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Hu Y, Yuan M, Julian A, Tuz K, Juárez O. Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions. Front Microbiol 2024; 15:1347466. [PMID: 38468849 PMCID: PMC10926992 DOI: 10.3389/fmicb.2024.1347466] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/08/2024] [Indexed: 03/13/2024] Open
Abstract
Pseudomonas aeruginosa is a common cause of urinary tract infections by strains that are often multidrug resistant, representing a major challenge to the world's health care system. This microorganism has a highly adaptable metabolism that allows it to colonize many environments, including the urinary tract. In this work, we have characterized the metabolic strategies used by stationary phase P. aeruginosa cells cultivated in urine-like media to understand the adaptations used by this microorganism to survive and produce disease. Our proteomics results show that cells rely on the Entner-Duodoroff pathway, pentose phosphate pathway, the Krebs cycle/ glyoxylate shunt and the aerobic oxidative phosphorylation to survive in urine-like media and other conditions. A deep characterization of the oxidative phosphorylation showed that the respiratory rate of stationary phase cells is increased 3-4 times compared to cells in the logarithmic phase of growth, indicating that the aerobic metabolism plays critical roles in the stationary phase of cells grown in urine like media. Moreover, the data show that respiratory complex III, succinate dehydrogenase and the NADH dehydrogenase NQR have important functions and could be used as targets to develop new antibiotics against this bacterium.
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Affiliation(s)
- Yuyao Hu
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
| | - Ming Yuan
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
| | - Alexander Julian
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
| | - Karina Tuz
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
| | - Oscar Juárez
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, United States
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2
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Hooper RW, Lin K, Veinot JGC, Michaelis VK. 3D to 0D cesium lead bromide: A 79/81Br NMR, NQR and theoretical investigation. J Magn Reson 2023; 352:107472. [PMID: 37186965 DOI: 10.1016/j.jmr.2023.107472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 05/17/2023]
Abstract
Inorganic metal halides offer unprecedented tunability through elemental variation of simple three-element compositions, but can exhibit complicated phase behaviour, degradation, and microscopic phenomena (disorder/dynamics) that play an integral role for the bulk-level chemical and physical properties of these materials. Understanding the halogen chemical environment in such materials is crucial to addressing many of the concerns regarding implementing these materials in commercial applications. In this study, a combined solid-state nuclear magnetic resonance, nuclear quadrupole resonance and quantum chemical computation approach is used to interrogate the Br chemical environment in a series of related inorganic lead bromide materials: CsPbBr3, CsPb2Br5, and Cs4PbBr6. The quadrupole coupling constants (CQ) were determined to range from 61 to 114 MHz for 81Br, with CsPbBr3 exhibiting the largest measured CQ and Cs4PbBr6 the smallest. GIPAW DFT was shown to be an excellent pre-screening tool for estimating the EFG of Br materials and can increase experimental efficiency by providing good starting estimates for acquisition. Finally, the combination of theory and experiment to inform the best methods for expanding further to the other quadrupolar halogens is discussed.
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Affiliation(s)
- Riley W Hooper
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Katherine Lin
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Jonathan G C Veinot
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Vladimir K Michaelis
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
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Yamada K, Masuda Y. A sulfur-33 nuclear quadrupole resonance study of 33 S 2 -labeled L-cystine. Magn Reson Chem 2023; 61:296-300. [PMID: 36650107 DOI: 10.1002/mrc.5333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 06/17/2023]
Abstract
The sulfur electric-field-gradient tensor for a disulfide bond in 33 S2 -labeled L-cystine has been investigated by 33 S nuclear quadrupole resonance (NQR). 33 S2 -labeled L-cystine is synthesized by introduction of disulfide ions prepared from elemental 33 S-sulfur into an amino acid derivative, the side chain of which is iodinated. In its NQR spectrum, sharp single peaks are observed at between 24.63 and 24.90 MHz in the temperature range from 80 to 298 K. The two-dimensional nutation echo 33 S NQR experiment is carried out at 160 K, and the quadrupole coupling constant, CQ , and the asymmetric parameter, ηQ , are obtained to be 46.9(9) MHz and 0.6(1), respectively. The calculated 33 S electric-field-gradient tensor components with respect to the molecular frame is briefly discussed.
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Affiliation(s)
- Kazuhiko Yamada
- Interdisciplinary Science Unit, Multidisciplinary Sciences Cluster, Research and Education Faculty, Kochi University, Kochi, Japan
| | - Yuichi Masuda
- Graduate School of Bioresources, Mie University, Tsu, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
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4
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Tuz K, Yuan M, Hu Y, Do TTT, Willow SY, DePaolo-Boisvert JA, Fuller JR, Minh DDL, Juárez O. Identification of the riboflavin-cofactor binding site in the Vibrio cholerae ion-pumping NQR complex: A novel structural motif in redox enzymes. J Biol Chem 2022; 298:102182. [PMID: 35752362 PMCID: PMC9293633 DOI: 10.1016/j.jbc.2022.102182] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/18/2022] Open
Abstract
The ion-pumping NQR complex is an essential respiratory enzyme in the physiology of many pathogenic bacteria. This enzyme transfers electrons from NADH to ubiquinone through several cofactors, including riboflavin (vitamin B2). NQR is the only enzyme reported that is able to use riboflavin as a cofactor. Moreover, the riboflavin molecule is found as a stable neutral semiquinone radical. The otherwise highly reactive unpaired electron is stabilized via an unknown mechanism. Crystallographic data suggested that riboflavin might be found in a superficially located site in the interface of NQR subunits B and E. However, this location is highly problematic, as the site does not have the expected physiochemical properties. In this work, we have located the riboflavin-binding site in an amphipathic pocket in subunit B, previously proposed to be the entry site of sodium. Here, we show that this site contains absolutely conserved residues, including N200, N203, and D346. Mutations of these residues decrease enzymatic activity and specifically block the ability of NQR to bind riboflavin. Docking analysis and molecular dynamics simulations indicate that these residues participate directly in riboflavin binding, establishing hydrogen bonds that stabilize the cofactor in the site. We conclude that riboflavin is likely bound in the proposed pocket, which is consistent with enzymatic characterizations, thermodynamic studies, and distance between cofactors.
