1
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Eldeeb MH, Camacho Lopez LJ, Fontanesi F. Mitochondrial respiratory supercomplexes of the yeast Saccharomyces cerevisiae. IUBMB Life 2024. [PMID: 38529880 DOI: 10.1002/iub.2817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/28/2024] [Indexed: 03/27/2024]
Abstract
The functional and structural relationship among the individual components of the mitochondrial respiratory chain constitutes a central aspect of our understanding of aerobic catabolism. This interplay has been a subject of intense debate for over 50 years. It is well established that individual respiratory enzymes associate into higher-order structures known as respiratory supercomplexes, which represent the evolutionarily conserved organizing principle of the mitochondrial respiratory chain. In the yeast Saccharomyces cerevisiae, supercomplexes are formed by a complex III homodimer flanked by one or two complex IV monomers, and their high-resolution structures have been recently elucidated. Despite the wealth of structural information, several proposed supercomplex functions remain speculative and our understanding of their physiological relevance is still limited. Recent advances in the field were made possible by the construction of yeast strains where the association of complex III and IV into supercomplexes is impeded, leading to diminished respiratory capacity and compromised cellular competitive fitness. Here, we discuss the experimental evidence and hypotheses relative to the functional roles of yeast respiratory supercomplexes. Moreover, we review the current models of yeast complex III and IV assembly in the context of supercomplex formation and highlight the data scattered throughout the literature suggesting the existence of cross talk between their biogenetic processes.
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Affiliation(s)
- Mazzen H Eldeeb
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Lizeth J Camacho Lopez
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
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2
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Li S, De Groote Tavares C, Tolar JG, Ajo-Franklin CM. Selective bioelectronic sensing of pharmacologically relevant quinones using extracellular electron transfer in Lactiplantibacillus plantarum. Biosens Bioelectron 2024; 243:115762. [PMID: 37875059 DOI: 10.1016/j.bios.2023.115762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/26/2023]
Abstract
Redox-active small molecules containing quinone functional groups play important roles as pharmaceuticals, but can be toxic if overdosed. Despite the need for a fast and quantitative method to detect quinone and its derivatives, current sensing strategies are often slow and struggle to differentiate between structural analogs. Leveraging the discovery that microorganisms use certain quinones to perform extracellular electron transfer (EET), we investigated the use of Lactiplantibacillus plantarum as a whole-cell bioelectronic sensor to selectively sense quinone analogs. By tailoring the native EET pathway in L. plantarum, we enabled quantitative quinone sensing of 1,4-dihydroxy-2-naphthoic acid (DHNA) - a gut bifidogenic growth stimulator. We found that L. plantarum could respond to environmental DHNA within seconds, producing concentration-dependent electrical signals. This sensing capacity was robust in different assay media and allowed for continuous monitoring of DHNA concentrations. In a simulated gut environment containing a mixed pool of quinone derivatives, this tailored EET pathway can selectively sense pharmacologically relevant quinone analogs, such as DHNA and menadione, amongst other structurally similar quinone derivatives. We also developed a multivariate model to describe the mechanism behind this selectivity and found a predictable correlation between quinone physiochemical properties and the corresponding electrical signals. Our work presents a new concept to selectively sense quinone using whole-cell bioelectronic sensors and opens the possibility of using probiotic L. plantarum for bioelectronic applications in human health.
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Affiliation(s)
- Siliang Li
- Department of BioSciences, Rice University, Houston, TX, USA
| | | | - Joe G Tolar
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Caroline M Ajo-Franklin
- Department of BioSciences, Rice University, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA; Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
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3
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Vishwakarma C, Ansari A, Pratap JV. Distinct oligomerization and NADPH binding modes observed between L. donovani and human quinone oxidoreductases. Biochem Biophys Res Commun 2024; 690:149096. [PMID: 37988924 DOI: 10.1016/j.bbrc.2023.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 11/23/2023]
Abstract
Electron-driven process helps the living organism in the generations of energy, biomass production and detoxification of synthetic compounds. Soluble quinone oxidoreductases (QORs) mediate the transfer of an electron from NADPH to various quinone and other compounds, helping in the detoxification of quinones. QORs play a crucial role in cellular metabolism and are thus potential targets for drug development. Here we report the crystal structure of the NADPH-dependent QOR from Leishmania donovani (LdQOR) at 2.05 Å. The enzyme exists as a homo-dimer, with each protomer consisting of two domains, responsible for binding NADPH cofactor and the substrate. Interestingly, the human QOR exists as a tetramer. Comparative analysis of the oligomeric interfaces of LdQOR with HsQOR shows no significant differences in the protomer/dimer assembly. The tetrameric interface of HsQOR is stabilized by salt bridges formed between Arg 169 and Glu 271 which is non-existent in LdQOR, with an Alanine replacing the glutamate. This distinct feature is conserved across other dimeric QORs, indicating the importance of this interaction for tetramer association. Among the homologs, the sequences of the loop region involved in the stabilization and binding of the adenine ring of the NADPH shows significant differences except for an Arginine & glycine residues. In dimer QORs, this Arginine acts as a gate to the co-factor, while the NADPH binding mode in the human homolog is distinct, stabilized by His 200 and Asn 229, which are not conserved in LdQOR. These distinct features have the potential to be utilized for therapeutic interventions.
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Affiliation(s)
- Chandan Vishwakarma
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Ahmadullah Ansari
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - J Venkatesh Pratap
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
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4
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Zhang S, Gou S, Zhang Q, Yong X, Gan B, Jia D. FSP1 oxidizes NADPH to suppress ferroptosis. Cell Res 2023; 33:967-970. [PMID: 37739993 PMCID: PMC10709417 DOI: 10.1038/s41422-023-00879-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/04/2023] [Indexed: 09/24/2023] Open
Affiliation(s)
- Sitao Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Shengsong Gou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Qian Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Xin Yong
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Boyi Gan
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China.
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5
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Peng W, Wang Z, Zhang Q, Yan S, Wang B. Unraveling the Valence State and Reactivity of Copper Centers in Membrane-Bound Particulate Methane Monooxygenase. J Am Chem Soc 2023; 145:25304-25317. [PMID: 37955571 DOI: 10.1021/jacs.3c08834] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Particulate methane monooxygenase (pMMO) plays a critical role in catalyzing the conversion of methane to methanol, constituting the initial step in the C1 metabolic pathway within methanotrophic bacteria. However, the membrane-bound pMMO's structure and catalytic mechanism, notably the copper's valence state and genuine active site for methane oxidation, have remained elusive. Based on the recently characterized structure of membrane-bound pMMO, extensive computational studies were conducted to address these long-standing issues. A comprehensive analysis comparing the quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulated structures with cryo-EM data indicates that both the CuC and CuD sites tend to stay in the Cu(I) valence state within the membrane environment. Additionally, the concurrent presence of Cu(I) at both CuC and CuD sites leads to the significant reduction of the ligand-binding cavity situated between them, making it less likely to accommodate a reductant molecule such as durohydroquinone (DQH2). Subsequent QM/MM calculations reveal that the CuD(I) site is more reactive than the CuC(I) site in oxygen activation, en route to H2O2 formation and the generation of Cu(II)-O•- species. Finally, our simulations demonstrate that the natural reductant ubiquinol (CoQH2) assumes a productive binding conformation at the CuD(I) site but not at the CuC(I) site. This provides evidence that the true active site of membrane-bound pMMOs may be CuD rather than CuC. These findings clarify pMMO's catalytic mechanism and emphasize the membrane environment's pivotal role in modulating the coordination structure and the activity of copper centers within pMMO.
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Affiliation(s)
- Wei Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
- Key Laboratory of Aerosol Chemistry and Physics, State Key Laboratory of Loess and Quaternary Geology (SKLLQG), Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, P. R. China
| | - Zikuan Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Qiaoyu Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
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6
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Nakamura T, Mishima E, Yamada N, Mourão ASD, Trümbach D, Doll S, Wanninger J, Lytton E, Sennhenn P, Nishida Xavier da Silva T, Angeli JPF, Sattler M, Proneth B, Conrad M. Integrated chemical and genetic screens unveil FSP1 mechanisms of ferroptosis regulation. Nat Struct Mol Biol 2023; 30:1806-1815. [PMID: 37957306 PMCID: PMC10643123 DOI: 10.1038/s41594-023-01136-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023]
Abstract
Ferroptosis, marked by iron-dependent lipid peroxidation, may present an Achilles heel for the treatment of cancers. Ferroptosis suppressor protein-1 (FSP1), as the second ferroptosis mainstay, efficiently prevents lipid peroxidation via NAD(P)H-dependent reduction of quinones. Because its molecular mechanisms have remained obscure, we studied numerous FSP1 mutations present in cancer or identified by untargeted random mutagenesis. This mutational analysis elucidates the FAD/NAD(P)H-binding site and proton-transfer function of FSP1, which emerged to be evolutionarily conserved among different NADH quinone reductases. Using random mutagenesis screens, we uncover the mechanism of action of next-generation FSP1 inhibitors. Our studies identify the binding pocket of the first FSP1 inhibitor, iFSP1, and introduce the first species-independent FSP1 inhibitor, targeting the NAD(P)H-binding pocket. Conclusively, our study provides new insights into the molecular functions of FSP1 and enables the rational design of FSP1 inhibitors targeting cancer cells.
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Affiliation(s)
- Toshitaka Nakamura
- Institute of Metabolism and Cell Death, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | - Eikan Mishima
- Institute of Metabolism and Cell Death, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
- Division of Nephrology, Rheumatology and Endocrinology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Naoya Yamada
- Institute of Metabolism and Cell Death, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | - André Santos Dias Mourão
- Institute of Structural Biology, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | - Dietrich Trümbach
- Institute of Metabolism and Cell Death, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | - Sebastian Doll
- Institute of Metabolism and Cell Death, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | - Jonas Wanninger
- Institute of Metabolism and Cell Death, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | - Elena Lytton
- Institute of Metabolism and Cell Death, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | | | - Thamara Nishida Xavier da Silva
- Rudolf Virchow Zentrum (RVZ), Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - José Pedro Friedmann Angeli
- Rudolf Virchow Zentrum (RVZ), Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Michael Sattler
- Institute of Structural Biology, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Bettina Proneth
- Institute of Metabolism and Cell Death, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | - Marcus Conrad
- Institute of Metabolism and Cell Death, Molecular Target and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany.
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7
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Lv Y, Liang C, Sun Q, Zhu J, Xu H, Li X, Li YY, Wang Q, Yuan H, Chu B, Zhu D. Structural insights into FSP1 catalysis and ferroptosis inhibition. Nat Commun 2023; 14:5933. [PMID: 37739943 PMCID: PMC10516921 DOI: 10.1038/s41467-023-41626-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 09/11/2023] [Indexed: 09/24/2023] Open
Abstract
Ferroptosis suppressor protein 1 (FSP1, also known as AIMF2, AMID or PRG3) is a recently identified glutathione-independent ferroptosis suppressor1-3, but its underlying structural mechanism remains unknown. Here we report the crystal structures of Gallus gallus FSP1 in its substrate-free and ubiquinone-bound forms. The structures reveal a FAD-binding domain and a NAD(P)H-binding domain, both of which are shared with AIF and NADH oxidoreductases4-9, and a characteristic carboxy-terminal domain as well. We demonstrate that the carboxy-terminal domain is crucial for the catalytic activity and ferroptosis inhibition of FSP1 by mediating the functional dimerization of FSP1, and the formation of two active sites located on two sides of FAD, which are responsible for ubiquinone reduction and a unique FAD hydroxylation respectively. We also identify that FSP1 can catalyze the production of H2O2 and the conversion of FAD to 6-hydroxy-FAD in the presence of oxygen and NAD(P)H in vitro, and 6-hydroxy-FAD directly inhibits ferroptosis in cells. Together, these findings further our understanding on the catalytic and ferroptosis suppression mechanisms of FSP1 and establish 6-hydroxy-FAD as an active cofactor in FSP1 and a potent radical-trapping antioxidant in ferroptosis inhibition.
