1
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García-Contreras R, de la Mora J, Mora-Montes HM, Martínez-Álvarez JA, Vicente-Gómez M, Padilla-Vaca F, Vargas-Maya NI, Franco B. The inorganic pyrophosphatases of microorganisms: a structural and functional review. PeerJ 2024; 12:e17496. [PMID: 38938619 PMCID: PMC11210485 DOI: 10.7717/peerj.17496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/09/2024] [Indexed: 06/29/2024] Open
Abstract
Pyrophosphatases (PPases) are enzymes that catalyze the hydrolysis of pyrophosphate (PPi), a byproduct of the synthesis and degradation of diverse biomolecules. The accumulation of PPi in the cell can result in cell death. Although the substrate is the same, there are variations in the catalysis and features of these enzymes. Two enzyme forms have been identified in bacteria: cytoplasmic or soluble pyrophosphatases and membrane-bound pyrophosphatases, which play major roles in cell bioenergetics. In eukaryotic cells, cytoplasmic enzymes are the predominant form of PPases (c-PPases), while membrane enzymes (m-PPases) are found only in protists and plants. The study of bacterial cytoplasmic and membrane-bound pyrophosphatases has slowed in recent years. These enzymes are central to cell metabolism and physiology since phospholipid and nucleic acid synthesis release important amounts of PPi that must be removed to allow biosynthesis to continue. In this review, two aims were pursued: first, to provide insight into the structural features of PPases known to date and that are well characterized, and to provide examples of enzymes with novel features. Second, the scientific community should continue studying these enzymes because they have many biotechnological applications. Additionally, in this review, we provide evidence that there are m-PPases present in fungi; to date, no examples have been characterized. Therefore, the diversity of PPase enzymes is still a fruitful field of research. Additionally, we focused on the roles of H+/Na+ pumps and m-PPases in cell bioenergetics. Finally, we provide some examples of the applications of these enzymes in molecular biology and biotechnology, especially in plants. This review is valuable for professionals in the biochemistry field of protein structure-function relationships and experts in other fields, such as chemistry, nanotechnology, and plant sciences.
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Affiliation(s)
- Rodolfo García-Contreras
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Javier de la Mora
- Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Héctor Manuel Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - José A. Martínez-Álvarez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Marcos Vicente-Gómez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Felipe Padilla-Vaca
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Naurú Idalia Vargas-Maya
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Bernardo Franco
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
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2
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Strauss J, Wilkinson C, Vidilaseris K, de Castro Ribeiro OM, Liu J, Hillier J, Wichert M, Malinen AM, Gehl B, Jeuken LJ, Pearson AR, Goldman A. Functional and structural asymmetry suggest a unifying principle for catalysis in membrane-bound pyrophosphatases. EMBO Rep 2024; 25:853-875. [PMID: 38182815 PMCID: PMC10897367 DOI: 10.1038/s44319-023-00037-x] [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: 08/24/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 01/07/2024] Open
Abstract
Membrane-bound pyrophosphatases (M-PPases) are homodimeric primary ion pumps that couple the transport of Na+- and/or H+ across membranes to the hydrolysis of pyrophosphate. Their role in the virulence of protist pathogens like Plasmodium falciparum makes them an intriguing target for structural and functional studies. Here, we show the first structure of a K+-independent M-PPase, asymmetric and time-dependent substrate binding in time-resolved structures of a K+-dependent M-PPase and demonstrate pumping-before-hydrolysis by electrometric studies. We suggest how key residues in helix 12, 13, and the exit channel loops affect ion selectivity and K+-activation due to a complex interplay of residues that are involved in subunit-subunit communication. Our findings not only explain ion selectivity in M-PPases but also why they display half-of-the-sites reactivity. Based on this, we propose, for the first time, a unified model for ion-pumping, hydrolysis, and energy coupling in all M-PPases, including those that pump both Na+ and H+.
