1
|
Kirschner H, Heister N, Zouatom M, Zhou T, Hofmann E, Scherkenbeck J, Stoll R. Toward More Selective Antibiotic Inhibitors: A Structural View of the Complexed Binding Pocket of E. coli Peptide Deformylase. J Med Chem 2024; 67:6384-6396. [PMID: 38574272 DOI: 10.1021/acs.jmedchem.3c02382] [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] [Indexed: 04/06/2024]
Abstract
Peptide deformylase (PDF) is involved in bacterial protein maturation processes. Originating from the interest in a new antibiotic, tremendous effort was put into the refinement of PDF inhibitors (PDFIs) and their selectivity. We obtained a full NMR backbone assignment the emergent additional protein backbone resonances of ecPDF 1-147 in complex with 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide (2), a potential new structural scaffold for more selective PDFIs. We also determined the complex crystal structures of E. coli PDF (ecPDF fl) and 2. Our structure suggests an alternative ligand conformation within the protein, a possible starting point for further selectivity optimization. The orientation of the second ligand conformation in the crystal structure points toward a small region of the S1' pocket, which differs between bacterial PDFs and human PDF. Moreover, we analyzed the binding mode of 2 via NMR TITAN line shape analysis, revealing an induced fit mechanism.
Collapse
Affiliation(s)
- Hendrik Kirschner
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR, and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, Bochum 44801, Germany
| | - Nicole Heister
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR, and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, Bochum 44801, Germany
| | - Manuela Zouatom
- Faculty of Mathematics and Natural Sciences, Bioorganic Chemistry, University of Wuppertal, Gaußstraße 20, Wuppertal 42119, Germany
| | - Tianyi Zhou
- Faculty of Mathematics and Natural Sciences, Bioorganic Chemistry, University of Wuppertal, Gaußstraße 20, Wuppertal 42119, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, Bochum 44801, Germany
| | - Jürgen Scherkenbeck
- Faculty of Mathematics and Natural Sciences, Bioorganic Chemistry, University of Wuppertal, Gaußstraße 20, Wuppertal 42119, Germany
| | - Raphael Stoll
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR, and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, Bochum 44801, Germany
| |
Collapse
|
2
|
Kirschner H, John M, Zhou T, Bachmann N, Schultz A, Hofmann E, Bandow JE, Scherkenbeck J, Metzler-Nolte N, Stoll R. Structural Insights into Antibacterial Payload Release from Gold Nanoparticles Bound to E. coli Peptide Deformylase. ChemMedChem 2024; 19:e202300538. [PMID: 38057137 DOI: 10.1002/cmdc.202300538] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/10/2023] [Indexed: 12/08/2023]
Abstract
The lack of new antibiotics and the rapidly rising number of pathogens resistant to antibiotics pose a serious problem to mankind. In bacteria, the cell membrane provides the first line of defence to antibiotics by preventing them from reaching their molecular target. To overcome this entrance barrier, it has been suggested[1] that small Gold-Nanoparticles (AuNP) could possibly function as drug delivery systems for antibiotic ligands. Using actinonin-based ligands, we provide here proof-of-principle of AuNP functionalisation, the capability to bind and inhibit the target protein of the ligand, and the possibility to selectively release the antimicrobial payload. To this end, we successfully synthesised AuNP coated with thio-functionalised actinonin and a derivative. Interactions between 15N-enriched His-peptide deformylase 1-147 from E. coli (His-ecPDF 1-147) and compound-coated AuNP were investigated via 2D 1H-15N-HSQC NMR spectra proving the direct binding to His-ecPDF 1-147. More importantly by adding dithiothreitol (DTT), we show that the derivative is successfully released from AuNPs while still bound to His-ecPDF 1-147. Our findings indicate that AuNP-conjugated ligands can address and bind intracellular target proteins. The system introduced here presents a new delivery platform for antibiotics and allows for the easy optimisation of ligand coated AuNPs.
Collapse
Affiliation(s)
- Hendrik Kirschner
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Milena John
- Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Tianyi Zhou
- Bioorganic Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Nathalie Bachmann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - André Schultz
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Julia Elisabeth Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Jürgen Scherkenbeck
- Bioorganic Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Nils Metzler-Nolte
- Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Raphael Stoll
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| |
Collapse
|
3
|
Brocks C, Das CK, Duan J, Yadav S, Apfel UP, Ghosh S, Hofmann E, Winkler M, Engelbrecht V, Schäfer LV, Happe T. A Dynamic Water Channel Affects O 2 Stability in [FeFe]-Hydrogenases. ChemSusChem 2024; 17:e202301365. [PMID: 37830175 DOI: 10.1002/cssc.202301365] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/14/2023]
Abstract
[FeFe]-hydrogenases are capable of reducing protons at a high rate. However, molecular oxygen (O2 ) induces the degradation of their catalytic cofactor, the H-cluster, which consists of a cubane [4Fe4S] subcluster (4FeH ) and a unique diiron moiety (2FeH ). Previous attempts to prevent O2 -induced damage have focused on enhancing the protein's sieving effect for O2 by blocking the hydrophobic gas channels that connect the protein surface and the 2FeH . In this study, we aimed to block an O2 diffusion pathway and shield 4FeH instead. Molecular dynamics (MD) simulations identified a novel water channel (WH ) surrounding the H-cluster. As this hydrophilic path may be accessible for O2 molecules we applied site-directed mutagenesis targeting amino acids along WH in proximity to 4FeH to block O2 diffusion. Protein film electrochemistry experiments demonstrate increased O2 stabilities for variants G302S and S357T, and MD simulations based on high-resolution crystal structures confirmed an enhanced local sieving effect for O2 in the environment of the 4FeH in both cases. The results strongly suggest that, in wild type proteins, O2 diffuses from the 4FeH to the 2FeH . These results reveal new strategies for improving the O2 stability of [FeFe]-hydrogenases by focusing on the O2 diffusion network near the active site.
Collapse
Affiliation(s)
- Claudia Brocks
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Chandan K Das
- Faculty of Chemistry and Biochemistry, Center for Theoretical Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Jifu Duan
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Shanika Yadav
- Faculty of Chemistry and Biochemistry, Inorganic Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Ulf-Peter Apfel
- Faculty of Chemistry and Biochemistry, Inorganic Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Subhasri Ghosh
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Eckhard Hofmann
- Faculty of Biology and Biotechnology, X-ray structure analysis of proteins, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Martin Winkler
- Electrobiotechnology, TUM Campus Straubing, Schulgasse 22, Straubing, 94315, Germany
| | - Vera Engelbrecht
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Lars V Schäfer
- Faculty of Chemistry and Biochemistry, Center for Theoretical Chemistry, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Thomas Happe
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| |
Collapse
|
4
|
Weber MSR, Duran Ramirez JJ, Hentzien M, Cavassini M, Bernasconi E, Hofmann E, Furrer H, Kovari H, Stöckle M, Schmid P, Haerry D, Braun DL, Günthard HF, Kusejko K. Time Trends in Causes of Death in People with HIV: Insights from the Swiss HIV Cohort Study. Clin Infect Dis 2024:ciae014. [PMID: 38214897 DOI: 10.1093/cid/ciae014] [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: 11/07/2023] [Revised: 12/21/2023] [Accepted: 01/10/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Advancements in access to antiretroviral therapy (ART) and human immunodeficiency virus (HIV) care have led to a decline in acquired immunodeficiency syndrome (AIDS)-related deaths among people with HIV (PWH) in Switzerland. However, data on the ongoing changes in causes of death among PWH over the past 15 years is scarce. METHODS We investigated all reported deaths in the Swiss HIV Cohort Study between 2005-2022. Causes of death were categorized using the Coding Causes of Death in HIV protocol. The statistical analysis included demographic stratification to identify time trends and logistic regression models to determine associated factors for the underlying cause of death. RESULTS In total, 1630 deaths were reported, with 23.7% of individuals assigned female at birth. Out of these deaths, 147 (9.0%) were HIV/AIDS-related, 373 (22.9%) due to non-AIDS, non-hepatic (NANH) cancers, 166 (10.2%) liver-related, and 158 (9.7%) cardiovascular-related. The median age at death increased from 45.0 [40.0,53.0] years in 2005-2007 to 61.0 [56.0,69.5] years in 2020-2022. HIV/AIDS and liver-related causes of death decreased, whereas deaths from NANH cancers increased, and cardiovascular-related deaths remained relatively stable. CONCLUSION The proportionally decreasing HIV/AIDS and liver-related deaths showcase the effectiveness of ART, comprehensive HIV patient care, and interventions targeting hepatitis C virus co-infection. Future research should focus on managing cancer and cardiovascular-related conditions as the new leading causes of death among PWH. Comprehensive healthcare strategies focusing on non-AIDS-related comorbidities, cancer management, and sustaining liver and cardiovascular health are needed to bridge the ongoing health disparities between PWH and the general population.
Collapse
Affiliation(s)
- M S R Weber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - J J Duran Ramirez
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - M Hentzien
- HIV/AIDS unit, Department of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland
- University of Geneva, Geneva, Switzerland
- Reims Champagne-Ardenne University, Reims, France
| | - M Cavassini
- Department of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
- University of Lausanne, Lausanne, Switzerland
| | - E Bernasconi
- Department of Infectious Diseases, Regional Hospital Lugano EOC, Lugano, Switzerland
- University of Geneva and University of Southern Switzerland, Lugano, Switzerland
| | - E Hofmann
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - H Furrer
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - H Kovari
- Center for Infectious Diseases, Klinik im Park, Zürich, Switzerland
| | - M Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - P Schmid
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - D Haerry
- Positive Council Switzerland, Zürich, Switzerland
| | - D L Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - H F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - K Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
5
|
Duan J, Veliju A, Lampret O, Liu L, Yadav S, Apfel UP, Armstrong FA, Hemschemeier A, Hofmann E. Insights into the Molecular Mechanism of Formaldehyde Inhibition of [FeFe]-Hydrogenases. J Am Chem Soc 2023; 145:26068-26074. [PMID: 37983562 DOI: 10.1021/jacs.3c07800] [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] [Indexed: 11/22/2023]
Abstract
[FeFe]-hydrogenases are efficient H2 converting biocatalysts that are inhibited by formaldehyde (HCHO). The molecular mechanism of this inhibition has so far not been experimentally solved. Here, we obtained high-resolution crystal structures of the HCHO-treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum, showing HCHO reacts with the secondary amine base of the catalytic cofactor and the cysteine C299 of the proton transfer pathway which both are very important for catalytic turnover. Kinetic assays via protein film electrochemistry show the CpI variant C299D is significantly less inhibited by HCHO, corroborating the structural results. By combining our data from protein crystallography, site-directed mutagenesis and protein film electrochemistry, a reaction mechanism involving the cofactor's amine base, the thiol group of C299 and HCHO can be deduced. In addition to the specific case of [FeFe]-hydrogenases, our study provides additional insights into the reactions between HCHO and protein molecules.