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Affiliation(s)
- Yun Lv
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Chunhui Liang
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Qichao Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Jing Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Haiyan Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Xiaoqing Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Yao-Yao Li
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Qihai Wang
- School of bioengineering, Jingchu University of Technology, Jingmen, 448000, China.
| | - Huiqing Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
- Key Laboratory of Experimental Teratology of Ministry of Education, Institute of Medical Sciences, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250031, China.
| | - Bo Chu
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
| | - Deyu Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
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8
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Mishima E, Nakamura T, Zheng J, Zhang W, Mourão ASD, Sennhenn P, Conrad M. DHODH inhibitors sensitize to ferroptosis by FSP1 inhibition. Nature 2023; 619:E9-E18. [PMID: 37407687 DOI: 10.1038/s41586-023-06269-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/30/2023] [Indexed: 07/07/2023]
Affiliation(s)
- Eikan Mishima
- Institute of Metabolism and Cell Death, Helmholtz Zentrum München, Neuherberg, Germany
- Division of Nephrology, Rheumatology and Endocrinology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Toshitaka Nakamura
- Institute of Metabolism and Cell Death, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jiashuo Zheng
- Institute of Metabolism and Cell Death, Helmholtz Zentrum München, Neuherberg, Germany
| | - Weijia Zhang
- Institute of Metabolism and Cell Death, Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Marcus Conrad
- Institute of Metabolism and Cell Death, Helmholtz Zentrum München, Neuherberg, Germany.
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9
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Sousa FM, Pires P, Barreto A, Refojo PN, Silva MS, Fernandes PB, Carapeto AP, Robalo TT, Rodrigues MS, Pinho MG, Cabrita EJ, Pereira MM. Unveiling the membrane bound dihydroorotate: Quinone oxidoreductase from Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148948. [PMID: 36481274 DOI: 10.1016/j.bbabio.2022.148948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Staphylococcus aureus is an opportunistic pathogen and one of the most frequent causes for community acquired and nosocomial bacterial infections. Even so, its energy metabolism is still under explored and its respiratory enzymes have been vastly overlooked. In this work, we unveil the dihydroorotate:quinone oxidoreductase (DHOQO) from S. aureus, the first example of a DHOQO from a Gram-positive organism. This protein was shown to be a FMN containing menaquinone reducing enzyme, presenting a Michaelis-Menten behaviour towards the two substrates, which was inhibited by Brequinar, Leflunomide, Lapachol, HQNO, Atovaquone and TFFA with different degrees of effectiveness. Deletion of the DHOQO coding gene (Δdhoqo) led to lower bacterial growth rates, and effected in cell morphology and metabolism, most importantly in the pyrimidine biosynthesis, here systematized for S. aureus MW2 for the first time. This work unveils the existence of a functional DHOQO in the respiratory chain of the pathogenic bacterium S. aureus, enlarging the understanding of its energy metabolism.
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Affiliation(s)
- Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Patrícia Pires
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Andreia Barreto
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Micael S Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro B Fernandes
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Ana P Carapeto
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Tiago T Robalo
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mário S Rodrigues
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mariana G Pinho
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Eurico J Cabrita
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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10
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Yang L, Rathnam C, Hidaka T, Hou Y, Conklin B, Pandian GN, Sugiyama H, Lee KB. Nanoparticle-Based Artificial Mitochondrial DNA Transcription Regulator: MitoScript. NANO LETTERS 2023; 23:2046-2055. [PMID: 36688839 DOI: 10.1021/acs.nanolett.2c03958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The growing knowledge of the links between aberrant mitochondrial gene transcription and human diseases necessitates both an effective and dynamic approach to control mitochondrial DNA (mtDNA) transcription. To address this challenge, we developed a nanoparticle-based synthetic mitochondrial transcription regulator (MitoScript). MitoScript provides great colloidal stability, excellent biocompatibility, efficient cell uptake, and selective mitochondria targeting and can be monitored in live cells using near-infrared fluorescence. Notably, MitoScript controlled mtDNA transcription in a human cell line in an effective and selective manner. MitoScript targeting the light strand promoter region of mtDNA resulted in the downregulation of ND6 gene silencing, which eventually affected cell redox status, with considerably increased reactive oxygen species (ROS) generation. In summary, we developed MitoScript for the efficient, nonviral modification of mitochondrial DNA transcription. Our platform technology can potentially contribute to understanding the fundamental mechanisms of mitochondrial disorders and developing effective treatments for mitochondrial diseases.
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Affiliation(s)
- Letao Yang
- Department of Chemistry and Chemical Biology, Rutgers University, 123 Bevier Road, Piscataway, New Jersey 08854, United States
| | - Christopher Rathnam
- Department of Chemistry and Chemical Biology, Rutgers University, 123 Bevier Road, Piscataway, New Jersey 08854, United States
| | - Takuya Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yannan Hou
- Department of Chemistry and Chemical Biology, Rutgers University, 123 Bevier Road, Piscataway, New Jersey 08854, United States
| | - Brandon Conklin
- Department of Chemistry and Chemical Biology, Rutgers University, 123 Bevier Road, Piscataway, New Jersey 08854, United States
| | - Ganesh N Pandian
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers University, 123 Bevier Road, Piscataway, New Jersey 08854, United States
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11
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Transgenic NADH dehydrogenase restores oxygen regulation of breathing in mitochondrial complex I-deficient mice. Nat Commun 2023; 14:1172. [PMID: 36859533 PMCID: PMC9977773 DOI: 10.1038/s41467-023-36894-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
The hypoxic ventilatory response (HVR) is a life-saving reflex, triggered by the activation of chemoreceptor glomus cells in the carotid body (CB) connected with the brainstem respiratory center. The molecular mechanisms underlying glomus cell acute oxygen (O2) sensing are unclear. Genetic disruption of mitochondrial complex I (MCI) selectively abolishes the HVR and glomus cell responsiveness to hypoxia. However, it is unknown what functions of MCI (metabolic, proton transport, or signaling) are essential for O2 sensing. Here we show that transgenic mitochondrial expression of NDI1, a single-molecule yeast NADH/quinone oxidoreductase that does not directly contribute to proton pumping, fully recovers the HVR and glomus cell sensitivity to hypoxia in MCI-deficient mice. Therefore, maintenance of mitochondrial NADH dehydrogenase activity and the electron transport chain are absolutely necessary for O2-dependent regulation of breathing. NDI1 expression also rescues other systemic defects caused by MCI deficiency. These data explain the role of MCI in acute O2 sensing by arterial chemoreceptors and demonstrate the optimal recovery of complex organismal functions by gene therapy.
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12
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Ding Q, Liu Q, Zhang Y, Li F, Song H. Modular Engineering Strategy to Redirect Electron Flux into the Electron-Transfer Chain for Enhancing Extracellular Electron Transfer in Shewanella oneidensis. ACS Synth Biol 2023; 12:471-481. [PMID: 36457250 DOI: 10.1021/acssynbio.2c00408] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Efficient extracellular electron transfer (EET) of exoelectrogens is critical for practical applications of various bioelectrochemical systems. However, the low efficiency of electron transfer remains a major bottleneck. In this study, a modular engineering strategy, including broadening the sources of the intracellular electron pool, enhancing intracellular nicotinamide adenine dinucleotide (NADH) regeneration, and promoting electron release from electron pools, was developed to redirect electron flux into the electron transfer chain in Shewanella oneidensis MR-1. Among them, four genes include gene SO1522 encoding a lactate transporter for broadening the sources of the intracellular electron pool, gene gapA encoding a glyceraldehyde-3-phosphate dehydrogenase and gene mdh encoding a malate dehydrogenase in the central carbon metabolism for enhancing intracellular NADH regeneration, and gene ndh encoding NADH dehydrogenase on the inner membrane for releasing electrons from intracellular electron pools into the electron-transport chain. Upon assembly of the four genes, electron flux was directly redirected from the electron donor to the electron-transfer chain, achieving 62% increase in intracellular NADH levels, which resulted in a 3.5-fold enhancement in the power density from 59.5 ± 3.2 mW/m2 (wild type) to 270.0 ± 12.7 mW/m2 (recombinant strain). This study confirmed that redirecting electron flux from the electron donor to the electron-transfer chain is a viable approach to enhance the EET rate of S. oneidensis.
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Affiliation(s)
- Qinran Ding
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
| | - Qijing Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
| | - Yan Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
| | - Hao Song
- Frontiers Science Center for Synthetic Biology (Ministry of Education), and Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin300072, China
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13
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A genome-wide CRISPR-Cas9 knockout screen identifies FSP1 as the warfarin-resistant vitamin K reductase. Nat Commun 2023; 14:828. [PMID: 36788244 PMCID: PMC9929328 DOI: 10.1038/s41467-023-36446-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/26/2023] [Indexed: 02/16/2023] Open
Abstract
Vitamin K is a vital micronutrient implicated in a variety of human diseases. Warfarin, a vitamin K antagonist, is the most commonly prescribed oral anticoagulant. Patients overdosed on warfarin can be rescued by administering high doses of vitamin K because of the existence of a warfarin-resistant vitamin K reductase. Despite the functional discovery of vitamin K reductase over eight decades ago, its identity remained elusive. Here, we report the identification of warfarin-resistant vitamin K reductase using a genome-wide CRISPR-Cas9 knockout screen with a vitamin K-dependent apoptotic reporter cell line. We find that ferroptosis suppressor protein 1 (FSP1), a ubiquinone oxidoreductase, is the enzyme responsible for vitamin K reduction in a warfarin-resistant manner, consistent with a recent discovery by Mishima et al. FSP1 inhibitor that inhibited ubiquinone reduction and thus triggered cancer cell ferroptosis, displays strong inhibition of vitamin K-dependent carboxylation. Intriguingly, dihydroorotate dehydrogenase, another ubiquinone-associated ferroptosis suppressor protein parallel to the function of FSP1, does not support vitamin K-dependent carboxylation. These findings provide new insights into selectively controlling the physiological and pathological processes involving electron transfers mediated by vitamin K and ubiquinone.
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14
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Yang C, Huang Z, Zhang X, Zhu C. Structural Insights into the NAD(P)H:Quinone Oxidoreductase from Phytophthora capsici. ACS OMEGA 2022; 7:25705-25714. [PMID: 35910145 PMCID: PMC9330140 DOI: 10.1021/acsomega.2c02954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Soluble quinone oxidoreductases catalyze transfer of electrons from NADPH to quinones. Transfer of electrons is essential for detoxification of synthetic compounds. Here, we present the crystal structure of a NADPH-dependent QOR from Phytophthora capsici (Pc) complexed with NADPH at 2.4 Å resolution. The enzyme exhibits a bi-modular architecture, containing a NADPH-binding groove and a substrate-binding pocket in each subunit. In the crystal, each asymmetric unit of PcQOR contains two molecules stabilized by intermolecular interactions. Gel filtration and ultracentrifugation analyses reveal that it functions as a tetramer in solution. Alignment of homologous structures exhibits a conserved topology. However, the active sites vary among the homologues, indicating differences in substrate specificities. Enzymatic assays indicate that PcQOR tends to catalyze the large substrates, like 9,10-phenanthrenequinone. Computational simulation associated with site-directed mutagenesis and enzymatic activity analysis declares a potential quinone-binding channel. The ability to reduce quinones probably helps P. capsici to detoxify some harmful chemicals encountered during invasion.
