex in which the N- and C-terminal domains of HycE were physically separated still retained most of its FHL activity, while the separation of NuoCD abolished complex I activity completely. Only the FHL complex tolerates physical separation of the HycE domains. Together, the findings strongly suggest that the N-terminal domains of these proteins are key determinants in complex assembly.
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Affiliation(s)
- Philipp Skorupa
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergGermany
| | - Ute Lindenstrauß
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergGermany
| | - Sabrina Burschel
- Institute of Biochemistry/Molecular BioenergeticsAlbert‐Ludwigs‐University FreiburgGermany
| | | | - Thorsten Friedrich
- Institute of Biochemistry/Molecular BioenergeticsAlbert‐Ludwigs‐University FreiburgGermany
| | - Constanze Pinske
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergGermany
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36
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Theßeling A, Burschel S, Wohlwend D, Friedrich T. The long Q‐loop ofEscherichia colicytochromebdoxidase is required for assembly and structural integrity. FEBS Lett 2020; 594:1577-1585. [DOI: 10.1002/1873-3468.13749] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/24/2020] [Accepted: 01/26/2020] [Indexed: 11/08/2022]
Affiliation(s)
| | - Sabrina Burschel
- Institut für Biochemie Albert‐Ludwigs‐Universität Freiburg Germany
| | - Daniel Wohlwend
- Institut für Biochemie Albert‐Ludwigs‐Universität Freiburg Germany
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Santos Seica AF, Schimpf J, Friedrich T, Hellwig P. Visualizing the movement of the amphipathic helix in the respiratory complex I using a nitrile infrared probe and SEIRAS. FEBS Lett 2019; 594:491-496. [PMID: 31556114 DOI: 10.1002/1873-3468.13620] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 01/22/2023]
Abstract
Conformational movements play an important role in enzyme catalysis. Respiratory complex I, an L-shaped enzyme, connects electron transfer from NADH to ubiquinone in its peripheral arm with proton translocation through its membrane arm by a coupling mechanism still under debate. The amphipathic helix across the membrane arm represents a unique structural feature. Here, we demonstrate a new way to study conformational changes by introducing a small and highly flexible nitrile infrared (IR) label to this helix to visualize movement with surface-enhanced IR absorption spectroscopy. We find that labeled residues K551CL and Y590CL move to a more hydrophobic environment upon NADH reduction of the enzyme, likely as a response to the reorganization of the antiporter-like subunits in the membrane arm.
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Affiliation(s)
- Ana Filipa Santos Seica
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, France
| | - Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Germany
| | | | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, France.,University of Strasbourg Institute for Advanced Studies (USIAS), France
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38
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Wilkening S, Schmitt FJ, Lenz O, Zebger I, Horch M, Friedrich T. Discriminating changes in intracellular NADH/NAD + levels due to anoxicity and H 2 supply in R. eutropha cells using the Frex fluorescence sensor. Biochim Biophys Acta Bioenerg 2019; 1860:148062. [PMID: 31419395 DOI: 10.1016/j.bbabio.2019.148062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/23/2019] [Accepted: 08/10/2019] [Indexed: 12/19/2022]
Abstract
The hydrogen-oxidizing "Knallgas" bacterium Ralstonia eutropha can thrive in aerobic and anaerobic environments and readily switches between heterotrophic and autotrophic metabolism, making it an attractive host for biotechnological applications including the sustainable H2-driven production of hydrocarbons. The soluble hydrogenase (SH), one out of four different [NiFe]-hydrogenases in R. eutropha, mediates H2 oxidation even in the presence of O2, thus providing an ideal model system for biological hydrogen production and utilization. The SH reversibly couples H2 oxidation with the reduction of NAD+ to NADH, thereby enabling the sustainable regeneration of this biotechnologically important nicotinamide cofactor. Thus, understanding the interaction of the SH with the cellular NADH/NAD+ pool is of high interest. Here, we applied the fluorescent biosensor Frex to measure changes in cytoplasmic [NADH] in R. eutropha cells under different gas supply conditions. The results show that Frex is well-suited to distinguish SH-mediated changes in the cytoplasmic redox status from effects of general anaerobiosis of the respiratory chain. Upon H2 supply, the Frex reporter reveals a robust fluorescence response and allows for monitoring rapid changes in cellular [NADH]. Compared to the Peredox fluorescence reporter, Frex displays a diminished NADH affinity, which prevents the saturation of the sensor under typical bacterial [NADH] levels. Thus, Frex is a valuable reporter for on-line monitoring of the [NADH]/[NAD+] redox state in living cells of R. eutropha and other proteobacteria. Based on these results, strategies for a rational optimization of fluorescent NADH sensors are discussed.
