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Martin FJO, Santiveri M, Hu H, Taylor NMI. Ion-driven rotary membrane motors: From structure to function. Curr Opin Struct Biol 2024; 88:102884. [PMID: 39053417 DOI: 10.1016/j.sbi.2024.102884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/16/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024]
Abstract
Ion-driven membrane motors, essential across all domains of life, convert a gradient of ions across a membrane into rotational energy, facilitating diverse biological processes including ATP synthesis, substrate transport, and bacterial locomotion. Herein, we highlight recent structural advances in the understanding of two classes of ion-driven membrane motors: rotary ATPases and 5:2 motors. The recent structure of the human F-type ATP synthase is emphasised along with the gained structural insight into clinically relevant mutations. Furthermore, we highlight the diverse roles of 5:2 motors and recent mechanistic understanding gained through the resolution of ions in the structure of a sodium-driven motor, combining insights into potential unifying mechanisms of ion selectivity and rotational torque generation in the context of their function as part of complex biological systems.
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Affiliation(s)
- Freddie J O Martin
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Mònica Santiveri
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Haidai Hu
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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2
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Reddy KD, Rasool B, Akher FB, Kutlešić N, Pant S, Boudker O. Evolutionary analysis reveals the origin of sodium coupling in glutamate transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.03.569786. [PMID: 38106174 PMCID: PMC10723334 DOI: 10.1101/2023.12.03.569786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Secondary active membrane transporters harness the energy of ion gradients to concentrate their substrates. Homologous transporters evolved to couple transport to different ions in response to changing environments and needs. The bases of such diversification, and thus principles of ion coupling, are unexplored. Employing phylogenetics and ancestral protein reconstruction, we investigated sodium-coupled transport in prokaryotic glutamate transporters, a mechanism ubiquitous across life domains and critical to neurotransmitter recycling in humans. We found that the evolutionary transition from sodium-dependent to independent substrate binding to the transporter preceded changes in the coupling mechanism. Structural and functional experiments suggest that the transition entailed allosteric mutations, making sodium binding dispensable without affecting ion-binding sites. Allosteric tuning of transporters' energy landscapes might be a widespread route of their functional diversification.
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Affiliation(s)
- Krishna D. Reddy
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Burha Rasool
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Farideh Badichi Akher
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Nemanja Kutlešić
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Swati Pant
- Dept. of Biochemistry, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
| | - Olga Boudker
- Dept. of Physiology & Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
- Howard Hughes Medical Institute, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
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3
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Ramadan AM, Al-Ghamdi KM, Alghamdi AJ, Amer M, Ibrahim MI, Atef A. Withania somnifera mitochondrial atp4 gene editing alters the ATP synthase b subunit, independent of salt stress. Saudi J Biol Sci 2023; 30:103817. [PMID: 37841665 PMCID: PMC10570708 DOI: 10.1016/j.sjbs.2023.103817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/05/2023] [Accepted: 09/21/2023] [Indexed: 10/17/2023] Open
Abstract
Numerous studies have shown that stress in plant cells and organelles with transport electron chains is related to RNA editing. The ATP synthase complex present in mitochondria plays a crucial role in cellular respiration and consists of several subunits. Among them is the b subunit, which is encoded by the mitochondrial atp4 gene. Computing-based analysis of the effects of RNA editing of the Withania somnifera atp4 gene in mitochondria leading to alterations in the b subunit of ATP synthase. Using the CLC Genomic Workbench 3, RNA editing analysis between the control and salt stress conditions was not significantly different. Depending on RNA editing, the tertiary structure model revealed a change in the states of the b subunit, reflecting differences in the central stalk and F1-catalytic domain. The study found that polar edits in the N-terminus of the b subunit allow for efficient H + ion selectivity and introduce a new coiled-coil alpha-helical structure that may help stabilize the complex. The most noteworthy finding of this study was the strong impact of these editing events on the tertiary structure of the b subunit, which has the potential to affect the ATPase activity and indicate that the editing in this subunit aimed to restore the original active protein and not as a response to salt stress.
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Affiliation(s)
- Ahmed M. Ramadan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Najla bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalid M. Al-Ghamdi
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdullah J. Alghamdi
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Marwa Amer
- Bioinformatics and Functional Genomics Department, College of Biotechnology, Misr University for Science and Technology (MUST), Egypt
| | - Mona I.M. Ibrahim
- Agricultural Biotechnology Department, College of Biotechnology, Misr University for Science and Technology (MUST), Egypt
| | - Ahmed Atef
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Najla bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
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4
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Direct observation of stepping rotation of V-ATPase reveals rigid component in coupling between V o and V 1 motors. Proc Natl Acad Sci U S A 2022; 119:e2210204119. [PMID: 36215468 PMCID: PMC9586324 DOI: 10.1073/pnas.2210204119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
V-ATPases are ion pumps consisting of two rotary motor proteins, Vo and V1, that actively transport ions across the cell membrane using the chemical energy of ATP. To understand how V-ATPases transduce the energy in the presence of a structural symmetry mismatch between Vo and V1, we simultaneously visualized the rotational pauses and forward and backward steps of Vo and V1 coupled with ion transport and ATP hydrolysis reactions, respectively. Our results suggest that V-ATPases with multiple peripheral stalks are more rigidly coupled than F-ATPases that have only one peripheral stalk and work as ATP synthases. Our high-speed/high-precision single-molecule imaging of rotary ATPases in action will pave the way for a comprehensive understanding of their energy transduction mechanisms. V-ATPases are rotary motor proteins that convert the chemical energy of ATP into the electrochemical potential of ions across cell membranes. V-ATPases consist of two rotary motors, Vo and V1, and Enterococcus hirae V-ATPase (EhVoV1) actively transports Na+ in Vo (EhVo) by using torque generated by ATP hydrolysis in V1 (EhV1). Here, we observed ATP-driven stepping rotation of detergent-solubilized EhVoV1 wild-type, aE634A, and BR350K mutants under various Na+ and ATP concentrations ([Na+] and [ATP], respectively) by using a 40-nm gold nanoparticle as a low-load probe. When [Na+] was low and [ATP] was high, under the condition that only Na+ binding to EhVo is rate limiting, wild-type and aE634A exhibited 10 pausing positions reflecting 10-fold symmetry of the EhVo rotor and almost no backward steps. Duration time before the forward steps was inversely proportional to [Na+], confirming that Na+ binding triggers the steps. When both [ATP] and [Na+] were low, under the condition that both Na+ and ATP bindings are rate limiting, aE634A exhibited 13 pausing positions reflecting 10- and 3-fold symmetries of EhVo and EhV1, respectively. The distribution of duration time before the forward step was fitted well by the sum of two exponential decay functions with distinct time constants. Furthermore, occasional backward steps smaller than 36° were observed. Small backward steps were also observed during three long ATP cleavage pauses of BR350K. These results indicate that EhVo and EhV1 do not share pausing positions, Na+ and ATP bindings occur at different angles, and the coupling between EhVo and EhV1 has a rigid component.
