1
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Maldonado M. Plant supercomplex I + III2 structure and function: implications for the growing field. Biochem Soc Trans 2024; 52:1647-1659. [PMID: 39177070 DOI: 10.1042/bst20230947] [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: 05/06/2024] [Revised: 08/01/2024] [Accepted: 08/07/2024] [Indexed: 08/24/2024]
Abstract
Mitochondrial respiration is major source of chemical energy for all free-living eukaryotes. Nevertheless, the mechanisms of the respiratory complexes and supercomplexes remain poorly understood. Here, I review recent structural and functional investigations of plant supercomplex I + III2 from Arabidopsis thaliana and Vigna radiata. I discuss commonalities, open questions and implications for complex I, complex III2 and supercomplexes in plants and non-plants. Studies across further clades will enhance our understanding of respiration and the potential universal mechanisms of its complexes and supercomplexes.
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Affiliation(s)
- Maria Maldonado
- Department of Plant Biology, University of California, Davis, Davis, CA, U.S.A
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2
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Wang P, Demaray J, Moroz S, Stuchebrukhov AA. Searching for proton transfer channels in respiratory complex I. Biophys J 2024:S0006-3495(24)00518-6. [PMID: 39095988 DOI: 10.1016/j.bpj.2024.07.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/19/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024] Open
Abstract
We have explored a strategy to identify potential proton transfer channels using computational analysis of a protein structure based on Voronoi partitioning and applied it for the analysis of proton transfer pathways in redox-driven proton-pumping respiratory complex I. The analysis results in a network of connected voids/channels, which represent the dual structure of the protein; we then hydrated the identified channels using our water placement program Dowser++. Many theoretical water molecules found in the channels perfectly match the observed experimental water molecules in the structure; some other predicted water molecules have not been resolved in the experiments. The channels are of varying cross sections. Some channels are big enough to accommodate water molecules that are suitable to conduct protons; others are too narrow to hold water but require only minor conformational changes to accommodate proton transfer. We provide a preliminary analysis of the proton conductivity of the network channels, classifying the proton transfer channels as open, closed, and partially open, and discuss possible conformational changes that can modulate, i.e., open and close, the channels.
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Affiliation(s)
- Panyue Wang
- Department of Chemistry, University of California at Davis, Davis, California
| | - Jackson Demaray
- Department of Chemistry, University of California at Davis, Davis, California
| | - Stanislav Moroz
- Department of Chemistry, University of California at Davis, Davis, California
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3
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Otani R, Masuya T, Miyoshi H, Murai M. Mitochondrial respiratory complex I can be inhibited via bypassing the ubiquinone-accessing tunnel. FEBS Lett 2024; 598:1989-1995. [PMID: 38924556 DOI: 10.1002/1873-3468.14967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/24/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Mitochondrial NADH-ubiquinone oxidoreductase (complex I) couples electron transfer from NADH to ubiquinone with proton translocation in its membrane part. Structural studies have identified a long (~ 30 Å), narrow, tunnel-like cavity within the enzyme, through which ubiquinone may access a deep reaction site. Although various inhibitors are considered to block the ubiquinone reduction by occupying the tunnel's interior, this view is still debatable. We synthesized a phosphatidylcholine-quinazoline hybrid compound (PC-Qz1), in which a quinazoline-type toxophore was attached to the sn-2 acyl chain to prevent it from entering the tunnel. However, PC-Qz1 inhibited complex I and suppressed photoaffinity labeling by another quinazoline derivative, [125I]AzQ. This study provides further experimental evidence that is difficult to reconcile with the canonical ubiquinone-accessing tunnel model.
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Affiliation(s)
- Ryohei Otani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Japan
| | - Takahiro Masuya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Japan
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Japan
| | - Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Japan
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4
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Chen P, Ding WL, Xu BW, Rehman MU, Liu KL, He YF, Li SY, Jian FC, Huang 黄 SC淑. Aflatoxin B1 as a complicit in intestinal damage caused by Eimeria ovinoidalis in lambs: Novel insights to reveal parasite-gut battle. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174539. [PMID: 38977103 DOI: 10.1016/j.scitotenv.2024.174539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/25/2024] [Accepted: 07/04/2024] [Indexed: 07/10/2024]
Abstract
Mycotoxins, unavoidable contaminants in feed and feed ingredients, have the potential to influence the incidence and severity of various diseases upon ingestion. Sheep coccidiosis is an enteric disease caused by protozoa of Eimeria spp. However, the extent to which the presence of aflatoxin b1 (AFB1) synergistically exacerbates damage to intestinal health in lambs with Eimeria remains unclear. 50-day-old female lambs were randomly assigned to a 2 × 2 factorial arrangement of treatments for 15 days to assess the impact of AFB1 exposure on lambs with or without Eimeria (E.) ovinoidalis infection. Our findings reveal that AFB1 synergistically intensifies damage to intestinal health in lambs challenged by E. ovinoidalis. This is evidenced by disruptions to the intestinal microbiota and reductions in the production of short-chain fatty acids. AFB1 further aggravates damage to the cecal mechanical barrier. Additionally, AFB1 contributes to the entry of lipopolysaccharide into the bloodstream, activating the inflammatory response. Interestingly, AFB1 exposure history results in an early peak of oocyst excretion and a decreased number of oocyst excretion in E. ovinoidalis infected lambs. This may be closely linked to the destruction of the intestinal epithelial cell structure and its apoptosis, as indicated by a decreased ratio of Bcl-2 to Bax and increased caspase-3 levels. Mechanistically, proteomics analysis identified mitochondrial dysfunction (inhibition of the oxidative phosphorylation pathway) as the primary factor intensifying intestinal epithelial cell destruction caused by coccidia, exacerbated by AFB1 through the inhibiting the conversion of NADH to NAD+ in the cecum of lambs via down-regulation of the PGC-1α/NRF1/TFAM pathway. Overall, these results offer novel insights into the AFB1 complicity in accelerating intestinal damage caused by E. ovinoidalis in lambs. Targeting the mitochondrial oxidative phosphorylation pathway of the intestine may represent a new therapeutic strategy against the detrimental effects of mycotoxin and coccidia.
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Affiliation(s)
- Pan Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Wen-Li Ding
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Bo-Wen Xu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Mujeeb Ur Rehman
- Directorate Planning & Development, Livestock and Dairy Development Department, Balochistan, Pakistan
| | - Kai-Li Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yan-Feng He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Sen-Yang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Fu-Chun Jian
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China.
| | - Shu-Cheng 淑成 Huang 黄
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China.
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5
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Zheng W, Chai P, Zhu J, Zhang K. High-resolution in situ structures of mammalian respiratory supercomplexes. Nature 2024; 631:232-239. [PMID: 38811722 PMCID: PMC11222160 DOI: 10.1038/s41586-024-07488-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes1-4. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: I1III2IV1, I1III2IV2, I2III2IV2 and I2III4IV2, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context.
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Affiliation(s)
- Wan Zheng
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jiapeng Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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6
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Vercellino I, Sazanov LA. SCAF1 drives the compositional diversity of mammalian respirasomes. Nat Struct Mol Biol 2024; 31:1061-1071. [PMID: 38575788 DOI: 10.1038/s41594-024-01255-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/16/2024] [Indexed: 04/06/2024]
Abstract
Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the 'canonical' respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the 'back' of CI, instead of the 'toe'. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.
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Affiliation(s)
- Irene Vercellino
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Klosterneuburg, Austria.
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7
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Dubinin MV, Chulkov AV, Igoshkina AD, Cherepanova AA, Mikina NV. Effect of 2-aminoethoxydiphenyl borate on the functions of mouse skeletal muscle mitochondria. Biochem Biophys Res Commun 2024; 712-713:149944. [PMID: 38636302 DOI: 10.1016/j.bbrc.2024.149944] [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: 02/13/2024] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
This work examined the effect of 2-aminoethoxydiphenyl borate (2-APB) on the functioning of isolated mouse skeletal muscle mitochondria and modeled its putative interaction with mitochondrial proteins. We have shown that 2-APB is able to dose-dependently suppress mitochondrial respiration in state 3 and 3UDNP driven by substrates of complex I and II. This effect of 2-APB was accompanied by a slight dose-dependent decrease in mitochondrial membrane potential and appears to be due to inhibition of complex I and complex III of the electron transport chain (ETC) with IC50 values of 200 and 120 μM, respectively. The results of molecular docking identified putative 2-APB interaction sites in these ETC complexes. 2-APB was shown to dose-dependently inhibit both mitochondrial Ca2+ uptake and Ca2+ efflux, which seems to be caused by a decrease in the membrane potential of the organelles. We have found that 2-APB has no significant effect on mitochondrial calcium retention capacity. On the other hand, 2-APB exhibited antioxidant effect by reducing mitochondrial hydrogen peroxide production but without affecting superoxide generation. It is concluded that the effect of 2-APB on mitochondrial targets should be taken into account when interpreting the results of cell and in vivo experiments.
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Affiliation(s)
- Mikhail V Dubinin
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El, 424001, Russia.
| | | | | | | | - Natalia V Mikina
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El, 424001, Russia
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8
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Grba DN, Wright JJ, Yin Z, Fisher W, Hirst J. Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I. Science 2024; 384:1247-1253. [PMID: 38870289 DOI: 10.1126/science.ado2075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
Abstract
Respiratory complex I is an efficient driver for oxidative phosphorylation in mammalian mitochondria, but its uncontrolled catalysis under challenging conditions leads to oxidative stress and cellular damage. Ischemic conditions switch complex I from rapid, reversible catalysis into a dormant state that protects upon reoxygenation, but the molecular basis for the switch is unknown. We combined precise biochemical definition of complex I catalysis with high-resolution cryo-electron microscopy structures in the phospholipid bilayer of coupled vesicles to reveal the mechanism of the transition into the dormant state, modulated by membrane interactions. By implementing a versatile membrane system to unite structure and function, attributing catalytic and regulatory properties to specific structural states, we define how a conformational switch in complex I controls its physiological roles.