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Affiliation(s)
- S Wilkening
- Technische Universität Berlin, Institut für Chemie PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - F-J Schmitt
- Technische Universität Berlin, Institut für Chemie PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - O Lenz
- Technische Universität Berlin, Institut für Chemie PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - I Zebger
- Technische Universität Berlin, Institut für Chemie PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - M Horch
- Technische Universität Berlin, Institut für Chemie PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany; Department of Chemistry and York Biomedical Research Institute, University of York, YO10 5DD, United Kingdom
| | - T Friedrich
- Technische Universität Berlin, Institut für Chemie PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany.
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Schulte M, Frick K, Gnandt E, Jurkovic S, Burschel S, Labatzke R, Aierstock K, Fiegen D, Wohlwend D, Gerhardt S, Einsle O, Friedrich T. A mechanism to prevent production of reactive oxygen species by Escherichia coli respiratory complex I. Nat Commun 2019; 10:2551. [PMID: 31186428 PMCID: PMC6560083 DOI: 10.1038/s41467-019-10429-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 05/08/2019] [Indexed: 11/21/2022] Open
Abstract
Respiratory complex I plays a central role in cellular energy metabolism coupling NADH oxidation to proton translocation. In humans its dysfunction is associated with degenerative diseases. Here we report the structure of the electron input part of Aquifex aeolicus complex I at up to 1.8 Å resolution with bound substrates in the reduced and oxidized states. The redox states differ by the flip of a peptide bond close to the NADH binding site. The orientation of this peptide bond is determined by the reduction state of the nearby [Fe-S] cluster N1a. Fixation of the peptide bond by site-directed mutagenesis led to an inactivation of electron transfer and a decreased reactive oxygen species (ROS) production. We suggest the redox-gated peptide flip to represent a previously unrecognized molecular switch synchronizing NADH oxidation in response to the redox state of the complex as part of an intramolecular feed-back mechanism to prevent ROS production. Respiratory complex I plays a central role in cellular energy metabolism coupling NADH oxidation to proton translocation. Here, the authors report the structure of the electron input part of Aquifex aeolicus complex I at up to 1.8 Å resolution with bound substrates in the reduced and oxidized states.
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Affiliation(s)
- Marius Schulte
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Klaudia Frick
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Emmanuel Gnandt
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Sascha Jurkovic
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Sabrina Burschel
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Ramona Labatzke
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Karoline Aierstock
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany.,Boehringer Ingelheim Pharma GmbH & Co. KG, Lead Identification and Optimization Sup, 88397, Biberach, Germany
| | - Dennis Fiegen
- Boehringer Ingelheim Pharma GmbH & Co. KG, Lead Identification and Optimization Sup, 88397, Biberach, Germany
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Stefan Gerhardt
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany.
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Wissig J, Grischin J, Bassler J, Schubert C, Friedrich T, Bähre H, Schultz JE, Unden G. CyaC, a redox‐regulated adenylate cyclase ofSinorhizobium melilotiwith a quinone responsive diheme‐B membrane anchor domain. Mol Microbiol 2019; 112:16-28. [DOI: 10.1111/mmi.14251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Juliane Wissig
- Microbiology and Wine Research, Institute for Molecular Physiology Johannes Gutenberg‐University of Mainz Becherweg 1555099Mainz Germany
| | - Julia Grischin
- Max‐Planck‐Institut für Entwicklungsbiologie, Abt. Proteinevolution Max‐Planck‐Ring 572076Tübingen Germany
| | - Jens Bassler
- Max‐Planck‐Institut für Entwicklungsbiologie, Abt. Proteinevolution Max‐Planck‐Ring 572076Tübingen Germany
| | - Christopher Schubert
- Microbiology and Wine Research, Institute for Molecular Physiology Johannes Gutenberg‐University of Mainz Becherweg 1555099Mainz Germany
| | | | - Heike Bähre
- Medizinische Hochschule Hannover Hannover Germany
| | - Joachim E. Schultz
- Pharmazeutisches Institut der Universität Tübingen Auf der Morgenstelle 872076Tübingen Germany
| | - Gottfried Unden