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The Mechanism of Energy Coupling in H +/Na +-Pumping Membrane Pyrophosphatase-Possibilities and Probabilities. Int J Mol Sci 2022; 23:ijms23169504. [PMID: 36012762 PMCID: PMC9408878 DOI: 10.3390/ijms23169504] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/12/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Membrane pyrophosphatases (mPPases) found in plant vacuoles and some prokaryotes and protists are ancient cation pumps that couple pyrophosphate hydrolysis with the H+ and/or Na+ transport out of the cytoplasm. Because this function is reversible, mPPases play a role in maintaining the level of cytoplasmic pyrophosphate, a known regulator of numerous metabolic reactions. mPPases arouse interest because they are among the simplest membrane transporters and have no homologs among known ion pumps. Detailed phylogenetic studies have revealed various subtypes of mPPases and suggested their roles in the evolution of the "sodium" and "proton" bioenergetics. This treatise focuses on the mechanistic aspects of the transport reaction, namely, the coupling step, the role of the chemically produced proton, subunit cooperation, and the relationship between the proton and sodium ion transport. The available data identify H+-PPases as the first non-oxidoreductase pump with a "direct-coupling" mechanism, i.e., the transported proton is produced in the coupled chemical reaction. They also support a "billiard" hypothesis, which unifies the H+ and Na+ transport mechanisms in mPPase and, probably, other transporters.
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Genomic and Functional Variation of the Chlorophyll d-Producing Cyanobacterium Acaryochloris marina. Microorganisms 2022; 10:microorganisms10030569. [PMID: 35336144 PMCID: PMC8949462 DOI: 10.3390/microorganisms10030569] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 02/01/2023] Open
Abstract
The Chlorophyll d-producing cyanobacterium Acaryochloris marina is widely distributed in marine environments enriched in far-red light, but our understanding of its genomic and functional diversity is limited. Here, we take an integrative approach to investigate A. marina diversity for 37 strains, which includes twelve newly isolated strains from previously unsampled locations in Europe and the Pacific Northwest of North America. A genome-wide phylogeny revealed both that closely related A. marina have migrated within geographic regions and that distantly related A. marina lineages can co-occur. The distribution of traits mapped onto the phylogeny provided evidence of a dynamic evolutionary history of gene gain and loss during A. marina diversification. Ancestral genes that were differentially retained or lost by strains include plasmid-encoded sodium-transporting ATPase and bidirectional NiFe-hydrogenase genes that may be involved in salt tolerance and redox balance under fermentative conditions, respectively. The acquisition of genes by horizontal transfer has also played an important role in the evolution of new functions, such as nitrogen fixation. Together, our results resolve examples in which genome content and ecotypic variation for nutrient metabolism and environmental tolerance have diversified during the evolutionary history of this unusual photosynthetic bacterium.
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Juhaszova M, Kobrinsky E, Zorov DB, Nuss HB, Yaniv Y, Fishbein KW, de Cabo R, Montoliu L, Gabelli SB, Aon MA, Cortassa S, Sollott SJ. ATP Synthase K +- and H +-Fluxes Drive ATP Synthesis and Enable Mitochondrial K +-"Uniporter" Function: I. Characterization of Ion Fluxes. FUNCTION (OXFORD, ENGLAND) 2021; 3:zqab065. [PMID: 35229078 PMCID: PMC8867323 DOI: 10.1093/function/zqab065] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 01/07/2023]
Abstract
ATP synthase (F1Fo) synthesizes daily our body's weight in ATP, whose production-rate can be transiently increased several-fold to meet changes in energy utilization. Using purified mammalian F1Fo-reconstituted proteoliposomes and isolated mitochondria, we show F1Fo can utilize both ΔΨm-driven H+- and K+-transport to synthesize ATP under physiological pH = 7.2 and K+ = 140 mEq/L conditions. Purely K+-driven ATP synthesis from single F1Fo molecules measured by bioluminescence photon detection could be directly demonstrated along with simultaneous measurements of unitary K+ currents by voltage clamp, both blocked by specific Fo inhibitors. In the presence of K+, compared to osmotically-matched conditions in which this cation is absent, isolated mitochondria display 3.5-fold higher rates of ATP synthesis, at the expense of 2.6-fold higher rates of oxygen consumption, these fluxes being driven by a 2.7:1 K+: H+ stoichiometry. The excellent agreement between the functional data obtained from purified F1Fo single molecule experiments and ATP synthase studied in the intact mitochondrion under unaltered OxPhos coupling by K+ presence, is entirely consistent with K+ transport through the ATP synthase driving the observed increase in ATP synthesis. Thus, both K+ (harnessing ΔΨm) and H+ (harnessing its chemical potential energy, ΔμH) drive ATP generation during normal physiology.