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Affiliation(s)
| | | | | | | | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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9
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Belosludtsev KN, Ilzorkina AI, Matveeva LA, Chulkov AV, Semenova AA, Dubinin MV, Belosludtseva NV. Effect of VBIT-4 on the functional activity of isolated mitochondria and cell viability. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184329. [PMID: 38679309 DOI: 10.1016/j.bbamem.2024.184329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/11/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
VBIT-4 is a new inhibitor of the oligomerization of VDAC proteins of the outer mitochondrial membrane preventing the development of oxidative stress, mitochondrial dysfunction, and cell death in various pathologies. However, as a VDAC inhibitor, VBIT-4 may itself cause mitochondrial dysfunction in healthy cells. The article examines the effect of VBIT-4 on the functional activity of rat liver mitochondria and cell cultures. We have demonstrated that high concentrations of VBIT-4 (15-30 μM) suppressed mitochondrial respiration in state 3 and 3UDNP driven by substrates of complex I and II. VBIT-4 induced depolarization of organelles fueled by substrates of complex I but not complex II of the respiratory chain. VBIT-4 has been found to inhibit the activity of complexes I, III, and IV of the respiratory chain. Molecular docking demonstrated that VBIT-4 interacts with the rotenone-binding site in complex I with similar affinity. 15-30 μM VBIT-4 caused an increase in H2O2 production in mitochondria, decreased the Ca2+ retention capacity, but increased the time of Ca2+-dependent mitochondrial swelling. We have found that the incubation of breast adenocarcinoma (MCF-7) with 30 μM VBIT-4 for 48 h led to the decrease of the mitochondrial membrane potential, an increase in ROS production and death of MCF-7 cells. The mechanism of action of VBIT-4 on mitochondria and cells is discussed.
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Affiliation(s)
| | - Anna I Ilzorkina
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, Pushchino, Moscow region 142290, Russia
| | | | | | - Alena A Semenova
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El 424001, Russia
| | - Mikhail V Dubinin
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El 424001, Russia
| | - Natalia V Belosludtseva
- Mari State University, pl. Lenina 1, Yoshkar-Ola, Mari El 424001, Russia; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Institutskaya 3, Pushchino, Moscow region 142290, Russia
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10
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Wang Y, Gao J, Tang B, Mo W, Gao H, Guo J, Kong X, Zhang W, Yin Y, Jiao Y, Sun L. A comparative study on the dose-effect of low-dose radiation based on microdosimetric analysis and single-cell sequencing technology. Sci Rep 2024; 14:11524. [PMID: 38773212 PMCID: PMC11109114 DOI: 10.1038/s41598-024-62501-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/17/2024] [Indexed: 05/23/2024] Open
Abstract
The biological mechanisms triggered by low-dose exposure still need to be explored in depth. In this study, the potential mechanisms of low-dose radiation when irradiating the BEAS-2B cell lines with a Cs-137 gamma-ray source were investigated through simulations and experiments. Monolayer cell population models were constructed for simulating and analyzing distributions of nucleus-specific energy within cell populations combined with the Monte Carlo method and microdosimetric analysis. Furthermore, the 10 × Genomics single-cell sequencing technology was employed to capture the heterogeneity of individual cell responses to low-dose radiation in the same irradiated sample. The numerical uncertainties can be found both in the specific energy distribution in microdosimetry and in differential gene expressions in radiation cytogenetics. Subsequently, the distribution of nucleus-specific energy was compared with the distribution of differential gene expressions to guide the selection of differential genes bioinformatics analysis. Dose inhomogeneity is pronounced at low doses, where an increase in dose corresponds to a decrease in the dispersion of cellular-specific energy distribution. Multiple screening of differential genes by microdosimetric features and statistical analysis indicate a number of potential pathways induced by low-dose exposure. It also provides a novel perspective on the selection of sensitive biomarkers that respond to low-dose radiation.
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Affiliation(s)
- Yidi Wang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China
| | - Jin Gao
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China
| | - Bo Tang
- Department of Public Health Surveillance and Evaluation, Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Wei Mo
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China
| | - Han Gao
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China
| | - Jiahao Guo
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China
| | - Xianghui Kong
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China
| | - Wenyue Zhang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China
| | - Yuchen Yin
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China
| | - Yang Jiao
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China.
| | - Liang Sun
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China.
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11
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Djurabekova A, Lasham J, Zdorevskyi O, Zickermann V, Sharma V. Long-range electron proton coupling in respiratory complex I - insights from molecular simulations of the quinone chamber and antiporter-like subunits. Biochem J 2024; 481:499-514. [PMID: 38572757 DOI: 10.1042/bcj20240009] [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: 01/11/2024] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024]
Abstract
Respiratory complex I is a redox-driven proton pump. Several high-resolution structures of complex I have been determined providing important information about the putative proton transfer paths and conformational transitions that may occur during catalysis. However, how redox energy is coupled to the pumping of protons remains unclear. In this article, we review biochemical, structural and molecular simulation data on complex I and discuss several coupling models, including the key unresolved mechanistic questions. Focusing both on the quinone-reductase domain as well as the proton-pumping membrane-bound domain of complex I, we discuss a molecular mechanism of proton pumping that satisfies most experimental and theoretical constraints. We suggest that protonation reactions play an important role not only in catalysis, but also in the physiologically-relevant active/deactive transition of complex I.
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Affiliation(s)
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, Helsinki, Finland
| | | | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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12
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Platonov M, Maximyuk O, Rayevsky A, Hurmach V, Iegorova O, Naumchyk V, Bulgakov E, Cherninskyi A, Ozheredov D, Ryabukhin SV, Krishtal O, Volochnyuk DM. 4-(Azolyl)-Benzamidines as a Novel Chemotype for ASIC1a Inhibitors. Int J Mol Sci 2024; 25:3584. [PMID: 38612396 PMCID: PMC11011685 DOI: 10.3390/ijms25073584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 03/03/2024] [Accepted: 03/13/2024] [Indexed: 04/14/2024] Open
Abstract
Acid-sensing ion channels (ASICs) play a key role in the perception and response to extracellular acidification changes. These proton-gated cation channels are critical for neuronal functions, like learning and memory, fear, mechanosensation and internal adjustments like synaptic plasticity. Moreover, they play a key role in neuronal degeneration, ischemic neuronal injury, seizure termination, pain-sensing, etc. Functional ASICs are homo or heterotrimers formed with (ASIC1-ASIC3) homologous subunits. ASIC1a, a major ASIC isoform in the central nervous system (CNS), possesses an acidic pocket in the extracellular region, which is a key regulator of channel gating. Growing data suggest that ASIC1a channels are a potential therapeutic target for treating a variety of neurological disorders, including stroke, epilepsy and pain. Many studies were aimed at identifying allosteric modulators of ASIC channels. However, the regulation of ASICs remains poorly understood. Using all available crystal structures, which correspond to different functional states of ASIC1, and a molecular dynamics simulation (MD) protocol, we analyzed the process of channel inactivation. Then we applied a molecular docking procedure to predict the protein conformation suitable for the amiloride binding. To confirm the effect of its sole active blocker against the ASIC1 state transition route we studied the complex with another MD simulation run. Further experiments evaluated various compounds in the Enamine library that emerge with a detectable ASIC inhibitory activity. We performed a detailed analysis of the structural basis of ASIC1a inhibition by amiloride, using a combination of in silico approaches to visualize its interaction with the ion pore in the open state. An artificial activation (otherwise, expansion of the central pore) causes a complex modification of the channel structure, namely its transmembrane domain. The output protein conformations were used as a set of docking models, suitable for a high-throughput virtual screening of the Enamine chemical library. The outcome of the virtual screening was confirmed by electrophysiological assays with the best results shown for three hit compounds.
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Affiliation(s)
- Maksym Platonov
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Zabolotnogo Str., 150, 03143 Kyiv, Ukraine; (M.P.); (V.H.)
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
| | - Oleksandr Maximyuk
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine; (O.M.); (O.I.); (A.C.); (O.K.)
| | - Alexey Rayevsky
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Zabolotnogo Str., 150, 03143 Kyiv, Ukraine; (M.P.); (V.H.)
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str., 2A, 04123 Kyiv, Ukraine;
| | - Vasyl Hurmach
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Zabolotnogo Str., 150, 03143 Kyiv, Ukraine; (M.P.); (V.H.)
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
| | - Olena Iegorova
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine; (O.M.); (O.I.); (A.C.); (O.K.)
| | - Vasyl Naumchyk
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, 01601 Kyiv, Ukraine
| | - Elijah Bulgakov
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str., 2A, 04123 Kyiv, Ukraine;
| | - Andrii Cherninskyi
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine; (O.M.); (O.I.); (A.C.); (O.K.)
| | - Danil Ozheredov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str., 2A, 04123 Kyiv, Ukraine;
| | - Serhiy V. Ryabukhin
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, 01601 Kyiv, Ukraine
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Academik Kukhar Str., 02660 Kyiv, Ukraine
| | - Oleg Krishtal
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine; (O.M.); (O.I.); (A.C.); (O.K.)
| | - Dmytro M. Volochnyuk
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, 01601 Kyiv, Ukraine
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Academik Kukhar Str., 02660 Kyiv, Ukraine
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13
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Lasham J, Djurabekova A, Zickermann V, Vonck J, Sharma V. Role of Protonation States in the Stability of Molecular Dynamics Simulations of High-Resolution Membrane Protein Structures. J Phys Chem B 2024; 128:2304-2316. [PMID: 38430110 PMCID: PMC11389979 DOI: 10.1021/acs.jpcb.3c07421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Classical molecular dynamics (MD) simulations provide unmatched spatial and time resolution of protein structure and function. However, the accuracy of MD simulations often depends on the quality of force field parameters and the time scale of sampling. Another limitation of conventional MD simulations is that the protonation states of titratable amino acid residues remain fixed during simulations, even though protonation state changes coupled to conformational dynamics are central to protein function. Due to the uncertainty in selecting protonation states, classical MD simulations are sometimes performed with all amino acids modeled in their standard charged states at pH 7. Here, we performed and analyzed classical MD simulations on high-resolution cryo-EM structures of two large membrane proteins that transfer protons by catalyzing protonation/deprotonation reactions. In simulations performed with titratable amino acids modeled in their standard protonation (charged) states, the structure diverges far from its starting conformation. In comparison, MD simulations performed with predetermined protonation states of amino acid residues reproduce the structural conformation, protein hydration, and protein-water and protein-protein interactions of the structure much better. The results support the notion that it is crucial to perform basic protonation state calculations, especially on structures where protonation changes play an important functional role, prior to the launch of any conventional MD simulations. Furthermore, the combined approach of fast protonation state prediction and MD simulations can provide valuable information about the charge states of amino acids in the cryo-EM sample. Even though accurate prediction of protonation states in proteinaceous environments currently remains a challenge, we introduce an approach of combining pKa prediction with cryo-EM density map analysis that helps in improving not only the protonation state predictions but also the atomic modeling of density data.