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Affiliation(s)
- Cancan Yang
- Shandong
Provincial Key Laboratory for Biology of Vegetable Diseases and Insect
Pests, College of Plant Protection, Shandong
Agricultural University, Taian 271018, China
| | - Zhenling Huang
- Shandong
Provincial Key Laboratory for Biology of Vegetable Diseases and Insect
Pests, College of Plant Protection, Shandong
Agricultural University, Taian 271018, China
| | - Xiuguo Zhang
- Shandong
Provincial Key Laboratory for Biology of Vegetable Diseases and Insect
Pests, College of Plant Protection, Shandong
Agricultural University, Taian 271018, China
| | - Chunyuan Zhu
- College
of Life Sciences, Shandong Agricultural
University, Taian 271018, China
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15
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Lu L, Åkerbladh L, Ahmad S, Konda V, Cao S, Vocat A, Maes L, Cole ST, Hughes D, Larhed M, Brandt P, Karlén A, Mowbray SL. Synthesis and In Vitro Biological Evaluation of Quinolinyl Pyrimidines Targeting Type II NADH-Dehydrogenase (NDH-2). ACS Infect Dis 2022; 8:482-498. [PMID: 35184552 PMCID: PMC8922281 DOI: 10.1021/acsinfecdis.1c00413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Type II NADH dehydrogenase
(NDH-2) is an essential component of
electron transfer in many microbial pathogens but has remained largely
unexplored as a potential drug target. Previously, quinolinyl pyrimidines
were shown to inhibit Mycobacterium tuberculosis NDH-2, as well as the growth of the bacteria [ShirudeP. S.; ACS Med. Chem. Lett.2012, 3, 736−74024900541]. Here, we synthesized a number of novel quinolinyl pyrimidines
and investigated their properties. In terms of inhibition of the NDH-2
enzymes from M. tuberculosis and Mycobacterium smegmatis, the best compounds were
of similar potency to previously reported inhibitors of the same class
(half-maximal inhibitory concentration (IC50) values in
the low-μM range). However, a number of the compounds had much
better activity against Gram-negative pathogens, with minimum inhibitory
concentrations (MICs) as low as 2 μg/mL. Multivariate analyses
(partial least-squares (PLS) and principle component analysis (PCA))
showed that overall ligand charge was one of the most important factors
in determining antibacterial activity, with patterns that varied depending
on the particular bacterial species. In some cases (e.g., mycobacteria), there was a clear correlation between the IC50 values and the observed MICs, while in other instances,
no such correlation was evident. When tested against a panel of protozoan
parasites, the compounds failed to show activity that was not linked
to cytotoxicity. Further, a strong correlation between hydrophobicity
(estimated as clog P) and cytotoxicity was
revealed; more hydrophobic analogues were more cytotoxic. By contrast,
antibacterial MIC values and cytotoxicity were not well correlated,
suggesting that the quinolinyl pyrimidines can be optimized further
as antimicrobial agents.
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Affiliation(s)
- Lu Lu
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Linda Åkerbladh
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, Box
574, SE-751 23 Uppsala, Sweden
| | - Shabbir Ahmad
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Vivek Konda
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, Box
574, SE-751 23 Uppsala, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
| | - Anthony Vocat
- École Polytechnique Fédérale de Lausanne, EPFL SV/GHI/UPCOL, Global Health Institute, Station no. 19, CH-1015 Lausanne, Switzerland
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Stewart T. Cole
- École Polytechnique Fédérale de Lausanne, EPFL SV/GHI/UPCOL, Global Health Institute, Station no. 19, CH-1015 Lausanne, Switzerland
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
| | - Mats Larhed
- Department of Medicinal Chemistry, Science for Life Laboratory, BMC, Uppsala University, Box
574, SE-751 23 Uppsala, Sweden
| | - Peter Brandt
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, Box
574, SE-751 23 Uppsala, Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, Box
574, SE-751 23 Uppsala, Sweden
| | - Sherry L. Mowbray
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
- Department of Cell and Molecular Biology, Science for Life Laboratory, BMC, Uppsala University, Box
596, SE-751 24 Uppsala, Sweden
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16
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Gu J, Liu T, Guo R, Zhang L, Yang M. The coupling mechanism of mammalian mitochondrial complex I. Nat Struct Mol Biol 2022; 29:172-182. [PMID: 35145322 DOI: 10.1038/s41594-022-00722-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/06/2022] [Indexed: 01/03/2023]
Abstract
Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in mitochondria. In the present study, we report cryo-electron microscopy structures of CI from Sus scrofa in six treatment conditions at a resolution of 2.4-3.5 Å, in which CI structures of each condition can be classified into two biochemical classes (active or deactive), with a notably higher proportion of active CI particles. These structures illuminate how hydrophobic ubiquinone-10 (Q10) with its long isoprenoid tail is bound and reduced in a narrow Q chamber comprising four different Q10-binding sites. Structural comparisons of active CI structures from our decylubiquinone-NADH and rotenone-NADH datasets reveal that Q10 reduction at site 1 is not coupled to proton pumping in the membrane arm, which might instead be coupled to Q10 oxidation at site 2. Our data overturn the widely accepted previous proposal about the coupling mechanism of CI.
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Affiliation(s)
- Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Tianya Liu
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Runyu Guo
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Laixing Zhang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing, China. .,SUSTech Cryo-EM Facility Center, Southern University of Science & Technology, Shenzhen, China.
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17
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Møller IM, Rasmusson AG, Van Aken O. Plant mitochondria - past, present and future. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:912-959. [PMID: 34528296 DOI: 10.1111/tpj.15495] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
The study of plant mitochondria started in earnest around 1950 with the first isolations of mitochondria from animal and plant tissues. The first 35 years were spent establishing the basic properties of plant mitochondria and plant respiration using biochemical and physiological approaches. A number of unique properties (compared to mammalian mitochondria) were observed: (i) the ability to oxidize malate, glycine and cytosolic NAD(P)H at high rates; (ii) the partial insensitivity to rotenone, which turned out to be due to the presence of a second NADH dehydrogenase on the inner surface of the inner mitochondrial membrane in addition to the classical Complex I NADH dehydrogenase; and (iii) the partial insensitivity to cyanide, which turned out to be due to an alternative oxidase, which is also located on the inner surface of the inner mitochondrial membrane, in addition to the classical Complex IV, cytochrome oxidase. With the appearance of molecular biology methods around 1985, followed by genomics, further unique properties were discovered: (iv) plant mitochondrial DNA (mtDNA) is 10-600 times larger than the mammalian mtDNA, yet it only contains approximately 50% more genes; (v) plant mtDNA has kept the standard genetic code, and it has a low divergence rate with respect to point mutations, but a high recombinatorial activity; (vi) mitochondrial mRNA maturation includes a uniquely complex set of activities for processing, splicing and editing (at hundreds of sites); (vii) recombination in mtDNA creates novel reading frames that can produce male sterility; and (viii) plant mitochondria have a large proteome with 2000-3000 different proteins containing many unique proteins such as 200-300 pentatricopeptide repeat proteins. We describe the present and fairly detailed picture of the structure and function of plant mitochondria and how the unique properties make their metabolism more flexible allowing them to be involved in many diverse processes in the plant cell, such as photosynthesis, photorespiration, CAM and C4 metabolism, heat production, temperature control, stress resistance mechanisms, programmed cell death and genomic evolution. However, it is still a challenge to understand how the regulation of metabolism and mtDNA expression works at the cellular level and how retrograde signaling from the mitochondria coordinates all those processes.
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Affiliation(s)
- Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
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18
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Leishmania type II dehydrogenase is essential for parasite viability irrespective of the presence of an active complex I. Proc Natl Acad Sci U S A 2021; 118:2103803118. [PMID: 34654744 DOI: 10.1073/pnas.2103803118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2021] [Indexed: 11/18/2022] Open
Abstract
Type II NADH dehydrogenases (NDH2) are monotopic enzymes present in the external or internal face of the mitochondrial inner membrane that contribute to NADH/NAD+ balance by conveying electrons from NADH to ubiquinone without coupled proton translocation. Herein, we characterize the product of a gene present in all species of the human protozoan parasite Leishmania as a bona fide, matrix-oriented, type II NADH dehydrogenase. Within mitochondria, this respiratory activity concurs with that of type I NADH dehydrogenase (complex I) in some Leishmania species but not others. To query the significance of NDH2 in parasite physiology, we attempted its genetic disruption in two parasite species, exhibiting a silent (Leishmania infantum, Li) and a fully operational (Leishmania major, Lm) complex I. Strikingly, this analysis revealed that NDH2 abrogation is not tolerated by Leishmania, not even by complex I-expressing Lm species. Conversely, complex I is dispensable in both species, provided that NDH2 is sufficiently expressed. That a type II dehydrogenase is essential even in the presence of an active complex I places Leishmania NADH metabolism into an entirely unique perspective and suggests unexplored functions for NDH2 that span beyond its complex I-overlapping activities. Notably, by showing that the essential character of NDH2 extends to the disease-causing stage of Leishmania, we genetically validate NDH2-an enzyme without a counterpart in mammals-as a candidate target for leishmanicidal drugs.
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19
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Yang Y, Tang T, Li X, Michel T, Ling L, Huang Z, Mulaka M, Wu Y, Gao H, Wang L, Zhou J, Meunier B, Ke H, Jiang L, Rao Y. Design, synthesis, and biological evaluation of multiple targeting antimalarials. Acta Pharm Sin B 2021; 11:2900-2913. [PMID: 34589403 PMCID: PMC8463279 DOI: 10.1016/j.apsb.2021.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/11/2021] [Accepted: 03/30/2021] [Indexed: 02/08/2023] Open
Abstract
Malaria still threatens global health seriously today. While the current discoveries of antimalarials are almost totally focused on single mode-of-action inhibitors, multi-targeting inhibitors are highly desired to overcome the increasingly serious drug resistance. Here, we performed a structure-based drug design on mitochondrial respiratory chain of Plasmodium falciparum and identified an extremely potent molecule, RYL-581, which binds to multiple protein binding sites of P. falciparum simultaneously (allosteric site of type II NADH dehydrogenase, Qo and Qi sites of cytochrome bc1). Antimalarials with such multiple targeting mechanism of action have never been reported before. RYL-581 kills various drug-resistant strains in vitro and shows good solubility as well as in vivo activity. This structure-based strategy for designing RYL-581 from starting compound may be helpful for other medicinal chemistry projects in the future, especially for drug discovery on membrane-associated targets.
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20
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Godoy-Hernandez A, McMillan DGG. The Profound Influence of Lipid Composition on the Catalysis of the Drug Target NADH Type II Oxidoreductase. MEMBRANES 2021; 11:membranes11050363. [PMID: 34067848 PMCID: PMC8156991 DOI: 10.3390/membranes11050363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 11/25/2022]
Abstract
Lipids play a pivotal role in cellular respiration, providing the natural environment in which an oxidoreductase interacts with the quinone pool. To date, it is generally accepted that negatively charged lipids play a major role in the activity of quinone oxidoreductases. By changing lipid compositions when assaying a type II NADH:quinone oxidoreductase, we demonstrate that phosphatidylethanolamine has an essential role in substrate binding and catalysis. We also reveal the importance of acyl chain composition, specifically c14:0, on membrane-bound quinone-mediated catalysis. This demonstrates that oxidoreductase lipid specificity is more diverse than originally thought and that the lipid environment plays an important role in the physiological catalysis of membrane-bound oxidoreductases.
