1
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Spassov DS. Binding Affinity Determination in Drug Design: Insights from Lock and Key, Induced Fit, Conformational Selection, and Inhibitor Trapping Models. Int J Mol Sci 2024; 25:7124. [PMID: 39000229 PMCID: PMC11240957 DOI: 10.3390/ijms25137124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Binding affinity is a fundamental parameter in drug design, describing the strength of the interaction between a molecule and its target protein. Accurately predicting binding affinity is crucial for the rapid development of novel therapeutics, the prioritization of promising candidates, and the optimization of their properties through rational design strategies. Binding affinity is determined by the mechanism of recognition between proteins and ligands. Various models, including the lock and key, induced fit, and conformational selection, have been proposed to explain this recognition process. However, current computational strategies to predict binding affinity, which are based on these models, have yet to produce satisfactory results. This article explores the connection between binding affinity and these protein-ligand interaction models, highlighting that they offer an incomplete picture of the mechanism governing binding affinity. Specifically, current models primarily center on the binding of the ligand and do not address its dissociation. In this context, the concept of ligand trapping is introduced, which models the mechanisms of dissociation. When combined with the current models, this concept can provide a unified theoretical framework that may allow for the accurate determination of the ligands' binding affinity.
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Affiliation(s)
- Danislav S Spassov
- Drug Design and Bioinformatics Lab, Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria
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2
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Hellemann E, Durrant JD. Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling. J Chem Theory Comput 2023; 19:5677-5689. [PMID: 37585617 PMCID: PMC10500992 DOI: 10.1021/acs.jctc.3c00478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Indexed: 08/18/2023]
Abstract
Structure-based virtual screening (VS) is an effective method for identifying potential small-molecule ligands, but traditional VS approaches consider only a single binding-pocket conformation. Consequently, they struggle to identify ligands that bind to alternate conformations. Ensemble docking helps address this issue by incorporating multiple conformations into the docking process, but it depends on methods that can thoroughly explore pocket flexibility. We here introduce Sub-Pocket EXplorer (SubPEx), an approach that uses weighted ensemble (WE) path sampling to accelerate binding-pocket sampling. As proof of principle, we apply SubPEx to three proteins relevant to drug discovery: heat shock protein 90, influenza neuraminidase, and yeast hexokinase 2. SubPEx is available free of charge without registration under the terms of the open-source MIT license: http://durrantlab.com/subpex/.
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Affiliation(s)
- Erich Hellemann
- Department of Biological
Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jacob D. Durrant
- Department of Biological
Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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3
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Dillenberger M, Werner AD, Velten AS, Rahlfs S, Becker K, Fritz-Wolf K. Structural Analysis of Plasmodium falciparum Hexokinase Provides Novel Information about Catalysis Due to a Plasmodium-Specific Insertion. Int J Mol Sci 2023; 24:12739. [PMID: 37628920 PMCID: PMC10454665 DOI: 10.3390/ijms241612739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
The protozoan parasite Plasmodium falciparum is the causative pathogen of the most severe form of malaria, for which novel strategies for treatment are urgently required. The primary energy supply for intraerythrocytic stages of Plasmodium is the production of ATP via glycolysis. Due to the parasite's strong dependence on this pathway and the significant structural differences of its glycolytic enzymes compared to its human counterpart, glycolysis is considered a potential drug target. In this study, we provide the first three-dimensional protein structure of P. falciparum hexokinase (PfHK) containing novel information about the mechanisms of PfHK. We identified for the first time a Plasmodium-specific insertion that lines the active site. Moreover, we propose that this insertion plays a role in ATP binding. Residues of the insertion further seem to affect the tetrameric interface and therefore suggest a special way of communication among the different monomers. In addition, we confirmed that PfHK is targeted and affected by oxidative posttranslational modifications (oxPTMs). Both S-glutathionylation and S-nitrosation revealed an inhibitory effect on the enzymatic activity of PfHK.
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Affiliation(s)
- Melissa Dillenberger
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, D-35392 Giessen, Germany; (M.D.)
| | - Anke-Dorothee Werner
- Institute of Virology, University of Marburg, Hans-Meerwein-Str. 2, D-35043 Marburg, Germany
| | - Ann-Sophie Velten
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, D-35392 Giessen, Germany; (M.D.)
| | - Stefan Rahlfs
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, D-35392 Giessen, Germany; (M.D.)
| | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, D-35392 Giessen, Germany; (M.D.)
| | - Karin Fritz-Wolf
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, D-35392 Giessen, Germany; (M.D.)