- Microbiology and Wine Research, Institute for Molecular Physiology Johannes Gutenberg‐University of Mainz Becherweg 1555099Mainz Germany
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Burschel S, Kreuzer Decovic D, Nuber F, Stiller M, Hofmann M, Zupok A, Siemiatkowska B, Gorka M, Leimkühler S, Friedrich T. Iron-sulfur cluster carrier proteins involved in the assembly of Escherichia coli
NADH:ubiquinone oxidoreductase (complex I). Mol Microbiol 2018; 111:31-45. [DOI: 10.1111/mmi.14137] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 09/10/2018] [Accepted: 09/19/2018] [Indexed: 01/26/2023]
Affiliation(s)
- Sabrina Burschel
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
| | - Doris Kreuzer Decovic
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
- Spemann Graduate School of Biology and Medicine (SGBM); University of Freiburg; Germany
| | - Franziska Nuber
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
| | - Marie Stiller
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
| | - Maud Hofmann
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
| | - Arkadiusz Zupok
- University of Potsdam; Institut für Biochemie und Biologie; Karl-Liebknecht-Str. 24-25 14476 Potsdam-Golm Germany
| | - Beata Siemiatkowska
- Max-Planck-Institute of Molecular Plant Physiology; Am Mühlenberg 1 14476 Potsdam-Golm Germany
| | - Michal Gorka
- Max-Planck-Institute of Molecular Plant Physiology; Am Mühlenberg 1 14476 Potsdam-Golm Germany
| | - Silke Leimkühler
- University of Potsdam; Institut für Biochemie und Biologie; Karl-Liebknecht-Str. 24-25 14476 Potsdam-Golm Germany
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität, Institut für Biochemie; Albertstr. 21 D-79104 Freiburg Germany
- Spemann Graduate School of Biology and Medicine (SGBM); University of Freiburg; Germany
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Roch PJ, Friedrich T, Bönninghoff R, Dinter D, Rickert A. [Laparoscopic resection of a giant colon diverticulum : Case report and review of the literature]. Chirurg 2018; 88:682-686. [PMID: 28374053 DOI: 10.1007/s00104-017-0412-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Giant diverticula are rare complications of diverticular disease. Current opinion regards operative therapy as the method of choice for the treatment of symptomatic giant diverticula; however, there is neither consensus about the technique nor about the necessary extent of resection. Based on a non-systematic review of the literature, an overview of giant diverticula in terms of epidemiology, pathology and classification is given. The current case is considered with respect to appropriate diagnostic procedures and possible therapeutic options. CASE PRESENTATION An 80-year-old female patient presented to the emergency department with abdominal pain and dyspnea. A computed tomography scan showed a large gas-filled structure in the upper left abdomen adjacent to the left colon. A giant colonic diverticulum was suspected and laparoscopy was performed. Intraoperatively, the diagnosis of a giant colon diverticulum located at the splenic flexure was confirmed. An unremarkable diverticulosis only was found in the descending colon. The giant diverticulum was treated by an atypical colon wedge resection and the postoperative course was uneventful. DISCUSSION This case report describes a laparoscopic atypical colon wedge resection as treatment of a giant colon diverticulum. Only four laparoscopic bowel resections in terms of sigmoid resections or hemicolectomy with primary anastomosis have been reported. Minimally invasive surgery can be a valuable alternative to open procedures. In the current case a laparoscopic atypical colon wedge resection was safely performed. This option might be considered as an alternative to extended resections of giant diverticula. Localization of the giant diverticulum and the simultaneous existence of diverticular disease are the main criteria for the decision between the different operative approaches.
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Affiliation(s)
- P J Roch
- Klinik für Allgemein-, Viszeral- und Transplantationschirurgie, Universitätsklinikums Heidelberg, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 110, 69120, Heidelberg, Deutschland
| | - T Friedrich
- Radiologische Abteilung des St. Josefskrankenhaus Heidelberg, St. Josefskrankenhaus Heidelberg, Landhausstraße 25, 69115, Heidelberg, Deutschland
| | - R Bönninghoff
- Chirurgische Abteilung des St. Josefskrankenhaus Heidelberg, St. Josefskrankenhaus Heidelberg, Landhausstraße 25, 69115, Heidelberg, Deutschland
| | - D Dinter
- Radiologie Schwetzingen, Bodelschwinghstr. 10, 68723, Schwetzingen, Deutschland
| | - A Rickert
- Chirurgische Abteilung des St. Josefskrankenhaus Heidelberg, St. Josefskrankenhaus Heidelberg, Landhausstraße 25, 69115, Heidelberg, Deutschland.