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21
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Boes DM, Godoy-Hernandez A, McMillan DGG. Peripheral Membrane Proteins: Promising Therapeutic Targets across Domains of Life. MEMBRANES 2021; 11:membranes11050346. [PMID: 34066904 PMCID: PMC8151925 DOI: 10.3390/membranes11050346] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 11/16/2022]
Abstract
Membrane proteins can be classified into two main categories—integral and peripheral membrane proteins—depending on the nature of their membrane interaction. Peripheral membrane proteins are highly unique amphipathic proteins that interact with the membrane indirectly, using electrostatic or hydrophobic interactions, or directly, using hydrophobic tails or GPI-anchors. The nature of this interaction not only influences the location of the protein in the cell, but also the function. In addition to their unique relationship with the cell membrane, peripheral membrane proteins often play a key role in the development of human diseases such as African sleeping sickness, cancer, and atherosclerosis. This review will discuss the membrane interaction and role of periplasmic nitrate reductase, CymA, cytochrome c, alkaline phosphatase, ecto-5’-nucleotidase, acetylcholinesterase, alternative oxidase, type-II NADH dehydrogenase, and dihydroorotate dehydrogenase in certain diseases. The study of these proteins will give new insights into their function and structure, and may ultimately lead to ground-breaking advances in the treatment of severe diseases.
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Affiliation(s)
- Deborah M. Boes
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
| | - Albert Godoy-Hernandez
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
| | - Duncan G. G. McMillan
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
- School of Fundamental Sciences, Massey University, Palmerston North, Private Bag 11 222, New Zealand
- Correspondence:
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22
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Abstract
Bacteria power their energy metabolism using membrane-bound respiratory enzymes that capture chemical energy and transduce it by pumping protons or Na+ ions across their cell membranes. Recent breakthroughs in molecular bioenergetics have elucidated the architecture and function of many bacterial respiratory enzymes, although key mechanistic principles remain debated. In this Review, we present an overview of the structure, function and bioenergetic principles of modular bacterial respiratory chains and discuss their differences from the eukaryotic counterparts. We also discuss bacterial supercomplexes, which provide central energy transduction systems in several bacteria, including important pathogens, and which could open up possible avenues for treatment of disease.
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23
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Kumar R, Chhikara BS, Gulia K, Chhillar M. Cleaning the molecular machinery of cells via proteostasis, proteolysis and endocytosis selectively, effectively, and precisely: intracellular self-defense and cellular perturbations. Mol Omics 2020; 17:11-28. [PMID: 33135707 DOI: 10.1039/d0mo00085j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Network coordinates of cellular processes (proteostasis, proteolysis, and endocytosis), and molecular chaperones are the key complements in the cell machinery and processes. Specifically, cellular pathways are responsible for the conformational maintenance, cellular concentration, interactions, protein synthesis, disposal of misfolded proteins, localization, folding, and degradation. The failure of cellular processes and pathways disturbs structural proteins and the nucleation of amyloids. These mishaps further initiate amyloid polymorphism, transmissibility, co-aggregation of pathogenic proteins in tissues and cells, prion strains, and mechanisms and pathways for toxicity. Consequently, these conditions favor and lead to the formation of elongated amyloid fibrils consisting of many-stranded β-sheets (N,N-terminus and C,C-terminus), and abnormal fibrous, extracellular, proteinaceous deposits. Finally, these β-sheets deposit, and cells fail to degrade them effectively. The essential torsion angles (φ, ψ, and ω) define the conformation of proteins and their architecture. Cells initiate several transformations and pathways during the regulation of protein homeostasis based on the requirements for the functioning of the cell, which are governed by ATP-dependent proteases. In this process, the kinetics of the molding/folding phenomenon is disturbed, and subsequently, it is dominated by cross-domain misfolding intermediates; however, simultaneously, it is opposed by small stretching forces, which naturally exist in the cell. The ubiquitin/proteasome system deals with damaged proteins, which are not refolded by the chaperone-type machinery. Ubiquitin-protein ligases (E3-Ub) participate in all the cellular activity initiated and governed by molecular chaperones to stabilize the cellular proteome and participate in the degradation phenomenon implemented for damaged proteins. Optical tweezers, a single-resolution based technique, disclose the folding pathway of linear chain proteins, which is how they convert themselves into a three-dimensional architecture. Further, DNA-protein conjugation analysis is performed to obtain folding energies as single-molecule kinetic and thermodynamic data.
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Affiliation(s)
- Rajiv Kumar
- NIET, National Institute of Medical Science, India.
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24
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Haapanen O, Reidelbach M, Sharma V. Coupling of quinone dynamics to proton pumping in respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148287. [PMID: 32777307 DOI: 10.1016/j.bbabio.2020.148287] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 12/12/2022]
Abstract
Respiratory complex I (NADH:quinone oxidoreductase) plays a central role in generating the proton electrochemical gradient in mitochondrial and bacterial membranes, which is needed to generate ATP. Several high-resolution structures of complex I have been determined, revealing its intricate architecture and complementing the biochemical and biophysical studies. However, the molecular mechanism of long-range coupling between ubiquinone (Q) reduction and proton pumping is not known. Computer simulations have been applied to decipher the dynamics of Q molecule in the ~30 Å long Q tunnel. In this short report, we discuss the binding and dynamics of Q at computationally predicted Q binding sites, many of which are supported by structural data on complex I. We suggest that the binding of Q at these sites is coupled to proton pumping by means of conformational rearrangements in the conserved loops of core subunits.
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Affiliation(s)
- Outi Haapanen
- Department of Physics, University of Helsinki, Finland
| | | | - Vivek Sharma
- Department of Physics, University of Helsinki, Finland; HiLIFE Institute of Biotechnology, University of Helsinki, Finland.
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25
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Juergens H, Hakkaart XDV, Bras JE, Vente A, Wu L, Benjamin KR, Pronk JT, Daran-Lapujade P, Mans R. Contribution of Complex I NADH Dehydrogenase to Respiratory Energy Coupling in Glucose-Grown Cultures of Ogataea parapolymorpha. Appl Environ Microbiol 2020; 86:e00678-20. [PMID: 32471916 PMCID: PMC7376551 DOI: 10.1128/aem.00678-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/04/2020] [Indexed: 12/31/2022] Open
Abstract
The thermotolerant yeast Ogataea parapolymorpha (formerly Hansenula polymorpha) is an industrially relevant production host that exhibits a fully respiratory sugar metabolism in aerobic batch cultures. NADH-derived electrons can enter its mitochondrial respiratory chain either via a proton-translocating complex I NADH-dehydrogenase or via three putative alternative NADH dehydrogenases. This respiratory entry point affects the amount of ATP produced per NADH/O2 consumed and therefore impacts the maximum yield of biomass and/or cellular products from a given amount of substrate. To investigate the physiological importance of complex I, a wild-type O. parapolymorpha strain and a congenic complex I-deficient mutant were grown on glucose in aerobic batch, chemostat, and retentostat cultures in bioreactors. In batch cultures, the two strains exhibited a fully respiratory metabolism and showed the same growth rates and biomass yields, indicating that, under these conditions, the contribution of NADH oxidation via complex I was negligible. Both strains also exhibited a respiratory metabolism in glucose-limited chemostat cultures, but the complex I-deficient mutant showed considerably reduced biomass yields on substrate and oxygen, consistent with a lower efficiency of respiratory energy coupling. In glucose-limited retentostat cultures at specific growth rates down to ∼0.001 h-1, both O. parapolymorpha strains showed high viability. Maintenance energy requirements at these extremely low growth rates were approximately 3-fold lower than estimated from faster-growing chemostat cultures, indicating a stringent-response-like behavior. Quantitative transcriptome and proteome analyses indicated condition-dependent expression patterns of complex I subunits and of alternative NADH dehydrogenases that were consistent with physiological observations.IMPORTANCE Since popular microbial cell factories have typically not been selected for efficient respiratory energy coupling, their ATP yields from sugar catabolism are often suboptimal. In aerobic industrial processes, suboptimal energy coupling results in reduced product yields on sugar, increased process costs for oxygen transfer, and volumetric productivity limitations due to limitations in gas transfer and cooling. This study provides insights into the contribution of mechanisms of respiratory energy coupling in the yeast cell factory Ogataea parapolymorpha under different growth conditions and provides a basis for rational improvement of energy coupling in yeast cell factories. Analysis of energy metabolism of O. parapolymorpha at extremely low specific growth rates indicated that this yeast reduces its energy requirements for cellular maintenance under extreme energy limitation. Exploration of the mechanisms for this increased energetic efficiency may contribute to an optimization of the performance of industrial processes with slow-growing eukaryotic cell factories.
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Affiliation(s)
- Hannes Juergens
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Xavier D V Hakkaart
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jildau E Bras
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - André Vente
- DSM Biotechnology Center, Delft, The Netherlands
| | - Liang Wu
- DSM Biotechnology Center, Delft, The Netherlands
| | | | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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26
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Linden A, Deckers M, Parfentev I, Pflanz R, Homberg B, Neumann P, Ficner R, Rehling P, Urlaub H. A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria. Mol Cell Proteomics 2020; 19:1161-1178. [PMID: 32332106 PMCID: PMC7338081 DOI: 10.1074/mcp.ra120.002028] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/24/2020] [Indexed: 12/13/2022] Open
Abstract
Protein cross-linking and the analysis of cross-linked peptides by mass spectrometry is currently receiving much attention. Not only is this approach applied to isolated complexes to provide information about spatial arrangements of proteins, but it is also increasingly applied to entire cells and their organelles. As in quantitative proteomics, the application of isotopic labeling further makes it possible to monitor quantitative changes in the protein-protein interactions between different states of a system. Here, we cross-linked mitochondria from Saccharomyces cerevisiae grown on either glycerol- or glucose-containing medium to monitor protein-protein interactions under non-fermentative and fermentative conditions. We investigated qualitatively the protein-protein interactions of the 400 most abundant proteins applying stringent data-filtering criteria, i.e. a minimum of two cross-linked peptide spectrum matches and a cut-off in the spectrum scoring of the used search engine. The cross-linker BS3 proved to be equally suited for connecting proteins in all compartments of mitochondria when compared with its water-insoluble but membrane-permeable derivative DSS. We also applied quantitative cross-linking to mitochondria of both the growth conditions using stable-isotope labeled BS3. Significant differences of cross-linked proteins under glycerol and glucose conditions were detected, however, mainly because of the different copy numbers of these proteins in mitochondria under both the conditions. Results obtained from the glycerol condition indicate that the internal NADH:ubiquinone oxidoreductase Ndi1 is part of an electron transport chain supercomplex. We have also detected several hitherto uncharacterized proteins and identified their interaction partners. Among those, Min8 was found to be associated with cytochrome c oxidase. BN-PAGE analyses of min8Δ mitochondria suggest that Min8 promotes the incorporation of Cox12 into cytochrome c oxidase.
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Affiliation(s)
- Andreas Linden
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Markus Deckers
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Iwan Parfentev
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ralf Pflanz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bettina Homberg
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany.