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Affiliation(s)
| | | | | | | | | | - Kenneth W Fishbein
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC), Biomedical Research Networking Center on Rare Diseases (CIBERER-ISCIII), 28049, Madrid, Spain
| | - Sandra B Gabelli
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Miguel A Aon
- Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, MD 21224, USA,Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Sonia Cortassa
- Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, MD 21224, USA
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8
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Nirody JA, Budin I, Rangamani P. ATP synthase: Evolution, energetics, and membrane interactions. J Gen Physiol 2021; 152:152111. [PMID: 32966553 PMCID: PMC7594442 DOI: 10.1085/jgp.201912475] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022] Open
Abstract
The synthesis of ATP, life’s “universal energy currency,” is the most prevalent chemical reaction in biological systems and is responsible for fueling nearly all cellular processes, from nerve impulse propagation to DNA synthesis. ATP synthases, the family of enzymes that carry out this endless task, are nearly as ubiquitous as the energy-laden molecule they are responsible for making. The F-type ATP synthase (F-ATPase) is found in every domain of life and has facilitated the survival of organisms in a wide range of habitats, ranging from the deep-sea thermal vents to the human intestine. Accordingly, there has been a large amount of work dedicated toward understanding the structural and functional details of ATP synthases in a wide range of species. Less attention, however, has been paid toward integrating these advances in ATP synthase molecular biology within the context of its evolutionary history. In this review, we present an overview of several structural and functional features of the F-type ATPases that vary across taxa and are purported to be adaptive or otherwise evolutionarily significant: ion channel selectivity, rotor ring size and stoichiometry, ATPase dimeric structure and localization in the mitochondrial inner membrane, and interactions with membrane lipids. We emphasize the importance of studying these features within the context of the enzyme’s particular lipid environment. Just as the interactions between an organism and its physical environment shape its evolutionary trajectory, ATPases are impacted by the membranes within which they reside. We argue that a comprehensive understanding of the structure, function, and evolution of membrane proteins—including ATP synthase—requires such an integrative approach.
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Affiliation(s)
- Jasmine A Nirody
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY.,All Souls College, University of Oxford, Oxford, UK
| | - Itay Budin
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA
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9
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Zubareva VM, Lapashina AS, Shugaeva TE, Litvin AV, Feniouk BA. Rotary Ion-Translocating ATPases/ATP Synthases: Diversity, Similarities, and Differences. BIOCHEMISTRY (MOSCOW) 2021; 85:1613-1630. [PMID: 33705299 DOI: 10.1134/s0006297920120135] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Ion-translocating ATPases and ATP synthases (F-, V-, A-type ATPases, and several P-type ATPases and ABC-transporters) catalyze ATP hydrolysis or ATP synthesis coupled with the ion transport across the membrane. F-, V-, and A-ATPases are protein nanomachines that combine transmembrane transport of protons or sodium ions with ATP synthesis/hydrolysis by means of a rotary mechanism. These enzymes are composed of two multisubunit subcomplexes that rotate relative to each other during catalysis. Rotary ATPases phosphorylate/dephosphorylate nucleotides directly, without the generation of phosphorylated protein intermediates. F-type ATPases are found in chloroplasts, mitochondria, most eubacteria, and in few archaea. V-type ATPases are eukaryotic enzymes present in a variety of cellular membranes, including the plasma membrane, vacuoles, late endosomes, and trans-Golgi cisternae. A-type ATPases are found in archaea and some eubacteria. F- and A-ATPases have two main functions: ATP synthesis powered by the proton motive force (pmf) or, in some prokaryotes, sodium-motive force (smf) and generation of the pmf or smf at the expense of ATP hydrolysis. In prokaryotes, both functions may be vitally important, depending on the environment and the presence of other enzymes capable of pmf or smf generation. In eukaryotes, the primary and the most crucial function of F-ATPases is ATP synthesis. Eukaryotic V-ATPases function exclusively as ATP-dependent proton pumps that generate pmf necessary for the transmembrane transport of ions and metabolites and are vitally important for pH regulation. This review describes the diversity of rotary ion-translocating ATPases from different organisms and compares the structural, functional, and regulatory features of these enzymes.
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Affiliation(s)
- V M Zubareva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A S Lapashina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - T E Shugaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A V Litvin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - B A Feniouk
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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10
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Doello S, Burkhardt M, Forchhammer K. The essential role of sodium bioenergetics and ATP homeostasis in the developmental transitions of a cyanobacterium. Curr Biol 2021; 31:1606-1615.e2. [PMID: 33571435 DOI: 10.1016/j.cub.2021.01.065] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/30/2020] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
The ability to resume growth after a dormant period is an important strategy for the survival and spreading of bacterial populations. Energy homeostasis is critical in the transition into and out of a quiescent state. Synechocystis sp. PCC 6803, a non-diazotrophic cyanobacterium, enters metabolic dormancy as a response to nitrogen starvation. We used Synechocystis as a model to investigate the regulation of ATP homeostasis during dormancy, and we unraveled a critical role for sodium bioenergetics in dormant cells. During nitrogen starvation, cells reduce their ATP levels and engage sodium bioenergetics to maintain the minimum ATP content required for viability. When nitrogen becomes available, energy requirements rise, and cells immediately increase ATP levels, employing sodium bioenergetics and glycogen catabolism. These processes allow them to restore the photosynthetic machinery and resume photoautotrophic growth. Our work reveals a precise regulation of the energy metabolism essential for bacterial survival during periods of nutrient deprivation.