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Affiliation(s)
- Jannik Strauss
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
- Numaferm GmbH, Düsseldorf, Germany
| | - Craig Wilkinson
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
| | - Keni Vidilaseris
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
| | - Orquidea M de Castro Ribeiro
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
| | - Jianing Liu
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
| | - James Hillier
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
- Bio-Rad Laboratories Ltd., Watford, UK
| | - Maximilian Wichert
- Leiden Institute of Chemistry, University Leiden, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Anssi M Malinen
- Department of Life Technologies, University of Turku, FIN-20014, Turku, Finland
| | - Bernadette Gehl
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
- Department of Applied Physics, Aalto University, FI-00076, AALTO, Espoo, Finland
| | - Lars Jc Jeuken
- Leiden Institute of Chemistry, University Leiden, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Arwen R Pearson
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761, Hamburg, Germany
| | - Adrian Goldman
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK.
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland.
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3
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Huang LK, Huang YC, Chen PC, Lee CH, Lin SM, Hsu YHH, Pan RL. Exploration of the Catalytic Cycle Dynamics of Vigna Radiata H +-Translocating Pyrophosphatases Through Hydrogen-Deuterium Exchange Mass Spectrometry. J Membr Biol 2023; 256:443-458. [PMID: 37955797 DOI: 10.1007/s00232-023-00295-9] [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: 04/25/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
Vigna radiata H+-translocating pyrophosphatases (VrH+-PPases, EC 3.6.1.1) are present in various endomembranes of plants, bacteria, archaea, and certain protozoa. They transport H+ into the lumen by hydrolyzing pyrophosphate, which is a by-product of many essential anabolic reactions. Although the crystal structure of H+-PPases has been elucidated, the H+ translocation mechanism of H+-PPases in the solution state remains unclear. In this study, we used hydrogen-deuterium exchange (HDX) coupled with mass spectrometry (MS) to investigate the dynamics of H+-PPases between the previously proposed R state (resting state, Apo form), I state (intermediate state, bound to a substrate analog), and T state (transient state, bound to inorganic phosphate). When hydrogen was replaced by proteins in deuterium oxide solution, the backbone hydrogen atoms, which were exchanged with deuterium, were identified through MS. Accordingly, we used deuterium uptake to examine the structural dynamics and conformational changes of H+-PPases in solution. In the highly conserved substrate binding and proton exit regions, HDX-MS revealed the existence of a compact conformation with deuterium exchange when H+-PPases were bound with a substrate analog and product. Thus, a novel working model was developed to elucidate the in situ catalytic mechanism of pyrophosphate hydrolysis and proton transport. In this model, a proton is released in the I state, and the TM5 inner wall serves as a proton piston.
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Affiliation(s)
- Li-Kun Huang
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No.101, Sec. 2, Kuangfu Rd., Hsinchu City, 30013, Taiwan, Republic of China
| | - Yi-Cyuan Huang
- Department of Chemistry, Tunghai University, No.1727, Sec. 4, Taiwan Boulevard, Taichung, 40704, Taiwan, Republic of China
| | - Pin-Chuan Chen
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No.101, Sec. 2, Kuangfu Rd., Hsinchu City, 30013, Taiwan, Republic of China
| | - Ching-Hung Lee
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No.101, Sec. 2, Kuangfu Rd., Hsinchu City, 30013, Taiwan, Republic of China
| | - Shih-Ming Lin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan, Republic of China
| | - Yuan-Hao Howard Hsu
- Department of Chemistry, Tunghai University, No.1727, Sec. 4, Taiwan Boulevard, Taichung, 40704, Taiwan, Republic of China.
| | - Rong-Long Pan
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No.101, Sec. 2, Kuangfu Rd., Hsinchu City, 30013, Taiwan, Republic of China.