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27
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Rasmusson AG, Escobar MA, Hao M, Podgórska A, Szal B. Mitochondrial NAD(P)H oxidation pathways and nitrate/ammonium redox balancing in plants. Mitochondrion 2020; 53:158-165. [PMID: 32485334 DOI: 10.1016/j.mito.2020.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/05/2020] [Accepted: 05/26/2020] [Indexed: 12/19/2022]
Abstract
Plant mitochondrial oxidative phosphorylation is characterised by alternative electron transport pathways with different energetic efficiencies, allowing turnover of cellular redox compounds like NAD(P)H. These electron transport chain pathways are profoundly affected by soil nitrogen availability, most commonly as oxidized nitrate (NO3-) and/or reduced ammonium (NH4+). The bioenergetic strategies involved in assimilating different N sources can alter redox homeostasis and antioxidant systems in different cellular compartments, including the mitochondria and the cell wall. Conversely, changes in mitochondrial redox systems can affect plant responses to N. This review explores the integration between N assimilation, mitochondrial redox metabolism, and apoplast metabolism.
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Affiliation(s)
- Allan G Rasmusson
- Lund University, Department of Biology, Sölvegatan 35B, 22362 Lund, Sweden.
| | - Matthew A Escobar
- California State University San Marcos, 333 S. Twin Oaks Valley Rd., San Marcos, CA 92096, USA
| | - Mengshu Hao
- Lund University, Department of Biology, Sölvegatan 35B, 22362 Lund, Sweden
| | - Anna Podgórska
- University of Warsaw, Faculty of Biology, Institute of Experimental Plant Biology and Biotechnology, Ilii Miecznikowa 1, 02-096 Warsaw, Poland
| | - Bożena Szal
- University of Warsaw, Faculty of Biology, Institute of Experimental Plant Biology and Biotechnology, Ilii Miecznikowa 1, 02-096 Warsaw, Poland
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28
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Wu M, Gu J, Zong S, Guo R, Liu T, Yang M. Research journey of respirasome. Protein Cell 2020; 11:318-338. [PMID: 31919741 PMCID: PMC7196574 DOI: 10.1007/s13238-019-00681-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
Respirasome, as a vital part of the oxidative phosphorylation system, undertakes the task of transferring electrons from the electron donors to oxygen and produces a proton concentration gradient across the inner mitochondrial membrane through the coupled translocation of protons. Copious research has been carried out on this lynchpin of respiration. From the discovery of individual respiratory complexes to the report of the high-resolution structure of mammalian respiratory supercomplex I1III2IV1, scientists have gradually uncovered the mysterious veil of the electron transport chain (ETC). With the discovery of the mammalian respiratory mega complex I2III2IV2, a new perspective emerges in the research field of the ETC. Behind these advances glitters the light of the revolution in both theory and technology. Here, we give a short review about how scientists 'see' the structure and the mechanism of respirasome from the macroscopic scale to the atomic scale during the past decades.
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Affiliation(s)
- Meng Wu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Shuai Zong
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Runyu Guo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Tianya Liu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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29
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Lencina AM, Gennis RB, Schurig-Briccio LA. The oligomeric state of the Caldivirga maquilingensis type III sulfide:Quinone Oxidoreductase is required for membrane binding. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148132. [PMID: 31816290 DOI: 10.1016/j.bbabio.2019.148132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/11/2019] [Accepted: 12/04/2019] [Indexed: 12/24/2022]
Abstract
Sulfide:quinone oxidoreductase (SQR) is a monotopic membrane flavoprotein present in all domains of life, with multiple roles including sulfide detoxification, homeostasis and energy generation by providing electrons to respiratory or photosynthetic electron transport chains. A type III SQR from the hyperthermophilic archeon Caldivirga maquilingensis has been previously characterized, and its C-terminal amphipathic helices were demonstrated to be responsible for membrane binding. Here, the oligomeric state of this protein was experimentally evaluated by size exclusion chromatography, native gels and crosslinking, and found to be a monomer-dimer-trimer equilibrium. Remarkably, mutant and truncated variants unable to bind to the membrane are able to maintain their oligomeric association. Thus, unlike other related monotopic membrane proteins, the region involved in membrane binding does not influence oligomerization. Furthermore, by studying heterodimers between the WT and mutants, it was concluded that membrane binding requires an oligomer with at least two copies of the protein with intact C-terminal amphipathic helices. A structural homology model of the C. maquilingensis SQR was used to define the flavin- and quinone-binding sites. CmGly12, CmGly16, CmAla77 and CmPro44 were determined to be important for flavin binding. Unexpectedly, CmGly299 is only important for quinone reduction despite its proximity to bound FAD. CmPhe337 and CmPhe362 are also important for quinone binding apparently by direct interaction with the quinone ring, whereas CmLys359, postulated to hydrogen bond to the quinone, seems to have a more structural role. The results presented differentiate the Type III CmSQR from some of its counterparts classified as Type I, II and V.
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Affiliation(s)
- Andrea M Lencina
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Lici A Schurig-Briccio
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA.
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30
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Nakatani Y, Shimaki Y, Dutta D, Muench SP, Ireton K, Cook GM, Jeuken LJC. Unprecedented Properties of Phenothiazines Unraveled by a NDH-2 Bioelectrochemical Assay Platform. J Am Chem Soc 2020; 142:1311-1320. [PMID: 31880924 DOI: 10.1021/jacs.9b10254] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Type II NADH:quinone oxidoreductase (NDH-2) plays a crucial role in the respiratory chains of many organisms. Its absence in mammalian cells makes NDH-2 an attractive new target for developing antimicrobials and antiprotozoal agents. We established a novel bioelectrochemical platform to characterize the catalytic behavior of NDH-2 from Caldalkalibacillus thermarum and Listeria monocytogenes strain EGD-e while bound to native-like lipid membranes. Catalysis of both NADH oxidation and lipophilic quinone reduction by membrane-bound NDH-2 followed the Michaelis-Menten model; however, the maximum turnover was only achieved when a high concentration of quinone (>3 mM) was present in the membrane, suggesting that quinone availability regulates NADH-coupled respiration activity. The quinone analogue 2-heptyl-4-hydroxyquinoline-N-oxide inhibited C. thermarum NDH-2 activity, and its potency is higher in a membrane environment compared to assays performed with water-soluble quinone analogues, demonstrating the importance of testing compounds under physiologically relevant conditions. Furthermore, when phenothiazines, one of the most commonly identified NDH-2 inhibitors, were tested, they did not inhibit membrane-bound NDH-2. Instead, our assay platform unexpectedly suggests a novel mode of phenothiazine action where chlorpromazine, a promising antitubercular agent and key medicine used to treat psychotic disorders, is able to disrupt pH gradients across bacterial membranes.
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Affiliation(s)
- Yoshio Nakatani
- Department of Microbiology and Immunology , University of Otago , Dunedin 9054 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
| | - Yosuke Shimaki
- Department of Microbiology and Immunology , University of Otago , Dunedin 9054 , New Zealand
| | - Debajyoti Dutta
- School of Biomedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Stephen P Muench
- School of Biomedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Keith Ireton
- Department of Microbiology and Immunology , University of Otago , Dunedin 9054 , New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology , University of Otago , Dunedin 9054 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
| | - Lars J C Jeuken
- School of Biomedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
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31
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Trisolini L, Gambacorta N, Gorgoglione R, Montaruli M, Laera L, Colella F, Volpicella M, De Grassi A, Pierri CL. FAD/NADH Dependent Oxidoreductases: From Different Amino Acid Sequences to Similar Protein Shapes for Playing an Ancient Function. J Clin Med 2019; 8:jcm8122117. [PMID: 31810296 PMCID: PMC6947548 DOI: 10.3390/jcm8122117] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 12/29/2022] Open
Abstract
Flavoprotein oxidoreductases are members of a large protein family of specialized dehydrogenases, which include type II NADH dehydrogenase, pyridine nucleotide-disulphide oxidoreductases, ferredoxin-NAD+ reductases, NADH oxidases, and NADH peroxidases, playing a crucial role in the metabolism of several prokaryotes and eukaryotes. Although several studies have been performed on single members or protein subgroups of flavoprotein oxidoreductases, a comprehensive analysis on structure-function relationships among the different members and subgroups of this great dehydrogenase family is still missing. Here, we present a structural comparative analysis showing that the investigated flavoprotein oxidoreductases have a highly similar overall structure, although the investigated dehydrogenases are quite different in functional annotations and global amino acid composition. The different functional annotation is ascribed to their participation in species-specific metabolic pathways based on the same biochemical reaction, i.e., the oxidation of specific cofactors, like NADH and FADH2. Notably, the performed comparative analysis sheds light on conserved sequence features that reflect very similar oxidation mechanisms, conserved among flavoprotein oxidoreductases belonging to phylogenetically distant species, as the bacterial type II NADH dehydrogenases and the mammalian apoptosis-inducing factor protein, until now retained as unique protein entities in Bacteria/Fungi or Animals, respectively. Furthermore, the presented computational analyses will allow consideration of FAD/NADH oxidoreductases as a possible target of new small molecules to be used as modulators of mitochondrial respiration for patients affected by rare diseases or cancer showing mitochondrial dysfunction, or antibiotics for treating bacterial/fungal/protista infections.
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Affiliation(s)
| | | | | | | | | | | | | | - Anna De Grassi
- Correspondence: (A.D.G.); or (C.L.P.); Tel.: +39-080-544-3614 (A.D.G. & C.L.P.); Fax: +39-080-544-2770 (A.D.G. & C.L.P.)
| | - Ciro Leonardo Pierri
- Correspondence: (A.D.G.); or (C.L.P.); Tel.: +39-080-544-3614 (A.D.G. & C.L.P.); Fax: +39-080-544-2770 (A.D.G. & C.L.P.)
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32
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Krishna PS, Morello G, Mamedov F. Characterization of the transient fluorescence wave phenomenon that occurs during H2 production in Chlamydomonas reinhardtii. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:6321-6336. [PMID: 31504725 PMCID: PMC6859737 DOI: 10.1093/jxb/erz380] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 08/14/2019] [Indexed: 05/10/2023]
Abstract
The redox state of the plastoquinone (PQ) pool in sulfur-deprived, H2-producing Chlamydomonas reinhardtii cells was studied using single flash-induced variable fluorescence decay kinetics. During H2 production, the fluorescence decay kinetics exhibited an unusual post-illumination rise of variable fluorescence, giving a wave-like appearance. The wave showed the transient fluorescence minimum at ~60 ms after the flash, followed by a rise, reaching the transient fluorescence maximum at ~1 s after the flash, before decaying back to the initial fluorescence level. Similar wave-like fluorescence decay kinetics have been reported previously in anaerobically incubated cyanobacteria but not in green algae. From several different electron and proton transfer inhibitors used, polymyxin B, an inhibitor of type II NAD(P)H dehydrogenase (NDA2), had the effect of eliminating the fluorescence wave feature, indicating involvement of NDA2 in this phenomenon. This was further confirmed by the absence of the fluorescence wave in the Δnda2 mutant lacking NDA2. Additionally, Δnda2 mutants have also shown delayed and diminished H2 production (only 23% if compared with the wild type). Our results show that the fluorescence wave phenomenon in C. reinhardtii is observed under highly reducing conditions and is induced by the NDA2-mediated electron flow from the reduced stromal components to the PQ pool. Therefore, the fluorescence wave phenomenon is a sensitive probe for the complex network of redox reactions at the PQ pool level in the thylakoid membrane. It could be used in further characterization and improvement of the electron transfer pathways leading to H2 production in C. reinhardtii.