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Affiliation(s)
- Jonathan Lasham
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Amina Djurabekova
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
- HiLIFE Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
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14
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Sirokha D, Rayevsky A, Gorodna O, Kalynovskyi V, Zelinska N, Samson O, Kwiatkowska K, Nef S, Jaruzelska J, Kusz-Zamelczyk K, Livshits L. Mutations in STARD8 (DLC3) May Cause 46,XY Gonadal Dysgenesis. Sex Dev 2024; 17:181-189. [PMID: 38447543 DOI: 10.1159/000537877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
INTRODUCTION 46,XY gonadal dysgenesis is a condition that is characterised by undeveloped testes in individuals with a male karyotype. Mutations in many genes that underlie this condition have been identified; however, there are still a considerable number of patients with an unknown genetic background. Recently, a mutation in the STARD8 X-linked gene in two sisters with 46,XY gonadal dysgenesis has been reported. It was localised within the START domain, whose homologue in Drosophila is responsible for maintaining testes integrity during their development. METHODS We analysed the potential pathogenicity of another STARD8 mutation, p.R887C, that was identified in a patient with 46,XY asymmetric gonadal dysgenesis. For this purpose, molecular dynamics simulations were performed. RESULTS These simulations revealed the full rearrangement of the helix containing the p.R887C substitution upstream from the START domain, which may cause STARD8 protein dysfunction and contribute to 46,XY gonadal dysgenesis. A comparison of the phenotypes of the three described 46,XY gonadal dysgenesis patients that harbour STARD8 mutations indicated that alterations of this gene can result in a partial or complete gonadal dysgenesis phenotype. CONCLUSION Based on these and previous results, it is reasonable to include STARD8 in gene panels for 46,XY gonadal dysgenesis.
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Affiliation(s)
- Dmytro Sirokha
- Department of Molecular Genetics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alexey Rayevsky
- Department of Molecular Genetics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Modeling, Enamine Ltd., Kyiv, Ukraine
| | - Olexandra Gorodna
- Department of Molecular Genetics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Vitalii Kalynovskyi
- Department of Pediatric Endocrinology, Ukrainian Scientific and Practical Center for Endocrine Surgery, Transplantation of Endocrine Organs and Tissues, Ministry of Health of Ukraine, Kyiv, Ukraine
| | - Nataliya Zelinska
- Department of Pediatric Endocrinology, Ukrainian Scientific and Practical Center for Endocrine Surgery, Transplantation of Endocrine Organs and Tissues, Ministry of Health of Ukraine, Kyiv, Ukraine
| | - Oksana Samson
- Endocrine Department, Shupyk National Healthcare University of Ukraine, Kyiv, Ukraine
| | | | - Serge Nef
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
| | | | | | - Ludmila Livshits
- Department of Molecular Genetics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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15
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Laube E, Schiller J, Zickermann V, Vonck J. Using cryo-EM to understand the assembly pathway of respiratory complex I. Acta Crystallogr D Struct Biol 2024; 80:159-173. [PMID: 38372588 PMCID: PMC10910544 DOI: 10.1107/s205979832400086x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/23/2024] [Indexed: 02/20/2024] Open
Abstract
Complex I (proton-pumping NADH:ubiquinone oxidoreductase) is the first component of the mitochondrial respiratory chain. In recent years, high-resolution cryo-EM studies of complex I from various species have greatly enhanced the understanding of the structure and function of this important membrane-protein complex. Less well studied is the structural basis of complex I biogenesis. The assembly of this complex of more than 40 subunits, encoded by nuclear or mitochondrial DNA, is an intricate process that requires at least 20 different assembly factors in humans. These are proteins that are transiently associated with building blocks of the complex and are involved in the assembly process, but are not part of mature complex I. Although the assembly pathways have been studied extensively, there is limited information on the structure and molecular function of the assembly factors. Here, the insights that have been gained into the assembly process using cryo-EM are reviewed.
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Affiliation(s)
- Eike Laube
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Jonathan Schiller
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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16
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Shin YC, Latorre-Muro P, Djurabekova A, Zdorevskyi O, Bennett CF, Burger N, Song K, Xu C, Sharma V, Liao M, Puigserver P. Structural basis of respiratory complexes adaptation to cold temperatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575914. [PMID: 38293190 PMCID: PMC10827213 DOI: 10.1101/2024.01.16.575914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
In response to cold, mammals activate brown fat for respiratory-dependent thermogenesis reliant on the electron transport chain (1, 2). Yet, the structural basis of respiratory complex adaptation to cold remains elusive. Herein we combined thermoregulatory physiology and cryo-EM to study endogenous respiratory supercomplexes exposed to different temperatures. A cold-induced conformation of CI:III 2 (termed type 2) was identified with a ∼25° rotation of CIII 2 around its inter-dimer axis, shortening inter-complex Q exchange space, and exhibiting different catalytic states which favor electron transfer. Large-scale supercomplex simulations in lipid membrane reveal how unique lipid-protein arrangements stabilize type 2 complexes to enhance catalytic activity. Together, our cryo-EM studies, multiscale simulations and biochemical analyses unveil the mechanisms and dynamics of respiratory adaptation at the structural and energetic level.
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17
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Braun HP, Klusch N. Promotion of oxidative phosphorylation by complex I-anchored carbonic anhydrases? TRENDS IN PLANT SCIENCE 2024; 29:64-71. [PMID: 37599162 DOI: 10.1016/j.tplants.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/12/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023]
Abstract
The mitochondrial NADH-dehydrogenase complex of the respiratory chain, known as complex I, includes a carbonic anhydrase (CA) module attached to its membrane arm on the matrix side in protozoans, algae, and plants. Its physiological role is so far unclear. Recent electron cryo-microscopy (cryo-EM) structures show that the CA module may directly provide protons for translocation across the inner mitochondrial membrane at complex I. CAs can have a central role in adjusting the proton concentration in the mitochondrial matrix. We suggest that CA anchoring in complex I represents the original configuration to secure oxidative phosphorylation (OXPHOS) in the context of early endosymbiosis. After development of 'modern mitochondria' with pronounced cristae structures, this anchoring became dispensable, but has been retained in protozoans, algae, and plants.
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Affiliation(s)
- Hans-Peter Braun
- Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany.
| | - Niklas Klusch
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt, Germany.
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18
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Yin Z, Agip ANA, Bridges HR, Hirst J. Structural insights into respiratory complex I deficiency and assembly from the mitochondrial disease-related ndufs4 -/- mouse. EMBO J 2024; 43:225-249. [PMID: 38177503 PMCID: PMC10897435 DOI: 10.1038/s44318-023-00001-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024] Open
Abstract
Respiratory complex I (NADH:ubiquinone oxidoreductase) is essential for cellular energy production and NAD+ homeostasis. Complex I mutations cause neuromuscular, mitochondrial diseases, such as Leigh Syndrome, but their molecular-level consequences remain poorly understood. Here, we use a popular complex I-linked mitochondrial disease model, the ndufs4-/- mouse, to define the structural, biochemical, and functional consequences of the absence of subunit NDUFS4. Cryo-EM analyses of the complex I from ndufs4-/- mouse hearts revealed a loose association of the NADH-dehydrogenase module, and discrete classes containing either assembly factor NDUFAF2 or subunit NDUFS6. Subunit NDUFA12, which replaces its paralogue NDUFAF2 in mature complex I, is absent from all classes, compounding the deletion of NDUFS4 and preventing maturation of an NDUFS4-free enzyme. We propose that NDUFAF2 recruits the NADH-dehydrogenase module during assembly of the complex. Taken together, the findings provide new molecular-level understanding of the ndufs4-/- mouse model and complex I-linked mitochondrial disease.
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Affiliation(s)
- Zhan Yin
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Ahmed-Noor A Agip
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Cambridge, UK
- Max-Planck-Institute of Biophysics, Frankfurt, 60438, Germany
| | - Hannah R Bridges
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Cambridge, UK.
- Structura Biotechnology Inc., Toronto, Canada.
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Cambridge, UK.
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Han H, Zhao C, Liu M, Zhu H, Meng F, Zhang Y, Wang G, Wang L, Di L, Mingyuen Lee S, Zhang Q, Cui G. Mitochondrial complex I inhibition by homoharringtonine: A novel strategy for suppression of chronic myeloid leukemia. Biochem Pharmacol 2023; 218:115875. [PMID: 37871881 DOI: 10.1016/j.bcp.2023.115875] [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: 08/29/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023]
Abstract
Chronic myeloid leukemia (CML) is a hematologic malignancy predominantly driven by the BCR-ABL fusion gene. One of the significant challenges in treating CML lies in the emergence of resistance to tyrosine kinase inhibitors (TKIs), especially those associated with the T315I mutation. Homoharringtonine (HHT) is an FDA-approved, naturally-derived drug with known anti-leukemic properties, but its precise mechanisms of action remain incompletely understood. In this study, we rigorously evaluated the anti-CML activity of HHT through both in vitro and in vivo assays, observing substantial anti-CML effects. To elucidate the molecular mechanisms underpinning these effects, we performed proteomic analysis on BCR-ABL T315I mutation-bearing cells treated with HHT. Comprehensive pathway enrichment analysis identified oxidative phosphorylation (OXPHOS) as the most significantly disrupted, suggesting a key role in the mechanism of action of HHT. Further bioinformatics exploration revealed a substantial downregulation of proteins localized within mitochondrial complex I (MCI), a critical OXPHOS component. These results were validated through Western blot analysis and were supplemented by marked reductions in MCI activity, ATP level, and oxygen consumption rate (OCR) upon HHT exposure. Collectively, our results shed light on the potent anti-CML properties of HHT, particularly its effectiveness against T315I mutant cells through MCI inhibition. Our study underscores a novel therapeutic strategy to overcome BCR-ABL T315I mutation resistance, illuminating a previously uncharted mechanism of action for HHT.