Collapse
Affiliation(s)
- Jifu Duan
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Astrit Veliju
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Oliver Lampret
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Lingling Liu
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Shanika Yadav
- Inorganic Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Inorganic Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Energy, Electrosynthesis Group, Fraunhofer UMSICHT, 46047 Oberhausen, Germany
| | - Fraser A Armstrong
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
| | - Anja Hemschemeier
- Photobiotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| |
Collapse
|
6
|
Frascogna F, Ledermann B, Hartmann J, Pérez Patallo E, Zeqiri F, Hofmann E, Frankenberg-Dinkel N. On the evolution of the plant phytochrome chromophore biosynthesis. Plant Physiol 2023; 193:246-258. [PMID: 37311159 DOI: 10.1093/plphys/kiad327] [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] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/15/2023]
Abstract
Phytochromes are biliprotein photoreceptors present in plants, algae, certain bacteria, and fungi. Land plant phytochromes use phytochromobilin (PΦB) as the bilin chromophore. Phytochromes of streptophyte algae, the clade within which land plants evolved, employ phycocyanobilin (PCB), leading to a more blue-shifted absorption spectrum. Both chromophores are synthesized by ferredoxin-dependent bilin reductases (FDBRs) starting from biliverdin IXα (BV). In cyanobacteria and chlorophyta, BV is reduced to PCB by the FDBR phycocyanobilin:ferredoxin oxidoreductase (PcyA), whereas, in land plants, BV is reduced to PФB by phytochromobilin synthase (HY2). However, phylogenetic studies suggested the absence of any ortholog of PcyA in streptophyte algae and the presence of only PФB biosynthesis-related genes (HY2). The HY2 of the streptophyte alga Klebsormidium nitens (formerly Klebsormidium flaccidum) has already indirectly been indicated to participate in PCB biosynthesis. Here, we overexpressed and purified a His6-tagged variant of K. nitens HY2 (KflaHY2) in Escherichia coli. Employing anaerobic bilin reductase activity assays and coupled phytochrome assembly assays, we confirmed the product and identified intermediates of the reaction. Site-directed mutagenesis revealed 2 aspartate residues critical for catalysis. While it was not possible to convert KflaHY2 into a PΦB-producing enzyme by simply exchanging the catalytic pair, the biochemical investigation of 2 additional members of the HY2 lineage enabled us to define 2 distinct clades, the PCB-HY2 and the PΦB-HY2 clade. Overall, our study gives insight into the evolution of the HY2 lineage of FDBRs.
Collapse
Affiliation(s)
- Federica Frascogna
- Department of Microbiology, University of Kaiserslautern-Landau, Kaiserslautern 67663, Germany
| | - Benjamin Ledermann
- Department of Microbiology, University of Kaiserslautern-Landau, Kaiserslautern 67663, Germany
| | - Jana Hartmann
- Department of Microbiology, University of Kaiserslautern-Landau, Kaiserslautern 67663, Germany
| | - Eugenio Pérez Patallo
- Department of Microbiology, University of Kaiserslautern-Landau, Kaiserslautern 67663, Germany
| | - Fjoralba Zeqiri
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum 44780, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum 44780, Germany
| | | |
Collapse
|
7
|
Geyer J, Hofmann E, Schmitt L. The Rauischholzhausen Transport Colloquium: membrane proteins from structure to function. Biol Chem 2023:hsz-2023-0208. [PMID: 37232577 DOI: 10.1515/hsz-2023-0208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Joachim Geyer
- Institute of Pharmacology and Toxicology, Biomedical Research Center Seltersberg, Justus Liebig University, Schubertstr. 81, D-35392 Giessen, Germany
| | - Eckhard Hofmann
- Department of Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| |
Collapse
|
8
|
Mann D, Labudda K, Zimmermann S, Vocke KU, Gasper R, Kötting C, Hofmann E. ATP binding and ATP hydrolysis in full-length MsbA monitored via time-resolved Fourier transform infrared spectroscopy. Biol Chem 2023:hsz-2023-0122. [PMID: 37185095 DOI: 10.1515/hsz-2023-0122] [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: 02/05/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023]
Abstract
The essential Escherichia coli ATPase MsbA is a lipid flippase that serves as a prototype for multi drug resistant ABC transporters. Its physiological function is the transport of lipopolisaccharides to build up the outer membranes of gram negative bacteria. Although several structural and biochemical studies of MsbA have been conducted previously, a detailed picture of the dynamic processes that link ATP hydrolysis to allocrit transport remains elusive. We report here for the first time time-resolved Fourier transform infrared (FTIR) spectroscopic measurements of the ATP binding and ATP hydrolysis reaction of full-length MsbA and determined reaction rates at 288 K of k 1 = 0.49 ± 0.28 s-1 and k 2 = 0.014 ± 0.003 s-1, respectively. We further verified these rates with photocaged NPEcgAppNHp where only nucleotide binding was observable and the negative mutant MsbA-H537A that showed slow hydrolysis (k 2 < 2 × 10-4 s-1). Besides single turnover kinetics, FTIR measurements also deliver IR signatures of all educts, products and the protein. ADP remains protein-bound after ATP hydrolysis. In addition, the spectral changes observed for the two variants MsbA-S378A and MsbA-S482A correlated with the loss of hydrogen bonding to the γ-phosphate of ATP. This study paves the way for FTIR-spectroscopic investigations of allocrite transport in full-length MsbA.
Collapse
Affiliation(s)
- Daniel Mann
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Forschungszentrum Jülich GmbH, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons / ER-C-3: Structural Biology, D-52425 Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute for Biological Information Processing / IBI-6 Cellular Structural Biology, D-52425 Jülich, Germany
| | - Kristin Labudda
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (PRODI), Biospectroscopy, D-44780 Bochum, Germany
| | - Sophie Zimmermann
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Kai Ulrich Vocke
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Raphael Gasper
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Max Planck Institute of Molecular Physiology, Crystallography and Biophysics Facility, D-44227 Dortmund, Germany
| | - Carsten Kötting
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (PRODI), Biospectroscopy, D-44780 Bochum, Germany
| | - Eckhard Hofmann
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
| |
Collapse
|
9
|
Duan J, Hemschemeier A, Burr DJ, Stripp ST, Hofmann E, Happe T. Cyanide Binding to [FeFe]-Hydrogenase Stabilizes the Alternative Configuration of the Proton Transfer Pathway. Angew Chem Int Ed Engl 2023; 62:e202216903. [PMID: 36464641 PMCID: PMC10107461 DOI: 10.1002/anie.202216903] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/02/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
Hydrogenases are H2 converting enzymes that harbor catalytic cofactors in which iron (Fe) ions are coordinated by biologically unusual carbon monoxide (CO) and cyanide (CN- ) ligands. Extrinsic CO and CN- , however, inhibit hydrogenases. The mechanism by which CN- binds to [FeFe]-hydrogenases is not known. Here, we obtained crystal structures of the CN- -treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum. The high resolution of 1.39 Å allowed us to distinguish intrinsic CN- and CO ligands and to show that extrinsic CN- binds to the open coordination site of the cofactor where CO is known to bind. In contrast to other inhibitors, CN- treated crystals show conformational changes of conserved residues within the proton transfer pathway which could allow a direct proton transfer between E279 and S319. This configuration has been proposed to be vital for efficient proton transfer, but has never been observed structurally.
Collapse
Affiliation(s)
- Jifu Duan
- Department of Plant Biochemistry, Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Anja Hemschemeier
- Department of Plant Biochemistry, Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - David J Burr
- Department of Physics, Experimental Biophysics and Space Sciences, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Sven T Stripp
- Department of Biophysics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Eckhard Hofmann
- Department of Biophysics, Faculty of Biology and Biotechnology, Protein Crystallography, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Thomas Happe
- Department of Plant Biochemistry, Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| |
Collapse
|
10
|
Duan J, Hemschemeier A, Burr DJ, Stripp ST, Hofmann E, Happe T. Cyanide Binding to [FeFe]‐Hydrogenase Stabilizes the Alternative Configuration of the Proton Transfer Pathway. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202216903] [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: 12/11/2022]
Affiliation(s)
- Jifu Duan
- Ruhr-Universität Bochum: Ruhr-Universitat Bochum Plant Biochemistry Universitätsstrasse 150 44801 Bochum GERMANY
| | - Anja Hemschemeier
- Ruhr-Universität Bochum: Ruhr-Universitat Bochum Department of Plant Biochemistry GERMANY
| | - David J. Burr
- Free University of Berlin: Freie Universitat Berlin Department of Biophysics GERMANY
| | - Sven T. Stripp
- Free University of Berlin: Freie Universitat Berlin Department of Biophysics GERMANY
| | - Eckhard Hofmann
- Ruhr University Bochum: Ruhr-Universitat Bochum Department of Biophysics GERMANY
| | - Thomas Happe
- Ruhr University Bochum: Ruhr-Universitat Bochum Department of Plant Biochemistry GERMANY
| |
Collapse
|
11
|
Yayci A, Bachmann N, Dirks T, Hofmann E, Bandow JE. Characterization of three novel DyP-type peroxidases from Streptomyces chartreusis NRRL 3882. J Appl Microbiol 2022; 133:2417-2429. [PMID: 35808848 DOI: 10.1111/jam.15707] [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: 05/04/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Abstract
AIMS Actinobacteria are known to produce extracellular enzymes including DyPs. We set out to identify and characterize novel peroxidases from Streptomyces chartreusis NRRL 3882, because S. chartreusis belongs to the small group of actinobacteria with three different DyPs. METHODS AND RESULTS The genome of the actinomycete Streptomyces chartreusis NRRL 3882 was mined for novel DyP-type peroxidases. Three genes encoding for DyP-type peroxidases were cloned and overexpressed in Escherichia coli. Subsequent characterization of the recombinant proteins included examination of operating conditions such as pH, temperature, and H2 O2 concentrations, as well as substrate spectrum. Despite their high sequence similarity, the enzymes named SCDYP1-SCDYP3 presented distinct preferences regarding their operating conditions. They showed great divergence in H2 O2 tolerance and stability, with SCDYP2 being most active at concentrations above 50 mmol l-1 . Moreover, SCDYP1 and SCDYP3 preferred acidic pH (typical for DyP-type peroxidases) whereas SCDYP2 was most active at pH 8. CONCLUSIONS Regarding the function of DyPs in nature, these results suggest that availability of different DyP variants with complementary activity profiles in one organism might convey evolutionary benefits. SIGNIFICANCE AND IMPACT OF STUDY DyP-type peroxidases are able to degrade xenobiotic compounds and thus can be applied in biocatalysis and bioremediation. However, the native function of DyPs and the benefits for their producers largely remain to be elucidated.