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Affiliation(s)
- Karina Tuz
- Department of Biological Sciences, Illinois Institute of Technology, Chicago IL
| | - Ming Yuan
- Department of Biological Sciences, Illinois Institute of Technology, Chicago IL
| | - Yuyao Hu
- Department of Biological Sciences, Illinois Institute of Technology, Chicago IL
| | - Tien T T Do
- Department of Chemistry, Illinois Institute of Technology, Chicago IL
| | | | | | - James R Fuller
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - David D L Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago IL
| | - Oscar Juárez
- Department of Biological Sciences, Illinois Institute of Technology, Chicago IL.
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5
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Willow SY, Yuan M, Juárez O, Minh DDL. Electrostatics and water occlusion regulate covalently-bound flavin mononucleotide cofactors of Vibrio cholerae respiratory complex NQR. Proteins 2021; 89:1376-1385. [PMID: 34091964 DOI: 10.1002/prot.26158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/20/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
Proteins like NADH:ubiquinone oxidoreductase (NQR), an essential enzyme and ion pump in the physiology of several pathogenic bacteria, tightly regulate the redox properties of their cofactors. Although flavin mononucleotide (FMN) is fully reduced in aqueous solution, FMN in subunits B and C of NQR exclusively undergo one-electron transitions during its catalytic cycle. Here, we perform ab initio calculations and molecular dynamics simulations to elucidate the mechanisms that regulate the redox state of FMN in NQR. QM/MM calculations show that binding site electrostatics disfavor anionic forms of FMNH2 , but permit a neutral form of the fully reduced flavin. The potential energy surface is unaffected by covalent bonding between FMN and threonine. Molecular dynamics simulations show that the FMN binding sites are inaccessible by water, suggesting that further reductions of the cofactors are limited or prohibited by the availability of water and other proton donors. These findings provide a deeper understanding of the mechanisms used by NQR to regulate electron transfer through the cofactors and perform its physiologic role. They also provide the first, to our knowledge, evidence of the simple concept that proteins regulate flavin redox states via water occlusion.
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Affiliation(s)
- Soohaeng Yoo Willow
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Ming Yuan
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Oscar Juárez
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, USA
| | - David D L Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, USA
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6
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Hetmańczyk Ł, Szklarz P, Kwocz A, Wierzejewska M, Pagacz-Kostrzewa M, Melnikov MY, Tolstoy PM, Filarowski A. Polymorphism and Conformational Equilibrium of Nitro-Acetophenone in Solid State and under Matrix Conditions. Molecules 2021; 26:molecules26113109. [PMID: 34067498 PMCID: PMC8197010 DOI: 10.3390/molecules26113109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/26/2022] Open
Abstract
Conformational and polymorphic states in the nitro-derivative of o-hydroxy acetophenone have been studied by experimental and theoretical methods. The potential energy curves for the rotation of the nitro group and isomerization of the hydroxyl group have been calculated by density functional theory (DFT) to estimate the barriers of the conformational changes. Two polymorphic forms of the studied compound were obtained by the slow and fast evaporation of polar and non-polar solutions, respectively. Both of the polymorphs were investigated by Infrared-Red (IR) and Raman spectroscopy, Incoherent Inelastic Neutron Scattering (IINS), X-ray diffraction, nuclear quadrupole resonance spectroscopy (NQR), differential scanning calorimetry (DSC) and density functional theory (DFT) methods. In one of the polymorphs, the existence of a phase transition was shown. The position of the nitro group and its impact on the crystal cell of the studied compound were analyzed. The conformational equilibrium determined by the reorientation of the hydroxyl group was observed under argon matrix isolation. An analysis of vibrational spectra was achieved for the interpretation of conformational equilibrium. The infrared spectra were measured in a wide temperature range to reveal the spectral bands that were the most sensitive to the phase transition and conformational equilibrium. The results showed the interrelations between intramolecular processes and macroscopic phenomena in the studied compound.
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Affiliation(s)
- Łukasz Hetmańczyk
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland;
| | - Przemysław Szklarz
- Faculty of Chemistry, Wrocław University, I14 F. Joliot-Curie st., 50-383 Wrocław, Poland; (P.S.); (A.K.); (M.W.); (M.P.-K.)
| | - Agnieszka Kwocz
- Faculty of Chemistry, Wrocław University, I14 F. Joliot-Curie st., 50-383 Wrocław, Poland; (P.S.); (A.K.); (M.W.); (M.P.-K.)
| | - Maria Wierzejewska
- Faculty of Chemistry, Wrocław University, I14 F. Joliot-Curie st., 50-383 Wrocław, Poland; (P.S.); (A.K.); (M.W.); (M.P.-K.)
| | - Magdalena Pagacz-Kostrzewa
- Faculty of Chemistry, Wrocław University, I14 F. Joliot-Curie st., 50-383 Wrocław, Poland; (P.S.); (A.K.); (M.W.); (M.P.-K.)
| | - Mikhail Ya. Melnikov
- Department of Chemistry, Moscow State University, F. Joliot-Curie 14, 119991 Moscow, Russia;
| | - Peter M. Tolstoy
- Institute of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 St. Petersburg, Russia;
| | - Aleksander Filarowski
- Faculty of Chemistry, Wrocław University, I14 F. Joliot-Curie st., 50-383 Wrocław, Poland; (P.S.); (A.K.); (M.W.); (M.P.-K.)
- Frank Laboratory of Neutron Physics, Joint Institute of Nuclear Research, 141980 Dubna, Russia
- Correspondence: ; Tel.: +48-71-3757283
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7
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Malone MW, Espy MA, He S, Janicke MT, Williams RF. The 1H T 1 dispersion curve of fentanyl citrate to identify NQR parameters. Solid State Nucl Magn Reson 2020; 110:101697. [PMID: 33075622 DOI: 10.1016/j.ssnmr.2020.101697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
We report the 1H T1 dispersion curve between 0 and 5 MHz for the synthetic opioid fentanyl citrate (C28H36N2O8). The structures in the curve can be used to estimate the 14N nuclear quadrupole resonance (NQR) frequencies of the material. Density functional theory predictions of the NQR parameters of several fentanyl citrate compounds are also reported. The predictions for the aniline nitrogen are consistent with structures in the observed T1 data. To help interpret the fentanyl citrate results the T1 dispersion curve for the explosive ammonium nitrate is also presented.