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Affiliation(s)
- Han Han
- School of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
| | - Chen Zhao
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau SAR, China
| | - Mengchen Liu
- School of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
| | - Hongxuan Zhu
- School of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
| | - Fancheng Meng
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau SAR, China
| | - Ying Zhang
- School of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
| | - Guibin Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Li Wang
- Faculty of Health sciences, University of Macau, Macau SAR, China
| | - Lijun Di
- Faculty of Health sciences, University of Macau, Macau SAR, China
| | - Simon Mingyuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau SAR, China
| | - Qingwen Zhang
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau SAR, China.
| | - Guozhen Cui
- School of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China.
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20
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Huang Y, Liang B, Li Z, Zhong Y, Wang B, Zhang B, Du J, Ye R, Xian H, Min W, Yan X, Deng Y, Feng Y, Bai R, Fan B, Yang X, Huang Z. Polystyrene nanoplastic exposure induces excessive mitophagy by activating AMPK/ULK1 pathway in differentiated SH-SY5Y cells and dopaminergic neurons in vivo. Part Fibre Toxicol 2023; 20:44. [PMID: 37993864 PMCID: PMC10664492 DOI: 10.1186/s12989-023-00556-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Microplastics and nanoplastics (MNPs) are emerging environmental contaminants detected in human samples, and have raised concerns regarding their potential risks to human health, particularly neurotoxicity. This study aimed to investigate the deleterious effects of polystyrene nanoplastics (PS-NPs, 50 nm) and understand their mechanisms in inducing Parkinson's disease (PD)-like neurodegeneration, along with exploring preventive strategies. METHODS Following exposure to PS-NPs (0.5-500 μg/mL), we assessed cytotoxicity, mitochondrial integrity, ATP levels, and mitochondrial respiration in dopaminergic-differentiated SH-SY5Y cells. Molecular docking and dynamic simulations explored PS-NPs' interactions with mitochondrial complexes. We further probed mitophagy's pivotal role in PS-NP-induced mitochondrial damage and examined melatonin's ameliorative potential in vitro. We validated melatonin's intervention (intraperitoneal, 10 mg/kg/d) in C57BL/6 J mice exposed to 250 mg/kg/d of PS-NPs for 28 days. RESULTS In our in vitro experiments, we observed PS-NP accumulation in cells, including mitochondria, leading to cell toxicity and reduced viability. Notably, antioxidant treatment failed to fully rescue viability, suggesting reactive oxygen species (ROS)-independent cytotoxicity. PS-NPs caused significant mitochondrial damage, characterized by altered morphology, reduced mitochondrial membrane potential, and decreased ATP production. Subsequent investigations pointed to PS-NP-induced disruption of mitochondrial respiration, potentially through interference with complex I (CI), a concept supported by molecular docking studies highlighting the influence of PS-NPs on CI. Rescue experiments using an AMPK pathway inhibitor (compound C) and an autophagy inhibitor (3-methyladenine) revealed that excessive mitophagy was induced through AMPK/ULK1 pathway activation, worsening mitochondrial damage and subsequent cell death in differentiated SH-SY5Y cells. Notably, we identified melatonin as a potential protective agent, capable of alleviating PS-NP-induced mitochondrial dysfunction. Lastly, our in vivo experiments demonstrated that melatonin could mitigate dopaminergic neuron loss and motor impairments by restoring mitophagy regulation in mice. CONCLUSIONS Our study demonstrated that PS-NPs disrupt mitochondrial function by affecting CI, leading to excessive mitophagy through the AMPK/ULK1 pathway, causing dopaminergic neuron death. Melatonin can counteract PS-NP-induced mitochondrial dysfunction and motor impairments by regulating mitochondrial autophagy. These findings offer novel insights into the MNP-induced PD-like neurodegenerative mechanisms, and highlight melatonin's protective potential in mitigating the MNP's environmental risk.
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Affiliation(s)
- Yuji Huang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Boxuan Liang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Zhiming Li
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Yizhou Zhong
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Bo Wang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Bingli Zhang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Jiaxin Du
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Rongyi Ye
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Hongyi Xian
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Weicui Min
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, People's Republic of China
| | - Xiliang Yan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, People's Republic of China
| | - Yanhong Deng
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Yu Feng
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Ruobing Bai
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Bingchi Fan
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Xingfen Yang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Food Safety and Health Research Center, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Zhenlie Huang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China.
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Yi JT, Wang P, Stuchebrukhov AA. Mutation at the entrance of the quinone cavity severely disrupts quinone binding in respiratory complex I. Sci Rep 2023; 13:20413. [PMID: 37989876 PMCID: PMC10663621 DOI: 10.1038/s41598-023-47314-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/12/2023] [Indexed: 11/23/2023] Open
Abstract
In all resolved structures of complex I, there exists a tunnel-like Q-chamber for ubiquinone binding and reduction. The entrance to the Q-chamber in ND1 subunit forms a narrow bottleneck, which is rather tight and requires thermal conformational changes for ubiquinone to get in and out of the binding chamber. The substitution of alanine with threonine at the bottleneck (AlaThr MUT), associated with 3460/ND1 mtDNA mutation in human complex I, is implicated in Leber's Hereditary Optic Neuropathy (LHON). Here, we show the AlaThr MUT further narrows the Q-chamber entrance cross-section area by almost 30%, increasing the activation free energy barrier of quinone passage by approximately 5 kJ mol-1. This severely disrupts quinone binding and reduction as quinone passage through the bottleneck is slowed down almost tenfold. Our estimate of the increase in free energy barrier is entirely due to the bottleneck narrowing, leading to a reduction of the transition state entropy between WT and MUT, and thus more difficult quinone passage. Additionally, we investigate details of possible water exchange between the Q-chamber and membrane. We find water exchange is dynamic in WT but may be severely slowed in MUT. We propose that LHON symptoms caused by 3460/ND1 mtDNA mutation are due to slowed quinone binding. This leads to an increased production of reactive oxidative species due to upstream electron backup at the FMN site of complex I, thus resulting in a mt bioenergetic defect.
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Affiliation(s)
- Jason Tae Yi
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Panyue Wang
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Alexei A Stuchebrukhov
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA.
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22
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Dong Y, Dong S, Yu C, Liu J, Gai S, Xie Y, Zhao Z, Qin X, Feng L, Yang P, Zhao Y. Mitochondria-targeting Cu 3VS 4 nanostructure with high copper ionic mobility for photothermoelectric therapy. SCIENCE ADVANCES 2023; 9:eadi9980. [PMID: 37910608 PMCID: PMC10619935 DOI: 10.1126/sciadv.adi9980] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
Thermoelectric therapy has emerged as a promising treatment strategy for oncology, but it is still limited by the low thermoelectric catalytic efficiency at human body temperature and the inevitable tumor thermotolerance. We present a photothermoelectric therapy (PTET) strategy based on triphenylphosphine-functionalized Cu3VS4 nanoparticles (CVS NPs) with high copper ionic mobility at room temperature. Under near-infrared laser irradiation, CVS NPs not only generate hyperthermia to ablate tumor cells but also catalytically yield superoxide radicals and induce endogenous NADH oxidation through the Seebeck effect. Notably, CVS NPs can accumulate inside mitochondria and deplete NADH, reducing ATP synthesis by competitively inhibiting the function of complex I, thereby down-regulating the expression of heat shock proteins to relieve tumor thermotolerance. Both in vitro and in vivo results show notable tumor suppression efficacy, indicating that the concept of integrating PTET and mitochondrial metabolism modulation is highly feasible and offers a translational promise for realizing precise and efficient cancer treatment.
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Affiliation(s)
- Yushan Dong
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, P. R. China
| | - Shuming Dong
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, P. R. China
| | - Chenghao Yu
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, P. R. China
| | - Jing Liu
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, P. R. China
| | - Shili Gai
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, P. R. China
| | - Ying Xie
- Key Laboratory of Functional Inorganic Material Chemistry, Ministry of Education, School of Chemistry and Materials Science, Heilongjiang University, Harbin, 150080, P. R. China
| | - Zhiyu Zhao
- Department of Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, P. R. China
| | - Xiran Qin
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, P. R. China
| | - Lili Feng
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, P. R. China
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Piaoping Yang
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin 150001, P. R. China
| | - Yanli Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
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23
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Kim H, Saura P, Pöverlein MC, Gamiz-Hernandez AP, Kaila VRI. Quinone Catalysis Modulates Proton Transfer Reactions in the Membrane Domain of Respiratory Complex I. J Am Chem Soc 2023; 145:17075-17086. [PMID: 37490414 PMCID: PMC10416309 DOI: 10.1021/jacs.3c03086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Indexed: 07/27/2023]
Abstract
Complex I is a redox-driven proton pump that drives electron transport chains and powers oxidative phosphorylation across all domains of life. Yet, despite recently resolved structures from multiple organisms, it still remains unclear how the redox reactions in Complex I trigger proton pumping up to 200 Å away from the active site. Here, we show that the proton-coupled electron transfer reactions during quinone reduction drive long-range conformational changes of conserved loops and trans-membrane (TM) helices in the membrane domain of Complex I from Yarrowia lipolytica. We find that the conformational switching triggers a π → α transition in a TM helix (TM3ND6) and establishes a proton pathway between the quinone chamber and the antiporter-like subunits, responsible for proton pumping. Our large-scale (>20 μs) atomistic molecular dynamics (MD) simulations in combination with quantum/classical (QM/MM) free energy calculations show that the helix transition controls the barrier for proton transfer reactions by wetting transitions and electrostatic effects. The conformational switching is enabled by re-arrangements of ion pairs that propagate from the quinone binding site to the membrane domain via an extended network of conserved residues. We find that these redox-driven changes create a conserved coupling network within the Complex I superfamily, with point mutations leading to drastic activity changes and mitochondrial disorders. On a general level, our findings illustrate how catalysis controls large-scale protein conformational changes and enables ion transport across biological membranes.