Collapse
Affiliation(s)
- Abdulkadir Yayci
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Nathalie Bachmann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Tim Dirks
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Julia E Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Germany
| |
Collapse
|
12
|
Ackermann B, Dünschede B, Pietzenuk B, Justesen BH, Krämer U, Hofmann E, Günther Pomorski T, Schünemann D. Chloroplast Ribosomes Interact With the Insertase Alb3 in the Thylakoid Membrane. Front Plant Sci 2021; 12:781857. [PMID: 35003166 PMCID: PMC8733628 DOI: 10.3389/fpls.2021.781857] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
Members of the Oxa1/YidC/Alb3 protein family are involved in the insertion, folding, and assembly of membrane proteins in mitochondria, bacteria, and chloroplasts. The thylakoid membrane protein Alb3 mediates the chloroplast signal recognition particle (cpSRP)-dependent posttranslational insertion of nuclear-encoded light harvesting chlorophyll a/b-binding proteins and participates in the biogenesis of plastid-encoded subunits of the photosynthetic complexes. These subunits are cotranslationally inserted into the thylakoid membrane, yet very little is known about the molecular mechanisms underlying docking of the ribosome-nascent chain complexes to the chloroplast SecY/Alb3 insertion machinery. Here, we show that nanodisc-embedded Alb3 interacts with ribosomes, while the homolog Alb4, also located in the thylakoid membrane, shows no ribosome binding. Alb3 contacts the ribosome with its C-terminal region and at least one additional binding site within its hydrophobic core region. Within the C-terminal region, two conserved motifs (motifs III and IV) are cooperatively required to enable the ribosome contact. Furthermore, our data suggest that the negatively charged C-terminus of the ribosomal subunit uL4c is involved in Alb3 binding. Phylogenetic analyses of uL4 demonstrate that this region newly evolved in the green lineage during the transition from aquatic to terrestrial life.
Collapse
Affiliation(s)
- Bernd Ackermann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Björn Pietzenuk
- Department of Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Bo Højen Justesen
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Ute Krämer
- Department of Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| |
Collapse
|
13
|
Tomazic N, Overkamp KE, Wegner H, Gu B, Mahler F, Aras M, Keller S, Pierik AJ, Hofmann E, Frankenberg-Dinkel N. Exchange of a single amino acid residue in the cryptophyte phycobiliprotein lyase GtCPES expands its substrate specificity. Biochim Biophys Acta Bioenerg 2021; 1862:148493. [PMID: 34537203 DOI: 10.1016/j.bbabio.2021.148493] [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: 06/02/2021] [Revised: 08/26/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Cryptophytes are among the few eukaryotes employing phycobiliproteins (PBP) for light harvesting during oxygenic photosynthesis. In contrast to cyanobacterial PBP that are organized in membrane-associated phycobilisomes, those from cryptophytes are soluble within the chloroplast thylakoid lumen. Their light-harvesting capacity is due to covalent linkage of several open-chain tetrapyrrole chromophores (phycobilins). Guillardia theta utilizes the PBP phycoerythrin 545 with 15,16-dihydrobiliverdin (DHBV) in addition to phycoerythrobilin (PEB) as chromophores. The assembly of PBPs in cryptophytes involves the action of PBP-lyases as shown for cyanobacterial PBP. PBP-lyases facilitate the attachment of the chromophore in the right configuration and stereochemistry. Here we present the functional characterization of the eukaryotic S-type PBP lyase GtCPES. We show GtCPES-mediated transfer and covalent attachment of PEB to the conserved Cys82 of the acceptor PBP β-subunit (PmCpeB) of Prochlorococcus marinus MED4. On the basis of the previously solved crystal structure, the GtCPES binding pocket was investigated using site-directed mutagenesis. Thereby, amino acid residues involved in phycobilin binding and transfer were identified. Interestingly, exchange of a single amino acid residue Met67 to Ala extended the substrate specificity to phycocyanobilin (PCB), most likely by enlarging the substrate-binding pocket. Variant GtCPES_M67A binds both PEB and PCB forming a stable, colored complex in vitro and produced in Escherichia coli. GtCPES_M67A is able to mediate PCB transfer to Cys82 of PmCpeB. Based on these findings, we postulate that this single amino acid residue has a crucial role for bilin binding specificity of S-type phycoerythrin lyases but additional factors regulate handover to the target protein.
Collapse
Affiliation(s)
- Natascha Tomazic
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Kristina E Overkamp
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Helen Wegner
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Bin Gu
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Florian Mahler
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Germany
| | - Marco Aras
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Germany; Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Antonio J Pierik
- Biochemistry, Faculty for Chemistry, Technische Universität Kaiserslautern (TUK), Germany
| | - Eckhard Hofmann
- Proteincrystallography, Faculty for Biology and Biotechnology, Ruhr-Universität Bochum, Germany
| | | |
Collapse
|
14
|
Lienkamp AC, Burnik J, Heine T, Hofmann E, Tischler D. Characterization of the Glutathione S-Transferases Involved in Styrene Degradation in Gordonia rubripertincta CWB2. Microbiol Spectr 2021; 9:e0047421. [PMID: 34319142 PMCID: PMC8552685 DOI: 10.1128/spectrum.00474-21] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 11/29/2022] Open
Abstract
The glutathione S-transferases carried on the plasmid for the styrene-specific degradation pathway in the Actinobacterium Gordonia rubripertincta CWB2 were heterologously expressed in Escherichia coli. Both enzymes were purified via affinity chromatography and subjected to activity investigations. StyI and StyJ displayed activity toward the commonly used glutathione S-transferase model substrate 1-chloro-2,4-dinitrobenzene (CDNB) with Km values of 0.0682 ± 0.0074 and 2.0281 ± 0.1301 mM and Vmax values of 0.0158 ± 0.0002 and 0.348 ± 0.008 U mg-1 for StyI and StyJ, respectively. The conversion of the natural substrate styrene oxide to the intermediate (1-phenyl-2-hydroxyethyl)glutathione was detected for StyI with 48.3 ± 2.9 U mg-1. This elucidates one more step in the not yet fully resolved styrene-specific degradation pathway of Gordonia rubripertincta CWB2. A characterization of both purified enzymes adds more insight into the scarce research field of actinobacterial glutathione S-transferases. Moreover, a sequence and phylogenetic analysis puts both enzymes into a physiological and evolutionary context. IMPORTANCE Styrene is a toxic compound that is used at a large scale by industry for plastic production. Bacterial degradation of styrene is a possibility for bioremediation and pollution prevention. Intermediates of styrene derivatives degraded in the styrene-specific pathways are precursors for valuable chemical compounds. The pathway in Gordonia rubripertincta CWB2 has proven to accept a broader substrate range than other bacterial styrene degraders. The enzymes characterized in this study, distinguish CWB2s pathway from other known styrene degradation routes and thus might be the main key for its ability to produce ibuprofen from the respective styrene derivative. A biotechnological utilization of this cascade could lead to efficient and sustainable production of drugs, flavors, and fragrances. Moreover, research on glutathione metabolism in Actinobacteria is rare. Here, a characterization of two glutathione S-transferases of actinobacterial origin is presented, and the utilization of glutathione in the metabolism of an Actinobacterium is proven.
Collapse
Affiliation(s)
- Anna C. Lienkamp
- Microbial Biotechnology, Ruhr-Universität Bochum, Bochum, Germany
| | - Jan Burnik
- X-Ray Structure Analysis of Proteins, Ruhr-Universität Bochum, Bochum, Germany
| | - Thomas Heine
- Environmental Microbiology, TU Bergakademie Freiberg, Freiberg, Germany
| | - Eckhard Hofmann
- X-Ray Structure Analysis of Proteins, Ruhr-Universität Bochum, Bochum, Germany
| | - Dirk Tischler
- Microbial Biotechnology, Ruhr-Universität Bochum, Bochum, Germany
| |
Collapse
|
15
|
Esselborn J, Kertess L, Apfel UP, Hofmann E, Happe T. Loss of Specific Active-Site Iron Atoms in Oxygen-Exposed [FeFe]-Hydrogenase Determined by Detailed X-ray Structure Analyses. J Am Chem Soc 2019; 141:17721-17728. [PMID: 31609603 DOI: 10.1021/jacs.9b07808] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The [FeFe]-hydrogenases catalyze the uptake and evolution of hydrogen with unmatched speed at low overpotential. However, oxygen induces the degradation of the unique [6Fe-6S] cofactor within the active site, termed the H-cluster. We used X-ray structural analyses to determine possible modes of irreversible oxygen-driven inactivation. To this end, we exposed crystals of the [FeFe]-hydrogenase CpI from Clostridium pasteurianum to oxygen and quantitatively investigated the effects on the H-cluster structure over several time points using multiple data sets, while correlating it to decreases in enzyme activity. Our results reveal the loss of specific Fe atoms from both the diiron (2FeH) and the [4Fe-4S] subcluster (4FeH) of the H-cluster. Within the 2FeH, the Fe atom more distal to the 4FeH is strikingly more affected than the more proximal Fe atom. The 4FeH interconverts to a [2Fe-2S] cluster in parts of the population of active CpIADT, but not in crystals of the inactive apoCpI initially lacking the 2FeH. We thus propose two parallel processes: dissociation of the distal Fe atom and 4FeH interconversion. Both pathways appear to play major roles in the oxidative damage of [FeFe]-hydrogenases under electron-donor deprived conditions probed by our experimental setup.
Collapse
|
16
|
Schmitt L, Hofmann E, Geyer J. Spotlight on biomembranes - the 11th Transport Colloquium. Biol Chem 2019; 400:1243. [PMID: 31408433 DOI: 10.1515/hsz-2019-0336] [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: 11/15/2022]
Affiliation(s)
- Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Chair of Biophysics, Ruhr University Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Joachim Geyer
- Institute of Pharmacology and Toxicology, Justus Liebig University, Schubertstr. 81, D-35392 Gießen, Germany
| |
Collapse
|
17
|
Sommerkamp JA, Frankenberg-Dinkel N, Hofmann E. Crystal structure of the first eukaryotic bilin reductase GtPEBB reveals a flipped binding mode of dihydrobiliverdin. J Biol Chem 2019; 294:13889-13901. [PMID: 31366727 PMCID: PMC6755814 DOI: 10.1074/jbc.ra119.009306] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 05/10/2019] [Revised: 07/26/2019] [Indexed: 01/11/2023] Open
Abstract
Phycobilins are light-harvesting pigments of cyanobacteria, red algae, and cryptophytes. The biosynthesis of phycoerythrobilin (PEB) is catalyzed by the subsequent action of two ferredoxin-dependent bilin reductases (FDBRs). Although 15,16-dihydrobiliverdin (DHBV):ferredoxin oxidoreductase (PebA) catalyzes the two-electron reduction of biliverdin IXα to 15,16-DHBV, PEB:ferredoxin oxidoreductase (PebB) reduces this intermediate further to PEB. Interestingly, marine viruses encode the FDBR PebS combining both activities within one enzyme. Although PebA and PebS share a canonical fold with similar substrate-binding pockets, the structural determinants for the stereo- and regiospecific modification of their tetrapyrrole substrates are incompletely understood, also because of the lack of a PebB structure. Here, we solved the X-ray crystal structures of both substrate-free and -bound PEBB from the cryptophyte Guillardia theta at 1.90 and 1.65 Å, respectively. The structures of PEBB exhibit the typical α/β/α-sandwich fold. Interestingly, the open-chain tetrapyrrole substrate DHBV is bound in an unexpected flipped orientation within the canonical FDBR active site. Biochemical analyses of the WT enzyme and active site variants identified two central aspartate residues Asp-99 and Asp-219 as essential for catalytic activity. In addition, the conserved Arg-215 plays a critical role in substrate specificity, binding orientation, and active site integrity. Because these critical residues are conserved within certain FDBRs displaying A-ring reduction activity, we propose that they present a conserved mechanism for this reaction. The flipped substrate-binding mode indicates that two-electron reducing FDBRs utilize the same primary site within the binding pocket and that substrate orientation is the determinant for A- or D-ring regiospecificity.