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4
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Holmes AOM, Goldman A, Kalli AC. mPPases create a conserved anionic membrane fingerprint as identified via multi-scale simulations. PLoS Comput Biol 2022; 18:e1010578. [PMID: 36191052 PMCID: PMC9560603 DOI: 10.1371/journal.pcbi.1010578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 10/13/2022] [Accepted: 09/16/2022] [Indexed: 11/06/2022] Open
Abstract
Membrane-integral pyrophosphatases (mPPases) are membrane-bound enzymes responsible for hydrolysing inorganic pyrophosphate and translocating a cation across the membrane. Their function is essential for the infectivity of clinically relevant protozoan parasites and plant maturation. Recent developments have indicated that their mechanism is more complicated than previously thought and that the membrane environment may be important for their function. In this work, we use multiscale molecular dynamics simulations to demonstrate for the first time that mPPases form specific anionic lipid interactions at 4 sites at the distal and interfacial regions of the protein. These interactions are conserved in simulations of the mPPases from Thermotoga maritima, Vigna radiata and Clostridium leptum and characterised by interactions with positive residues on helices 1, 2, 3 and 4 for the distal site, or 9, 10, 13 and 14 for the interfacial site. Due to the importance of these helices in protein stability and function, these lipid interactions may play a crucial role in the mPPase mechanism and enable future structural and functional studies.
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Affiliation(s)
- Alexandra O. M. Holmes
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Adrian Goldman
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- Research Program in Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland
| | - Antreas C. Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine and Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
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5
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Malinen AM, Anashkin VA, Orlov VN, Bogachev AV, Lahti R, Baykov AA. Pre‐steady‐state kinetics and solvent isotope effects support the “billiard‐type” transport mechanism in
Na
+
‐translocating pyrophosphatase. Protein Sci 2022; 31:e4394. [PMID: 36040263 PMCID: PMC9405524 DOI: 10.1002/pro.4394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/23/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022]
Abstract
Membrane‐bound pyrophosphatase (mPPase) found in microbes and plants is a membrane H+ pump that transports the H+ ion generated in coupled pyrophosphate hydrolysis out of the cytoplasm. Certain bacterial and archaeal mPPases can in parallel transport Na+ via a hypothetical “billiard‐type” mechanism, also involving the hydrolysis‐generated proton. Here, we present the functional evidence supporting this coupling mechanism. Rapid‐quench and pulse‐chase measurements with [32P]pyrophosphate indicated that the chemical step (pyrophosphate hydrolysis) is rate‐limiting in mPPase catalysis and is preceded by a fast isomerization of the enzyme‐substrate complex. Na+, whose binding is a prerequisite for the hydrolysis step, is not required for substrate binding. Replacement of H2O with D2O decreased the rates of pyrophosphate hydrolysis by both Na+‐ and H+‐transporting bacterial mPPases, the effect being more significant than with a non‐transporting soluble pyrophosphatase. We also show that the Na+‐pumping mPPase of Thermotoga maritima resembles other dimeric mPPases in demonstrating negative kinetic cooperativity and the requirement for general acid catalysis. The findings point to a crucial role for the hydrolysis‐generated proton both in H+‐pumping and Na+‐pumping by mPPases.