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Affiliation(s)
- Sofia Doello
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Markus Burkhardt
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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11
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Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
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12
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Conserved binding site in the N-lobe of prokaryotic MATE transporters suggests a role for Na + in ion-coupled drug efflux. J Biol Chem 2021; 296:100262. [PMID: 33837745 PMCID: PMC7949106 DOI: 10.1016/j.jbc.2021.100262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/18/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
In both prokaryotes and eukaryotes, multidrug and toxic-compound extrusion (MATE) transporters catalyze the efflux of a broad range of cytotoxic compounds, including human-made antibiotics and anticancer drugs. MATEs are secondary-active antiporters, i.e., their drug-efflux activity is coupled to, and powered by, the uptake of ions down a preexisting transmembrane electrochemical gradient. Key aspects of this mechanism, however, remain to be delineated, such as its ion specificity and stoichiometry. We previously revealed the existence of a Na+-binding site in a MATE transporter from Pyroccocus furiosus (PfMATE) and hypothesized that this site might be broadly conserved among prokaryotic MATEs. Here, we evaluate this hypothesis by analyzing VcmN and ClbM, which along with PfMATE are the only three prokaryotic MATEs whose molecular structures have been determined at atomic resolution, i.e. better than 3 Å. Reinterpretation of existing crystallographic data and molecular dynamics simulations indeed reveal an occupied Na+-binding site in the N-terminal lobe of both structures, analogous to that identified in PfMATE. We likewise find this site to be strongly selective against K+, suggesting it is mechanistically significant. Consistent with these computational results, DEER spectroscopy measurements for multiple doubly-spin-labeled VcmN constructs demonstrate Na+-dependent changes in protein conformation. The existence of this binding site in three MATE orthologs implicates Na+ in the ion-coupled drug-efflux mechanisms of this class of transporters. These results also imply that observations of H+-dependent activity likely stem either from a site elsewhere in the structure, or from H+ displacing Na+ under certain laboratory conditions, as has been noted for other Na+-driven transport systems.
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13
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The 3 × 120° rotary mechanism of Paracoccus denitrificans F 1-ATPase is different from that of the bacterial and mitochondrial F 1-ATPases. Proc Natl Acad Sci U S A 2020; 117:29647-29657. [PMID: 33168750 PMCID: PMC7703542 DOI: 10.1073/pnas.2003163117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The rotation of Paracoccus denitrificans F1-ATPase (PdF1) was studied using single-molecule microscopy. At all concentrations of adenosine triphosphate (ATP) or a slowly hydrolyzable ATP analog (ATPγS), above or below K m, PdF1 showed three dwells per turn, each separated by 120°. Analysis of dwell time between steps showed that PdF1 executes binding, hydrolysis, and probably product release at the same dwell. The comparison of ATP binding and catalytic pauses in single PdF1 molecules suggested that PdF1 executes both elementary events at the same rotary position. This point was confirmed in an inhibition experiment with a nonhydrolyzable ATP analog (AMP-PNP). Rotation assays in the presence of adenosine diphosphate (ADP) or inorganic phosphate at physiological concentrations did not reveal any obvious substeps. Although the possibility of the existence of substeps remains, all of the datasets show that PdF1 is principally a three-stepping motor similar to bacterial vacuolar (V1)-ATPase from Thermus thermophilus This contrasts with all other known F1-ATPases that show six or nine dwells per turn, conducting ATP binding and hydrolysis at different dwells. Pauses by persistent Mg-ADP inhibition or the inhibitory ζ-subunit were also found at the same angular position of the rotation dwell, supporting the simplified chemomechanical scheme of PdF1 Comprehensive analysis of rotary catalysis of F1 from different species, including PdF1, suggests a clear trend in the correlation between the numbers of rotary steps of F1 and Fo domains of F-ATP synthase. F1 motors with more distinctive steps are coupled with proton-conducting Fo rings with fewer proteolipid subunits, giving insight into the design principle the F1Fo of ATP synthase.
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14
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Xu X, Shi H, Gong X, Chen P, Gao Y, Zhang X, Xiang S. Structural insights into sodium transport by the oxaloacetate decarboxylase sodium pump. eLife 2020; 9:53853. [PMID: 32459174 PMCID: PMC7274780 DOI: 10.7554/elife.53853] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/22/2020] [Indexed: 12/16/2022] Open
Abstract
The oxaloacetate decarboxylase sodium pump (OAD) is a unique primary-active transporter that utilizes the free energy derived from oxaloacetate decarboxylation for sodium transport across the cell membrane. It is composed of 3 subunits: the α subunit catalyzes carboxyl-transfer from oxaloacetate to biotin, the membrane integrated β subunit catalyzes the subsequent carboxyl-biotin decarboxylation and the coupled sodium transport, the γ subunit interacts with the α and β subunits and stabilizes the OAD complex. We present here structure of the Salmonella typhimurium OAD βγ sub-complex. The structure revealed that the β and γ subunits form a β3γ3 hetero-hexamer with extensive interactions between the subunits and shed light on the OAD holo-enzyme assembly. Structure-guided functional studies provided insights into the sodium binding sites in the β subunit and the coupling between carboxyl-biotin decarboxylation and sodium transport by the OAD β subunit.