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Na S, Jurkovic S, Friedrich T, Koslowski T. Charge transfer through a fragment of the respiratory complex I and its regulation: an atomistic simulation approach. Phys Chem Chem Phys 2018; 20:20023-20032. [PMID: 30022212 DOI: 10.1039/c8cp02420k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We simulate electron transfer within a fragment of the NADH:ubiquinone oxidoreductase (respiratory complex I) of the hyperthermophilic bacterium Aquifex aeolicus. We apply molecular dynamics simulations, thermodynamic integration, and a thermodynamic network least squares analysis to compute two key parameters of Marcus' theory of charge transfer, the thermodynamic driving force and the reorganization energy. Intramolecular contributions to the Gibbs free energy differences of electron and hydrogen transfer processes, ΔG, are accessed by calibrating against experimental redox titration data. This approach permits the computation of the interactions between the species NAD+, FMNH2, N1a-, and N3-, and the construction of a free energy surface for the flow of electrons within the fragment. We find NAD+ to be a strong candidate for the regulation of charge transfer.
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Affiliation(s)
- Sehee Na
- Institut für Physikalische Chemie, Universität Freiburg, Albertstraße23a, 79104 Freiburg im Breisgau, Germany.
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Affiliation(s)
- A. Kassam
- School of Agriculture, Policy and Development, University of Reading, UK
| | - T. Friedrich
- Food and Agriculture Organization (FAO) of the United Nations, La Paz, Bolivia
| | - R. Derpsch
- International Consultant for Conservation Agriculture/No-till, Asunción, Paraguay
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Hoeser J, Gnandt E, Friedrich T. Low cost, microcontroller based heating device for multi-wavelength differential scanning fluorimetry. Sci Rep 2018; 8:1457. [PMID: 29362420 PMCID: PMC5780519 DOI: 10.1038/s41598-018-19702-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/02/2018] [Indexed: 11/09/2022] Open
Abstract
Differential scanning fluorimetry is a popular method to estimate the stability of a protein in distinct buffer conditions by determining its ‘melting point’. The method requires a temperature controlled fluorescence spectrometer or a RT-PCR machine. Here, we introduce a low-budget version of a microcontroller based heating device implemented into a 96-well plate reader that is connected to a standard fluorescence spectrometer. We demonstrate its potential to determine the ‘melting point’ of soluble and membranous proteins at various buffer conditions.
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Affiliation(s)
- Jo Hoeser
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg i. Br., Germany. .,Luxembourg Science Center, 50 rue Emile Mark, 4620, Differdange, Luxembourg.
| | - Emmanuel Gnandt
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg i. Br., Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg i. Br., Germany.
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Friedrich T, Bochmann A, Dinger J, Teichert S. Application of the pattern matching approach for EBSD calibration and orientation mapping, utilising dynamical EBSP simulations. Ultramicroscopy 2018; 184:44-51. [DOI: 10.1016/j.ultramic.2017.10.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/05/2017] [Accepted: 10/10/2017] [Indexed: 11/28/2022]
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Llorente-Garcia I, Lenn T, Erhardt H, Harriman OL, Liu LN, Robson A, Chiu SW, Matthews S, Willis NJ, Bray CD, Lee SH, Shin JY, Bustamante C, Liphardt J, Friedrich T, Mullineaux CW, Leake MC. Corrigendum to "Single-molecule in vivo imaging of bacterial respiratory complexes indicates delocalized oxidative phosphorylation" [Biochim. Biophys. Acta 1837(6) (2014) 811-824 DOI: 10.1016/j.bbabio.2014.01.020]. Biochim Biophys Acta Bioenerg 2017; 1859:164. [PMID: 29175561 DOI: 10.1016/j.bbabio.2017.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Isabel Llorente-Garcia
- Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, UK; Department of Physics and Astronomy, University College London, Gower St., London, WC1E 6BT, UK
| | - Tchern Lenn
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK; QB3 University of California, Berkeley CA94720, USA
| | | | | | - Lu-Ning Liu
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Alex Robson
- Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, UK
| | - Sheng-Wen Chiu
- Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, UK
| | - Sarah Matthews
- Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, UK
| | - Nicky J Willis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Christopher D Bray
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | | | - Jae Yen Shin
- QB3 University of California, Berkeley CA94720, USA
| | | | - Jan Liphardt
- QB3 University of California, Berkeley CA94720, USA
| | | | - Conrad W Mullineaux
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Mark C Leake
- Biological Physical Sciences Institute (BPSI), University of York, York YO10 5DD, UK.