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Affiliation(s)
- Anssi M. Malinen
- Department of Life Technologies University of Turku Turku Finland
| | - Viktor A. Anashkin
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
| | - Victor N. Orlov
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
| | - Alexander V. Bogachev
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
| | - Reijo Lahti
- Department of Life Technologies University of Turku Turku Finland
| | - Alexander A. Baykov
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
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6
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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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7
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Guo L, He J, Lin P, Huang SY, Wang J. TRScore: a three-dimensional RepVGG-based scoring method for ranking protein docking models. Bioinformatics 2022; 38:2444-2451. [PMID: 35199137 DOI: 10.1093/bioinformatics/btac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/19/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Protein-protein interactions (PPI) play important roles in cellular activities. Due to the technical difficulty and high cost of experimental methods, there are considerable interests towards the development of computational approaches, such as protein docking, to decipher PPI patterns. One of the important and difficult aspects in protein docking is recognizing near-native conformations from a set of decoys, but unfortunately traditional scoring functions still suffer from limited accuracy. Therefore, new scoring methods are pressingly needed in methodological and/or practical implications. RESULTS We present a new deep learning-based scoring method for ranking protein-protein docking models based on a three-dimensional (3D) RepVGG network, named TRScore. To recognize near-native conformations from a set of decoys, TRScore voxelizes the protein-protein interface into a 3D grid labeled by the number of atoms in different physicochemical classes. Benefiting from the deep convolutional RepVGG architecture, TRScore can effectively capture the subtle differences between energetically favorable near-native models and unfavorable non-native decoys without needing extra information. TRScore was extensively evaluated on diverse test sets including protein-protein docking benchmark 5.0 update set, DockGround decoy set, as well as realistic CAPRI decoy set, and overall obtained a significant improvement over existing methods in cross validation and independent evaluations. AVAILABILITY Codes available at: https://github.com/BioinformaticsCSU/TRScore.
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Affiliation(s)
- Linyuan Guo
- School of Computer Science, Central South University, Changsha, Hunan 410083, China
| | - Jiahua He
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Peicong Lin
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jianxin Wang
- School of Computer Science, Central South University, Changsha, Hunan 410083, China
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8
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A Lumenal Loop Associated with Catalytic Asymmetry in Plant Vacuolar H +-Translocating Pyrophosphatase. Int J Mol Sci 2021; 22:ijms222312902. [PMID: 34884707 PMCID: PMC8657866 DOI: 10.3390/ijms222312902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/27/2021] [Indexed: 12/13/2022] Open
Abstract
Membrane-integral inorganic pyrophosphatases (mPPases) couple pyrophosphate hydrolysis with H+ and Na+ pumping in plants and microbes. mPPases are homodimeric transporters with two catalytic sites facing the cytoplasm and demonstrating highly different substrate-binding affinities and activities. The structural aspects of the functional asymmetry are still poorly understood because the structure of the physiologically relevant dimer form with only one active site occupied by the substrate is unknown. We addressed this issue by molecular dynamics (MD) simulations of the H+-transporting mPPase of Vigna radiata, starting from its crystal structure containing a close substrate analog (imidodiphosphate, IDP) in both active sites. The MD simulations revealed pre-existing subunit asymmetry, which increased upon IDP binding to one subunit and persisted in the fully occupied dimer. The most significant asymmetrical change caused by IDP binding is a ‘rigid body’-like displacement of the lumenal loop connecting α-helices 2 and 3 in the partner subunit and opening its exit channel for water. This highly conserved 14–19-residue loop is found only in plant vacuolar mPPases and may have a regulatory function, such as pH sensing in the vacuole. Our data define the structural link between the loop and active sites and are consistent with the published structural and functional data.
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9
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Johansson NG, Dreano L, Vidilaseris K, Khattab A, Liu J, Lasbleiz A, Ribeiro O, Kiriazis A, Boije af Gennäs G, Meri S, Goldman A, Yli‐Kauhaluoma J, Xhaard H. Exploration of Pyrazolo[1,5-a]pyrimidines as Membrane-Bound Pyrophosphatase Inhibitors. ChemMedChem 2021; 16:3360-3367. [PMID: 34459148 PMCID: PMC8597055 DOI: 10.1002/cmdc.202100392] [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: 06/01/2021] [Revised: 08/03/2021] [Indexed: 11/08/2022]
Abstract
Inhibition of membrane-bound pyrophosphatase (mPPase) with small molecules offer a new approach in the fight against pathogenic protozoan parasites. mPPases are absent in humans, but essential for many protists as they couple pyrophosphate hydrolysis to the active transport of protons or sodium ions across acidocalcisomal membranes. So far, only few nonphosphorus inhibitors have been reported. Here, we explore the chemical space around previous hits using a combination of screening and synthetic medicinal chemistry, identifying compounds with low micromolar inhibitory activities in the Thermotoga maritima mPPase test system. We furthermore provide early structure-activity relationships around a new scaffold having a pyrazolo[1,5-a]pyrimidine core. The most promising pyrazolo[1,5-a]pyrimidine congener was further investigated and found to inhibit Plasmodium falciparum mPPase in membranes as well as the growth of P. falciparum in an ex vivo survival assay.