Collapse
Affiliation(s)
- Johannes A Sommerkamp
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Nicole Frankenberg-Dinkel
- Department of Biology, Microbiology, Technical University Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| |
Collapse
|
18
|
Duan J, Mebs S, Laun K, Wittkamp F, Heberle J, Happe T, Hofmann E, Apfel UP, Winkler M, Senger M, Haumann M, Stripp ST. Geometry of the Catalytic Active Site in [FeFe]-Hydrogenase Is Determined by Hydrogen Bonding and Proton Transfer. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02203] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jifu Duan
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Stefan Mebs
- Department of Physics, Biophysics of Metalloenzymes, Freie Universität Berlin, 14195 Berlin, Germany
| | - Konstantin Laun
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Florian Wittkamp
- Faculty of Chemistry and Biochemistry, Inorganic Chemistry I, Ruhr University Bochum, 44801 Bochum, Germany
| | - Joachim Heberle
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Thomas Happe
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Eckhard Hofmann
- Faculty of Biology and Biotechnology, Protein Crystallography, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Faculty of Chemistry and Biochemistry, Inorganic Chemistry I, Ruhr University Bochum, 44801 Bochum, Germany
- Fraunhofer UMSICHT, 46047 Oberhausen, Germany
| | - Martin Winkler
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Moritz Senger
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Michael Haumann
- Department of Physics, Biophysics of Metalloenzymes, Freie Universität Berlin, 14195 Berlin, Germany
| | - Sven T. Stripp
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
| |
Collapse
|
19
|
Nischwitz SP, Bernardelli de Mattos I, Hofmann E, Groeber-Becker F, Funk M, Mohr GJ, Branski LK, Mautner SI, Kamolz LP. Continuous pH monitoring in wounds using a composite indicator dressing - A feasibility study. Burns 2019; 45:1336-1341. [PMID: 31371230 DOI: 10.1016/j.burns.2019.02.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/05/2019] [Accepted: 02/27/2019] [Indexed: 11/17/2022]
Abstract
PURPOSE Modern burn care strives for new means to guarantee optimised wound healing. Several studies have shown a correlation between the pH value in a (burn) wound and successful wound healing. A multitude of devices to monitor pH is available, all requiring direct wound contact and removal of the dressing for pH monitoring. The aim of this feasibility study was to create a sterile and easy to handle method for pH monitoring while simultaneously using an advanced wound dressing. MATERIALS AND METHODS Dressing sheets of biotechnologically generated nanofibrillar cellulose (epicitehydro) were chemically functionalised with the indicator dye GJM-534. pH-donors with increasing pH were subsequently applied to the created indicator dressing. To investigate temporal resolution and continuous monitoring we used circular pH-donors with different pH (7 and 10) and decreasing diameters that were placed on another dressing sheet. Clinically relevant spatial resolution was checked by a wound bed simulation with small areas (8 mm) of higher pH (10) on a field of lower pH (7) and vice versa. RESULTS The indicator dressing showed a gradual colouring from yellow to dark orange with increasing pH in steps of 0.3. After conversion of digital pictures to greyscale values, a sigmoidal distribution with a pKa-value of 8.4 was obtained. A ring-like pattern with alternating colour change corresponding to the pH was observed in the continuous monitoring experiment and the wound bed simulation delivered excellent local resolution. CONCLUSION Since the pH of a (burn) wound can have a significant influence on wound healing, a pH indicator was successfully linked to an advanced, temporary, alloplastic wound dressing material. We were able to show the possibility of pH monitoring by the dressing itself. Additional testing, including studies with large case numbers for optimisation are necessary before clinical implementation.
Collapse
Affiliation(s)
- S P Nischwitz
- COREMED - Cooperative Centre for Regenerative Medicine, Joanneum Research Forschungsgesellschaft mbH, Graz, Austria; Division of Plastic, Aesthetic and Reconstructive Surgery, Department of Surgery, Medical University of Graz, Graz, Austria.
| | - I Bernardelli de Mattos
- Fraunhofer Institute for Silicate Research ISC, Translational Center Regenerative Therapies, Wuerzburg, Germany
| | - E Hofmann
- COREMED - Cooperative Centre for Regenerative Medicine, Joanneum Research Forschungsgesellschaft mbH, Graz, Austria; Division of Plastic, Aesthetic and Reconstructive Surgery, Department of Surgery, Medical University of Graz, Graz, Austria
| | - F Groeber-Becker
- Fraunhofer Institute for Silicate Research ISC, Translational Center Regenerative Therapies, Wuerzburg, Germany
| | - M Funk
- QRSKIN GmbH, Wuerzburg, Germany
| | - G J Mohr
- MATERIALS - Institute for Surface Technologies and Photonics, Joanneum Research Forschungsgesellschaft mbH, Weiz, Austria
| | - L K Branski
- Division of Plastic, Aesthetic and Reconstructive Surgery, Department of Surgery, Medical University of Graz, Graz, Austria; Department of Surgery, University of Texas Medical Branch and Shriners Hospitals for Children-Galveston®, Galveston, TX, USA
| | - S I Mautner
- Division of Plastic, Aesthetic and Reconstructive Surgery, Department of Surgery, Medical University of Graz, Graz, Austria; HEALTH - Institute for Biomedicine and Health Sciences, Joanneum Research Forschungsgesellschaft mbH, Graz, Austria
| | - L P Kamolz
- COREMED - Cooperative Centre for Regenerative Medicine, Joanneum Research Forschungsgesellschaft mbH, Graz, Austria; Division of Plastic, Aesthetic and Reconstructive Surgery, Department of Surgery, Medical University of Graz, Graz, Austria
| |
Collapse
|
20
|
Rehic E, Hoenig D, Kamba BE, Goehring A, Hofmann E, Gasper R, Matena A, Bayer P. Structural Analysis of the 42 kDa Parvulin of Trypanosoma brucei. Biomolecules 2019; 9:biom9030093. [PMID: 30866577 PMCID: PMC6468809 DOI: 10.3390/biom9030093] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 02/28/2019] [Accepted: 02/28/2019] [Indexed: 11/16/2022] Open
Abstract
Trypanosoma brucei is a unicellular eukaryotic parasite, which causes the African sleeping sickness in humans. The recently discovered trypanosomal protein Parvulin 42 (TbPar42) plays a key role in parasite cell proliferation. Homologues of this two-domain protein are exclusively found in protozoa species. TbPar42 exhibits an N-terminal forkhead associated (FHA)-domain and a peptidyl-prolyl-cis/trans-isomerase (PPIase) domain, both connected by a linker. Using NMR and X-ray analysis as well as activity assays, we report on the structures of the single domains of TbPar42, discuss their intra-molecular interplay, and give some initial hints as to potential cellular functions of the protein.
Collapse
Affiliation(s)
- Edisa Rehic
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Dana Hoenig
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Bianca E Kamba
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Anna Goehring
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Raphael Gasper
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany.
- Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany.
| | - Anja Matena
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| | - Peter Bayer
- University Duisburg-Essen, Research Group Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.
| |
Collapse
|
21
|
Rodríguez-Maciá P, Kertess L, Burnik J, Birrell JA, Hofmann E, Lubitz W, Happe T, Rüdiger O. His-Ligation to the [4Fe–4S] Subcluster Tunes the Catalytic Bias of [FeFe] Hydrogenase. J Am Chem Soc 2018; 141:472-481. [DOI: 10.1021/jacs.8b11149] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Patricia Rodríguez-Maciá
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Leonie Kertess
- Photobiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Jan Burnik
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - James A. Birrell
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Thomas Happe
- Photobiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
22
|
Duan J, Senger M, Esselborn J, Engelbrecht V, Wittkamp F, Apfel UP, Hofmann E, Stripp ST, Happe T, Winkler M. Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases. Nat Commun 2018; 9:4726. [PMID: 30413719 PMCID: PMC6226526 DOI: 10.1038/s41467-018-07140-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [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: 06/25/2018] [Accepted: 10/18/2018] [Indexed: 11/29/2022] Open
Abstract
The unmatched catalytic turnover rates of [FeFe]-hydrogenases require an exceptionally efficient proton-transfer (PT) pathway to shuttle protons as substrates or products between bulk water and catalytic center. For clostridial [FeFe]-hydrogenase CpI such a pathway has been proposed and analyzed, but mainly on a theoretical basis. Here, eleven enzyme variants of two different [FeFe]-hydrogenases (CpI and HydA1) with substitutions in the presumptive PT-pathway are examined kinetically, spectroscopically, and crystallographically to provide solid experimental proof for its role in hydrogen-turnover. Targeting key residues of the PT-pathway by site directed mutagenesis significantly alters the pH-activity profile of these variants and in presence of H2 their cofactor is trapped in an intermediate state indicative of precluded proton-transfer. Furthermore, crystal structures coherently explain the individual levels of residual activity, demonstrating e.g. how trapped H2O molecules rescue the interrupted PT-pathway. These features provide conclusive evidence that the targeted positions are indeed vital for catalytic proton-transfer. [FeFe]-hydrogenases catalyze H2-evolution and -oxidation at very high turnover-rates. Here the authors provide experimental evidence for the proposed proton-transfer (PT) pathway by kinetically, spectroscopically, and crystallographically characterizing eleven mutants from the two [FeFe]-hydrogenases CpI and HydA1.
Collapse
Affiliation(s)
- Jifu Duan
- Department of Plant Biochemistry, Photobiotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Moritz Senger
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Julian Esselborn
- Department of Plant Biochemistry, Photobiotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Vera Engelbrecht
- Department of Plant Biochemistry, Photobiotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Florian Wittkamp
- Department of Chemistry and Biochemistry, Inorganic Chemistry Ι, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Ulf-Peter Apfel
- Department of Chemistry and Biochemistry, Inorganic Chemistry Ι, Ruhr-Universität Bochum, 44801, Bochum, Germany.,Fraunhofer UMSICHT, Osterfelder Straße, 346047, Oberhausen, Germany
| | - Eckhard Hofmann
- Department of Biophysics, Protein Crystallography, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Sven T Stripp
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Thomas Happe
- Department of Plant Biochemistry, Photobiotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany.
| | - Martin Winkler
- Department of Plant Biochemistry, Photobiotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany.
| |
Collapse
|
23
|
Mhaindarkar D, Gasper R, Lupilov N, Hofmann E, Leichert LI. Loss of a conserved salt bridge in bacterial glycosyl hydrolase BgIM-G1 improves substrate binding in temperate environments. Commun Biol 2018; 1:171. [PMID: 30345395 PMCID: PMC6192996 DOI: 10.1038/s42003-018-0167-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/13/2018] [Indexed: 11/09/2022] Open
Abstract
Salt bridges are the strongest electrostatic interactions in proteins. They substantially contribute to a protein's structural stability. Thus, mutations of salt bridges are typically selected against. Here, we report on the evolutionary loss of a highly conserved salt bridge in the GH1 family glycosyl hydrolase BglM-G1. BglM-G1's gene was found in the bacterial metagenome of a temperate, seasonally cold marine habitat. In BglM-G1, arginine 75 is replaced by a histidine. While fully retaining β-glucosidase activity, BglM-G1 is less heat stable than an H75R variant, in which the salt bridge was artificially re-introduced. However, the K m toward its substrates was lower in wild type, leading to an overall higher catalytic efficiency. Our results indicate that this loss of the salt bridge leads to higher flexibility in BglM-G1's active site, trading structural stability at high temperatures, a trait not needed in a temperate, seasonally cold habitat, for a more effective catalytic activity.