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Affiliation(s)
- Pilla Sankara Krishna
- Molecular Biomimetics, Department of Chemistry – Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Giorgio Morello
- Molecular Biomimetics, Department of Chemistry – Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Fikret Mamedov
- Molecular Biomimetics, Department of Chemistry – Ångström Laboratory, Uppsala University, Uppsala, Sweden
- Correspondence:
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33
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Godoy-Hernandez A, Tate DJ, McMillan DGG. Revealing the Membrane-Bound Catalytic Oxidation of NADH by the Drug Target Type-II NADH Dehydrogenase. Biochemistry 2019; 58:4272-4275. [PMID: 31592658 PMCID: PMC6812066 DOI: 10.1021/acs.biochem.9b00752] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Type-II NADH:quinone
oxidoreductases (NDH-2s) are an important
element of microbial pathogen electron transport chains and an attractive
drug target. Despite being widely studied, its mechanism and catalysis
are still poorly understood in a hydrophobic membrane environment.
A recent report for the Escherichia coli NDH-2 showed
NADH oxidation in a solution-based assay but apparently showed the
reverse reaction in electrochemical studies, calling into question
the validity of the electrochemical approach. Here we report electrochemical
catalysis in the well-studied NDH-2 from Caldalkalibacillus
thermarum (CthNDH-2). In agreement with
previous reports, we demonstrated CthNDH-2 NADH oxidation
in a solution assay and electrochemical assays revealed a system artifact
in the absence of quinone that was absent in a membrane system. However,
in the presence of either immobilized quinone or mobile quinone in
a membrane, NADH oxidation was observed as in solution-phase assays.
This conclusively establishes surface-based electrochemistry as a
viable approach for interrogating electron transfer chain drug targets.
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Affiliation(s)
- Albert Godoy-Hernandez
- Department of Biotechnology , Delft University of Technology , Van der Maasweg 9 , Delft 2629 HZ , The Netherlands
| | - Daniel J Tate
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , United Kingdom
| | - Duncan G G McMillan
- Department of Biotechnology , Delft University of Technology , Van der Maasweg 9 , Delft 2629 HZ , The Netherlands.,Department of Applied Chemistry, Graduate School of Engineering , The University of Tokyo , Tokyo 113-8656 , Japan
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34
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Xie T, Wu Z, Gu J, Guo R, Yan X, Duan H, Liu X, Liu W, Liang L, Wan H, Luo Y, Tang D, Shi H, Hu J. The global motion affecting electron transfer in Plasmodium falciparum type II NADH dehydrogenases: a novel non-competitive mechanism for quinoline ketone derivative inhibitors. Phys Chem Chem Phys 2019; 21:18105-18118. [PMID: 31396604 DOI: 10.1039/c9cp02645b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
With the emergence of drug-resistant Plasmodium falciparum, the treatment of malaria has become a significant challenge; therefore, the development of antimalarial drugs acting on new targets is extremely urgent. In Plasmodium falciparum, type II nicotinamide adenine dinucleotide (NADH) dehydrogenase (NDH-2) is responsible for catalyzing the transfer of two electrons from NADH to flavin adenine dinucleotide (FAD), which in turn transfers the electrons to coenzyme Q (CoQ). As an entry enzyme for oxidative phosphorylation, NDH-2 has become one of the popular targets for the development of new antimalarial drugs. In this study, reliable motion trajectories of the NDH-2 complex with its co-factors (NADH and FAD) and inhibitor, RYL-552, were obtained by comparative molecular dynamics simulations. The influence of cofactor binding on the global motion of NDH-2 was explored through conformational clustering, principal component analysis and free energy landscape. The molecular interactions of NDH-2 before and after its binding with the inhibitor RYL-552 were analyzed, and the key residues and important hydrogen bonds were also determined. The results show that the association of RYL-552 results in the weakening of intramolecular hydrogen bonds and large allosterism of NDH-2. There was a significant positive correlation between the angular change of the key pocket residues in the NADH-FAD-pockets that represents the global functional motion and the change in distance between NADH-C4 and FAD-N5 that represents the electron transfer efficiency. Finally, the possible non-competitive inhibitory mechanism of RYL-552 was proposed. Specifically, the association of inhibitors with NDH-2 significantly affects the global motion mode of NDH-2, leading to widening of the distance between NADH and FAD through cooperative motion induction; this reduces the electron transfer efficiency of the mitochondrial respiratory chain. The simulation results provide useful theoretical guidance for subsequent antimalarial drug design based on the NDH-2 structure and the respiratory chain electron transfer mechanism.
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Affiliation(s)
- Tao Xie
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, 610106, China.
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35
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Lencina AM, Koepke J, Preu J, Muenke C, Gennis RB, Michel H, Schurig-Briccio LA. Characterization and X-ray structure of the NADH-dependent coenzyme A disulfide reductase from Thermus thermophilus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148080. [PMID: 31520616 DOI: 10.1016/j.bbabio.2019.148080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/28/2019] [Accepted: 09/08/2019] [Indexed: 11/25/2022]
Abstract
The crystal structure of the enzyme previously characterized as a type-2 NADH:menaquinone oxidoreductase (NDH-2) from Thermus thermophilus has been solved at a resolution of 2.9 Å and revealed that this protein is, in fact, a coenzyme A-disulfide reductase (CoADR). Coenzyme A (CoASH) replaces glutathione as the major low molecular weight thiol in Thermus thermophilus and is maintained in the reduced state by this enzyme (CoADR). Although the enzyme does exhibit NADH:menadione oxidoreductase activity expected for NDH-2 enzymes, the specific activity with CoAD as an electron acceptor is about 5-fold higher than with menadione. Furthermore, the crystal structure contains coenzyme A covalently linked Cys44, a catalytic intermediate (Cys44-S-S-CoA) reduced by NADH via the FAD cofactor. Soaking the crystals with menadione shows that menadione can bind to a site near the redox active FAD, consistent with the observed NADH:menadione oxidoreductase activity. CoADRs from other species were also examined and shown to have measurable NADH:menadione oxidoreductase activity. Although a common feature of this family of enzymes, no biological relevance is proposed. The CoADR from T. thermophilus is a soluble homodimeric enzyme. Expression of the recombinant TtCoADR at high levels in E. coli results in a small fraction that co-purifies with the membrane fraction, which was used previously to isolate the enzyme wrongly identified as a membrane-bound NDH-2. It is concluded that T. thermophilus does not contain an authentic NDH-2 component in its aerobic respiratory chain.
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Affiliation(s)
- Andrea M Lencina
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Juergen Koepke
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Julia Preu
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Cornelia Muenke
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany.
| | - Lici A Schurig-Briccio
- Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA.
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Bausewein T, Nussberger S, Kühlbrandt W. Cryo-EM structure of Neurospora crassa respiratory complex IV. IUCRJ 2019; 6:773-780. [PMID: 31316820 PMCID: PMC6608615 DOI: 10.1107/s2052252519007486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/23/2019] [Indexed: 05/13/2023]
Abstract
In fungi, the mitochondrial respiratory chain complexes (complexes I-IV) are responsible for oxidative phosphorylation, as in higher eukaryotes. Cryo-EM was used to identify a 200 kDa membrane protein from Neurospora crassa in lipid nanodiscs as cytochrome c oxidase (complex IV) and its structure was determined at 5.5 Å resolution. The map closely resembles the cryo-EM structure of complex IV from Saccharomyces cerevisiae. Its ten subunits are conserved in S. cerevisiae and Bos taurus, but other transmembrane subunits are missing. The different structure of the Cox5a subunit is typical for fungal complex IV and may affect the interaction with complex III in a respiratory supercomplex. Additional density was found between the matrix domains of the Cox4 and Cox5a subunits that appears to be specific to N. crassa.
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Affiliation(s)
- Thomas Bausewein
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Stephan Nussberger
- Abteilung Biophysik, Institut für Biomaterialien und biomolekulare Systeme, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
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Garavito MF, Narvaez-Ortiz HY, Pulido DC, Löffler M, Judelson HS, Restrepo S, Zimmermann BH. Phytophthora infestans Dihydroorotate Dehydrogenase Is a Potential Target for Chemical Control - A Comparison With the Enzyme From Solanum tuberosum. Front Microbiol 2019; 10:1479. [PMID: 31316493 PMCID: PMC6611227 DOI: 10.3389/fmicb.2019.01479] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/13/2019] [Indexed: 01/04/2023] Open
Abstract
The oomycete Phytophthora infestans is the causal agent of tomato and potato late blight, a disease that causes tremendous economic losses in the production of solanaceous crops. The similarities between oomycetes and the apicomplexa led us to hypothesize that dihydroorotate dehydrogenase (DHODH), the enzyme catalyzing the fourth step in pyrimidine biosynthetic pathway, and a validated drug target in treatment of malaria, could be a potential target for controlling P. infestans growth. In eukaryotes, class 2 DHODHs are mitochondrially associated ubiquinone-linked enzymes that catalyze the fourth, and only redox step of de novo pyrimidine biosynthesis. We characterized the enzymes from both the pathogen and a host, Solanum tuberosum. Plant DHODHs are known to be class 2 enzymes. Sequence analysis suggested that the pathogen enzyme (PiDHODHs) also belongs to this class. We confirmed the mitochondrial localization of GFP-PiDHODH showing colocalization with mCherry-labeled ATPase in a transgenic pathogen. N-terminally truncated versions of the two DHODHs were overproduced in E. coli, purified, and kinetically characterized. StDHODH exhibited a apparent specific activity of 41 ± 1 μmol min-1 mg-1, a kcatapp of 30 ± 1 s-1, and a Kmapp of 20 ± 1 μM for L-dihydroorotate, and a Kmapp= 30 ± 3 μM for decylubiquinone (Qd). PiDHODH exhibited an apparent specific activity of 104 ± 1 μmol min-1 mg-1, a kcatapp of 75 ± 1 s-1, and a Kmapp of 57 ± 3 μM for L-dihydroorotate, and a Kmapp of 15 ± 1 μM for Qd. The two enzymes exhibited different activities with different quinones and napthoquinone derivatives, and different sensitivities to compounds known to cause inhibition of DHODHs from other organisms. The IC50 for A77 1726, a nanomolar inhibitor of human DHODH, was 2.9 ± 0.6 mM for StDHODH, and 79 ± 1 μM for PiDHODH. In vivo, 0.5 mM A77 1726 decreased mycelial growth by approximately 50%, after 92 h. Collectively, our findings suggest that the PiDHODH could be a target for selective inhibitors and we provide a biochemical background for the development of compounds that could be helpful for the control of the pathogen, opening the way to protein crystallization.
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Affiliation(s)
- Manuel F Garavito
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia.,Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
| | | | - Dania Camila Pulido
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Monika Löffler
- Faculty of Medicine, Department of Biology, University of Marburg, Marburg, Germany
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
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Santoso KT, Cheung CY, Hards K, Cook GM, Stocker BL, Timmer MSM. Synthesis and Investigation of Phthalazinones as Antitubercular Agents. Chem Asian J 2019; 14:1278-1285. [PMID: 30680937 DOI: 10.1002/asia.201801805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/16/2019] [Indexed: 11/08/2022]
Abstract
A series of 2- and 7-substituted phthalazinones was synthesised and their potential as anti-tubercular drugs assessed via Mycobacterium tuberculosis (mc2 6230) growth inhibition assays. All phthalazinones tested showed growth inhibitory activity (MIC <100 μm), and those compounds containing lipophilic and electron-withdrawing groups generally exhibited better anti-tubercular activity. Several lead compounds were identified, including 7-((2-amino-6-(4-fluorophenyl)pyrimidin-4-yl)amino)-2-heptylphthalazin-1(2H)-one (MIC=1.6 μm), 4-tertbutylphthalazin-2(1H)-one (MIC=3 μm), and 7-nitro-phthalazin-1(2H)-one (MIC=3 μm). Mode of action studies indicated that selected pyrimidinyl-phthalazinones may interfere with NADH oxidation, however, the mode of action of the lead compound is independent of this enzyme. MIC=minimum inhibitory concentration.