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Affiliation(s)
- Niklas G. Johansson
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
| | - Loïc Dreano
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
| | - Keni Vidilaseris
- Department of Biosciences, Division of BiochemistryUniversity of HelsinkiP.O. Box 56 (Viikinkaari 9)00014HelsinkiFinland
| | - Ayman Khattab
- Malaria Research Laboratory, Translational Immunology Research Program, Department of Bacteriology and Immunology, Haartman InstituteUniversity of HelsinkiP.O. Box 21 (Haartmaninkatu 3)00014HelsinkiFinland
| | - Jianing Liu
- Department of Biosciences, Division of BiochemistryUniversity of HelsinkiP.O. Box 56 (Viikinkaari 9)00014HelsinkiFinland
| | - Arthur Lasbleiz
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
| | - Orquidea Ribeiro
- Department of Biosciences, Division of BiochemistryUniversity of HelsinkiP.O. Box 56 (Viikinkaari 9)00014HelsinkiFinland
| | - Alexandros Kiriazis
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
| | - Gustav Boije af Gennäs
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
| | - Seppo Meri
- Malaria Research Laboratory, Translational Immunology Research Program, Department of Bacteriology and Immunology, Haartman InstituteUniversity of HelsinkiP.O. Box 21 (Haartmaninkatu 3)00014HelsinkiFinland
| | - Adrian Goldman
- Department of Biosciences, Division of BiochemistryUniversity of HelsinkiP.O. Box 56 (Viikinkaari 9)00014HelsinkiFinland
- School of Biomedical Sciences and Astbury Centre for Structural Molecular BiologyUniversity of Leeds, Clarendon WayLeeds LS2 9JTUK
| | - Jari Yli‐Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
| | - Henri Xhaard
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of PharmacyUniversity of HelsinkiP.O. Box 56 (Viikinkaari 5 E)00014HelsinkiFinland
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10
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Anashkin VA, Malinen AM, Bogachev AV, Baykov AA. Catalytic Asymmetry in Homodimeric H +-Pumping Membrane Pyrophosphatase Demonstrated by Non-Hydrolyzable Pyrophosphate Analogs. Int J Mol Sci 2021; 22:ijms22189820. [PMID: 34575984 PMCID: PMC8469034 DOI: 10.3390/ijms22189820] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/23/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023] Open
Abstract
Membrane-bound inorganic pyrophosphatase (mPPase) resembles the F-ATPase in catalyzing polyphosphate-energized H+ and Na+ transport across lipid membranes, but differs structurally and mechanistically. Homodimeric mPPase likely uses a “direct coupling” mechanism, in which the proton generated from the water nucleophile at the entrance to the ion conductance channel is transported across the membrane or triggers Na+ transport. The structural aspects of this mechanism, including subunit cooperation, are still poorly understood. Using a refined enzyme assay, we examined the inhibition of K+-dependent H+-transporting mPPase from Desulfitobacterium hafniensee by three non-hydrolyzable PPi analogs (imidodiphosphate and C-substituted bisphosphonates). The kinetic data demonstrated negative cooperativity in inhibitor binding to two active sites, and reduced active site performance when the inhibitor or substrate occupied the other active site. The nonequivalence of active sites in PPi hydrolysis in terms of the Michaelis constant vanished at a low (0.1 mM) concentration of Mg2+ (essential cofactor). The replacement of K+, the second metal cofactor, by Na+ increased the substrate and inhibitor binding cooperativity. The detergent-solubilized form of mPPase exhibited similar active site nonequivalence in PPi hydrolysis. Our findings support the notion that the mPPase mechanism combines Mitchell’s direct coupling with conformational coupling to catalyze cation transport across the membrane.