Collapse
Affiliation(s)
- Dipali Mhaindarkar
- Ruhr University Bochum, Fakultät für Medizin, Institute for Biochemistry and Pathobiochemistry, Microbial Biochemistry, Universitätsstr. 150, 44780, Bochum, Germany
| | - Raphael Gasper
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Department of Biophysics, Protein Crystallography, Universitätsstr. 150, 44780, Bochum, Germany
| | - Natalie Lupilov
- Ruhr University Bochum, Fakultät für Medizin, Institute for Biochemistry and Pathobiochemistry, Microbial Biochemistry, Universitätsstr. 150, 44780, Bochum, Germany
| | - Eckhard Hofmann
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Department of Biophysics, Protein Crystallography, Universitätsstr. 150, 44780, Bochum, Germany
| | - Lars I Leichert
- Ruhr University Bochum, Fakultät für Medizin, Institute for Biochemistry and Pathobiochemistry, Microbial Biochemistry, Universitätsstr. 150, 44780, Bochum, Germany.
| |
Collapse
|
24
|
Vinklárek IS, Bornemann TLV, Lokstein H, Hofmann E, Alster J, Pšenčík J. Temperature Dependence of Chlorophyll Triplet Quenching in Two Photosynthetic Light-Harvesting Complexes from Higher Plants and Dinoflagellates. J Phys Chem B 2018; 122:8834-8845. [PMID: 30179014 DOI: 10.1021/acs.jpcb.8b06751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Chlorophyll (Chl) triplet states generated in photosynthetic light-harvesting complexes (LHCs) can be quenched by carotenoids to prevent the formation of reactive singlet oxygen. Although this quenching occurs with an efficiency close to 100% at physiological temperatures, the Chl triplets are often observed at low temperatures. This might be due to the intrinsic temperature dependence of the Dexter mechanism of excitation energy transfer, which governs triplet quenching, or by temperature-induced conformational changes. Here, we report about the temperature dependence of Chl triplet quenching in two LHCs. We show that both the effects contribute significantly. In LHC II of higher plants, the core Chls are quenched with a high efficiency independent of temperature. A different subpopulation of Chls, which increases with lowering temperature, is not quenched at all. This is probably caused by the conformational changes which detach these Chls from the energy-transfer chain. In a membrane-intrinsic LHC of dinoflagellates, similarly two subpopulations of Chls were observed. In addition, another part of Chl triplets is quenched by carotenoids with a rate which decreases with temperature. This allowed us to study the temperature dependence of Dexter energy transfer. Finally, a part of Chls was quenched by triplet-triplet annihilation, a phenomenon which was not observed for LHCs before.
Collapse
Affiliation(s)
- Ivo S Vinklárek
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics , Charles University , Ke Karlovu 3 , 121 16 Prague 2 , Czech Republic
| | - Till L V Bornemann
- Protein Crystallography, Faculty of Biology and Biotechnology , Ruhr-University Bochum , D-44780 Bochum , Germany
| | - Heiko Lokstein
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics , Charles University , Ke Karlovu 3 , 121 16 Prague 2 , Czech Republic
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology , Ruhr-University Bochum , D-44780 Bochum , Germany
| | - Jan Alster
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics , Charles University , Ke Karlovu 3 , 121 16 Prague 2 , Czech Republic
| | - Jakub Pšenčík
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics , Charles University , Ke Karlovu 3 , 121 16 Prague 2 , Czech Republic
| |
Collapse
|
25
|
Kertess L, Wittkamp F, Sommer C, Esselborn J, Rüdiger O, Reijerse EJ, Hofmann E, Lubitz W, Winkler M, Happe T, Apfel UP. Chalcogenide substitution in the [2Fe] cluster of [FeFe]-hydrogenases conserves high enzymatic activity. Dalton Trans 2018; 46:16947-16958. [PMID: 29177350 DOI: 10.1039/c7dt03785f] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
[FeFe]-Hydrogenases efficiently catalyze the uptake and evolution of H2 due to the presence of an inorganic [6Fe-6S]-cofactor (H-cluster). This cofactor is comprised of a [4Fe-4S] cluster coupled to a unique [2Fe] cluster where the catalytic turnover of H2/H+ takes place. We herein report on the synthesis of a selenium substituted [2Fe] cluster [Fe2{μ(SeCH2)2NH}(CO)4(CN)2]2- (ADSe) and its successful in vitro integration into the native protein scaffold of [FeFe]-hydrogenases HydA1 from Chlamydomonas reinhardtii and CpI from Clostridium pasteurianum yielding fully active enzymes (HydA1-ADSe and CpI-ADSe). FT-IR spectroscopy and X-ray structure analysis confirmed the presence of structurally intact ADSe at the active site. Electrochemical assays reveal that the selenium containing enzymes are more biased towards hydrogen production than their native counterparts. In contrast to previous chalcogenide exchange studies, the S to Se exchange herein is not based on a simple reconstitution approach using ionic cluster constituents but on the in vitro maturation with a pre-synthesized selenium-containing [2Fe] mimic. The combination of biological and chemical methods allowed for the creation of a novel [FeFe]-hydrogenase with a [2Fe2Se]-active site which confers individual catalytic features.
Collapse
Affiliation(s)
- L Kertess
- Ruhr-Universität Bochum, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Universitätsstraße 150, 44801 Bochum, Germany.
| | - F Wittkamp
- Ruhr-Universität Bochum, Anorganische Chemie I/Bioanorganische Chemie, Universitätsstraße 150, 44801 Bochum, Germany.
| | - C Sommer
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - J Esselborn
- Ruhr-Universität Bochum, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Universitätsstraße 150, 44801 Bochum, Germany.
| | - O Rüdiger
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - E J Reijerse
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - E Hofmann
- Ruhr-Universität Bochum, Lehrstuhl für Biophysik, AG Röntgenstrukturanalyse an Proteinen, Universitätsstraße 150, 44801 Bochum, Germany
| | - W Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - M Winkler
- Ruhr-Universität Bochum, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Universitätsstraße 150, 44801 Bochum, Germany.
| | - T Happe
- Ruhr-Universität Bochum, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Universitätsstraße 150, 44801 Bochum, Germany.
| | - U-P Apfel
- Ruhr-Universität Bochum, Anorganische Chemie I/Bioanorganische Chemie, Universitätsstraße 150, 44801 Bochum, Germany.
| |
Collapse
|
26
|
Hofmann E, Failing K, Wehrend A. Veränderungen an Vulva und Vestibulum bei Mutterkühen und Färsen in den letzten sieben Tagen vor der Geburt. Tierarztl Prax Ausg G Grosstiere Nutztiere 2018. [DOI: 10.1055/s-0037-1621051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Zusammenfassung:
Gegenstand und Ziel: Ziel dieser Untersuchung war zu überprüfen, inwiefern die Ödematisierung der Vulva, Austritt von Sekret aus der Rima vulvae unddie Veränderung der Schleimhautfarbe im Vestibulum dazu geeignet sind, bei Mutterkühen den genauen Geburtszeitpunktzu bestimmen. Weiterhin sollte die Frage beantwortetwerden,ob ein Rasse- und ein Paritätseinfluss auf diese Parameter bestehen. Material und Methoden: An 105 Tieren (10 Färsen; 95 Kühe, davon 68 Fleckvieh-Kühe und 27 Kreuzungstiere Fleckvieh x Limousin) wurden während der letzten 168 Stunden ante partum alle acht Stunden folgende Merkmale untersucht: Grad der Vulvaödematisierung, Schleimaustritt aus der Rima vulvae und Farbe der Vestibu- larschleimhaut. Ergebnisse: Alle Tiere zeigten eine ÖdematisierteVulva. DerAnteilvon Tieren mit hochgradiger Ödematisierung nahm mit nahender Geburt zu (p <0,001). Zwischen Kühen und Färsen sowie den Rassen ließ sich kein Unterschied nachweisen. Mit zeitlicher Annäherung an den Partus erhöhte sich derAn- teil der Tiere mit Schleimaustritt aus der Rima vulvae nicht (p >0,05). Die Intensitätdes Schleimaustritts war bei Kühen stärker alsbei Färsen (p < 0,05). Rasseunterschiede bestanden nicht. Statistisch signifikante Veränderungen der Schleimhautfarbe des Vestibulums konnten nicht festgestellt werden. Zwischen Kühen und Färsen und zwischen den Rassen fanden sich keine Unterschiede. Schlussfolgerung und klinische Relevanz: Der Grad der Vulvaödematisierung zeigt eine starke zeitliche Bindung zum Abkalbetermin. Sie ist jedoch nicht dazu geeignet,den Zeitpunktdes Partus genauer zu terminieren. Keine zeitliche Bindung besteht zwischen der Veränderung der Vestibularschleimhautfarbe sowie dem Austritt vonSchleimaus der Rima vulvae in der letzten Woche ante partum und dem Geburtszeitpunkt.
Collapse
|
27
|
Ledermann B, Schwan M, Sommerkamp JA, Hofmann E, Béjà O, Frankenberg-Dinkel N. Evolution and molecular mechanism of four-electron reducing ferredoxin-dependent bilin reductases from oceanic phages. FEBS J 2017; 285:339-356. [PMID: 29156487 DOI: 10.1111/febs.14341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 09/29/2017] [Revised: 11/06/2017] [Accepted: 11/16/2017] [Indexed: 01/17/2023]
Abstract
Ferredoxin-dependent bilin reductases (FDBRs) are a class of enzymes reducing the heme metabolite biliverdin IXα (BV) to form open-chain tetrapyrroles used for light-perception and light-harvesting in photosynthetic organisms. Thus far, seven FDBR families have been identified, each catalysing a distinct reaction and either transferring two or four electrons from ferredoxin onto the substrate. The newest addition to the family is PcyX, originally identified from metagenomics data derived from phage. Phylogenetically, PcyA is the closest relative catalysing the reduction of BV to phycocyanobilin. PcyX, however, converts the same substrate to phycoerythrobilin, resembling the reaction catalysed by cyanophage PebS. Within this study, we aimed at understanding the evolution of catalytic activities within FDBRs using PcyX as an example. Additional members of the PcyX clade and a remote member of the PcyA family were investigated to gain insights into catalysis. Biochemical data in combination with the PcyX crystal structure revealed that a conserved aspartate-histidine pair is critical for activity. Interestingly, the same residues are part of a catalytic Asp-His-Glu triad in PcyA, including an additional Glu. While this Glu residue is replaced by Asp in PcyX, it is not involved in catalysis. Substitution back to a Glu failed to convert PcyX to a PcyA. Therefore, the change in regiospecificity is not only caused by individual catalytic amino acid residues. Rather the combination of the architecture of the active site with the positioning of the substrate triggers specific proton transfer yielding the individual phycobilin products. ENZYMES Suggested EC number for PcyX: 1.3.7.6 DATABASES: The PcyX X-ray structure was deposited in the PDB with the accession code 5OWG.