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Affiliation(s)
| | | | - Sun He
- Washington University in St Louis, St Louis, MO, USA
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8
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Rodriguez Castillo DA, Ansari JN, Cooper RJ, Lee GJ, Prescott DW, Sauer KL. Homogeneous fields: Double expansion method, 3D printing/CNC realization, and verification by atomic magnetometry. J Magn Reson 2020; 315:106738. [PMID: 32417414 DOI: 10.1016/j.jmr.2020.106738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
In low-field magnetic resonance applications there is often an interest in creating homogeneous magnetic fields over unusual geometries, particularly when quantum magnetometers are involved. In this paper a design method is proposed, where both the surface current and magnetic field are expanded to find current coefficients that cancel out higher order field terms. Two coils are designed using this double expansion methodology: (1) a tuning field for a half-meter-long atomic magnetometer array and (2) a null field for a magnetometer to operate adjacent to an excitation solenoid. The field verification of the former shows the accuracy of CNC milling and the method proposed; a close analysis of the field signature in the latter revealed the limitations of 3D printing for precise scientific applications. Both coils are designed to be fifth-order error systems or better.
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Affiliation(s)
- Daniel A Rodriguez Castillo
- Department of Physics and Astronomy, Quantum Science and Engineering Center, George Mason University, Fairfax, VA 22030, United States
| | - Jaafar N Ansari
- Department of Physics and Astronomy, Quantum Science and Engineering Center, George Mason University, Fairfax, VA 22030, United States
| | - Robert J Cooper
- Department of Physics and Astronomy, Quantum Science and Engineering Center, George Mason University, Fairfax, VA 22030, United States
| | - Garrett J Lee
- Department of Physics and Astronomy, Quantum Science and Engineering Center, George Mason University, Fairfax, VA 22030, United States
| | - David W Prescott
- Department of Physics and Astronomy, Quantum Science and Engineering Center, George Mason University, Fairfax, VA 22030, United States
| | - Karen L Sauer
- Department of Physics and Astronomy, Quantum Science and Engineering Center, George Mason University, Fairfax, VA 22030, United States.
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9
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Apih T, Žagar V, Seliger J. NMR and NQR study of polymorphism in carbamazepine. Solid State Nucl Magn Reson 2020; 107:101653. [PMID: 32101778 DOI: 10.1016/j.ssnmr.2020.101653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
Four polymorphic forms of carbamazepine have been simultaneously investigated by 1H NMR and 14N NQR. The results show that the proton spin-lattice relaxation time and the 14N NQR spectra can be used to differentiate between various polymorphic forms. Spontaneous transformations from Form II to Form III and from Form IV to Form III have been investigated through their influence on the 14N NQR spectrum and the proton NMR signal and spin-lattice relaxation. The 14N NQR spectra prove that in the observed polymorphic forms of carbamazepine the hydrogen bonded dimers of carbamazepine molecules are the basic elements of the crystal structure. The dimers are centrosymmetric in Forms III and IV and in metastable polymorphic form occurring during the transformation of Form IV to Form III. Two non-equivalent molecular positions are observed in Form II with the occupation ratio 1:1 and in Form I with the occupation ratio either 2:1 or 3:1. The 14N NQR data are related to the published crystal structures. Possible reasons for the mismatch of the X-ray and NQR data for Forms I and II are discussed.
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Affiliation(s)
- Tomaž Apih
- "Jožef Stefan" Institute, Jamova 39, Ljubljana, Slovenia
| | - Veselko Žagar
- "Jožef Stefan" Institute, Jamova 39, Ljubljana, Slovenia
| | - Janez Seliger
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia.
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Ito T, Gallegos R, Matano LM, Butler NL, Hantman N, Kaili M, Coyne MJ, Comstock LE, Malamy MH, Barquera B. Genetic and Biochemical Analysis of Anaerobic Respiration in Bacteroides fragilis and Its Importance In Vivo. mBio 2020; 11:e03238-19. [PMID: 32019804 PMCID: PMC7002350 DOI: 10.1128/mbio.03238-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 12/14/2022] Open
Abstract
In bacteria, the respiratory pathways that drive molecular transport and ATP synthesis include a variety of enzyme complexes that utilize different electron donors and acceptors. This property allows them to vary the efficiency of energy conservation and to generate different types of electrochemical gradients (H+ or Na+). We know little about the respiratory pathways in Bacteroides species, which are abundant in the human gut, and whether they have a simple or a branched pathway. Here, we combined genetics, enzyme activity measurements, and mammalian gut colonization assays to better understand the first committed step in respiration, the transfer of electrons from NADH to quinone. We found that a model gut Bacteroides species, Bacteroides fragilis, has all three types of putative NADH dehydrogenases that typically transfer electrons from the highly reducing molecule NADH to quinone. Analyses of NADH oxidation and quinone reduction in wild-type and deletion mutants showed that two of these enzymes, Na+-pumping NADH:quinone oxidoreductase (NQR) and NADH dehydrogenase II (NDH2), have NADH dehydrogenase activity, whereas H+-pumping NADH:ubiquinone oxidoreductase (NUO) does not. Under anaerobic conditions, NQR contributes more than 65% of the NADH:quinone oxidoreductase activity. When grown in rich medium, none of the single deletion mutants had a significant growth defect; however, the double Δnqr Δndh2 mutant, which lacked almost all NADH:quinone oxidoreductase activity, had a significantly increased doubling time. Despite unaltered in vitro growth, the single nqr deletion mutant was unable to competitively colonize the gnotobiotic mouse gut, confirming the importance of NQR to respiration in B. fragilis and the overall importance of respiration to this abundant gut symbiont.IMPORTANCEBacteroides species are abundant in the human intestine and provide numerous beneficial properties to their hosts. The ability of Bacteroides species to convert host and dietary glycans and polysaccharides to energy is paramount to their success in the human gut. We know a great deal about the molecules that these bacteria extract from the human gut but much less about how they convert those molecules into energy. Here, we show that B. fragilis has a complex respiratory pathway with two different enzymes that transfer electrons from NADH to quinone and a third enzyme complex that may use an electron donor other than NADH. Although fermentation has generally been believed to be the main mechanism of energy generation in Bacteroides, we found that a mutant lacking one of the NADH:quinone oxidoreductases was unable to compete with the wild type in the mammalian gut, revealing the importance of respiration to these abundant gut symbionts.