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Affiliation(s)
- Viktor A. Anashkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia; (V.A.A.); (A.V.B.)
| | - Anssi M. Malinen
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland;
| | - Alexander V. Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia; (V.A.A.); (A.V.B.)
| | - Alexander A. Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia; (V.A.A.); (A.V.B.)
- Correspondence:
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11
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Cecchetti C, Strauss J, Stohrer C, Naylor C, Pryor E, Hobbs J, Tanley S, Goldman A, Byrne B. A novel high-throughput screen for identifying lipids that stabilise membrane proteins in detergent based solution. PLoS One 2021; 16:e0254118. [PMID: 34252116 PMCID: PMC8274869 DOI: 10.1371/journal.pone.0254118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/20/2021] [Indexed: 12/29/2022] Open
Abstract
Membrane proteins have a range of crucial biological functions and are the target of about 60% of all prescribed drugs. For most studies, they need to be extracted out of the lipid-bilayer, e.g. by detergent solubilisation, leading to the loss of native lipids, which may disturb important protein-lipid/bilayer interactions and thus functional and structural integrity. Relipidation of membrane proteins has proven extremely successful for studying challenging targets, but the identification of suitable lipids can be expensive and laborious. Therefore, we developed a screen to aid the high-throughput identification of beneficial lipids. The screen covers a large lipid space and was designed to be suitable for a range of stability assessment methods. Here, we demonstrate its use as a tool for identifying stabilising lipids for three membrane proteins: a bacterial pyrophosphatase (Tm-PPase), a fungal purine transporter (UapA) and a human GPCR (A2AR). A2AR is stabilised by cholesteryl hemisuccinate, a lipid well known to stabilise GPCRs, validating the approach. Additionally, our screen also identified a range of new lipids which stabilised our test proteins, providing a starting point for further investigation and demonstrating its value as a novel tool for membrane protein research. The pre-dispensed screen will be made commercially available to the scientific community in future and has a number of potential applications in the field.
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Affiliation(s)
- Cristina Cecchetti
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Jannik Strauss
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Claudia Stohrer
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | | | - Edward Pryor
- Anatrace, Maumee, Ohio, United States of America
| | | | | | - Adrian Goldman
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
- MIBS, Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- * E-mail: (AG); (BB)
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail: (AG); (BB)
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12
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Johansson NG, Turku A, Vidilaseris K, Dreano L, Khattab A, Ayuso Pérez D, Wilkinson A, Zhang Y, Tamminen M, Grazhdankin E, Kiriazis A, Fishwick CWG, Meri S, Yli-Kauhaluoma J, Goldman A, Boije af Gennäs G, Xhaard H. Discovery of Membrane-Bound Pyrophosphatase Inhibitors Derived from an Isoxazole Fragment. ACS Med Chem Lett 2020; 11:605-610. [PMID: 32292570 PMCID: PMC7153278 DOI: 10.1021/acsmedchemlett.9b00537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/10/2020] [Indexed: 12/21/2022] Open
Abstract
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Membrane-bound
pyrophosphatases (mPPases) regulate energy homeostasis
in pathogenic protozoan parasites and lack human homologues, which
makes them promising targets in e.g. malaria. Yet
only few nonphosphorus inhibitors have been reported so far. Here,
we explore an isoxazole fragment hit, leading to the discovery of
small mPPase inhibitors with 6–10 μM IC50 values
in the Thermotoga maritima test system. Promisingly,
the compounds retained activity against Plasmodium falciparum mPPase in membranes and inhibited parasite growth.