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Affiliation(s)
- Hyunho Kim
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | | | - Ana P. Gamiz-Hernandez
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Ville R. I. Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
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24
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Grba DN, Chung I, Bridges HR, Agip ANA, Hirst J. Investigation of hydrated channels and proton pathways in a high-resolution cryo-EM structure of mammalian complex I. SCIENCE ADVANCES 2023; 9:eadi1359. [PMID: 37531432 PMCID: PMC10396290 DOI: 10.1126/sciadv.adi1359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023]
Abstract
Respiratory complex I, a key enzyme in mammalian metabolism, captures the energy released by reduction of ubiquinone by NADH to drive protons across the inner mitochondrial membrane, generating the proton-motive force for ATP synthesis. Despite remarkable advances in structural knowledge of this complicated membrane-bound enzyme, its mechanism of catalysis remains controversial. In particular, how ubiquinone reduction is coupled to proton pumping and the pathways and mechanisms of proton translocation are contested. We present a 2.4-Å resolution cryo-EM structure of complex I from mouse heart mitochondria in the closed, active (ready-to-go) resting state, with 2945 water molecules modeled. By analyzing the networks of charged and polar residues and water molecules present, we evaluate candidate pathways for proton transfer through the enzyme, for the chemical protons for ubiquinone reduction, and for the protons transported across the membrane. Last, we compare our data to the predictions of extant mechanistic models, and identify key questions to answer in future work to test them.
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25
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Ikunishi R, Otani R, Masuya T, Shinzawa-Itoh K, Shiba T, Murai M, Miyoshi H. Respiratory complex I in mitochondrial membrane catalyzes oversized ubiquinones. J Biol Chem 2023; 299:105001. [PMID: 37394006 PMCID: PMC10416054 DOI: 10.1016/j.jbc.2023.105001] [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: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/04/2023] Open
Abstract
NADH-ubiquinone (UQ) oxidoreductase (complex I) couples electron transfer from NADH to UQ with proton translocation in its membrane part. The UQ reduction step is key to triggering proton translocation. Structural studies have identified a long, narrow, tunnel-like cavity within complex I, through which UQ may access a deep reaction site. To elucidate the physiological relevance of this UQ-accessing tunnel, we previously investigated whether a series of oversized UQs (OS-UQs), whose tail moiety is too large to enter and transit the narrow tunnel, can be catalytically reduced by complex I using the native enzyme in bovine heart submitochondrial particles (SMPs) and the isolated enzyme reconstituted into liposomes. Nevertheless, the physiological relevance remained unclear because some amphiphilic OS-UQs were reduced in SMPs but not in proteoliposomes, and investigation of extremely hydrophobic OS-UQs was not possible in SMPs. To uniformly assess the electron transfer activities of all OS-UQs with the native complex I, here we present a new assay system using SMPs, which were fused with liposomes incorporating OS-UQ and supplemented with a parasitic quinol oxidase to recycle reduced OS-UQ. In this system, all OS-UQs tested were reduced by the native enzyme, and the reduction was coupled with proton translocation. This finding does not support the canonical tunnel model. We propose that the UQ reaction cavity is flexibly open in the native enzyme to allow OS-UQs to access the reaction site, but their access is obstructed in the isolated enzyme as the cavity is altered by detergent-solubilizing from the mitochondrial membrane.
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Affiliation(s)
- Ryo Ikunishi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Ryohei Otani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takahiro Masuya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kyoko Shinzawa-Itoh
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
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26
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Zdorevskyi O, Djurabekova A, Lasham J, Sharma V. Horizontal proton transfer across the antiporter-like subunits in mitochondrial respiratory complex I. Chem Sci 2023; 14:6309-6318. [PMID: 37325138 PMCID: PMC10266447 DOI: 10.1039/d3sc01427d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Respiratory complex I is a redox-driven proton pump contributing to about 40% of total proton motive force required for mitochondrial ATP generation. Recent high-resolution cryo-EM structural data revealed the positions of several water molecules in the membrane domain of the large enzyme complex. However, it remains unclear how protons flow in the membrane-bound antiporter-like subunits of complex I. Here, we performed multiscale computer simulations on high-resolution structural data to model explicit proton transfer processes in the ND2 subunit of complex I. Our results show protons can travel the entire width of antiporter-like subunits, including at the subunit-subunit interface, parallel to the membrane. We identify a previously unrecognized role of conserved tyrosine residues in catalyzing horizontal proton transfer, and that long-range electrostatic effects assist in reducing energetic barriers of proton transfer dynamics. Results from our simulations warrant a revision in several prevailing proton pumping models of respiratory complex I.
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Affiliation(s)
| | | | - Jonathan Lasham
- Department of Physics, University of Helsinki Helsinki Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki Helsinki Finland
- HiLIFE Institute of Biotechnology, University of Helsinki Helsinki Finland
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27
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Han F, Hu Y, Wu M, He Z, Tian H, Zhou L. Structures of Tetrahymena thermophila respiratory megacomplexes on the tubular mitochondrial cristae. Nat Commun 2023; 14:2542. [PMID: 37248254 DOI: 10.1038/s41467-023-38158-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/19/2023] [Indexed: 05/31/2023] Open
Abstract
Tetrahymena thermophila, a classic ciliate model organism, has been shown to possess tubular mitochondrial cristae and highly divergent electron transport chain involving four transmembrane protein complexes (I-IV). Here we report cryo-EM structures of its ~8 MDa megacomplex IV2 + (I + III2 + II)2, as well as a ~ 10.6 MDa megacomplex (IV2 + I + III2 + II)2 at lower resolution. In megacomplex IV2 + (I + III2 + II)2, each CIV2 protomer associates one copy of supercomplex I + III2 and one copy of CII, forming a half ring-shaped architecture that adapts to the membrane curvature of mitochondrial cristae. Megacomplex (IV2 + I + III2 + II)2 defines the relative position between neighbouring half rings and maintains the proximity between CIV2 and CIII2 cytochrome c binding sites. Our findings expand the current understanding of divergence in eukaryotic electron transport chain organization and how it is related to mitochondrial morphology.
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Affiliation(s)
- Fangzhu Han
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Yiqi Hu
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Mengchen Wu
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Zhaoxiang He
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Hongtao Tian
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China
| | - Long Zhou
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China.
- Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310058, China.
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28
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Strotmann L, Harter C, Gerasimova T, Ritter K, Jessen HJ, Wohlwend D, Friedrich T. H 2O 2 selectively damages the binuclear iron-sulfur cluster N1b of respiratory complex I. Sci Rep 2023; 13:7652. [PMID: 37169846 PMCID: PMC10175503 DOI: 10.1038/s41598-023-34821-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023] Open
Abstract
NADH:ubiquinone oxidoreductase, respiratory complex I, plays a major role in cellular energy metabolism by coupling electron transfer with proton translocation. Electron transfer is catalyzed by a flavin mononucleotide and a series of iron-sulfur (Fe/S) clusters. As a by-product of the reaction, the reduced flavin generates reactive oxygen species (ROS). It was suggested that the ROS generated by the respiratory chain in general could damage the Fe/S clusters of the complex. Here, we show that the binuclear Fe/S cluster N1b is specifically damaged by H2O2, however, only at high concentrations. But under the same conditions, the activity of the complex is hardly affected, since N1b can be easily bypassed during electron transfer.
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Affiliation(s)
- Lisa Strotmann
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Caroline Harter
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Tatjana Gerasimova
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Kevin Ritter
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Henning J Jessen
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany.
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29
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Pereira CS, Teixeira MH, Russell DA, Hirst J, Arantes GM. Mechanism of rotenone binding to respiratory complex I depends on ligand flexibility. Sci Rep 2023; 13:6738. [PMID: 37185607 PMCID: PMC10130173 DOI: 10.1038/s41598-023-33333-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Respiratory complex I is a major cellular energy transducer located in the inner mitochondrial membrane. Its inhibition by rotenone, a natural isoflavonoid, has been used for centuries by indigenous peoples to aid in fishing and, more recently, as a broad-spectrum pesticide or even a possible anticancer therapeutic. Unraveling the molecular mechanism of rotenone action will help to design tuned derivatives and to understand the still mysterious catalytic mechanism of complex I. Although composed of five fused rings, rotenone is a flexible molecule and populates two conformers, bent and straight. Here, a rotenone derivative locked in the straight form was synthesized and found to inhibit complex I with 600-fold less potency than natural rotenone. Large-scale molecular dynamics and free energy simulations of the pathway for ligand binding to complex I show that rotenone is more stable in the bent conformer, either free in the membrane or bound to the redox active site in the substrate-binding Q-channel. However, the straight conformer is necessary for passage from the membrane through the narrow entrance of the channel. The less potent inhibition of the synthesized derivative is therefore due to its lack of internal flexibility, and interconversion between bent and straight forms is required to enable efficient kinetics and high stability for rotenone binding. The ligand also induces reconfiguration of protein loops and side-chains inside the Q-channel similar to structural changes that occur in the open to closed conformational transition of complex I. Detailed understanding of ligand flexibility and interactions that determine rotenone binding may now be exploited to tune the properties of synthetic derivatives for specific applications.
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Affiliation(s)
- Caroline S Pereira
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-900, Brazil
| | - Murilo H Teixeira
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-900, Brazil
| | - David A Russell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK.
| | - Guilherme M Arantes
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-900, Brazil.