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Affiliation(s)
- Kristiana T Santoso
- School of Chemical and Physical Sciences, Victoria University of Wellington, P.O. Box 600, 6140, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, P.O. Box 600, 6140, Wellington, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Kiel Hards
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Bridget L Stocker
- School of Chemical and Physical Sciences, Victoria University of Wellington, P.O. Box 600, 6140, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, P.O. Box 600, 6140, Wellington, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Mattie S M Timmer
- School of Chemical and Physical Sciences, Victoria University of Wellington, P.O. Box 600, 6140, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, P.O. Box 600, 6140, Wellington, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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Antos-Krzeminska N, Jarmuszkiewicz W. Alternative Type II NAD(P)H Dehydrogenases in the Mitochondria of Protists and Fungi. Protist 2018; 170:21-37. [PMID: 30553126 DOI: 10.1016/j.protis.2018.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/12/2018] [Accepted: 11/04/2018] [Indexed: 01/11/2023]
Abstract
Plants, fungi, and some protists possess a more branched electron transport chain in their mitochondria compared to canonical one. In these organisms, the electron transport chain contains several rotenone-insensitive NAD(P)H dehydrogenases. Some are located on the outer surface, and others are located on the inner surface of the inner mitochondrial membrane. The putative role of these enzymes still remains elusive, but they may prevent the overreduction of the electron transport chain components and decrease the production of reaction oxygen species as a consequence. The last two decades resulted in the discovery of alternative rotenone-insensitive NAD(P)H dehydrogenases present in representatives of fungi and protozoa. The aim of this review is to gather and focus on current information concerning molecular and functional properties, regulation, and the physiological role of fungal and protozoan alternative NAD(P)H dehydrogenases.
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Affiliation(s)
- Nina Antos-Krzeminska
- Department of Bioenergetics, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland.
| | - Wieslawa Jarmuszkiewicz
- Department of Bioenergetics, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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40
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Larosa V, Remacle C. Insights into the respiratory chain and oxidative stress. Biosci Rep 2018; 38:BSR20171492. [PMID: 30201689 PMCID: PMC6167499 DOI: 10.1042/bsr20171492] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/15/2018] [Accepted: 09/05/2018] [Indexed: 01/13/2023] Open
Abstract
Reactive oxygen species (ROS) are highly reactive reduced oxygen molecules that result from aerobic metabolism. The common forms are the superoxide anion (O2∙-) and hydrogen peroxide (H2O2) and their derived forms, hydroxyl radical (HO∙) and hydroperoxyl radical (HOO∙). Their production sites in mitochondria are reviewed. Even though being highly toxic products, ROS seem important in transducing information from dysfunctional mitochondria. Evidences of signal transduction mediated by ROS in mitochondrial deficiency contexts are then presented in different organisms such as yeast, mammals or photosynthetic organisms.
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Affiliation(s)
- Véronique Larosa
- Genetics and Physiology of Microalgae, UR InBios/Phytosystems, Chemin de la Vallée, 4, University of Liège, Liège 4000, Belgium
| | - Claire Remacle
- Genetics and Physiology of Microalgae, UR InBios/Phytosystems, Chemin de la Vallée, 4, University of Liège, Liège 4000, Belgium
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Matuz-Mares D, Matus-Ortega G, Cárdenas-Monroy C, Romero-Aguilar L, Villalobos-Rocha JC, Vázquez-Meza H, Guerra-Sánchez G, Peña-Díaz A, Pardo JP. Expression of alternative NADH dehydrogenases (NDH-2) in the phytopathogenic fungus Ustilago maydis. FEBS Open Bio 2018; 8:1267-1279. [PMID: 30221129 PMCID: PMC6134880 DOI: 10.1002/2211-5463.12475] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/27/2018] [Accepted: 06/11/2018] [Indexed: 11/17/2022] Open
Abstract
Type 2 alternative NADH dehydrogenases (NDH‐2) participate indirectly in the generation of the electrochemical proton gradient by transferring electrons from NADH and NADPH into the ubiquinone pool. Due to their structural simplicity, alternative NADH dehydrogenases have been proposed as useful tools for gene therapy of cells with defects in the respiratory complex I. In this work, we report the presence of three open reading frames, which correspond to NDH‐2 genes in the genome of Ustilago maydis. These three genes were constitutively transcribed in cells cultured in YPD and minimal medium with glucose, ethanol, or lactate as carbon sources. Proteomic analysis showed that only two of the three NDH‐2 were associated with isolated mitochondria in all culture media. Oxygen consumption by permeabilized cells using NADH or NADPH was different for each condition, opening the possibility of posttranslational regulation. We confirmed the presence of both external and internal NADH dehydrogenases, as well as an external NADPH dehydrogenase insensitive to calcium. Higher oxygen consumption rates were observed during the exponential growth phase, suggesting that the activity of NADH and NADPH dehydrogenases is coupled to the dynamics of cell growth.
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Affiliation(s)
- Deyamira Matuz-Mares
- Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Genaro Matus-Ortega
- Departamento de Genética Molecular Instituto de Fisiología Celular Universidad Nacional Autónoma de México Ciudad de México México
| | - Christian Cárdenas-Monroy
- Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Lucero Romero-Aguilar
- Bioquímica de hongos Escuela Nacional de Ciencias Biológicas Instituto Politécnico Nacional Ciudad de México México
| | | | - Héctor Vázquez-Meza
- Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Guadalupe Guerra-Sánchez
- Bioquímica de hongos Escuela Nacional de Ciencias Biológicas Instituto Politécnico Nacional Ciudad de México México
| | - Antonio Peña-Díaz
- Departamento de Genética Molecular Instituto de Fisiología Celular Universidad Nacional Autónoma de México Ciudad de México México
| | - Juan Pablo Pardo
- Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
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Type 2 NADH Dehydrogenase Is the Only Point of Entry for Electrons into the Streptococcus agalactiae Respiratory Chain and Is a Potential Drug Target. mBio 2018; 9:mBio.01034-18. [PMID: 29970468 PMCID: PMC6030563 DOI: 10.1128/mbio.01034-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The opportunistic pathogen Streptococcus agalactiae is the major cause of meningitis and sepsis in a newborn’s first week, as well as a considerable cause of pneumonia, urinary tract infections, and sepsis in immunocompromised adults. This pathogen respires aerobically if heme and quinone are available in the environment, and a functional respiratory chain is required for full virulence. Remarkably, it is shown here that the entire respiratory chain of S. agalactiae consists of only two enzymes, a type 2 NADH dehydrogenase (NDH-2) and a cytochrome bd oxygen reductase. There are no respiratory dehydrogenases other than NDH-2 to feed electrons into the respiratory chain, and there is only one respiratory oxygen reductase to reduce oxygen to water. Although S. agalactiae grows well in vitro by fermentative metabolism, it is shown here that the absence of NDH-2 results in attenuated virulence, as observed by reduced colonization in heart and kidney in a mouse model of systemic infection. The lack of NDH-2 in mammalian mitochondria and its important role for virulence suggest this enzyme may be a potential drug target. For this reason, in this study, S. agalactiae NDH-2 was purified and biochemically characterized, and the isolated enzyme was used to screen for inhibitors from libraries of FDA-approved drugs. Zafirlukast was identified to successfully inhibit both NDH-2 activity and aerobic respiration in intact cells. This compound may be useful as a laboratory tool to inhibit respiration in S. agalactiae and, since it has few side effects, it might be considered a lead compound for therapeutics development. S. agalactiae is part of the human intestinal microbiota and is present in the vagina of ~30% of healthy women. Although a commensal, it is also the leading cause of septicemia and meningitis in neonates and immunocompromised adults. This organism can aerobically respire, but only using external sources of heme and quinone, required to have a functional electron transport chain. Although bacteria usually have a branched respiratory chain with multiple dehydrogenases and terminal oxygen reductases, here we establish that S. agalactiae utilizes only one type 2 NADH dehydrogenase (NDH-2) and one cytochrome bd oxygen reductase to perform respiration. NADH-dependent respiration plays a critical role in the pathogen in maintaining NADH/NAD+ redox balance in the cell, optimizing ATP production, and tolerating oxygen. In summary, we demonstrate the essential role of NDH-2 in respiration and its contribution to S. agalactiae virulence and propose it as a potential drug target.
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Petri J, Shimaki Y, Jiao W, Bridges HR, Russell ER, Parker EJ, Aragão D, Cook GM, Nakatani Y. Structure of the NDH-2 - HQNO inhibited complex provides molecular insight into quinone-binding site inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2018; 1859:482-490. [PMID: 29621505 PMCID: PMC6167311 DOI: 10.1016/j.bbabio.2018.03.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/22/2018] [Accepted: 03/29/2018] [Indexed: 11/23/2022]
Abstract
Type II NADH:quinone oxidoreductase (NDH-2) is a proposed drug-target of major pathogenic microorganisms such as Mycobacterium tuberculosis and Plasmodium falciparum. Many NDH-2 inhibitors have been identified, but rational drug development is impeded by the lack of information regarding their mode of action and associated inhibitor-bound NDH-2 structure. We have determined the crystal structure of NDH-2 complexed with a quinolone inhibitor 2-heptyl-4-hydroxyquinoline-N-oxide (HQNO). HQNO is nested into the slot-shaped tunnel of the Q-site, in which the quinone-head group is clamped by Q317 and I379 residues, and hydrogen-bonds to FAD. The interaction of HQNO with bacterial NDH-2 is very similar to the native substrate ubiquinone (UQ1) interactions in the yeast Ndi1-UQ1 complex structure, suggesting a conserved mechanism for quinone binding. Further, the structural analysis provided insight how modifications of quinolone scaffolds improve potency (e.g. quinolinyl pyrimidine derivatives) and suggests unexplored target space for the rational design of new NDH-2 inhibitors.
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Affiliation(s)
- Jessica Petri
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Yosuke Shimaki
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Wanting Jiao
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Hannah R Bridges
- MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Euan R Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - David Aragão
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria, VIC3168, Australia
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand.
| | - Yoshio Nakatani
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand.
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In Silico Discovery of a Substituted 6-Methoxy-quinalidine with Leishmanicidal Activity in Leishmania infantum. Molecules 2018; 23:molecules23040772. [PMID: 29584709 PMCID: PMC6017605 DOI: 10.3390/molecules23040772] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 03/21/2018] [Accepted: 03/26/2018] [Indexed: 11/29/2022] Open
Abstract
There is an urgent need for the discovery of new antileishmanial drugs with a new mechanism of action. Type 2 NADH dehydrogenase from Leishmania infantum (LiNDH2) is an enzyme of the parasite’s respiratory system, which catalyzes the electron transfer from NADH to ubiquinone without coupled proton pumping. In previous studies of the related NADH: ubiquinone oxidoreductase crystal structure from Saccharomyces cerevisiae, two ubiquinone-binding sites (UQI and UQII) were identified and shown to play an important role in the NDH-2-catalyzed oxidoreduction reaction. Based on the available structural data, we developed a three-dimensional structural model of LiNDH2 using homology detection methods and performed an in silico virtual screening campaign to search for potential inhibitors targeting the LiNDH2 ubiquinone-binding site 1–UQI. Selected compounds displaying favorable properties in the computational screening experiments were assayed for inhibitory activity in the structurally similar recombinant NDH-2 from S. aureus and leishmanicidal activity was determined in the wild-type axenic amastigotes and promastigotes of L. infantum. The identified compound, a substituted 6-methoxy-quinalidine, showed promising nanomolar leishmanicidal activity on wild-type axenic promastigotes and amastigotes of L. infantum and the potential for further development.