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Affiliation(s)
- Takeshi Ito
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Rene Gallegos
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Leigh M Matano
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicole L Butler
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Noam Hantman
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Matthew Kaili
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Michael J Coyne
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Laurie E Comstock
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael H Malamy
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Blanca Barquera
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
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11
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Agarwal S, Bernt M, Toulouse C, Kurz H, Pfannstiel J, D'Alvise P, Hasselmann M, Block AM, Häse CC, Fritz G, Steuber J. Impact of Na +-Translocating NADH:Quinone Oxidoreductase on Iron Uptake and nqrM Expression in Vibrio cholerae. J Bacteriol 2020; 202:e00681-19. [PMID: 31712283 DOI: 10.1128/JB.00681-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 12/28/2022] Open
Abstract
The Na+ ion-translocating NADH:quinone oxidoreductase (NQR) from Vibrio cholerae is a membrane-bound respiratory enzyme which harbors flavins and Fe-S clusters as redox centers. The NQR is the main producer of the sodium motive force (SMF) and drives energy-dissipating processes such as flagellar rotation, substrate uptake, ATP synthesis, and cation-proton antiport. The NQR requires for its maturation, in addition to the six structural genes nqrABCDEF, a flavin attachment gene, apbE, and the nqrM gene, presumably encoding a Fe delivery protein. We here describe growth studies and quantitative real-time PCR for the V. cholerae O395N1 wild-type (wt) strain and its mutant Δnqr and ΔubiC strains, impaired in respiration. In a comparative proteome analysis, FeoB, the membrane subunit of the uptake system for Fe2+ (Feo), was increased in V. cholerae Δnqr In this study, the upregulation was confirmed on the mRNA level and resulted in improved growth rates of V. cholerae Δnqr with Fe2+ as an iron source. We studied the expression of feoB on other respiratory enzyme deletion mutants such as the ΔubiC mutant to determine whether iron transport is specific to the absence of NQR resulting from impaired respiration. We show that the nqr operon comprises, in addition to the structural nqrABCDEF genes, the downstream apbE and nqrM genes on the same operon and demonstrate induction of the nqr operon by iron in V. cholerae wt. In contrast, expression of the nqrM gene in V. cholerae Δnqr is repressed by iron. The lack of functional NQR has a strong impact on iron homeostasis in V. cholerae and demonstrates that central respiratory metabolism is interwoven with iron uptake and regulation.IMPORTANCE Investigating strategies of iron acquisition, storage, and delivery in Vibrio cholerae is a prerequisite to understand how this pathogen thrives in hostile, iron-limited environments such as the human host. In addition to highlighting the maturation of the respiratory complex NQR, this study points out the influence of NQR on iron metabolism, thereby making it a potential drug target for antibiotics.
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12
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Ramu L, Kuppan N, Ramesh KP, Chandramani R, Ramananda D. 35 Cl NQR frequency and spin lattice relaxation study in 3,4-dichloronitrobenzene as a function of temperature and pressure. Magn Reson Chem 2019; 57:499-505. [PMID: 31038234 DOI: 10.1002/mrc.4881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/22/2019] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
35 Cl NQR frequency and spin lattice relaxation time in 3,4-dichloronitrobenzene have been measured as a function of temperature and pressure. Two NQR signals were observed in the temperature range 77 to 300 K and pressure up to 5.1 kbar at 300 K. The contributions to the relaxation from the torsional motion of the molecule and reorientational motion of the nitro group have been analyzed on the basis of the Woessner and Gutowsky model. The temperature dependence of the average torsional lifetimes of the molecules, transition probabilities, and the activation energy for the reorientation of the nitro group was estimated. The pressure dependence of the NQR frequency in 3,4-Dichloronitrobenzene shows a nonlinear increase in NQR frequency with increase in pressure, indicating increased contribution from the static effects at higher pressures. A thermodynamic analysis of the data was carried out to determine the constant-volume temperature coefficients of the NQR frequency. The spin-lattice relaxation was found to be weakly dependent on pressure.
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Affiliation(s)
- Loganathan Ramu
- Department of Physics,MES college of Arts,Commerce and Science, Bangalore University, Bangalore, India
| | - Narendra Kuppan
- Department of Botany, Annamalai University, Chidambaram, Tamil Nadu, India
- Department of Biology, MES College of Arts, Commerce and Science, Bangalore, India
| | | | | | - Daivagna Ramananda
- Department of Physics, Bhandarkar's Arts and Science College, Karnataka, India
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Cardona L, Itozaki H, Jiménez J, Vanegas N, Sato-Akaba H. Spectral descriptors and supervised classifier for ammonium nitrate detection in landmines by nuclear quadrupole resonance. J Magn Reson 2019; 305:104-111. [PMID: 31252239 DOI: 10.1016/j.jmr.2019.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/07/2019] [Accepted: 06/17/2019] [Indexed: 06/09/2023]
Abstract
The high specificity of Nuclear Quadrupole Resonance (NQR) makes it very suited for the detection of antipersonnel mines, where the intensity of the signal spectrum around the resonance frequency of the target substance is the standard decision parameter; however, radiofrequency interference, soil effects on the search coil, landmine size, burial depth, and target temperature affect signal intensity. To overcome this, the use of spectral descriptors and a supervised classifier are proposed in this work, where an assembly of decision trees was trained with NQR data collected on places where a target filled with ammonium nitrate was present and where it was not. A statistical test, comparing the proposed classifier and the solution based solely on the intensity of the signal spectrum, showed with significant evidence that the proposed classifier outperforms the traditional solution. A final blind experiment was conducted in a rural region of Colombia, where five landmines of different size filled with ammonium nitrate were shallowly buried in an area of 1.9 × 1.52 m, and the system with the proposed classifier detected four of them with three false alarms. This work is also novel in detecting ammonium nitrate in antipersonnel mines, which are typical in Colombia, the second most mined country in the world.