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Affiliation(s)
- Xin Xu
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Huigang Shi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaowen Gong
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Pu Chen
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Ying Gao
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Song Xiang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
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15
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Novitskaia O, Buslaev P, Gushchin I. Assembly of Spinach Chloroplast ATP Synthase Rotor Ring Protein-Lipid Complex. Front Mol Biosci 2019; 6:135. [PMID: 31850368 PMCID: PMC6896225 DOI: 10.3389/fmolb.2019.00135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/13/2019] [Indexed: 11/19/2022] Open
Abstract
Rotor ATPases are large multisubunit membrane protein complexes found in all kingdoms of life. The membrane parts of these ATPases include a ring-like assembly, so-called c-ring, consisting of several subunits c, plugged by a patch of phospholipids. In this report, we use a nature-inspired approach to model the assembly of the spinach (Spinacia oleracea) c14 ring protein-lipid complex, where partially assembled oligomers are pulled toward each other using a biasing potential. The resulting assemblies contain 23 to 26 encapsulated plug lipids, general position of which corresponds well to experimental maps. However, best fit to experimental data is achieved with 15 to 17 lipids inside the c-ring. In all of the simulations, the lipids from one leaflet (loop side of the c subunit) are ordered and static, whereas the lipids from the other leaflet are disordered and dynamic. Spontaneous permeation of water molecules toward Glu61 at the active site is also observed. The presented assembly approach is expected to be generalizable to other protein complexes with encapsulated lipid patches.
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Affiliation(s)
- Olga Novitskaia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Pavel Buslaev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Nanoscience Center, Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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16
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Guo H, Suzuki T, Rubinstein JL. Structure of a bacterial ATP synthase. eLife 2019; 8:43128. [PMID: 30724163 PMCID: PMC6377231 DOI: 10.7554/elife.43128] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/02/2019] [Indexed: 01/20/2023] Open
Abstract
ATP synthases produce ATP from ADP and inorganic phosphate with energy from a transmembrane proton motive force. Bacterial ATP synthases have been studied extensively because they are the simplest form of the enzyme and because of the relative ease of genetic manipulation of these complexes. We expressed the Bacillus PS3 ATP synthase in Eschericia coli, purified it, and imaged it by cryo-EM, allowing us to build atomic models of the complex in three rotational states. The position of subunit ε shows how it is able to inhibit ATP hydrolysis while allowing ATP synthesis. The architecture of the membrane region shows how the simple bacterial ATP synthase is able to perform the same core functions as the equivalent, but more complicated, mitochondrial complex. The structures reveal the path of transmembrane proton translocation and provide a model for understanding decades of biochemical analysis interrogating the roles of specific residues in the enzyme.
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Affiliation(s)
- Hui Guo
- The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Medical Biophysics, The University of Toronto, Toronto, Canada
| | - Toshiharu Suzuki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.,Department of Molecular Bioscience, Kyoto-Sangyo University, Kyoto, Japan
| | - John L Rubinstein
- The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Medical Biophysics, The University of Toronto, Toronto, Canada.,Department of Biochemistry, The University of Toronto, Toronto, Canada
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17
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Sielaff H, Yanagisawa S, Frasch WD, Junge W, Börsch M. Structural Asymmetry and Kinetic Limping of Single Rotary F-ATP Synthases. Molecules 2019; 24:E504. [PMID: 30704145 PMCID: PMC6384691 DOI: 10.3390/molecules24030504] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/12/2022] Open
Abstract
F-ATP synthases use proton flow through the FO domain to synthesize ATP in the F₁ domain. In Escherichia coli, the enzyme consists of rotor subunits γεc10 and stator subunits (αβ)₃δab₂. Subunits c10 or (αβ)₃ alone are rotationally symmetric. However, symmetry is broken by the b₂ homodimer, which together with subunit δa, forms a single eccentric stalk connecting the membrane embedded FO domain with the soluble F₁ domain, and the central rotating and curved stalk composed of subunit γε. Although each of the three catalytic binding sites in (αβ)₃ catalyzes the same set of partial reactions in the time average, they might not be fully equivalent at any moment, because the structural symmetry is broken by contact with b₂δ in F₁ and with b₂a in FO. We monitored the enzyme's rotary progression during ATP hydrolysis by three single-molecule techniques: fluorescence video-microscopy with attached actin filaments, Förster resonance energy transfer between pairs of fluorescence probes, and a polarization assay using gold nanorods. We found that one dwell in the three-stepped rotary progression lasting longer than the other two by a factor of up to 1.6. This effect of the structural asymmetry is small due to the internal elastic coupling.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
| | - Seiga Yanagisawa
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wayne D Frasch
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wolfgang Junge
- Department of Biology & Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
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18
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Nguyen NL, Yu WJ, Gwak JH, Kim SJ, Park SJ, Herbold CW, Kim JG, Jung MY, Rhee SK. Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils. Front Microbiol 2018; 9:1982. [PMID: 30210468 PMCID: PMC6119699 DOI: 10.3389/fmicb.2018.01982] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/06/2018] [Indexed: 01/08/2023] Open
Abstract
Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs (Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.