Collapse
Affiliation(s)
- Benjamin Ledermann
- Department of Biology, Microbiology, Technical University Kaiserslautern, Germany
| | - Meike Schwan
- Department of Biology, Microbiology, Technical University Kaiserslautern, Germany
| | - Johannes A Sommerkamp
- Protein Crystallography, Faculty for Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty for Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | | |
Collapse
|
28
|
Hofmann E, Loza-Gomez A, Lam J, Menchine M. 38 Does EMS Transport of Septic Patients Improve Downstream Processes of Care? Ann Emerg Med 2017. [DOI: 10.1016/j.annemergmed.2017.07.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
29
|
Winkler M, Senger M, Duan J, Esselborn J, Wittkamp F, Hofmann E, Apfel UP, Stripp ST, Happe T. Accumulating the hydride state in the catalytic cycle of [FeFe]-hydrogenases. Nat Commun 2017; 8:16115. [PMID: 28722011 PMCID: PMC5524980 DOI: 10.1038/ncomms16115] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [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: 02/04/2017] [Accepted: 05/30/2017] [Indexed: 01/07/2023] Open
Abstract
H2 turnover at the [FeFe]-hydrogenase cofactor (H-cluster) is assumed to follow a reversible heterolytic mechanism, first yielding a proton and a hydrido-species which again is double-oxidized to release another proton. Three of the four presumed catalytic intermediates (Hox, Hred/Hred and Hsred) were characterized, using various spectroscopic techniques. However, in catalytically active enzyme, the state containing the hydrido-species, which is eponymous for the proposed heterolytic mechanism, has yet only been speculated about. We use different strategies to trap and spectroscopically characterize this transient hydride state (Hhyd) for three wild-type [FeFe]-hydrogenases. Applying a novel set-up for real-time attenuated total-reflection Fourier-transform infrared spectroscopy, we monitor compositional changes in the state-specific infrared signatures of [FeFe]-hydrogenases, varying buffer pH and gas composition. We selectively enrich the equilibrium concentration of Hhyd, applying Le Chatelier’s principle by simultaneously increasing substrate and product concentrations (H2/H+). Site-directed manipulation, targeting either the proton-transfer pathway or the adt ligand, significantly enhances Hhyd accumulation independent of pH. Of the four intermediates in the catalytic cycle of [FeFe]-hydrogenases, the hydride state still has eluded characterization. Here, the authors shift the reaction equilibrium for three hydrogenases and enrich the hydride-bound species, characterizing them using a real-time IR spectroscopic technique.
Collapse
Affiliation(s)
- Martin Winkler
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Moritz Senger
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jifu Duan
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Julian Esselborn
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Florian Wittkamp
- Fakultät für Chemie und Biochemie, Lehrstuhl für Anorganische Chemie I/Bioanorganische Chemie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Eckhard Hofmann
- AG Proteinkristallographie, Lehrstuhl für Biophysik, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Ulf-Peter Apfel
- Fakultät für Chemie und Biochemie, Lehrstuhl für Anorganische Chemie I/Bioanorganische Chemie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Sven Timo Stripp
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Thomas Happe
- AG Photobiotechnologie, Lehrstuhl für Biochemie der Pflanzen, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| |
Collapse
|
30
|
Schmitt L, Geyer J, Hofmann E. Highlight: the transporter colloquium – spotlight on membrane proteins. Biol Chem 2017; 398:143. [DOI: 10.1515/hsz-2016-0335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
31
|
Gasper R, Schwach J, Hartmann J, Holtkamp A, Wiethaus J, Riedel N, Hofmann E, Frankenberg-Dinkel N. Distinct Features of Cyanophage-encoded T-type Phycobiliprotein Lyase ΦCpeT: THE ROLE OF AUXILIARY METABOLIC GENES. J Biol Chem 2017; 292:3089-3098. [PMID: 28073912 DOI: 10.1074/jbc.m116.769703] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 11/28/2016] [Revised: 01/03/2017] [Indexed: 11/06/2022] Open
Abstract
Auxiliary metabolic genes (AMG) are commonly found in the genomes of phages that infect cyanobacteria and increase the fitness of the cyanophage. AMGs are often homologs of host genes, and also typically related to photosynthesis. For example, the ΦcpeT gene in the cyanophage P-HM1 encodes a putative phycobiliprotein lyase related to cyanobacterial T-type lyases, which facilitate attachment of linear tetrapyrrole chromophores to Cys-155 of phycobiliprotein β-subunits, suggesting that ΦCpeT may also help assemble light-harvesting phycobiliproteins during infection. To investigate this possibility, we structurally and biochemically characterized recombinant ΦCpeT. The solved crystal structure of ΦCpeT at 1.8-Å resolution revealed that the protein adopts a similar fold as the cyanobacterial T-type lyase CpcT from Nostoc sp. PCC7120 but overall is more compact and smaller. ΦCpeT specifically binds phycoerythrobilin (PEB) in vitro leading to a tight complex that can also be formed in Escherichia coli when it is co-expressed with genes encoding PEB biosynthesis (i.e. ho1 and pebS). The formed ΦCpeT·PEB complex was very stable as the chromophore was not lost during chromatography and displayed a strong red fluorescence with a fluorescence quantum yield of ΦF = 0.3. This complex was not directly able to transfer PEB to the host phycobiliprotein β-subunit. However, it could assist the host lyase CpeS in its function by providing a pool of readily available PEB, a feature that might be important for fast phycobiliprotein assembly during phage infection.
Collapse
Affiliation(s)
| | - Julia Schwach
- Physiology of Microorganisms Group, Faculty for Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum
| | - Jana Hartmann
- Department of Biology, Division for Microbiology, Technical University Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Andrea Holtkamp
- Physiology of Microorganisms Group, Faculty for Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum
| | - Jessica Wiethaus
- Physiology of Microorganisms Group, Faculty for Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum
| | - Natascha Riedel
- Department of Biology, Division for Microbiology, Technical University Kaiserslautern, 67663 Kaiserslautern, Germany
| | | | - Nicole Frankenberg-Dinkel
- Physiology of Microorganisms Group, Faculty for Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum; Department of Biology, Division for Microbiology, Technical University Kaiserslautern, 67663 Kaiserslautern, Germany.
| |
Collapse
|
32
|
Hofmann E, Di Fazio P, Bartsch DK, Gress T, Wissniowski TT. Cux1 confers resistance to apoptotic cell death in liver cancer cells. Z Gastroenterol 2016. [DOI: 10.1055/s-0036-1597464] [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] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- E Hofmann
- Philipps University Marburg, Department of Visceral, Thoracic and Vascular Surgery, Marburg, Germany
| | - P Di Fazio
- Philipps University Marburg, Department of Visceral, Thoracic and Vascular Surgery, Marburg, Germany
| | - DK Bartsch
- Philipps University Marburg, Department of Visceral, Thoracic and Vascular Surgery, Marburg, Germany
| | - T Gress
- Philipps University Marburg, Department of Gastroenterology, Marburg, Germany
| | - TT Wissniowski
- Philipps University Marburg, Department of Gastroenterology, Marburg, Germany
| |
Collapse
|
33
|
Gasper R, Effenberger I, Kolesinski P, Terlecka B, Hofmann E, Schaller A. Dirigent Protein Mode of Action Revealed by the Crystal Structure of AtDIR6. Plant Physiol 2016; 172:2165-2175. [PMID: 27756822 PMCID: PMC5129718 DOI: 10.1104/pp.16.01281] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/15/2016] [Indexed: 05/02/2023]
Abstract
Dirigent proteins impart stereoselectivity to phenoxy radical coupling reactions in plants and, thus, play an essential role in the biosynthesis of biologically active natural products. This includes the regioselective and enantioselective coupling and subsequent cyclization of two coniferyl alcohol radicals to pinoresinol as the committed step of lignan biosynthesis. The reaction is controlled by dirigent proteins, which, depending on the species and protein, direct the reaction to either (+)- or (-)-pinoresinol. We present the crystal structure of the (-)-pinoresinol forming DIRIGENT PROTEIN6 (AtDIR6) from Arabidopsis (Arabidopsis thaliana) with data to 1.4 Å resolution. The structure shows AtDIR6 as an eight-stranded antiparallel β-barrel that forms a trimer with spatially well-separated cavities for substrate binding. The binding cavities are two lobed, exhibiting two opposing pockets, each lined with a set of hydrophilic and potentially catalytic residues, including essential aspartic acids. These residues are conserved between (+) and (-)-pinoresinol-forming DIRs and required for activity. The structure supports a model in which two substrate radicals bind to each of the DIR monomers. With the aromatic rings fixed in the two pockets, the propionyl side chains face each other for radical-radical coupling, and stereoselectivity is determined by the exact positioning of the side chains. Extensive mutational analysis supports a previously unrecognized function for DIRs in catalyzing the cyclization of the bis-quinone methide reaction intermediate to yield (+)- or (-)-pinoresinol.
Collapse
Affiliation(s)
- Raphael Gasper
- Ruhr University Bochum, AG Protein Crystallography, Biophysics, 44801 Bochum, Germany (R.G., B.T., E.H.)
- University of Hohenheim, Institute of Plant Physiology and Biotechnology, 70593 Stuttgart, Germany (I.E., A.S); and
- University of Wroclaw, Laboratory of Biophysics, Faculty of Biotechnology, 50-383 Wroclaw, Poland (P.K.)
| | - Isabelle Effenberger
- Ruhr University Bochum, AG Protein Crystallography, Biophysics, 44801 Bochum, Germany (R.G., B.T., E.H.)
- University of Hohenheim, Institute of Plant Physiology and Biotechnology, 70593 Stuttgart, Germany (I.E., A.S); and
- University of Wroclaw, Laboratory of Biophysics, Faculty of Biotechnology, 50-383 Wroclaw, Poland (P.K.)
| | - Piotr Kolesinski
- Ruhr University Bochum, AG Protein Crystallography, Biophysics, 44801 Bochum, Germany (R.G., B.T., E.H.)
- University of Hohenheim, Institute of Plant Physiology and Biotechnology, 70593 Stuttgart, Germany (I.E., A.S); and
- University of Wroclaw, Laboratory of Biophysics, Faculty of Biotechnology, 50-383 Wroclaw, Poland (P.K.)
| | - Barbara Terlecka
- Ruhr University Bochum, AG Protein Crystallography, Biophysics, 44801 Bochum, Germany (R.G., B.T., E.H.)