- Max-Planck Institute for Medical Research, Jahnstr. 29, D-69120 Heidelberg, Germany
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4
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Hellemann E, Durrant JD. Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539330. [PMID: 37251500 PMCID: PMC10214482 DOI: 10.1101/2023.05.03.539330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Structure-based virtual screening (VS) is an effective method for identifying potential small-molecule ligands, but traditional VS approaches consider only a single binding-pocket conformation. Consequently, they struggle to identify ligands that bind to alternate conformations. Ensemble docking helps address this issue by incorporating multiple conformations into the docking process, but it depends on methods that can thoroughly explore pocket flexibility. We here introduce Sub-Pocket EXplorer (SubPEx), an approach that uses weighted ensemble (WE) path sampling to accelerate binding-pocket sampling. As proof of principle, we apply SubPEx to three proteins relevant to drug discovery: heat shock protein 90, influenza neuraminidase, and yeast hexokinase 2. SubPEx is available free of charge without registration under the terms of the open-source MIT license: http://durrantlab.com/subpex/.
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Affiliation(s)
- Erich Hellemann
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, United States
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, United States
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5
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Hellemann E, Walker JL, Lesko MA, Chandrashekarappa DG, Schmidt MC, O’Donnell AF, Durrant JD. Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics. PLoS Comput Biol 2022; 18:e1009929. [PMID: 35235554 PMCID: PMC8920189 DOI: 10.1371/journal.pcbi.1009929] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/14/2022] [Accepted: 02/16/2022] [Indexed: 01/16/2023] Open
Abstract
Glucose is central to many biological processes, serving as an energy source and a building block for biosynthesis. After glucose enters the cell, hexokinases convert it to glucose-6-phosphate (Glc-6P) for use in anaerobic fermentation, aerobic oxidative phosphorylation, and the pentose-phosphate pathway. We here describe a genetic screen in Saccharomyces cerevisiae that generated a novel spontaneous mutation in hexokinase-2, hxk2G238V, that confers resistance to the toxic glucose analog 2-deoxyglucose (2DG). Wild-type hexokinases convert 2DG to 2-deoxyglucose-6-phosphate (2DG-6P), but 2DG-6P cannot support downstream glycolysis, resulting in a cellular starvation-like response. Curiously, though the hxk2G238V mutation encodes a loss-of-function allele, the affected amino acid does not interact directly with bound glucose, 2DG, or ATP. Molecular dynamics simulations suggest that Hxk2G238V impedes sugar binding by altering the protein dynamics of the glucose-binding cleft, as well as the large-scale domain-closure motions required for catalysis. These findings shed new light on Hxk2 dynamics and highlight how allosteric changes can influence catalysis, providing new structural insights into this critical regulator of carbohydrate metabolism. Given that hexokinases are upregulated in some cancers and that 2DG and its derivatives have been studied in anti-cancer trials, the present work also provides insights that may apply to cancer biology and drug resistance. Glucose fuels many of the energy-production processes required for normal cell growth. Before glucose can participate in these processes, it must first be chemically modified by proteins called hexokinases. To better understand how hexokinases modify glucose—and how mutations in hexokinase genes might confer drug resistance—we evolved resistance in yeast to a toxic hexokinase-binding molecule called 2DG. We discovered a mutation in the hexokinase gene that confers 2DG resistance and reduces the protein’s ability to modify glucose. Biochemical analyses and computer simulations of the hexokinase protein suggest that the mutation diminishes glucose binding by altering enzyme flexibility. This work shows how cells can evolve resistance to toxins via only modest changes to protein structures. Furthermore, because cancer-cell hexokinases are particularly active, 2DG has been studied as cancer chemotherapy. Thus, the insights this work provides might also apply to cancer biology.