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Affiliation(s)
- Ngoc-Loi Nguyen
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Woon-Jong Yu
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Joo-Han Gwak
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - So-Jeong Kim
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju City, South Korea
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Jong-Geol Kim
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Man-Young Jung
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
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19
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Broadly conserved Na +-binding site in the N-lobe of prokaryotic multidrug MATE transporters. Proc Natl Acad Sci U S A 2018; 115:E6172-E6181. [PMID: 29915058 DOI: 10.1073/pnas.1802080115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Multidrug and toxic-compound extrusion (MATE) proteins comprise an important but largely uncharacterized family of secondary-active transporters. In both eukaryotes and prokaryotes, these transporters protect the cell by catalyzing the efflux of a broad range of cytotoxic compounds, including human-made antibiotics and anticancer drugs. MATEs are thus potential pharmacological targets against drug-resistant pathogenic bacteria and tumor cells. The activity of MATEs is powered by transmembrane electrochemical ion gradients, but their molecular mechanism and ion specificity are not understood, in part because high-quality structural information is limited. Here, we use computational methods to study PfMATE, from Pyrococcus furiosus, whose structure is the best resolved to date. Analysis of available crystallographic data and additional molecular dynamics simulations unequivocally reveal an occupied Na+-binding site in the N-lobe of this transporter, which had not been previously recognized. We find this site to be selective against K+ and broadly conserved among prokaryotic MATEs, including homologs known to be Na+-dependent such as NorM-VC, VmrA, and ClbM, for which the location of the Na+ site had been debated. We note, however, that the chemical makeup of the proposed Na+ site indicates it is weakly specific against H+, explaining why MATEs featuring this Na+-binding motif may be solely driven by H+ in laboratory conditions. We further posit that the concurrent coupling to H+ and Na+ gradients observed for some Na+-driven MATEs owes to a second H+-binding site, within the C-lobe. In summary, our study provides insights into the structural basis for the complex ion dependency of MATE transporters.
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20
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Zhou W, Faraldo-Gómez JD. Membrane plasticity facilitates recognition of the inhibitor oligomycin by the mitochondrial ATP synthase rotor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:789-796. [PMID: 29630891 DOI: 10.1016/j.bbabio.2018.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/13/2018] [Accepted: 03/23/2018] [Indexed: 12/11/2022]
Abstract
Enzymes in the respiratory chain are increasingly seen as potential targets against multi-drug resistance of human pathogens and cancerous cells. However, a detailed understanding of the mechanism and specificity determinants of known inhibitors is still lacking. Oligomycin, for example, has been known to be an inhibitor of the membrane motor of the mitochondrial ATP synthase for over five decades, and yet little is known about its mode of action at the molecular level. In a recent breakthrough, a crystal structure of the S. cerevisiae c-subunit ring with bound oligomycin revealed the inhibitor docked on the outer face of the proton-binding sites, deep into the transmembrane region. However, the structure of the complex was obtained in an organic solvent rather than detergent or a lipid bilayer, and therefore it has been unclear whether this mode of recognition is physiologically relevant. Here, we use molecular dynamics simulations to address this question and gain insights into the mechanism of oligomycin inhibition. Our findings lead us to propose that oligomycin naturally partitions into the lipid/water interface, and that in this environment the inhibitor can indeed bind to any of the c-ring proton-carrying sites that are exposed to the membrane, thereby becoming an integral component of the proton-coordinating network. As the c-ring rotates within the membrane, driven either by downhill proton permeation or ATP hydrolysis, one of the protonated, oligomycin-bound sites eventually reaches the subunit-a interface and halts the rotary mechanism of the enzyme.
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Affiliation(s)
- Wenchang Zhou
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Room 5N307A, Bethesda, MD 20892, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Room 5N307A, Bethesda, MD 20892, United States.
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21
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Sedwick C. A symporter’s secrets shown. J Gen Physiol 2017; 149:967. [PMID: 29054865 PMCID: PMC5677104 DOI: 10.1085/jgp.201711922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
New JGP study explores the thermodynamic cycle and cation preference of the sugar symporter MelB.
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22
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Hariharan P, Guan L. Thermodynamic cooperativity of cosubstrate binding and cation selectivity of Salmonella typhimurium MelB. J Gen Physiol 2017; 149:1029-1039. [PMID: 29054867 PMCID: PMC5677108 DOI: 10.1085/jgp.201711788] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 08/17/2017] [Accepted: 09/13/2017] [Indexed: 12/20/2022] Open
Abstract
The melibiose symporter MelB couples melibiose transport to that of cations such as Na+. Hariharan and Guan show that the binding of Na+ and melibiose is thermodynamically cooperative and that Na+ coupling is based on ion concentrations and competitive binding, but not ion selectivity. The Na+-coupled melibiose symporter MelB, which can also be coupled to H+ or Li+ transport, is a prototype for the glycoside-pentoside-hexuronide:cation symporter family. Although the 3-D x-ray crystal structure of Salmonella typhimurium MelB (MelBSt) has been determined, the symport mechanisms for the obligatory coupled transport are not well understood. Here, we apply isothermal titration calorimetry to determine the energetics of Na+ and melibiose binding to MelBSt, as well as protonation of this transporter. Studies of the thermodynamic cycle for the formation of the Na+–MelBSt–melibiose ternary complex at pH 7.45 reveal that the binding of Na+ and melibiose is cooperative. The binding affinity for one substrate (Na+ or melibiose) is increased by the presence of the other by about eightfold. The coupling free energies (ΔΔG) of either substrate binding are ∼5 kJ/mol, and binding of both substrates releases a free energy of ∼35 kJ/mol. Measurements of the Na+-binding enthalpy at three different pH values, including the pKa value of MelB, indicate that the binding of one Na+ displaces one H+ per MelBSt molecule. In addition, the absolute dissociation constants for Na+ and H+, determined by competitive binding, show that MelBSt is selective for H+ over Na+ by ∼1,000-fold at a pKa of 6.25. Thus, the Na+ coupling in MelBSt is based not on ion selectivity but on ion concentrations and competitive binding because of a much higher Na+ concentration under physiological conditions. Such a selectivity feature seems to be common for membrane transport proteins that can bind both H+ and Na+ at a common site.