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Affiliation(s)
- Niklas G. Johansson
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Ainoleena Turku
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Keni Vidilaseris
- Department of Biosciences, Division of Biochemistry, University of Helsinki, P.O. Box 56
(Viikinkaari 9), FI-00014 Helsinki, Finland
| | - Loïc Dreano
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Ayman Khattab
- Malaria Research Laboratory, Translational Immunology Research Program, Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, P.O. Box 21
(Haartmaninkatu 3), FI-00014 Helsinki, Finland
| | - Daniel Ayuso Pérez
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Aaron Wilkinson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Yuezhou Zhang
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Matti Tamminen
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Evgeni Grazhdankin
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Alexandros Kiriazis
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Colin W. G. Fishwick
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Seppo Meri
- Malaria Research Laboratory, Translational Immunology Research Program, Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, P.O. Box 21
(Haartmaninkatu 3), FI-00014 Helsinki, Finland
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Adrian Goldman
- Department of Biosciences, Division of Biochemistry, University of Helsinki, P.O. Box 56
(Viikinkaari 9), FI-00014 Helsinki, Finland
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Clarendon Way, Leeds LS2 9JT, United Kingdom
| | - Gustav Boije af Gennäs
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
| | - Henri Xhaard
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), FI-00014 Helsinki, Finland
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13
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Baykov AA. Energy Coupling in Cation-Pumping Pyrophosphatase-Back to Mitchell. FRONTIERS IN PLANT SCIENCE 2020; 11:107. [PMID: 32117404 PMCID: PMC7034417 DOI: 10.3389/fpls.2020.00107] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
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14
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Holmes AOM, Kalli AC, Goldman A. The Function of Membrane Integral Pyrophosphatases From Whole Organism to Single Molecule. Front Mol Biosci 2019; 6:132. [PMID: 31824962 PMCID: PMC6882861 DOI: 10.3389/fmolb.2019.00132] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/08/2019] [Indexed: 12/02/2022] Open
Abstract
Membrane integral pyrophosphatases (mPPases) are responsible for the hydrolysis of pyrophosphate. This enzymatic mechanism is coupled to the pumping of H+ or Na+ across membranes in a process that can be K+ dependent or independent. Understanding the movements and dynamics throughout the mPPase catalytic cycle is important, as this knowledge is essential for improving or impeding protein function. mPPases have been shown to play a crucial role in plant maturation and abiotic stress tolerance, and so have the potential to be engineered to improve plant survival, with implications for global food security. mPPases are also selectively toxic drug targets, which could be pharmacologically modulated to reduce the virulence of common human pathogens. The last few years have seen the publication of many new insights into the function and structure of mPPases. In particular, there is a new body of evidence that the catalytic cycle is more complex than originally proposed. There are structural and functional data supporting a mechanism involving half-of-the-sites reactivity, inter-subunit communication, and exit channel motions. A more advanced and in-depth understanding of mPPases has begun to be uncovered, leaving the field of research with multiple interesting avenues for further exploration and investigation.
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Affiliation(s)
- Alexandra O. M. Holmes
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Antreas C. Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine and Astbury Centre for Structural Biology, University of Leeds, Leeds, United Kingdom
| | - Adrian Goldman
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- Research Program in Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland
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15
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Glutamate transporters: a broad review of the most recent archaeal and human structures. Biochem Soc Trans 2019; 47:1197-1207. [PMID: 31383819 DOI: 10.1042/bst20190316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 12/11/2022]
Abstract
Glutamate transporters play important roles in bacteria, archaea and eukaryotes. Their function in the mammalian central nervous system is essential for preventing excitotoxicity, and their dysregulation is implicated in many diseases, such as epilepsy and Alzheimer's. Elucidating their transport mechanism would further the understanding of these transporters and promote drug design as they provide compelling targets for understanding the pathophysiology of diseases and may have a direct role in the treatment of conditions involving glutamate excitotoxicity. This review outlines the insights into the transport cycle, uncoupled chloride conductance and modulation, as well as identifying areas that require further investigation.
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