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Affiliation(s)
- Lorena Cardona
- Department of Mechanics, School of Engineering, Institución Universitaria Pascual Bravo, Calle 73 No. 73A - 226, Medellín, Antioquia, Colombia.
| | - Hideo Itozaki
- Department of Systems Innovation, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Jovani Jiménez
- Department of Computation and Decision Science, School of Mines, Universidad Nacional de Colombia, Carrera 80 No. 65-223, Medellin, Antioquia, Colombia
| | - Nelson Vanegas
- Department of Mechanical Engineering, School of Mines, Universidad Nacional de Colombia, Carrera 64 No. 63-120, Medellin, Antioquia, Colombia
| | - Hideo Sato-Akaba
- Department of Systems Innovation, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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14
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Fang X, Osipiuk J, Chakravarthy S, Yuan M, Menzer WM, Nissen D, Liang P, Raba DA, Tuz K, Howard AJ, Joachimiak A, Minh DDL, Juarez O. Conserved residue His-257 of Vibrio cholerae flavin transferase ApbE plays a critical role in substrate binding and catalysis. J Biol Chem 2019; 294:13800-13810. [PMID: 31350338 DOI: 10.1074/jbc.ra119.008261] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/23/2019] [Indexed: 12/22/2022] Open
Abstract
The flavin transferase ApbE plays essential roles in bacterial physiology, covalently incorporating FMN cofactors into numerous respiratory enzymes that use the integrated cofactors as electron carriers. In this work we performed a detailed kinetic and structural characterization of Vibrio cholerae WT ApbE and mutants of the conserved residue His-257, to understand its role in substrate binding and in the catalytic mechanism of this family. Bi-substrate kinetic experiments revealed that ApbE follows a random Bi Bi sequential kinetic mechanism, in which a ternary complex is formed, indicating that both substrates must be bound to the enzyme for the reaction to proceed. Steady-state kinetic analyses show that the turnover rates of His-257 mutants are significantly smaller than those of WT ApbE, and have increased Km values for both substrates, indicating that the His-257 residue plays important roles in catalysis and in enzyme-substrate complex formation. Analyses of the pH dependence of ApbE activity indicate that the pKa of the catalytic residue (pK ES1) increases by 2 pH units in the His-257 mutants, suggesting that this residue plays a role in substrate deprotonation. The crystal structures of WT ApbE and an H257G mutant were determined at 1.61 and 1.92 Å resolutions, revealing that His-257 is located in the catalytic site and that the substitution does not produce major conformational changes. We propose a reaction mechanism in which His-257 acts as a general base that deprotonates the acceptor residue, which subsequently performs a nucleophilic attack on FAD for flavin transfer.
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Affiliation(s)
- Xuan Fang
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Jerzy Osipiuk
- Center for Structural Genomics of Infectious Diseases (CSGID), Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60637.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439
| | - Srinivas Chakravarthy
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616.,Biophysics Collaborative Access Team, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439
| | - Ming Yuan
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - William M Menzer
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Devin Nissen
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Pingdong Liang
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Daniel A Raba
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Karina Tuz
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Andrew J Howard
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases (CSGID), Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60637.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439
| | - David D L Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Oscar Juarez
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
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15
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Deusch S, Bok E, Schleicher L, Seifert J, Steuber J. Occurrence and Function of the Na +-Translocating NADH:Quinone Oxidoreductase in Prevotella spp. Microorganisms 2019; 7:E117. [PMID: 31035603 DOI: 10.3390/microorganisms7050117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/08/2019] [Accepted: 04/25/2019] [Indexed: 12/18/2022] Open
Abstract
Strictly anaerobic Prevotella spp. are characterized by their vast metabolic potential. As members of the Prevotellaceae family, they represent the most abundant organisms in the rumen and are typically found in monogastrics such as pigs and humans. Within their largely anoxic habitats, these bacteria are considered to rely primarily on fermentation for energy conservation. A recent study of the rumen microbiome identified multiple subunits of the Na+-translocating NADH:quinone oxidoreductase (NQR) belonging to different Prevotella spp. Commonly, the NQR is associated with biochemical energy generation by respiration. The existence of this Na+ pump in Prevotella spp. may indicate an important role for electrochemical Na+ gradients in their anaerobic metabolism. However, detailed information about the potential activity of the NQR in Prevotella spp. is not available. Here, the presence of a functioning NQR in the strictly anaerobic model organism P. bryantii B14 was verified by conducting mass spectrometric, biochemical, and kinetic experiments. Our findings propose that P. bryantii B14 and other Prevotella spp. retrieved from the rumen operate a respiratory NQR together with a fumarate reductase which suggests that these ruminal bacteria utilize a sodium motive force generated during respiratory NADH:fumarate oxidoreduction.
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16
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Toulouse C, Schmucker S, Metesch K, Pfannstiel J, Michel B, Starke I, Möller HM, Stefanski V, Steuber J. Mechanism and impact of catecholamine conversion by Vibrio cholerae. Biochim Biophys Acta Bioenerg 2019; 1860:478-487. [PMID: 30986392 DOI: 10.1016/j.bbabio.2019.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/02/2019] [Accepted: 04/10/2019] [Indexed: 02/06/2023]
Abstract
Bacterial pathogens are influenced by signaling molecules including the catecholamines adrenaline and noradrenaline which are host-derived hormones and neurotransmitters. Adrenaline and noradrenaline modulate growth, motility and virulence of bacteria. We show that adrenaline is converted by the pathogen Vibrio cholerae to adrenochrome in the course of respiration, and demonstrate that superoxide produced by the respiratory, Na+ - translocating NADH:quinone oxidoreductase (NQR) acts as electron acceptor in the oxidative conversion of adrenaline to adrenochrome. Adrenochrome stimulates growth of V. cholerae, and triggers specific responses in V. cholerae and in immune cells. We performed a quantitative proteome analysis of V. cholerae grown in minimal medium with glucose as carbon source without catecholamines, or with adrenaline, noradrenaline or adrenochrome. Significant regulation of proteins participating in iron transport and iron homeostasis, in energy metabolism, and in signaling was observed upon exposure to adrenaline, noradrenaline or adrenochrome. On the host side, adrenochrome inhibited lipopolysaccharide-triggered formation of TNF-α by THP-1 monocytes, though to a lesser extent than adrenaline. It is proposed that adrenochrome produced from adrenaline by respiring V. cholerae functions as effector molecule in pathogen-host interaction.