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30
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Lou X, Zhou Y, Liu Z, Xie Y, Zhang L, Zhao S, Gong S, Zhuo X, Wang J, Dai L, Ren X, Tong X, Jiang L, Fang H, Fang F, Lyu J. De novo frameshift variant in MT-ND1 causes a mitochondrial complex I deficiency associated with MELAS syndrome. Gene 2023; 860:147229. [PMID: 36717040 DOI: 10.1016/j.gene.2023.147229] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/04/2023] [Accepted: 01/24/2023] [Indexed: 01/29/2023]
Abstract
BACKGROUND The variant m.3571_3572insC/MT-ND1 thus far only reported in oncocytic tumors of different tissues. However, the role of m.3571_3572insC in inherited mitochondrial diseases has yet to be elucidated. METHODS A patient diagnosed with MELAS syndrome was recruited, and detailed medical records were collected and reviewed. The muscle was biopsied for mitochondrial respiratory chain enzyme activity. Series of fibroblast clones bearing different m.3571_3572insC variant loads were generated from patient-derived fibroblasts and subjected to functional assays. RESULTS Complex I deficiency was confirmed in the patient's muscle via mitochondrial respiratory chain enzyme activity assay. The m.3571_3572insC was filtered for the candidate variant of the patient according to the guidelines for mitochondrial mRNA variants interpretation. Three cell clones with different m.3571_3572insC variant loads were generated to evaluate mitochondrial function. Blue native PAGE analysis revealed that m.3571_3572insC caused a deficiency in the mitochondrial complex I. Oxygen consumption rate, ATP production, and lactate assays found an impairment of cellular bioenergetic capacity due to m.3571_3572insC. Mitochondrial membrane potential was decreased, and mitochondrial reactive oxygen species production was increased with the variant of m.3571_3572insC. According to the competitive cell growth assay, the mutant cells had impaired cell growth capacity compared to wild type. CONCLUSIONS A novel variant m.3571_3572insC was identified in a patient diagnosed with MELAS syndrome, and the variant impaired mitochondrial respiration by decreasing the activity of complex I. In conclusion, the genetic spectrum of mitochondrial diseases was expanded by including m.3571_3572insC/MT-ND1.
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Affiliation(s)
- Xiaoting Lou
- Center for Reproductive Medicine, Department of Genetic and Genomic Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China; Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Yuwei Zhou
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zhimei Liu
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100069, China
| | - Yaojun Xie
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Luyi Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Suzhou Zhao
- Fujungenetics Technologies Co., Ltd, Beijing 100176, China
| | - Shuai Gong
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100069, China
| | - Xiuwei Zhuo
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100069, China
| | - Junling Wang
- Department of Pediatrics, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Lifang Dai
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100069, China
| | - Xiaotun Ren
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100069, China
| | - Xiao Tong
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100069, China
| | - Liangliang Jiang
- Pediatric Neurology, Anhui Provincial Children's Hospital, Hefei, Anhui 230022, China
| | - Hezhi Fang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Fang Fang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100069, China.
| | - Jianxin Lyu
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China; Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
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31
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Tunnel dynamics of quinone derivatives and its coupling to protein conformational rearrangements in respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148951. [PMID: 36509126 DOI: 10.1016/j.bbabio.2022.148951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
Respiratory complex I in mitochondria and bacteria catalyzes the transfer of electrons from NADH to quinone (Q). The free energy available from the reaction is used to pump protons and to establish a membrane proton electrochemical gradient, which drives ATP synthesis. Even though several high-resolution structures of complex I have been resolved, how Q reduction is linked with proton pumping, remains unknown. Here, microsecond long molecular dynamics (MD) simulations were performed on Yarrowia lipolytica complex I structures where Q molecules have been resolved in the ~30 Å long Q tunnel. MD simulations of several different redox/protonation states of Q reveal the coupling between the Q dynamics and the restructuring of conserved loops and ion pairs. Oxidized quinone stabilizes towards the N2 FeS cluster, a binding mode not previously described in Yarrowia lipolytica complex I structures. On the other hand, reduced (and protonated) species tend to diffuse towards the Q binding sites closer to the tunnel entrance. Mechanistic and physiological relevance of these results are discussed.
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32
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Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL. Structure of mycobacterial respiratory complex I. Proc Natl Acad Sci U S A 2023; 120:e2214949120. [PMID: 36952383 PMCID: PMC10068793 DOI: 10.1073/pnas.2214949120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/10/2023] [Indexed: 03/24/2023] Open
Abstract
Oxidative phosphorylation, the combined activity of the electron transport chain (ETC) and adenosine triphosphate synthase, has emerged as a valuable target for the treatment of infection by Mycobacterium tuberculosis and other mycobacteria. The mycobacterial ETC is highly branched with multiple dehydrogenases transferring electrons to a membrane-bound pool of menaquinone and multiple oxidases transferring electrons from the pool. The proton-pumping type I nicotinamide adenine dinucleotide (NADH) dehydrogenase (Complex I) is found in low abundance in the plasma membranes of mycobacteria in typical in vitro culture conditions and is often considered dispensable. We found that growth of Mycobacterium smegmatis in carbon-limited conditions greatly increased the abundance of Complex I and allowed isolation of a rotenone-sensitive preparation of the enzyme. Determination of the structure of the complex by cryoEM revealed the "orphan" two-component response regulator protein MSMEG_2064 as a subunit of the assembly. MSMEG_2064 in the complex occupies a site similar to the proposed redox-sensing subunit NDUFA9 in eukaryotic Complex I. An apparent purine nucleoside triphosphate within the NuoG subunit resembles the GTP-derived molybdenum cofactor in homologous formate dehydrogenase enzymes. The membrane region of the complex binds acyl phosphatidylinositol dimannoside, a characteristic three-tailed lipid from the mycobacterial membrane. The structure also shows menaquinone, which is preferentially used over ubiquinone by gram-positive bacteria, in two different positions along the quinone channel, comparable to ubiquinone in other structures and suggesting a conserved quinone binding mechanism.
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Affiliation(s)
- Yingke Liang
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
- Department of Biochemistry, University of Toronto, TorontoM5S 1A8, Canada
| | - Alicia Plourde
- Department of Molecular and Cellular Biology, University of Guelph, TorontoN1G 2W1, Canada
| | - Stephanie A. Bueler
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, TorontoM5S 1A8, Canada
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91Stockholm, Sweden
| | - Siavash Vahidi
- Department of Molecular and Cellular Biology, University of Guelph, TorontoN1G 2W1, Canada
| | - John L. Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
- Department of Biochemistry, University of Toronto, TorontoM5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, TorontoM5G 1L7, Canada
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33
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Bridges HR, Blaza JN, Yin Z, Chung I, Pollak MN, Hirst J. Structural basis of mammalian respiratory complex I inhibition by medicinal biguanides. Science 2023; 379:351-357. [PMID: 36701435 PMCID: PMC7614227 DOI: 10.1126/science.ade3332] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The molecular mode of action of biguanides, including the drug metformin, which is widely used in the treatment of diabetes, is incompletely characterized. Here, we define the inhibitory drug-target interaction(s) of a model biguanide with mammalian respiratory complex I by combining cryo-electron microscopy and enzyme kinetics. We interpret these data to explain the selectivity of biguanide binding to different enzyme states. The primary inhibitory site is in an amphipathic region of the quinone-binding channel, and an additional binding site is in a pocket on the intermembrane-space side of the enzyme. An independent local chaotropic interaction, not previously described for any drug, displaces a portion of a key helix in the membrane domain. Our data provide a structural basis for biguanide action and enable the rational design of medicinal biguanides.
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Affiliation(s)
- Hannah R. Bridges
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK,Authors for correspondence: and
| | - James N. Blaza
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK,Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, The University of York, YO10 5DD, UK
| | - Zhan Yin
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Injae Chung
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Michael N. Pollak
- Lady Davis Institute of the Jewish General Hospital and Department of Oncology, McGill University, Montreal, QC H3T 1E2, Canada
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK,Authors for correspondence: and
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Agip ANA, Chung I, Sanchez-Martinez A, Whitworth AJ, Hirst J. Cryo-EM structures of mitochondrial respiratory complex I from Drosophila melanogaster. eLife 2023; 12:e84424. [PMID: 36622099 PMCID: PMC9977279 DOI: 10.7554/elife.84424] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
Respiratory complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from NADH oxidation by ubiquinone to drive protons across an energy-transducing membrane. Drosophila melanogaster is a candidate model organism for complex I due to its high evolutionary conservation with the mammalian enzyme, well-developed genetic toolkit, and complex physiology for studies in specific cell types and tissues. Here, we isolate complex I from Drosophila and determine its structure, revealing a 43-subunit assembly with high structural homology to its 45-subunit mammalian counterpart, including a hitherto unknown homologue to subunit NDUFA3. The major conformational state of the Drosophila enzyme is the mammalian-type 'ready-to-go' active resting state, with a fully ordered and enclosed ubiquinone-binding site, but a subtly altered global conformation related to changes in subunit ND6. The mammalian-type 'deactive' pronounced resting state is not observed: in two minor states, the ubiquinone-binding site is unchanged, but a deactive-type π-bulge is present in ND6-TMH3. Our detailed structural knowledge of Drosophila complex I provides a foundation for new approaches to disentangle mechanisms of complex I catalysis and regulation in bioenergetics and physiology.
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Affiliation(s)
- Ahmed-Noor A Agip
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Injae Chung
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Alvaro Sanchez-Martinez
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Alexander J Whitworth
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
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Wikström M, Djurabekova A, Sharma V. On the role of ubiquinone in the proton translocation mechanism of respiratory complex I. FEBS Lett 2023; 597:224-236. [PMID: 36180980 DOI: 10.1002/1873-3468.14506] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 01/26/2023]
Abstract
Complex I converts oxidoreduction energy into a proton electrochemical gradient across the inner mitochondrial or bacterial cell membrane. This gradient is the primary source of energy for aerobic synthesis of ATP. Oxidation of reduced nicotinamide adenine dinucleotide (NADH) by ubiquinone (Q) yields NAD+ and ubiquinol (QH2 ), which is tightly coupled to translocation of four protons from the negatively to the positively charged side of the membrane. Electrons from NADH oxidation reach the iron-sulfur centre N2 positioned near the bottom of a tunnel that extends circa 30 Å from the membrane domain into the hydrophilic domain of the complex. The tunnel is occupied by ubiquinone, which can take a distal position near the N2 centre or proximal positions closer to the membrane. Here, we review important structural, kinetic and thermodynamic properties of ubiquinone that define its role in complex I function. We suggest that this function exceeds that of a mere substrate or electron acceptor and propose that ubiquinone may be the redox element of complex I coupling electron transfer to proton translocation.