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Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX
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23
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Zhekova HR, Ngo V, da Silva MC, Salahub D, Noskov S. Selective ion binding and transport by membrane proteins – A computational perspective. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.03.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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24
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Zhou W, Marinelli F, Nief C, Faraldo-Gómez JD. Atomistic simulations indicate the c-subunit ring of the F 1F o ATP synthase is not the mitochondrial permeability transition pore. eLife 2017; 6. [PMID: 28186490 PMCID: PMC5323039 DOI: 10.7554/elife.23781] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/09/2017] [Indexed: 12/03/2022] Open
Abstract
Pathological metabolic conditions such as ischemia induce the rupture of the mitochondrial envelope and the release of pro-apoptotic proteins, leading to cell death. At the onset of this process, the inner mitochondrial membrane becomes depolarized and permeable to osmolytes, proposedly due to the opening of a non-selective protein channel of unknown molecular identity. A recent study purports that this channel, referred to as Mitochondrial Permeability Transition Pore (MPTP), is formed within the c-subunit ring of the ATP synthase, upon its dissociation from the catalytic domain of the enzyme. Here, we examine this claim for two c-rings of different lumen width, through calculations of their ion conductance and selectivity based on all-atom molecular dynamics simulations. We also quantify the likelihood that the lumen of these c-rings is in a hydrated, potentially conducting state rather than empty or blocked by lipid molecules. These calculations demonstrate that the structure and biophysical properties of a correctly assembled c-ring are inconsistent with those attributed to the MPTP. DOI:http://dx.doi.org/10.7554/eLife.23781.001
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Affiliation(s)
- Wenchang Zhou
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Fabrizio Marinelli
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Corrine Nief
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
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25
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Leone V, Faraldo-Gómez JD. Structure and mechanism of the ATP synthase membrane motor inferred from quantitative integrative modeling. J Gen Physiol 2016; 148:441-457. [PMID: 27821609 PMCID: PMC5129741 DOI: 10.1085/jgp.201611679] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/13/2016] [Indexed: 01/31/2023] Open
Abstract
The ATP synthase is a molecular rotor that recycles ADP into ATP. Leone and Faraldo-Gómez use structural modeling to reinterpret and reconcile recent cryo-EM data for its membrane domain with other experimental evidence, gaining insights into its mechanism and the mode of inhibition by oligomycin. Two subunits within the transmembrane domain of the ATP synthase—the c-ring and subunit a—energize the production of 90% of cellular ATP by transducing an electrochemical gradient of H+ or Na+ into rotational motion. The nature of this turbine-like energy conversion mechanism has been elusive for decades, owing to the lack of definitive structural information on subunit a or its c-ring interface. In a recent breakthrough, several structures of this complex were resolved by cryo–electron microscopy (cryo-EM), but the modest resolution of the data has led to divergent interpretations. Moreover, the unexpected architecture of the complex has cast doubts on a wealth of earlier biochemical analyses conducted to probe this structure. Here, we use quantitative molecular-modeling methods to derive a structure of the a–c complex that is not only objectively consistent with the cryo-EM data, but also with correlated mutation analyses of both subunits and with prior cross-linking and cysteine accessibility measurements. This systematic, integrative approach reveals unambiguously the topology of subunit a and its relationship with the c-ring. Mapping of known Cd2+ block sites and conserved protonatable residues onto the structure delineates two noncontiguous pathways across the complex, connecting two adjacent proton-binding sites in the c-ring to the space on either side of the membrane. The location of these binding sites and of a strictly conserved arginine on subunit a, which serves to prevent protons from hopping between them, explains the directionality of the rotary mechanism and its strict coupling to the proton-motive force. Additionally, mapping of mutations conferring resistance to oligomycin unexpectedly reveals that this prototypical inhibitor may bind to two distinct sites at the a–c interface, explaining its ability to block the mechanism of the enzyme irrespective of the direction of rotation of the c-ring. In summary, this study is a stepping stone toward establishing the mechanism of the ATP synthase at the atomic level.
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Affiliation(s)
- Vanessa Leone
- Theoretical Molecular Biophysics Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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26
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Zhou W, Leone V, Krah A, Faraldo-Gómez JD. Predicted Structures of the Proton-Bound Membrane-Embedded Rotor Rings of the Saccharomyces cerevisiae and Escherichia coli ATP Synthases. J Phys Chem B 2016; 121:3297-3307. [PMID: 27715045 DOI: 10.1021/acs.jpcb.6b08051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent years have witnessed a renewed interest in the ATP synthase as a drug target against human pathogens. Indeed, clinical, biochemical, and structural data indicate that hydrophobic inhibitors targeting the membrane-embedded proton-binding sites of the c-subunit ring could serve as last-resort antibiotics against multidrug resistant strains. However, because inhibition of the mitochondrial ATP synthase in humans is lethal, it is essential that these inhibitors be not only potent but also highly selective for the bacterial enzyme. To this end, a detailed understanding of the structure of this protein target is arguably instrumental. Here, we use computational methods to predict the atomic structures of the proton-binding sites in two prototypical c-rings: that of the ATP synthase from Saccharomyces cerevisiae, which is a model system for mitochondrial enzymes, and that from Escherichia coli, which can be pathogenic for humans. Our study reveals the structure of these binding sites loaded with protons and in the context of the membrane, that is, in the state that would mediate the recognition of a potential inhibitor. Both structures reflect a mode of proton coordination unlike those previously observed in other c-ring structures, whether experimental or modeled.