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Affiliation(s)
| | - Sonja Schmucker
- Behavioral Physiology of Livestock, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Kristina Metesch
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany
| | - Jens Pfannstiel
- Mass Spectrometry Core Facility, University of Hohenheim, Stuttgart, Germany
| | - Bernd Michel
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany
| | - Ines Starke
- Institute of Chemistry, University of Potsdam, Potsdam, Germany
| | - Heiko M Möller
- Institute of Chemistry, University of Potsdam, Potsdam, Germany
| | - Volker Stefanski
- Behavioral Physiology of Livestock, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Julia Steuber
- Institute of Microbiology, University of Hohenheim, Stuttgart, Germany.
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17
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Toulouse C, Metesch K, Pfannstiel J, Steuber J. Metabolic Reprogramming of Vibrio cholerae Impaired in Respiratory NADH Oxidation Is Accompanied by Increased Copper Sensitivity. J Bacteriol 2018; 200:e00761-17. [PMID: 29735761 DOI: 10.1128/JB.00761-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/01/2018] [Indexed: 11/20/2022] Open
Abstract
The electrogenic, sodium ion-translocating NADH:quinone oxidoreductase (NQR) from Vibrio cholerae is frequent in pathogenic bacteria and a potential target for antibiotics. NQR couples the oxidation of NADH to the formation of a sodium motive force (SMF) and therefore drives important processes, such as flagellar rotation, substrate uptake, and energy-dissipating cation-proton antiport. We performed a quantitative proteome analysis of V. cholerae O395N1 compared to its variant lacking the NQR using minimal medium with glucose as the carbon source. We found 84 proteins (regulation factor of ≥2) to be changed in abundance. The loss of NQR resulted in a decrease in the abundance of enzymes of the oxidative branch of the tricarboxylic acid (TCA) cycle and an increase in abundance of virulence factors AcfC and TcpA. Most unexpected, the copper resistance proteins CopA, CopG, and CueR were decreased in the nqr deletion strain. As a consequence, the mutant exhibited diminished resistance to copper compared to the reference strain, as confirmed in growth studies using either glucose or mixed amino acids as carbon sources. We propose that the observed adaptations of the nqr deletion strain represent a coordinated response which counteracts a drop in transmembrane voltage that challenges V. cholerae in its different habitats.IMPORTANCE The importance of the central metabolism for bacterial virulence has raised interest in studying catabolic enzymes not present in the host, such as NQR, as putative targets for antibiotics. Vibrio cholerae lacking the NQR, which is studied here, is a model to estimate the impact of specific NQR inhibitors on the phenotype of a pathogen. Our comparative proteomic study provides a framework to evaluate the chances of success of compounds directed against NQR with respect to their bacteriostatic or bactericidal action.
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18
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Chen C, Zhang F, Bhunia S, Mandal S. Broadband quantitative NQR for authentication of vitamins and dietary supplements. J Magn Reson 2017; 278:67-79. [PMID: 28371759 DOI: 10.1016/j.jmr.2017.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 01/13/2017] [Revised: 03/12/2017] [Accepted: 03/20/2017] [Indexed: 06/07/2023]
Abstract
We describe hardware, pulse sequences, and algorithms for nuclear quadrupole resonance (NQR) spectroscopy of medicines and dietary supplements. Medicine and food safety is a pressing problem that has drawn more and more attention. NQR is an ideal technique for authenticating these substances because it is a non-invasive method for chemical identification. We have recently developed a broadband NQR front-end that can excite and detect 14N NQR signals over a wide frequency range; its operating frequency can be rapidly set by software, while sensitivity is comparable to conventional narrowband front-ends over the entire range. This front-end improves the accuracy of authentication by enabling multiple-frequency experiments. We have also developed calibration and signal processing techniques to convert measured NQR signal amplitudes into nuclear spin densities, thus enabling its use as a quantitative technique. Experimental results from several samples are used to illustrate the proposed methods.
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Affiliation(s)
- Cheng Chen
- Case Western Reserve University, Cleveland, OH 44106, USA.