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Affiliation(s)
- Mårten Wikström
- HiLIFE Institute of Biotechnology, University of Helsinki, Finland
| | | | - Vivek Sharma
- HiLIFE Institute of Biotechnology, University of Helsinki, Finland.,Department of Physics, University of Helsinki, Finland
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36
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Stuchebrukhov AA, Hayashi T. Single protonation of the reduced quinone in respiratory complex I drives four-proton pumping. FEBS Lett 2023; 597:237-245. [PMID: 36251339 PMCID: PMC9877130 DOI: 10.1002/1873-3468.14518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 01/29/2023]
Abstract
Complex I is a key proton-pumping enzyme in bacterial and mitochondrial respiratory electron transport chains. Using quantum chemistry and electrostatic calculations, we have examined the pKa of the reduced quinone QH-/QH2 in the catalytic cavity of complex I. We find that pKa (QH-/QH2) is very high, above 20. This means that the energy of a single protonation reaction of the doubly reduced quinone (i.e. the reduced semiquinone QH-) is sufficient to drive four protons across the membrane with a potential of 180 mV. Based on these calculations, we propose a possible scheme of redox-linked proton pumping by complex I. The model explains how the energy of the protonation reaction can be divided equally among four pumping units of the pump, and how a single proton can drive translocation of four additional protons in multiple pumping blocks.
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Affiliation(s)
| | - Tomoyuki Hayashi
- Department of Chemistry, University of California, Davis, CA 95616
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Chung I, Grba DN, Wright JJ, Hirst J. Making the leap from structure to mechanism: are the open states of mammalian complex I identified by cryoEM resting states or catalytic intermediates? Curr Opin Struct Biol 2022; 77:102447. [PMID: 36087446 PMCID: PMC7614202 DOI: 10.1016/j.sbi.2022.102447] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/07/2022] [Accepted: 07/26/2022] [Indexed: 12/14/2022]
Abstract
Respiratory complex I (NADH:ubiquinone oxidoreductase) is a multi-subunit, energy-transducing mitochondrial enzyme that is essential for oxidative phosphorylation and regulating NAD+/NADH pools. Despite recent advances in structural knowledge and a long history of biochemical analyses, the mechanism of redox-coupled proton translocation by complex I remains unknown. Due to its ability to separate molecules in a mixed population into distinct classes, single-particle electron cryomicroscopy has enabled identification and characterisation of different complex I conformations. However, deciding on their catalytic and/or regulatory properties to underpin mechanistic hypotheses, especially without detailed biochemical characterisation of the structural samples, has proven challenging. In this review we explore different mechanistic interpretations of the closed and open states identified in cryoEM analyses of mammalian complex I.
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Affiliation(s)
- Injae Chung
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Daniel N Grba
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - John J Wright
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK.
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Laube E, Meier-Credo J, Langer JD, Kühlbrandt W. Conformational changes in mitochondrial complex I of the thermophilic eukaryote Chaetomium thermophilum. SCIENCE ADVANCES 2022; 8:eadc9952. [PMID: 36427319 PMCID: PMC9699679 DOI: 10.1126/sciadv.adc9952] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/07/2022] [Indexed: 05/23/2023]
Abstract
Mitochondrial complex I is a redox-driven proton pump that generates proton-motive force across the inner mitochondrial membrane, powering oxidative phosphorylation and ATP synthesis in eukaryotes. We report the structure of complex I from the thermophilic fungus Chaetomium thermophilum, determined by cryoEM up to 2.4-Å resolution. We show that the complex undergoes a transition between two conformations, which we refer to as state 1 and state 2. The conformational switch is manifest in a twisting movement of the peripheral arm relative to the membrane arm, but most notably in substantial rearrangements of the Q-binding cavity and the E-channel, resulting in a continuous aqueous passage from the E-channel to subunit ND5 at the far end of the membrane arm. The conformational changes in the complex interior resemble those reported for mammalian complex I, suggesting a highly conserved, universal mechanism of coupling electron transport to proton pumping.
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Affiliation(s)
- Eike Laube
- Max-Planck-Institute of Biophysics, Frankfurt 60438, Germany
| | - Jakob Meier-Credo
- Max-Planck-Institute of Biophysics, Frankfurt 60438, Germany
- Max-Planck-Institute for Brain Research, Frankfurt 60438, Germany
| | - Julian D. Langer
- Max-Planck-Institute of Biophysics, Frankfurt 60438, Germany
- Max-Planck-Institute for Brain Research, Frankfurt 60438, Germany
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Alkhaldi HA, Phan DH, Vik SB. Analysis of Human Clinical Mutations of Mitochondrial ND1 in a Bacterial Model System for Complex I. Life (Basel) 2022; 12:1934. [PMID: 36431069 PMCID: PMC9696053 DOI: 10.3390/life12111934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
The most common causes of mitochondrial dysfunction and disease include mutations in subunits and assembly factors of Complex I. Numerous mutations in the mitochondrial gene ND1 have been identified in humans. Currently, a bacterial model system provides the only method for rapid construction and analysis of mutations in homologs of human ND1. In this report, we have identified nine mutations in human ND1 that are reported to be pathogenic and are located at subunit interfaces. Our hypothesis was that these mutations would disrupt Complex I assembly. Seventeen mutations were constructed in the homologous nuoH gene in an E. coli model system. In addition to the clinical mutations, alanine substitutions were constructed in order to distinguish between a deleterious effect from the introduction of the mutant residue and the loss of the original residue. The mutations were moved to an expression vector containing all thirteen genes of the E. coli nuo operon coding for Complex I. Membrane vesicles were prepared and rates of deamino-NADH oxidase activity and proton translocation were measured. Samples were also tested for assembly by native gel electrophoresis and for expression of NuoH by immunoblotting. A range of outcomes was observed: Mutations at four of the sites allow normal assembly with moderate activity (50−76% of wild type). Mutations at the other sites disrupt assembly and/or activity, and in some cases the outcomes depend upon the amino acid introduced. In general, the outcomes are consistent with the proposed pathogenicity in humans.
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Affiliation(s)
| | | | - Steven B. Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA
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Alkhaldi HA, Vik SB. Subunits E-F-G of E. coli Complex I can form an active complex when expressed alone, but in time-delayed assembly co-expression of B-CD-E-F-G is optimal. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148593. [PMID: 35850264 PMCID: PMC9783743 DOI: 10.1016/j.bbabio.2022.148593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/15/2022] [Accepted: 07/11/2022] [Indexed: 12/27/2022]
Abstract
Respiratory Complex I from E. coli is a proto-type of the mitochondrial enzyme, consisting of a 6-subunit peripheral arm (B-CD-E-F-G-I) and a 7-subunit membrane arm. When subunits E-F-G (N-module), were expressed alone they formed an active complex as determined by co-immunoprecipitation and native gel electrophoresis. When co-expressed with subunits B and CD, only a complex of E-F-G was found. When these five subunits were co-expressed with subunit I and two membrane subunits, A and H, a complex of B-CD-E-F-G-I was membrane-bound, constituting the N- and Q-modules. Assembly of Complex I was also followed by splitting the genes between two plasmids, in three different groupings, and expressing them simultaneously, or with time-delay of expression from one plasmid. When the B-CD-E-F-G genes were co-expressed after a time-delay, assembly was over 90 % of that when the whole operon was expressed together. In summary, E-F-G was the only soluble subcomplex detected in these studies, but assembly was not optimal when these subunits were expressed either first or last. Co-expression of subunits B and CD with E-F-G provided a higher level of assembly, indicating that integrated assembly of N- and Q-modules provides a more efficient pathway.
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Affiliation(s)
- Hind A Alkhaldi
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Steven B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA.
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Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov L. A universal coupling mechanism of respiratory complex I. Nature 2022; 609:808-814. [DOI: 10.1038/s41586-022-05199-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/05/2022] [Indexed: 11/09/2022]
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Binding of Natural Inhibitors to Respiratory Complex I. Pharmaceuticals (Basel) 2022; 15:ph15091088. [PMID: 36145309 PMCID: PMC9503403 DOI: 10.3390/ph15091088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022] Open
Abstract
NADH:ubiquinone oxidoreductase (respiratory complex I) is a redox-driven proton pump with a central role in mitochondrial oxidative phosphorylation. The ubiquinone reduction site of complex I is located in the matrix arm of this large protein complex and connected to the membrane via a tunnel. A variety of chemically diverse compounds are known to inhibit ubiquinone reduction by complex I. Rotenone, piericidin A, and annonaceous acetogenins are representatives of complex I inhibitors from biological sources. The structure of complex I is determined at high resolution, and inhibitor binding sites are described in detail. In this review, we summarize the state of knowledge of how natural inhibitors bind in the Q reduction site and the Q access pathway and how their inhibitory mechanisms compare with that of a synthetic anti-cancer agent.
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43
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cAMP/PKA Signaling Modulates Mitochondrial Supercomplex Organization. Int J Mol Sci 2022; 23:ijms23179655. [PMID: 36077053 PMCID: PMC9455794 DOI: 10.3390/ijms23179655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
The oxidative phosphorylation (OXPHOS) system couples the transfer of electrons to oxygen with pumping of protons across the inner mitochondrial membrane, ensuring the ATP production. Evidence suggests that respiratory chain complexes may also assemble into supramolecular structures, called supercomplexes (SCs). The SCs appear to increase the efficiency/capacity of OXPHOS and reduce the reactive oxygen species (ROS) production, especially that which is produced by complex I. Studies suggest a mutual regulation between complex I and SCs, while SCs organization is important for complex I assembly/stability, complex I is involved in the supercomplex formation. Complex I is a pacemaker of the OXPHOS system, and it has been shown that the PKA-dependent phosphorylation of some of its subunits increases the activity of the complex, reducing the ROS production. In this work, using in ex vivo and in vitro models, we show that the activation of cAMP/PKA cascade resulted in an increase in SCs formation associated with an enhanced capacity of electron flux and ATP production rate. This is also associated with the phosphorylation of the NDUFS4 subunit of complex I. This aspect highlights the key role of complex I in cellular energy production.