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Sena FV, Sousa FM, Oliveira ASF, Soares CM, Catarino T, Pereira MM. Regulation of the mechanism of Type-II NADH: Quinone oxidoreductase from S. aureus. Redox Biol 2018. [PMID: 29524843 PMCID: PMC5857484 DOI: 10.1016/j.redox.2018.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Type-II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins involved in respiratory chains and the only enzymes with NADH:quinone oxidoreductase activity expressed in Staphylococcus aureus (S. aureus), one of the most common causes of clinical infections. NDH-2s are members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, having a flavin adenine dinucleotide, FAD, as prosthetic group and NAD(P)H as substrate. The establishment of a Charge-Transfer Complex (CTC) between the isoalloxazine ring of the reduced flavin and the nicotinamide ring of NAD+ in NDH-2 was described, and in this work we explored its role in the kinetic mechanism using different electron donors and electron acceptors. We observed that CTC slows down the rate of the second half reaction (quinone reduction) and determines the effect of HQNO, an inhibitor. Also, protonation equilibrium simulations clearly indicate that the protonation probability of an important residue for proton transfer to the active site (D302) is influenced by the presence of the CTC. We propose that CTC is critical for the overall mechanism of NDH-2 and possibly relevant to keep a low quinol/quinone ratio and avoid excessive ROS production in vivo.
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Affiliation(s)
- Filipa V Sena
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - A Sofia F Oliveira
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Cláudio M Soares
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Teresa Catarino
- Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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Yamashita T, Inaoka DK, Shiba T, Oohashi T, Iwata S, Yagi T, Kosaka H, Miyoshi H, Harada S, Kita K, Hirano K. Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors. Sci Rep 2018; 8:2427. [PMID: 29402945 PMCID: PMC5799168 DOI: 10.1038/s41598-018-20775-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/24/2018] [Indexed: 12/20/2022] Open
Abstract
Yeast Ndi1 is a monotopic alternative NADH dehydrogenase. Its crystal structure in complex with the electron acceptor, ubiquinone, has been determined. However, there has been controversy regarding the ubiquinone binding site. To address these points, we identified the first competitive inhibitor of Ndi1, stigmatellin, along with new mixed-type inhibitors, AC0-12 and myxothiazol, and thereby determined the crystal structures of Ndi1 in complexes with the inhibitors. Two separate binding sites of stigmatellin, STG-1 and STG-2, were observed. The electron density at STG-1, located at the vicinity of the FAD cofactor, further demonstrated two binding modes: STG-1a and STG-1b. AC0-12 and myxothiazol are also located at the vicinity of FAD. The comparison of the binding modes among stigmatellin at STG-1, AC0-12, and myxothiazol revealed a unique position for the aliphatic tail of stigmatellin at STG-1a. Mutations of amino acid residues that interact with this aliphatic tail at STG-1a reduced the affinity of Ndi1 for ubiquinone. In conclusion, the position of the aliphatic tail of stigmatellin at STG-1a provides a structural basis for its competitive inhibition of Ndi1. The inherent binding site of ubiquinone is suggested to overlap with STG-1a that is distinct from the binding site for NADH.
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Affiliation(s)
- Tetsuo Yamashita
- Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, 761-0793, Japan.
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8523, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, 606-8585, Japan
| | - Takumi Oohashi
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - So Iwata
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London, SW7 2AZ, UK
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire, OX11 0DE, UK
- Japan Science and Technology Agency, Exploratory Research for Advanced Technology, Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-Ku, Kyoto, 606-8501, Japan
- Systems and Structural Biology Centre, RIKEN, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takao Yagi
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Hiroaki Kosaka
- Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, 761-0793, Japan
- Osaka Jikei College, 1-2-8 Miyahara, Yodogawa-Ku, Osaka, 532-0003, Japan
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, 606-8585, Japan.
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8523, Japan
| | - Katsuya Hirano
- Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, 761-0793, Japan
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A Role for the Respiratory Chain in Regulating Meiosis Initiation in Saccharomyces cerevisiae. Genetics 2018; 208:1181-1194. [PMID: 29301906 DOI: 10.1534/genetics.118.300689] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 12/29/2017] [Indexed: 01/01/2023] Open
Abstract
Meiosis is a specific type of cell division that is essential for sexual reproduction in most eukaryotes. Mitochondria are crucial cellular organelles that play important roles in reproduction, though the detailed mechanism by which the mitochondrial respiratory chain functions during meiosis remains elusive. Here, we show that components of the respiratory chain (Complexes I-V) play essential roles in meiosis initiation during the sporulation of budding yeast, Saccharomyces cerevisiae Any functional defects in the Complex I component Ndi1p resulted in the abolishment of sporulation. Further studies revealed that respiratory deficiency resulted in the failure of premeiotic DNA replication due to insufficient IME1 expression. In addition, respiration promoted the expression of RIM101, whose product inhibits Smp1p, a negative transcriptional regulator of IME1, to promote meiosis initiation. In summary, our studies unveiled the close relationship between mitochondria and sporulation, and uncover a novel meiosis initiation pathway that is regulated by the respiratory chain.
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48
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Oxidative Phosphorylation as a Target Space for Tuberculosis: Success, Caution, and Future Directions. Microbiol Spectr 2017; 5. [PMID: 28597820 DOI: 10.1128/microbiolspec.tbtb2-0014-2016] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The emergence and spread of drug-resistant pathogens, and our inability to develop new antimicrobials to combat resistance, have inspired scientists to seek out new targets for drug development. The Mycobacterium tuberculosis complex is a group of obligately aerobic bacteria that have specialized for inhabiting a wide range of intracellular and extracellular environments. Two fundamental features in this adaptation are the flexible utilization of energy sources and continued metabolism in the absence of growth. M. tuberculosis is an obligately aerobic heterotroph that depends on oxidative phosphorylation for growth and survival. However, several studies are redefining the metabolic breadth of the genus. Alternative electron donors and acceptors may provide the maintenance energy for the pathogen to maintain viability in hypoxic, nonreplicating states relevant to latent infection. This hidden metabolic flexibility may ultimately decrease the efficacy of drugs targeted against primary dehydrogenases and terminal oxidases. However, it may also open up opportunities to develop novel antimycobacterials targeting persister cells. In this review, we discuss the progress in understanding the role of energetic targets in mycobacterial physiology and pathogenesis and the opportunities for drug discovery.
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Hartuti ED, Inaoka DK, Komatsuya K, Miyazaki Y, Miller RJ, Xinying W, Sadikin M, Prabandari EE, Waluyo D, Kuroda M, Amalia E, Matsuo Y, Nugroho NB, Saimoto H, Pramisandi A, Watanabe YI, Mori M, Shiomi K, Balogun EO, Shiba T, Harada S, Nozaki T, Kita K. Biochemical studies of membrane bound Plasmodium falciparum mitochondrial L-malate:quinone oxidoreductase, a potential drug target. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1859:191-200. [PMID: 29269266 DOI: 10.1016/j.bbabio.2017.12.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/13/2017] [Accepted: 12/16/2017] [Indexed: 11/30/2022]
Abstract
Plasmodium falciparum is an apicomplexan parasite that causes the most severe malaria in humans. Due to a lack of effective vaccines and emerging of drug resistance parasites, development of drugs with novel mechanisms of action and few side effects are imperative. To this end, ideal drug targets are those essential to parasite viability as well as absent in their mammalian hosts. The mitochondrial electron transport chain (ETC) of P. falciparum is one source of such potential targets because enzymes, such as L-malate:quinone oxidoreductase (PfMQO), in this pathway are absent humans. PfMQO catalyzes the oxidation of L-malate to oxaloacetate and the simultaneous reduction of ubiquinone to ubiquinol. It is a membrane protein, involved in three pathways (ETC, the tricarboxylic acid cycle and the fumarate cycle) and has been shown to be essential for parasite survival, at least, in the intra-erythrocytic asexual stage. These findings indicate that PfMQO would be a valuable drug target for development of antimalarial with novel mechanism of action. Up to this point in time, difficulty in producing active recombinant mitochondrial MQO has hampered biochemical characterization and targeted drug discovery with MQO. Here we report for the first time recombinant PfMQO overexpressed in bacterial membrane and the first biochemical study. Furthermore, about 113 compounds, consisting of ubiquinone binding site inhibitors and antiparasitic agents, were screened resulting in the discovery of ferulenol as a potent PfMQO inhibitor. Finally, ferulenol was shown to inhibit parasite growth and showed strong synergism in combination with atovaquone, a well-described anti-malarial and bc1 complex inhibitor.
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Affiliation(s)
- Endah Dwi Hartuti
- Master program of Biomedical Science, Faculty of Medicine, University of Indonesia, Indonesia; Biotech Center, Agency for the Assessment and Application of Technology, Jakarta, Indonesia
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.
| | - Keisuke Komatsuya
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukiko Miyazaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Russell J Miller
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Wang Xinying
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Mohamad Sadikin
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | | | - Danang Waluyo
- Biotech Center, Agency for the Assessment and Application of Technology, Jakarta, Indonesia
| | - Marie Kuroda
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eri Amalia
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuichi Matsuo
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Nuki B Nugroho
- Biotech Center, Agency for the Assessment and Application of Technology, Jakarta, Indonesia
| | - Hiroyuki Saimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Amila Pramisandi
- Biotech Center, Agency for the Assessment and Application of Technology, Jakarta, Indonesia; Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Yoh-Ichi Watanabe
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mihoko Mori
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Kazuro Shiomi
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Emmanuel Oluwadare Balogun
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
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50
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Nakatani Y, Jiao W, Aragão D, Shimaki Y, Petri J, Parker EJ, Cook GM. Crystal structure of type II NADH:quinone oxidoreductase from Caldalkalibacillus thermarum with an improved resolution of 2.15 Å. Acta Crystallogr F Struct Biol Commun 2017; 73:541-549. [PMID: 28994401 PMCID: PMC5633920 DOI: 10.1107/s2053230x17013073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/12/2017] [Indexed: 11/11/2022] Open
Abstract
Type II NADH:quinone oxidoreductase (NDH-2) is a respiratory enzyme found in the electron-transport chain of many species, with the exception of mammals. It is a 40-70 kDa single-subunit monotopic membrane protein that catalyses the oxidation of NADH and the reduction of quinone molecules via the cofactor FAD. NDH-2 is a promising new target for drug development given its essential role in many bacterial species and intracellular parasites. Only two bacterial NDH-2 structures have been reported and these structures are at moderate resolution (2.3-2.5 Å). In this communication, a new crystallization platform is reported that produced high-quality NDH-2 crystals that diffracted to high resolution (2.15 Å). The high-resolution NDH-2 structure was used for in silico quinone substrate-docking studies to investigate the binding poses of menadione and ubiquinone molecules. These studies revealed that a very limited number of molecular interactions occur at the quinone-binding site of NDH-2. Given that the conformation of the active site is well defined, this high-resolution structure is potentially suitable for in silico inhibitor-compound screening and ligand-docking applications.
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Affiliation(s)
- Yoshio Nakatani
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - Wanting Jiao
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - David Aragão
- Australian Synchrotron, 800 Blackburn Road, Clayton 3168, Australia
| | - Yosuke Shimaki
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
| | - Jessica Petri
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - Emily J. Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Gregory M. Cook
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
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