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19
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Bain AD. Quadrupole interactions: NMR, NQR, and in between from a single viewpoint. Magn Reson Chem 2017; 55:198-205. [PMID: 26891414 DOI: 10.1002/mrc.4418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 01/07/2016] [Accepted: 01/16/2016] [Indexed: 06/05/2023]
Abstract
Nuclear spins with quantum numbers >1/2 can interact with a static magnetic field, or a local electric field gradient, to produce quantized energy levels. If the magnetic field interaction dominates, we are doing nuclear magnetic resonance (NMR). If the interaction of the nuclear electric quadrupole with electric field gradients is much stronger, this is nuclear quadrupole resonance (NQR). The two are extremes of a continuum, as the ratio of one interaction to the other changes. In this work, we look at this continuum from a single, unified viewpoint based on a Liouville-space approach: the direct method. This method does not require explicit operators and their commutators, unlike Hamiltonian methods. We derive both the quadrupole-perturbed NMR solution and also the Zeeman-perturbed NQR results. Furthermore, we examine the polarization of these signals, because this is different between pure NMR and pure NQR spectroscopy. Spin 3/2 is the focus here, but the approach is perfectly general and can be applied to any spin. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Alex D Bain
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. West, Hamilton, Ontario, L8S 4M1, Canada
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20
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Gregorovič A, Apih T, Seliger J. (1)H-(14)N cross-relaxation spectrum analysis in sildenafil and sildenafil citrate. Solid State Nucl Magn Reson 2016; 78:16-23. [PMID: 27379753 DOI: 10.1016/j.ssnmr.2016.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 03/24/2016] [Accepted: 05/19/2016] [Indexed: 06/06/2023]
Abstract
Here we describe a method for the extraction of (14)N quadrupole parameters from a (1)H-(14)N cross-relaxation spectrum by fitting the lineshapes of the (14)N quadrupole transitions. The procedures used typically to fit quadrupole lineshapes are not directly applicable to fit the (1)H-(14)N cross-relaxation spectrum, because the presence of proton homonuclear dipolar interaction broadens the lineshapes considerably and prevents a reliable determination of Cq and η from a single lineshape. Instead, one must fit two or even three lineshapes originating from the same nitrogen site simultaneously. The problem is to identify which lineshapes belong together when many are observed due to the existence of several nitrogen sites. We solve this problem by fitting the spectrum for all possible combinations and find the best-fitting one. This combination then most likely correctly identifies lineshapes belonging to the same nitrogen site. There are two main advantages of our method compared to the typically used method, which relies only on lineshape singularities: (i) the method is "automatic" and does not require knowledge of nitrogen quadrupole parameters in similar environments to aid dip pairing and (ii) the accuracy of quadrupole parameters is better, as proton linewidth is included in the fits. We use sildenafil and sildenafil citrate as model compounds, each with six non-equivalent nitrogen sites.
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Affiliation(s)
- Alan Gregorovič
- Institute "Jožef Stefan", Jamova 39, 1000 Ljubljana, Slovenia.
| | - Tomaž Apih
- Institute "Jožef Stefan", Jamova 39, 1000 Ljubljana, Slovenia
| | - Janez Seliger
- Institute "Jožef Stefan", Jamova 39, 1000 Ljubljana, Slovenia; Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
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21
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Bastow TJ, Lehmann-Horn JA, Miljak DG. (121,123)Sb and (75)As NMR and NQR investigation of the tetrahedrite (Cu12Sb4S13)--Tennantite (Cu12As4S13) system and other metal arsenides. Solid State Nucl Magn Reson 2015; 71:55-60. [PMID: 26453410 DOI: 10.1016/j.ssnmr.2015.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/25/2015] [Accepted: 09/29/2015] [Indexed: 06/05/2023]
Abstract
This work is motivated by the recent developments in online minerals analysis in the mining and minerals processing industry via nuclear quadrupole resonance (NQR). Here we describe a nuclear magnetic resonance (NMR) and NQR study of the minerals tennantite (Cu12As4S13) and tetrahedrite (Cu12 Sb4S13). In the first part NQR lines associated with (75)As in tennantite and (121,123)Sb isotopes in tetrahedrite are reported. The spectroscopy has been restricted to an ambient temperature studies in accord with typical industrial conditions. The second part of this contribution reports nuclear quadrupole-perturbed NMR findings on further, only partially characterised, metal arsenides. The findings enhance the detection capabilities of NQR based analysers for online measurement applications and may aid to control arsenic and antimony concentrations in metal processing stages.
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Affiliation(s)
- T J Bastow
- CSIRO Manufacturing, Clayton 3168, Victoria, Australia.
| | | | - D G Miljak
- CSIRO Mineral Resources, Lucas Heights 2234, NSW, Australia
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22
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Rafiee M, Javaheri M. A theoretical study of benzaldehyde derivatives as tyrosinase inhibitors using Ab initio calculated NQCC parameters. Mol Biol Res Commun 2015; 4:151-9. [PMID: 27844007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Tyrosinase is a multifunctional copper-containing enzyme. It can catalyze two distinct reactions of melanin synthesis and benzaldehyde derivatives, which are potential tyrosinase inhibitors. To find the relationships between charge distributions of benzaldehyde and their pharmaceutical behavior, the present study aimed at investigating nuclear quadrupole coupling constants of quadrupolare nuclei in the functional benzaldehyde group and calculating some its derivatives. In addition, the differences between the electronic structures of various derivatives of this depigmenting drug were examined. All ab initio calculations were carried out using Gaussian 03. The results predicted benzaldehyde derivatives to be bicentral inhibitors; nevertheless, the oxygen or hydrogen contents of the aldehyde group were not found to be the only active sites. Furthermore with the presence of the aldehyde group, the terminal methoxy group in C4 was found to contribute to tyrosinase inhibitory activities. In addition, an oxygen atom with high charge density in the side chain was found to play an important role in its inhibitory effect.
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Aissani S, Guendouz L, Marande PL, Canet D. ¹⁴N Quadrupole Resonance line broadening due to the earth magnetic field, occuring only in the case of an axially symmetric electric field gradient tensor. Solid State Nucl Magn Reson 2015; 68-69:57-60. [PMID: 25910551 DOI: 10.1016/j.ssnmr.2015.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/31/2015] [Accepted: 04/02/2015] [Indexed: 06/04/2023]
Abstract
As demonstrated before, the application of a weak static B0 magnetic field (less than 10 G) may produce definite effects on the ¹⁴N Quadrupole Resonance line when the electric field gradient tensor at the nitrogen nucleus level is of axial symmetry. Here, we address more precisely the problem of the relative orientation of the two magnetic fields (the static field and the radio-frequency field of the pure NQR experiment). For a field of 6G, the evolution of the signal intensity, as a function of this relative orientation, is in very good agreement with the theoretical predictions. There is in particular an intensity loss by a factor of three when going from the parallel configuration to the perpendicular configuration. By contrast, when dealing with a very weak magnetic field (as the earth field, around 0.5 G), this effect drops to ca. 1.5 in the case Hexamethylenetetramine (HMT).This is explained by the fact that the Zeeman shift (due to the very weak magnetic field) becomes comparable to the natural line-width. The latter can therefore be determined by accounting for this competition. Still in the case of HMT, the estimated natural line-width is half the observed line-width. The extra broadening is thus attributed to earth magnetic field. The latter constitutes therefore the main cause of the difference between the natural transverse relaxation time (T₂) and the transverse relaxation time derived from the observed line-width (T₂(⁎)).