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44
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Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint for the mechanism. Curr Opin Struct Biol 2022; 74:102350. [PMID: 35316665 PMCID: PMC7613608 DOI: 10.1016/j.sbi.2022.102350] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/25/2022] [Accepted: 02/08/2022] [Indexed: 11/26/2022]
Abstract
Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I.
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Tragni V, Primiano G, Tummolo A, Cafferati Beltrame L, La Piana G, Sgobba MN, Cavalluzzi MM, Paterno G, Gorgoglione R, Volpicella M, Guerra L, Marzulli D, Servidei S, De Grassi A, Petrosillo G, Lentini G, Pierri CL. Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs. Molecules 2022; 27:3494. [PMID: 35684429 PMCID: PMC9182050 DOI: 10.3390/molecules27113494] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial diseases (MDs) may result from mutations affecting nuclear or mitochondrial genes, encoding mitochondrial proteins, or non-protein-coding mitochondrial RNA. Despite the great variability of affected genes, in the most severe cases, a neuromuscular and neurodegenerative phenotype is observed, and no specific therapy exists for a complete recovery from the disease. The most used treatments are symptomatic and based on the administration of antioxidant cocktails combined with antiepileptic/antipsychotic drugs and supportive therapy for multiorgan involvement. Nevertheless, the real utility of antioxidant cocktail treatments for patients affected by MDs still needs to be scientifically demonstrated. Unfortunately, clinical trials for antioxidant therapies using α-tocopherol, ascorbate, glutathione, riboflavin, niacin, acetyl-carnitine and coenzyme Q have met a limited success. Indeed, it would be expected that the employed antioxidants can only be effective if they are able to target the specific mechanism, i.e., involving the central and peripheral nervous system, responsible for the clinical manifestations of the disease. Noteworthily, very often the phenotypes characterizing MD patients are associated with mutations in proteins whose function does not depend on specific cofactors. Conversely, the administration of the antioxidant cocktails might determine the suppression of endogenous oxidants resulting in deleterious effects on cell viability and/or toxicity for patients. In order to avoid toxicity effects and before administering the antioxidant therapy, it might be useful to ascertain the blood serum levels of antioxidants and cofactors to be administered in MD patients. It would be also worthwhile to check the localization of mutations affecting proteins whose function should depend (less or more directly) on the cofactors to be administered, for estimating the real need and predicting the success of the proposed cofactor/antioxidant-based therapy.
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Affiliation(s)
- Vincenzo Tragni
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Guido Primiano
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (S.S.)
- Dipartimento Universitario di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Albina Tummolo
- Department of Metabolic Diseases, Clinical Genetics and Diabetology, Giovanni XXIII Children Hospital, Azienda Ospedaliero-Universitaria Consorziale, Via Amendola 207, 70126 Bari, Italy; (A.T.); (G.P.)
| | - Lucas Cafferati Beltrame
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Gianluigi La Piana
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Maria Noemi Sgobba
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Maria Maddalena Cavalluzzi
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy;
| | - Giulia Paterno
- Department of Metabolic Diseases, Clinical Genetics and Diabetology, Giovanni XXIII Children Hospital, Azienda Ospedaliero-Universitaria Consorziale, Via Amendola 207, 70126 Bari, Italy; (A.T.); (G.P.)
| | - Ruggiero Gorgoglione
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Mariateresa Volpicella
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Lorenzo Guerra
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Domenico Marzulli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Serenella Servidei
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (S.S.)
- Dipartimento Universitario di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Giuseppe Petrosillo
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Giovanni Lentini
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy;
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
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Uno S, Masuya T, Zdorevskyi O, Ikunishi R, Shinzawa-Itoh K, Lasham J, Sharma V, Murai M, Miyoshi H. Diverse reaction behaviors of artificial ubiquinones in mitochondrial respiratory complex I. J Biol Chem 2022; 298:102075. [PMID: 35643318 PMCID: PMC9243180 DOI: 10.1016/j.jbc.2022.102075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 11/24/2022] Open
Abstract
The ubiquinone (UQ) reduction step catalyzed by NADH-UQ oxidoreductase (mitochondrial respiratory complex I) is key to triggering proton translocation across the inner mitochondrial membrane. Structural studies have identified a long, narrow, UQ-accessing tunnel within the enzyme. We previously demonstrated that synthetic oversized UQs, which are unlikely to transit this narrow tunnel, are catalytically reduced by native complex I embedded in submitochondrial particles but not by the isolated enzyme. To explain this contradiction, we hypothesized that access of oversized UQs to the reaction site is obstructed in the isolated enzyme because their access route is altered following detergent solubilization from the inner mitochondrial membrane. In the present study, we investigated this using two pairs of photoreactive UQs (pUQm-1/pUQp-1 and pUQm-2/pUQp-2), with each pair having the same chemical properties except for a ∼1.0 Å difference in side-chain widths. Despite this subtle difference, reduction of the wider pUQs by the isolated complex was significantly slower than of the narrower pUQs, but both were similarly reduced by the native enzyme. In addition, photoaffinity-labeling experiments using the four [125I]pUQs demonstrated that their side chains predominantly label the ND1 subunit with both enzymes but at different regions around the tunnel. Finally, we show that the suppressive effects of different types of inhibitors on the labeling significantly changed depending on [125I]pUQs used, indicating that [125I]pUQs and these inhibitors do not necessarily share a common binding cavity. Altogether, we conclude that the reaction behaviors of pUQs cannot be simply explained by the canonical UQ tunnel model.
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Affiliation(s)
- Shinpei Uno
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takahiro Masuya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Ryo Ikunishi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kyoko Shinzawa-Itoh
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
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Wang P, Leontyev I, Stuchebrukhov AA. Mechanical Allosteric Couplings of Redox-Induced Conformational Changes in Respiratory Complex I. J Phys Chem B 2022; 126:4080-4088. [PMID: 35612955 DOI: 10.1021/acs.jpcb.2c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We apply linear response theory to calculate mechanical allosteric couplings in respiratory complex I between the iron sulfur cluster N2, located in the catalytic cavity, and the membrane part of the enzyme, separated from it by more than 50 Å. According to our hypothesis, the redox reaction of ubiquinone in the catalytic cavity of the enzyme generates an unbalanced charge that via repulsion of the charged redox center N2 produces local mechanical stress that transmits into the membrane part of the enzyme where it induces proton pumping. Using coarse-grained simulations of the enzyme, we calculated mechanistic allosteric couplings that reveal the pathways of the mechanical transmission of the stress along the enzyme. The results shed light on the recent experimental studies where a stabilization of the enzyme with an introduced disulfide bridge resulted in the abolishing of proton pumping. Simulation of the disulfide bond action indicates a dramatic change of the mechanistic coupling pathways in line with experimental findings.
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Affiliation(s)
- Panyue Wang
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Igor Leontyev
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Alexei A Stuchebrukhov
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
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48
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Zhang F, Dang QCL, Vik SB. Human clinical mutations in mitochondrially encoded subunits of Complex I can be successfully modeled in E. coli. Mitochondrion 2022; 64:59-72. [PMID: 35306226 PMCID: PMC9035099 DOI: 10.1016/j.mito.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/21/2022] [Accepted: 03/15/2022] [Indexed: 11/28/2022]
Abstract
Respiratory Complex I is the site of a large fraction of the mutations that appear to cause mitochondrial disease. Seven of its subunits are mitochondrially encoded, and therefore, such mutants are particularly difficult to construct in cell-culture model systems. We have selected 13 human clinical mutations found in ND2, ND3, ND4, ND4L, ND5 and ND6 that are generally found at subunit interfaces, and not in critical residues. These mutations have been modeled in E. coli subunits of Complex I, nuoN, nuoA, nuoM, nuoK, nuoL, and nuoJ, respectively. All mutants were expressed from a plasmid encoding the entire nuo operon, and membrane vesicles were analyzed for deamino-NADH oxidase activity, and proton translocation activity. ND5 mutants were also analyzed using a time-delayed expression system, recently described by this lab. Other mutants were analyzed for the ability to associate in subcomplexes, after expression of subsets of the genes. For most mutants there was a positive correlation between those that were previously determined to be pathogenic, or likely to be pathogenic, and those that we found with compromised Complex I activity or subunit interactions in E. coli. In conclusion, this approach provides another way to explore the deleterious effects of human mitochondrial mutations, and it can contribute to molecular understanding of such mutations.
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Affiliation(s)
- Fang Zhang
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Quynh-Chi L Dang
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Steven B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA.
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49
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Djurabekova A, Galemou Yoga E, Nyman A, Pirttikoski A, Zickermann V, Haapanen O, Sharma V. Docking and molecular simulations reveal a quinone binding site on the surface of respiratory complex I. FEBS Lett 2022; 596:1133-1146. [PMID: 35363885 DOI: 10.1002/1873-3468.14346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/11/2022] [Accepted: 03/24/2022] [Indexed: 11/07/2022]
Abstract
The first component of the mitochondrial electron transport chain is respiratory complex I. Several high-resolution structures of complex I from different species have been resolved. However, despite these significant achievements, the mechanism of redox-coupled proton pumping remains elusive. Here, we combined atomistic docking, molecular dynamics simulations and site-directed mutagenesis on respiratory complex I from Yarrowia lipolytica to identify a quinone (Q) binding site on its surface near the horizontal amphipathic helices of ND1 and NDUFS7 subunits. The surface-bound Q makes stable interactions with conserved charged and polar residues, including the highly conserved Arg72 from the NDUFS7 subunit. The binding and dynamics of a Q molecule at the surface-binding site raises interesting possibilities about the mechanism of complex I, which are discussed.
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Affiliation(s)
| | - Etienne Galemou Yoga
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Aino Nyman
- Department of Physics, University of Helsinki, Finland
| | | | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - 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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