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Affiliation(s)
- Wenchang Zhou
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Vanessa Leone
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Alexander Krah
- Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics , 60438 Frankfurt am Main, Germany
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.,Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics , 60438 Frankfurt am Main, Germany
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27
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Two independent evolutionary routes to Na+/H+ cotransport function in membrane pyrophosphatases. Biochem J 2016; 473:3099-111. [DOI: 10.1042/bcj20160529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 08/03/2016] [Indexed: 11/17/2022]
Abstract
Membrane-bound pyrophosphatases (mPPases) hydrolyze pyrophosphate (PPi) to transport H+, Na+ or both and help organisms to cope with stress conditions, such as high salinity or limiting nutrients. Recent elucidation of mPPase structure and identification of subfamilies that have fully or partially switched from Na+ to H+ pumping have established mPPases as versatile models for studying the principles governing the mechanism, specificity and evolution of cation transporters. In the present study, we constructed an accurate phylogenetic map of the interface of Na+-transporting PPases (Na+-PPases) and Na+- and H+-transporting PPases (Na+,H+-PPases), which guided our experimental exploration of the variations in PPi hydrolysis and ion transport activities during evolution. Surprisingly, we identified two mPPase lineages that independently acquired physiologically significant Na+ and H+ cotransport function. Na+,H+-PPases of the first lineage transport H+ over an extended [Na+] range, but progressively lose H+ transport efficiency at high [Na+]. In contrast, H+-transport by Na+,H+-PPases of the second lineage is not inhibited by up to 100 mM Na+. With the identification of Na+,H+-PPase subtypes, the mPPases protein superfamily appears as a continuum, ranging from monospecific Na+ transporters to transporters with tunable levels of Na+ and H+ cotransport and further to monospecific H+ transporters. Our results lend credence to the concept that Na+ and H+ are transported by similar mechanisms, allowing the relative efficiencies of Na+ and H+ transport to be modulated by minor changes in protein structure during the course of adaptation to a changing environment.
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Mamedov MD, Mamedov AM, Bertsova YV, Bogachev AV. A single mutation converts bacterial Na(+) -transporting rhodopsin into an H(+) transporter. FEBS Lett 2016; 590:2827-35. [PMID: 27447358 DOI: 10.1002/1873-3468.12324] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/10/2016] [Accepted: 07/13/2016] [Indexed: 11/10/2022]
Abstract
Na(+) -rhodopsins are light-driven pumps used by marine bacteria to extrude Na(+) ions from the cytoplasm. We show here that replacement of Gln123 on the cytoplasmic side of the ion-conductance channel with aspartate or glutamate confers H(+) transport activity to the Na(+) -rhodopsin from Dokdonia sp. PRO95. The Q123E variant could transport H(+) out of Escherichia coli cells in a medium containing 100 mm Na(+) and SCN(-) as the penetrating anion. The rates of the photocycle steps of this variant were only marginally dependent on Na(+) , and the major electrogenic steps were the decays of the K and O intermediates.
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Affiliation(s)
- Mahir D Mamedov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
| | - Adalyat M Mamedov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
| | - Yulia V Bertsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
| | - Alexander V Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
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Refaeli B, Giladi M, Hiller R, Khananshvili D. Structure-Based Engineering of Lithium-Transport Capacity in an Archaeal Sodium–Calcium Exchanger. Biochemistry 2016; 55:1673-6. [DOI: 10.1021/acs.biochem.6b00119] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bosmat Refaeli
- Department of Physiology
and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel
| | - Moshe Giladi
- Department of Physiology
and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel
| | - Reuben Hiller
- Department of Physiology
and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel
| | - Daniel Khananshvili
- Department of Physiology
and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel
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Castro PJ, Silva AF, Marreiros BC, Batista AP, Pereira MM. Respiratory complex I: A dual relation with H(+) and Na(+)? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:928-37. [PMID: 26711319 DOI: 10.1016/j.bbabio.2015.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 12/10/2015] [Accepted: 12/17/2015] [Indexed: 10/22/2022]
Abstract
Respiratory complex I couples NADH:quinone oxidoreduction to ion translocation across the membrane, contributing to the buildup of the transmembrane difference of electrochemical potential. H(+) is well recognized to be the coupling ion of this system but some studies suggested that this role could be also performed by Na(+). We have previously observed NADH-driven Na(+) transport opposite to H(+) translocation by menaquinone-reducing complexes I, which indicated a Na(+)/H(+) antiporter activity in these systems. Such activity was also observed for the ubiquinone-reducing mitochondrial complex I in its deactive form. The relation of Na(+) with complex I may not be surprising since the enzyme has three subunits structurally homologous to bona fide Na(+)/H(+) antiporters and translocation of H(+) and Na(+) ions has been described for members of most types of ion pumps and transporters. Moreover, no clearly distinguishable motifs for the binding of H(+) or Na(+) have been recognized yet. We noticed that in menaquinone-reducing complexes I, less energy is available for ion translocation, compared to ubiquinone-reducing complexes I. Therefore, we hypothesized that menaquinone-reducing complexes I perform Na(+)/H(+) antiporter activity in order to achieve the stoichiometry of 4H(+)/2e(-). In agreement, the organisms that use ubiquinone, a high potential quinone, would have kept such Na(+)/H(+) antiporter activity, only operative under determined conditions. This would imply a physiological role(s) of complex I besides a simple "coupling" of a redox reaction and ion transport, which could account for the sophistication of this enzyme. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Paulo J Castro
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Andreia F Silva
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Bruno C Marreiros
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Ana P Batista
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal.
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