- University of Hohenheim, Institute of Plant Physiology and Biotechnology, 70593 Stuttgart, Germany (I.E., A.S); and
- University of Wroclaw, Laboratory of Biophysics, Faculty of Biotechnology, 50-383 Wroclaw, Poland (P.K.)
| | - Eckhard Hofmann
- Ruhr University Bochum, AG Protein Crystallography, Biophysics, 44801 Bochum, Germany (R.G., B.T., E.H.);
- University of Hohenheim, Institute of Plant Physiology and Biotechnology, 70593 Stuttgart, Germany (I.E., A.S); and
- University of Wroclaw, Laboratory of Biophysics, Faculty of Biotechnology, 50-383 Wroclaw, Poland (P.K.)
| | - Andreas Schaller
- Ruhr University Bochum, AG Protein Crystallography, Biophysics, 44801 Bochum, Germany (R.G., B.T., E.H.);
- University of Hohenheim, Institute of Plant Physiology and Biotechnology, 70593 Stuttgart, Germany (I.E., A.S); and
- University of Wroclaw, Laboratory of Biophysics, Faculty of Biotechnology, 50-383 Wroclaw, Poland (P.K.)
| |
Collapse
|
34
|
Hofmann E, Milano P, Desai S, Lam C, Kim H, Eiting E, Menchine M. 199 Is Time to Antibiotics in Sepsis a Waste of Time? Ann Emerg Med 2016. [DOI: 10.1016/j.annemergmed.2016.08.212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
35
|
Noth J, Esselborn J, Güldenhaupt J, Brünje A, Sawyer A, Apfel UP, Gerwert K, Hofmann E, Winkler M, Happe T. [FeFe]-Hydrogenase with Chalcogenide Substitutions at the H-Cluster Maintains Full H2
Evolution Activity. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511896] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jens Noth
- Ruhr Universität Bochum; Lehrstuhl für Biochemie der Pflanzen; AG Photobiotechnologie; Universitätsstrasse 150 44801 Bochum Germany
| | - Julian Esselborn
- Ruhr Universität Bochum; Lehrstuhl für Biochemie der Pflanzen; AG Photobiotechnologie; Universitätsstrasse 150 44801 Bochum Germany
| | - Jörn Güldenhaupt
- Ruhr Universität Bochum; Lehrstuhl für Biophysik, AG Spektroskopie; Universitätsstrasse 150 44801 Bochum Germany
| | - Annika Brünje
- Ruhr Universität Bochum; Lehrstuhl für Biochemie der Pflanzen; AG Photobiotechnologie; Universitätsstrasse 150 44801 Bochum Germany
| | - Anne Sawyer
- Ruhr Universität Bochum; Lehrstuhl für Biochemie der Pflanzen; AG Photobiotechnologie; Universitätsstrasse 150 44801 Bochum Germany
| | - Ulf-Peter Apfel
- Ruhr Universität Bochum; Fakultät für Chemie und Biochemie; Lehrstuhl für Anorganische Chemie I/ Bioanorganische Chemie; Universitätsstrasse 150 44801 Bochum Germany
| | - Klaus Gerwert
- Ruhr Universität Bochum; Lehrstuhl für Biophysik, AG Spektroskopie; Universitätsstrasse 150 44801 Bochum Germany
| | - Eckhard Hofmann
- Ruhr Universität Bochum; Lehrstuhl für Biophysik; AG Röntgenstrukturanalyse an Proteinen; Universitätsstrasse 150 44801 Bochum Germany
| | - Martin Winkler
- Ruhr Universität Bochum; Lehrstuhl für Biochemie der Pflanzen; AG Photobiotechnologie; Universitätsstrasse 150 44801 Bochum Germany
| | - Thomas Happe
- Ruhr Universität Bochum; Lehrstuhl für Biochemie der Pflanzen; AG Photobiotechnologie; Universitätsstrasse 150 44801 Bochum Germany
| |
Collapse
|
36
|
Noth J, Esselborn J, Güldenhaupt J, Brünje A, Sawyer A, Apfel UP, Gerwert K, Hofmann E, Winkler M, Happe T. [FeFe]-Hydrogenase with Chalcogenide Substitutions at the H-Cluster Maintains Full H2 Evolution Activity. Angew Chem Int Ed Engl 2016; 55:8396-400. [PMID: 27214763 DOI: 10.1002/anie.201511896] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [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: 12/23/2015] [Revised: 03/27/2016] [Indexed: 01/08/2023]
Abstract
The [FeFe]-hydrogenase HYDA1 from Chlamydomonas reinhardtii is particularly amenable to biochemical and biophysical characterization because the H-cluster in the active site is the only inorganic cofactor present. Herein, we present the complete chemical incorporation of the H-cluster into the HYDA1-apoprotein scaffold and, furthermore, the successful replacement of sulfur in the native [4FeH ] cluster with selenium. The crystal structure of the reconstituted pre-mature HYDA1[4Fe4Se]H protein was determined, and a catalytically intact artificial H-cluster variant was generated upon in vitro maturation. Full hydrogen evolution activity as well as native-like composition and behavior of the redesigned enzyme were verified through kinetic assays, FTIR spectroscopy, and X-ray structure analysis. These findings reveal that even a bioinorganic active site with exceptional complexity can exhibit a surprising level of compositional plasticity.
Collapse
Affiliation(s)
- Jens Noth
- Ruhr Universität Bochum, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Julian Esselborn
- Ruhr Universität Bochum, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Jörn Güldenhaupt
- Ruhr Universität Bochum, Lehrstuhl für Biophysik, AG Spektroskopie, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Annika Brünje
- Ruhr Universität Bochum, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Anne Sawyer
- Ruhr Universität Bochum, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Ulf-Peter Apfel
- Ruhr Universität Bochum, Fakultät für Chemie und Biochemie, Lehrstuhl für Anorganische Chemie I/ Bioanorganische Chemie, Universitätsstrasse 150, 44801, Bochum, Germany.
| | - Klaus Gerwert
- Ruhr Universität Bochum, Lehrstuhl für Biophysik, AG Spektroskopie, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Eckhard Hofmann
- Ruhr Universität Bochum, Lehrstuhl für Biophysik, AG Röntgenstrukturanalyse an Proteinen, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Martin Winkler
- Ruhr Universität Bochum, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Thomas Happe
- Ruhr Universität Bochum, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Universitätsstrasse 150, 44801, Bochum, Germany.
| |
Collapse
|
37
|
Yip KT, Zhong XY, Seibel N, Pütz S, Autzen J, Gasper R, Hofmann E, Scherkenbeck J, Stoll R. Small Molecules Antagonise the MIA-Fibronectin Interaction in Malignant Melanoma. Sci Rep 2016; 6:25119. [PMID: 27151361 PMCID: PMC4858652 DOI: 10.1038/srep25119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/11/2016] [Indexed: 02/01/2023] Open
Abstract
Melanoma inhibitory activity (MIA), an extracellular protein highly expressed by malignant melanoma cells, plays an important functional role in melanoma development, progression, and metastasis. After its secretion, MIA directly interacts with extracellular matrix proteins, such as fibronectin (FN). By this mechanism, MIA actively facilitates focal cell detachment from surrounding structures and strongly promotes tumour cell invasion and migration. Hence, the molecular understanding of MIA's function provides a promising target for the development of new strategies in malignant melanoma therapy. Here, we describe for the first time the discovery of small molecules that are able to disrupt the MIA-FN complex by selectively binding to a new druggable pocket, which we could identify on MIA by structural analysis and fragment-based screening. Our findings may inspire novel drug discovery efforts aiming at a therapeutically effective treatment of melanoma by targeting MIA.
Collapse
Affiliation(s)
- King Tuo Yip
- Ruhr University of Bochum, Faculty of Chemistry and Biochemistry, Bochum, 44780, Germany
| | - Xue Yin Zhong
- Ruhr University of Bochum, Faculty of Chemistry and Biochemistry, Bochum, 44780, Germany
| | - Nadia Seibel
- Ruhr University of Bochum, Faculty of Chemistry and Biochemistry, Bochum, 44780, Germany
| | - Stefanie Pütz
- Ruhr University of Bochum, Faculty of Chemistry and Biochemistry, Bochum, 44780, Germany
| | - Jasmin Autzen
- University of Wuppertal, Faculty of Chemistry, Wuppertal, 42119, Germany
| | - Raphael Gasper
- Ruhr University of Bochum, Faculty of Biology and Biotechnology, Bochum, 44801, Germany
| | - Eckhard Hofmann
- Ruhr University of Bochum, Faculty of Biology and Biotechnology, Bochum, 44801, Germany
| | | | - Raphael Stoll
- Ruhr University of Bochum, Faculty of Chemistry and Biochemistry, Bochum, 44780, Germany
| |
Collapse
|
38
|
Kvíčalová Z, Alster J, Hofmann E, Khoroshyy P, Litvín R, Bína D, Polívka T, Pšenčík J. Triplet–triplet energy transfer from chlorophylls to carotenoids in two antenna complexes from dinoflagellate Amphidinium carterae. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2016; 1857:341-9. [DOI: 10.1016/j.bbabio.2016.01.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/08/2016] [Accepted: 01/17/2016] [Indexed: 11/24/2022]
|
39
|
Hofmann E. Bildgebung vor endonasaler NNH-Chirurgie. ROFO-FORTSCHR RONTG 2016. [DOI: 10.1055/s-0036-1581593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
40
|
Hofmann E. Bildgebung bei entzündlichen Erkrankungen. ROFO-FORTSCHR RONTG 2016. [DOI: 10.1055/s-0036-1581583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
41
|
Buisson C, Duclaux M, Hofmann E, Reynier O, Savarino D, Hatem O, Garcia-Larrea L. ID 228 – Combining evoked potentials and EEG reactivity for coma prognosis. Clin Neurophysiol 2016. [DOI: 10.1016/j.clinph.2015.11.348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
42
|
Hirschinger V, Hanke S, Hirschfelder U, Hofmann E. Artifacts in orthodontic bracket systems in cone-beam computed tomography and multislice computed tomography. J Orofac Orthop 2016; 76:152-60, 162-3. [PMID: 25744093 DOI: 10.1007/s00056-014-0278-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVES The purpose of this study was to quantify artifacts caused by different bracket systems in cone-beam computed tomography (CBCT) and multislice computed tomography (MSCT) scans. METHODS Orthodontic brackets of four different systems were consecutively bonded to the surface of a residual molar on a human cadaveric mandible. One MSCT system and three CBCT units were used to scan each of the four bonded brackets, in addition to obtaining a blank reference scan of the tooth surface. All datasets were registered to the reference dataset using visualization software (Analyze 11.0® by AnalyzeDirect). Artifact-related reductions in image quality were expressed in percent of theoretical maximum standard deviations (SD) obtained for the gray values of the adjacent voxels, with higher percentages correlating more pronounced artifacts. RESULTS Both the SD percentages for three defined line profiles and their mean values were almost invariably higher with the MSCT system than with the CBCT units. Looking into the individual SD percentages, two of the CBCT units (Pax Zenith 3D® and Picasso Trio®; both Vatech) produced higher values than the MSCT system (SOMATOM Definition AS+®; Siemens) in some line profiles. The titanium bracket, in particular, was associated with marked differences between the two scanner technologies, as the mean artifact intensities from this bracket were particularly high with the MSCT unit and relatively low with the CBCT units. The artifact intensities observed with the other three bracket systems varied widely depending on which scanner was used. CONCLUSION Different artifact intensities were noted depending on the composition of the bracket system and on the scanner technology (MSCT/CBCT). While the artifacts manifested themselves differently with different scanners, their adverse effects were comparable. However, given the variable severity of the artifacts observed depending on the materials scanned and the scanners used, a blanket recommendation for or against MSCT or CBCT units cannot be given on the basis of this study.