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Boscary J, Friedrich T, Greuner H, Schulmeyer W, Stadler R, Mendelevitch B, Junghanns P, Ehrke G. Summary of the production of the divertor target elements of Wendelstein 7-X. Fusion Engineering and Design 2017. [DOI: 10.1016/j.fusengdes.2017.03.084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Sokol O, Scifoni E, Tinganelli W, Kraft-Weyrather W, Wiedemann J, Maier A, Boscolo D, Friedrich T, Brons S, Durante M, Krämer M. Oxygen beams for therapy: advanced biological treatment planning and experimental verification. Phys Med Biol 2017; 62:7798-7813. [PMID: 28841579 DOI: 10.1088/1361-6560/aa88a0] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nowadays there is a rising interest towards exploiting new therapeutical beams beyond carbon ions and protons. In particular, [Formula: see text]O ions are being widely discussed due to their increased LET distribution. In this contribution, we report on the first experimental verification of biologically optimized treatment plans, accounting for different biological effects, generated with the TRiP98 planning system with [Formula: see text]O beams, performed at HIT and GSI. This implies the measurements of 3D profiles of absorbed dose as well as several biological measurements. The latter includes the measurements of relative biological effectiveness along the range of linear energy transfer values from ≈20 up to ≈750 keV μ [Formula: see text], oxygen enhancement ratio values and the verification of the kill-painting approach, to overcome hypoxia, with a phantom imitating an unevenly oxygenated target. With the present implementation, our treatment planning system is able to perform a comparative analysis of different ions, according to any given condition of the target. For the particular cases of low target oxygenation, [Formula: see text]O ions demonstrate a higher peak-to-entrance dose ratio for the same cell killing in the target region compared to [Formula: see text]C ions. Based on this phenomenon, we performed a short computational analysis to reveal the potential range of treatment plans, where [Formula: see text]O can benefit over lighter modalities. It emerges that for more hypoxic target regions (partial oxygen pressure of ≈0.15% or lower) and relatively low doses (≈4 Gy or lower) the choice of [Formula: see text]O over [Formula: see text]C or [Formula: see text]He may be justified.
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Affiliation(s)
- O Sokol
- Biophysics Department, GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, D-64291 Darmstadt, Germany
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Hunter P, Delbaere M, O’Connell ME, Cammer A, Seaton JX, Friedrich T, Fick F. Did online publishers "get it right"? Using a naturalistic search strategy to review cognitive health promotion content on internet webpages. BMC Geriatr 2017; 17:125. [PMID: 28619010 PMCID: PMC5472889 DOI: 10.1186/s12877-017-0515-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 06/06/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND One of the most common uses of the Internet is to search for health-related information. Although scientific evidence pertaining to cognitive health promotion has expanded rapidly in recent years, it is unclear how much of this information has been made available to Internet users. Thus, the purpose of our study was to assess the reliability and quality of information about cognitive health promotion encountered by typical Internet users. METHODS To generate a list of relevant search terms employed by Internet users, we entered seed search terms in Google Trends and recorded any terms consistently used in the prior 2 years. To further approximate the behaviour of typical Internet users, we entered each term in Google and sampled the first two relevant results. This search, completed in October 2014, resulted in a sample of 86 webpages, 48 of which had content related to cognitive health promotion. An interdisciplinary team rated the information reliability and quality of these webpages using a standardized measure. RESULTS We found that information reliability and quality were moderate, on average. Just one retrieved page mentioned best practice, national recommendations, or consensus guidelines by name. Commercial content (i.e., product promotion, advertising content, or non-commercial) was associated with differences in reliability and quality, with product promoter webpages having the lowest mean reliability and quality ratings. CONCLUSIONS As efforts to communicate the association between lifestyle and cognitive health continue to expand, we offer these results as a baseline assessment of the reliability and quality of cognitive health promotion on the Internet.
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Affiliation(s)
- P.V. Hunter
- St. Thomas More College, University of Saskatchewan, 1437 College Drive, Saskatoon, SK S7M 0W6 Canada
| | - M. Delbaere
- Edwards School of Business, University of Saskatchewan, 25 Campus Drive, Saskatoon, SK S7N 5A7 Canada
| | - M. E. O’Connell
- Psychology, University of Saskatchewan, 9 Campus Drive, Saskatoon, SK S7N 5A5 Canada
| | - A. Cammer
- College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9 Canada
| | - J. X. Seaton
- Interdisciplinary Studies, University of Saskatchewan, 176 Thorvaldson Building, 110 Science Place, Saskatoon, SK S7N 5C9 Canada
| | - T. Friedrich
- Psychology, University of Saskatchewan, 9 Campus Drive, Saskatoon, SK S7N 5A5 Canada
| | - F. Fick
- Psychology, University of Saskatchewan, 9 Campus Drive, Saskatoon, SK S7N 5A5 Canada
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