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Affiliation(s)
- Sarra Aissani
- Méthodologie RMN (CRM(2); UMR 7036, UL-CNRS), Université de Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandœuvre-lès-Nancy (cedex), France; Mesures et architectures électroniques (IJL; UMR 7198, UL-CNRS), Université de Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandœuvre-lès-Nancy (cedex), France
| | - Laouès Guendouz
- Mesures et architectures électroniques (IJL; UMR 7198, UL-CNRS), Université de Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandœuvre-lès-Nancy (cedex), France
| | - Pierre-Louis Marande
- Méthodologie RMN (CRM(2); UMR 7036, UL-CNRS), Université de Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandœuvre-lès-Nancy (cedex), France
| | - Daniel Canet
- Institut Jean Barriol (FR CNRS 2843), Université de Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandœuvre-lès-Nancy (cedex), France.
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Strickland M, Juárez O, Neehaul Y, Cook DA, Barquera B, Hellwig P. The conformational changes induced by ubiquinone binding in the Na+-pumping NADH:ubiquinone oxidoreductase (Na+- NQR) are kinetically controlled by conserved glycines 140 and 141 of the NqrB subunit. J Biol Chem 2014; 289:23723-33. [PMID: 25006248 DOI: 10.1074/jbc.m114.574640] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Na(+)-pumping NADH:ubiquinone oxidoreductase (Na(+)-NQR) is responsible for maintaining a sodium gradient across the inner bacterial membrane. This respiratory enzyme, which couples sodium pumping to the electron transfer between NADH and ubiquinone, is not present in eukaryotes and as such could be a target for antibiotics. In this paper it is shown that the site of ubiquinone reduction is conformationally coupled to the NqrB subunit, which also hosts the final cofactor in the electron transport chain, riboflavin. Previous work showed that mutations in conserved NqrB glycine residues 140 and 141 affect ubiquinone reduction and the proper functioning of the sodium pump. Surprisingly, these mutants did not affect the dissociation constant of ubiquinone or its analog HQNO (2-n-heptyl-4-hydroxyquinoline N-oxide) from Na(+)-NQR, which indicates that these residues do not participate directly in the ubiquinone binding site but probably control its accessibility. Indeed, redox-induced difference spectroscopy showed that these mutations prevented the conformational change involved in ubiquinone binding but did not modify the signals corresponding to bound ubiquinone. Moreover, data are presented that demonstrate the NqrA subunit is able to bind ubiquinone but with a low non-catalytically relevant affinity. It is also suggested that Na(+)-NQR contains a single catalytic ubiquinone binding site and a second site that can bind ubiquinone but is not active.
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Affiliation(s)
- Madeleine Strickland
- From the Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CNRS Université de Strasbourg, Strasbourg, France, 67000 and
| | - Oscar Juárez
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Yashvin Neehaul
- From the Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CNRS Université de Strasbourg, Strasbourg, France, 67000 and
| | - Darcie A Cook
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Blanca Barquera
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Petra Hellwig
- From the Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CNRS Université de Strasbourg, Strasbourg, France, 67000 and
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25
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Mandal S, Song YQ. Two-dimensional NQR using ultra-broadband electronics. J Magn Reson 2014; 240:16-23. [PMID: 24495675 DOI: 10.1016/j.jmr.2014.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 11/15/2013] [Revised: 01/02/2014] [Accepted: 01/06/2014] [Indexed: 06/03/2023]
Abstract
We have recently developed an ultra-broadband instrument that can effectively excite and detect NMR and NQR signals over a wide frequency range. Our current system operates between 100 kHz and 3.2 MHz using an un-tuned sample coil. The major benefits of this instrument compared to conventional NQR/NMR systems include increased robustness, ease of use (in particular for multi-frequency experiments), and elimination of the need for tuning adjustments in the hardware. Here we describe its use for performing two-dimensional (2D) scans, which allow improved interpretation of complex NQR spectra by detecting the connected resonances. Our method relies on population transfers between the three energy levels of spin-1 nuclei (such as (14)N) by using multi-frequency excitation and a single RF coil. Experimental results on pure samples and mixtures are also presented.
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Affiliation(s)
- S Mandal
- Schlumberger-Doll Research, Cambridge, MA 02139, USA.
| | - Y-Q Song
- Schlumberger-Doll Research, Cambridge, MA 02139, USA.
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Guendouz L, Aissani S, Marêché JF, Retournard A, Marande PL, Canet D. Effect of a weak static magnetic field on nitrogen-14 quadrupole resonance in the case of an axially symmetric electric field gradient tensor. Solid State Nucl Magn Reson 2013; 55-56:84-90. [PMID: 24183810 DOI: 10.1016/j.ssnmr.2013.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 09/28/2013] [Accepted: 10/02/2013] [Indexed: 06/02/2023]
Abstract
The application of a weak static B0 magnetic field (less than 1 mT) may produce a well-defined splitting of the (14)N Quadrupole Resonance line when the electric field gradient tensor at the nitrogen nucleus level is of axial symmetry. It is theoretically shown and experimentally confirmed that the actual splitting (when it exists) as well as the line-shape and the signal intensity depends on three factors: (i) the amplitude of B0, (ii) the amplitude and pulse duration of the radio-frequency field, B1, used for detecting the NQR signal, and (iii) the relative orientation of B0 and B1. For instance, when B0 is parallel to B1 and regardless of the B0 value, the signal intensity is three times larger than when B0 is perpendicular to B1. This point is of some importance in practice since NQR measurements are almost always performed in the earth field. Moreover, in the course of this study, it has been recognized that important pieces of information regarding line-shape are contained in data points at the beginning of the free induction decay (fid) which, in practice, are eliminated for avoiding spurious signals due to probe ringing. It has been found that these data points can generally be retrieved by linear prediction (LP) procedures. As a further LP benefit, the signal intensity loss (by about a factor of three) is regained.
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Affiliation(s)
- Laouès Guendouz
- Mesures et architectures électroniques (IJL; UMR 7198, UL-CNRS), Université de Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandœuvre-lès-Nancy (cedex), France
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