Collapse
Affiliation(s)
- V Hirschinger
- Department of Orthodontics and Orofacial Orthopedics, Zahnklinik 3 - Kieferorthopädie, Universitätsklinikum Erlangen, Glückstr. 11, 91054, Erlangen, Germany
| | | | | | | |
Collapse
|
43
|
Croy I, Luong A, Triscoli C, Hofmann E, Olausson H, Sailer U. Interpersonal stroking touch is targeted to C tactile afferent activation. Behav Brain Res 2016; 297:37-40. [DOI: 10.1016/j.bbr.2015.09.038] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/22/2015] [Accepted: 09/27/2015] [Indexed: 01/31/2023]
|
44
|
Esselborn J, Muraki N, Klein K, Engelbrecht V, Metzler-Nolte N, Apfel UP, Hofmann E, Kurisu G, Happe T. A structural view of synthetic cofactor integration into [FeFe]-hydrogenases. Chem Sci 2015; 7:959-968. [PMID: 29896366 PMCID: PMC5954619 DOI: 10.1039/c5sc03397g] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [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: 09/09/2015] [Accepted: 10/26/2015] [Indexed: 12/20/2022] Open
Abstract
Crystal structures of semisynthetic [FeFe]-hydrogenases with variations in the [2Fe] cluster show little structural differences despite strong effects on activity.
[FeFe]-hydrogenases are nature's fastest catalysts for the evolution or oxidation of hydrogen. Numerous synthetic model complexes for the [2Fe] subcluster (2FeH) of their active site are known, but so far none of these could compete with the enzymes. The complex Fe2[μ-(SCH2)2X](CN)2(CO)42– with X = NH was shown to integrate into the apo-form of [FeFe]-hydrogenases to yield a fully active enzyme. Here we report the first crystal structures of the apo-form of the bacterial [FeFe]-hydrogenase CpI from Clostridium pasteurianum at 1.60 Å and the active semisynthetic enzyme, CpIADT, at 1.63 Å. The structures illustrate the significant changes in ligand coordination upon integration and activation of the [2Fe] complex. These changes are induced by a rigid 2FeH cavity as revealed by the structure of apoCpI, which is remarkably similar to CpIADT. Additionally we present the high resolution crystal structures of the semisynthetic bacterial [FeFe]-hydrogenases CpIPDT (X = CH2), CpIODT (X = O) and CpISDT (X = S) with changes in the headgroup of the dithiolate bridge in the 2FeH cofactor. The structures of these inactive enzymes demonstrate that the 2FeH-subcluster and its protein environment remain largely unchanged when compared to the active enzyme CpIADT. As the active site shows an open coordination site in all structures, the absence of catalytic activity is probably not caused by steric obstruction. This demonstrates that the chemical properties of the dithiolate bridge are essential for enzyme activity.
Collapse
Affiliation(s)
- J Esselborn
- AG Photobiotechnologie , Fakultät für Biologie und Biotechnologie , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| | - N Muraki
- Laboratory of Protein Crystallography , Institute for Protein Research , Osaka University , Suita , Osaka 565-0871 , Japan .
| | - K Klein
- Lehrstuhl für Anorganische Chemie I-Bioanorganische Chemie , Fakultät für Chemie und Biochemie , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| | - V Engelbrecht
- AG Photobiotechnologie , Fakultät für Biologie und Biotechnologie , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| | - N Metzler-Nolte
- Lehrstuhl für Anorganische Chemie I-Bioanorganische Chemie , Fakultät für Chemie und Biochemie , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| | - U-P Apfel
- Lehrstuhl für Anorganische Chemie I-Bioanorganische Chemie , Fakultät für Chemie und Biochemie , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| | - E Hofmann
- AG Proteinkristallographie , Fakultät für Biologie und Biotechnologie , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany
| | - G Kurisu
- Laboratory of Protein Crystallography , Institute for Protein Research , Osaka University , Suita , Osaka 565-0871 , Japan .
| | - T Happe
- AG Photobiotechnologie , Fakultät für Biologie und Biotechnologie , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany .
| |
Collapse
|
45
|
Hofmann E. Anatomie der Schädelbasis. ROFO-FORTSCHR RONTG 2015. [DOI: 10.1055/s-0035-1551300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
46
|
Hofmann E. Schwindel und Tinnitus. ROFO-FORTSCHR RONTG 2015. [DOI: 10.1055/s-0035-1551173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
47
|
|
48
|
Dünschede B, Träger C, Schröder CV, Ziehe D, Walter B, Funke S, Hofmann E, Schünemann D. Chloroplast SRP54 Was Recruited for Posttranslational Protein Transport via Complex Formation with Chloroplast SRP43 during Land Plant Evolution. J Biol Chem 2015; 290:13104-14. [PMID: 25833951 DOI: 10.1074/jbc.m114.597922] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Indexed: 01/05/2023] Open
Abstract
In bacteria, membrane proteins are targeted cotranslationally via a signal recognition particle (SRP). During the evolution of higher plant chloroplasts from cyanobacteria, the SRP pathway underwent striking adaptations that enable the posttranslational transport of the abundant light-harvesting chlorophyll-a/b-binding proteins (LHCPs). The conserved 54-kDa SRP subunit in higher plant chloroplasts (cpSRP54) is not bound to an SRP RNA, an essential SRP component in bacteria, but forms a stable heterodimer with the chloroplast-specific cpSRP43. This heterodimeric cpSRP recognizes LHCP and delivers it to the thylakoid membrane whereby cpSRP43 plays a central role. This study shows that the cpSRP system in the green alga Chlamydomonas reinhardtii differs significantly from that of higher plants as cpSRP43 is not complexed to cpSRP54 in Chlamydomonas and cpSRP54 is not involved in LHCP recognition. This divergence is attributed to altered residues within the cpSRP54 tail and the second chromodomain of cpSRP43 that are crucial for the formation of the binding interface in Arabidopsis. These changes are highly conserved among chlorophytes, whereas all land plants contain cpSRP proteins with typical interaction motifs. These data demonstrate that the coevolution of LHCPs and cpSRP43 occurred independently of complex formation with cpSRP54 and that the interaction between cpSRP54 and cpSRP43 evolved later during the transition from chlorophytes to land plants. Furthermore, our data show that in higher plants a heterodimeric form of cpSRP is required for the formation of a low molecular weight transit complex with LHCP.
Collapse
Affiliation(s)
| | | | | | | | - Björn Walter
- From the Molecular Biology of Plant Organelles and
| | - Silke Funke
- From the Molecular Biology of Plant Organelles and
| | - Eckhard Hofmann
- Protein Crystallography, Ruhr University Bochum, 44780 Bochum, Germany
| | | |
Collapse
|
49
|
Lell MM, May MS, Brand M, Eller A, Buder T, Hofmann E, Uder M, Wuest W. Imaging the Parasinus Region with a Third-Generation Dual-Source CT and the Effect of Tin Filtration on Image Quality and Radiation Dose. AJNR Am J Neuroradiol 2015; 36:1225-30. [PMID: 25814658 DOI: 10.3174/ajnr.a4270] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 12/14/2014] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND PURPOSE CT is the imaging technique of choice in the evaluation of midface trauma or inflammatory disease. We performed a systematic evaluation of scan protocols to optimize image quality and radiation exposure on third-generation dual-source CT. MATERIALS AND METHODS CT protocols with different tube voltage (70-150 kV), current (25-300 reference mAs), prefiltration, pitch value, and rotation time were systematically evaluated. All images were reconstructed with iterative reconstruction (Advanced Modeled Iterative Reconstruction, level 2). To individually compare results with otherwise identical factors, we obtained all scans on a frozen human head. Conebeam CT was performed for image quality and dose comparison with multidetector row CT. Delineation of important anatomic structures and incidental pathologic conditions in the cadaver head was evaluated. RESULTS One hundred kilovolts with tin prefiltration demonstrated the best compromise between dose and image quality. The most dose-effective combination for trauma imaging was Sn100 kV/250 mAs (volume CT dose index, 2.02 mGy), and for preoperative sinus surgery planning, Sn100 kV/150 mAs (volume CT dose index, 1.22 mGy). "Sn" indicates an additional prefiltration of the x-ray beam with a tin filter to constrict the energy spectrum. Exclusion of sinonasal disease was possible with even a lower dose by using Sn100 kV/25 mAs (volume CT dose index, 0.2 mGy). CONCLUSIONS High image quality at very low dose levels can be achieved by using a Sn100-kV protocol with iterative reconstruction. The effective dose is comparable with that of conventional radiography, and the high image quality at even lower radiation exposure favors multidetector row CT over conebeam CT.
Collapse
Affiliation(s)
- M M Lell
- From the Departments of Radiology (M.M.L., M.S.M., M.B., A.E., M.U., W.W.) Imaging Science Institute (M.M.L., M.U.), University Erlangen, Erlangen, Germany.
| | - M S May
- From the Departments of Radiology (M.M.L., M.S.M., M.B., A.E., M.U., W.W.)
| | - M Brand
- From the Departments of Radiology (M.M.L., M.S.M., M.B., A.E., M.U., W.W.)
| | - A Eller
- From the Departments of Radiology (M.M.L., M.S.M., M.B., A.E., M.U., W.W.)
| | - T Buder
- Department I (T.B.), Institute of Anatomy
| | - E Hofmann
- Orthodontics and Orofacial Orthopedics (E.H.)
| | - M Uder
- From the Departments of Radiology (M.M.L., M.S.M., M.B., A.E., M.U., W.W.) Imaging Science Institute (M.M.L., M.U.), University Erlangen, Erlangen, Germany
| | - W Wuest
- From the Departments of Radiology (M.M.L., M.S.M., M.B., A.E., M.U., W.W.)
| |
Collapse
|
50
|
Liauw P, Kannchen D, Gasper R, Dyczmons-Nowaczyk N, Nowaczyk MM, Hofmann E. Cloning, expression, crystallization and preliminary X-ray studies of a superfolder GFP fusion of cyanobacterial Psb32. Acta Crystallogr F Struct Biol Commun 2015; 71:409-13. [PMID: 25849501 DOI: 10.1107/s2053230x15003970] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/25/2015] [Indexed: 11/10/2022]
Abstract
A fusion of Psb32 from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (TePsb32) with superfolder GFP was created for enhanced solubility and improved detection and purification. The fusion protein readily formed large hexagonal crystals belonging to space group P6₁22. A full data set extending to 2.3 Å resolution was collected at the Swiss Light Source. The phase problem could be solved by using only the sfGFP fusion partner or by using GFP and AtTLP18.3 from Arabidopsis thaliana as search models. Based on this expression construct, a versatile library of 24 vectors combining four different superfolder GFP variants and three affinity tags was generated to facilitate expression and screening of fluorescent fusion proteins.
Collapse
Affiliation(s)
- Pasqual Liauw
- Department of Plant Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Daniela Kannchen
- Department of Plant Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Raphael Gasper
- Department of Biophysics, Ruhr-University Bochum, 44780 Bochum, Germany
| | | | - Marc M Nowaczyk
- Department of Plant Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Eckhard Hofmann
- Department of Biophysics, Ruhr-University Bochum, 44780 Bochum, Germany
| |
Collapse
|