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Affiliation(s)
- Erich Hellemann
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jennifer L. Walker
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mitchell A. Lesko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Dakshayini G. Chandrashekarappa
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Martin C. Schmidt
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Allyson F. O’Donnell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (AFO); (JDD)
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (AFO); (JDD)
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6
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van Tatenhove-Pel RJ, Zwering E, Boreel DF, Falk M, van Heerden JH, Kes MBMJ, Kranenburg CI, Botman D, Teusink B, Bachmann H. Serial propagation in water-in-oil emulsions selects for Saccharomyces cerevisiae strains with a reduced cell size or an increased biomass yield on glucose. Metab Eng 2021; 64:1-14. [PMID: 33418011 DOI: 10.1016/j.ymben.2020.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/26/2020] [Accepted: 12/15/2020] [Indexed: 11/19/2022]
Abstract
In S. cerevisiae and many other micro-organisms an increase in metabolic efficiency (i.e. ATP yield on carbon) is accompanied by a decrease in growth rate. From a fundamental point of view, studying these yield-rate trade-offs provides insight in for example microbial evolution and cellular regulation. From a biotechnological point of view, increasing the ATP yield on carbon might increase the yield of anabolic products. We here aimed to select S. cerevisiae mutants with an increased biomass yield. Serial propagation of individual cells in water-in-oil emulsions previously enabled the selection of lactococci with increased biomass yields, and adapting this protocol for yeast allowed us to enrich an engineered Crabtree-negative S. cerevisiae strain with a high biomass yield on glucose. When we started the selection with an S. cerevisiae deletion collection, serial propagation in emulsion enriched hxk2Δ and reg1Δ strains with an increased biomass yield on glucose. Surprisingly, a tps1Δ strain was highly abundant in both emulsion- and suspension-propagated populations. In a separate experiment we propagated a chemically mutagenized S. cerevisiae population in emulsion, which resulted in mutants with a higher cell number yield on glucose, but no significantly changed biomass yield. Genome analyses indicate that genes involved in glucose repression and cell cycle processes play a role in the selected phenotypes. The repeated identification of mutations in genes involved in glucose-repression indicates that serial propagation in emulsion is a valuable tool to study metabolic efficiency in S. cerevisiae.
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Affiliation(s)
- Rinke Johanna van Tatenhove-Pel
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Emile Zwering
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Daan Floris Boreel
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Martijn Falk
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Johan Hendrik van Heerden
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Mariah B M J Kes
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Cindy Iris Kranenburg
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Dennis Botman
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands
| | - Herwig Bachmann
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV Amsterdam, the Netherlands; NIZO Food Research, Kernhemseweg 2, 6718ZB, Ede, the Netherlands.
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7
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Ha EJ, Lwin CT, Durrant JD. LigGrep: a tool for filtering docked poses to improve virtual-screening hit rates. J Cheminform 2020; 12:69. [PMID: 33292486 PMCID: PMC7656723 DOI: 10.1186/s13321-020-00471-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/19/2020] [Indexed: 01/21/2023] Open
Abstract
Structure-based virtual screening (VS) uses computer docking to prioritize candidate small-molecule ligands for subsequent experimental testing. Docking programs evaluate molecular binding in part by predicting the geometry with which a given compound might bind a target receptor (e.g., the docked "pose" relative to a protein target). Candidate ligands predicted to participate in the same intermolecular interactions typical of known ligands (or ligands that bind related proteins) are arguably more likely to be true binders. Some docking programs allow users to apply constraints during the docking process with the goal of prioritizing these critical interactions. But these programs often have restrictive and/or expensive licenses, and many popular open-source docking programs (e.g., AutoDock Vina) lack this important functionality. We present LigGrep, a free, open-source program that addresses this limitation. As input, LigGrep accepts a protein receptor file, a directory containing many docked-compound files, and a list of user-specified filters describing critical receptor/ligand interactions. LigGrep evaluates each docked pose and outputs the names of the compounds with poses that pass all filters. To demonstrate utility, we show that LigGrep can improve the hit rates of test VS targeting H. sapiens poly(ADPribose) polymerase 1 (HsPARP1), H. sapiens peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (HsPin1p), and S. cerevisiae hexokinase-2 (ScHxk2p). We hope that LigGrep will be a useful tool for the computational biology community. A copy is available free of charge at http://durrantlab.com/liggrep/ .
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Affiliation(s)
- Emily J Ha
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, United States
| | - Cara T Lwin
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, United States
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, United States.
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8
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Zhou L, Wen Z, Wang Z, Zhang Y, Ledesma-Amaro R, Jin M. Evolutionary Engineering Improved d-Glucose/Xylose Cofermentation of Yarrowia lipolytica. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c00896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Linlin Zhou
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Zedi Wang
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | - Yuwei Zhang
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
| | | | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
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9
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Garcia SN, Guedes RC, Marques MM. Unlocking the Potential of HK2 in Cancer Metabolism and Therapeutics. Curr Med Chem 2020; 26:7285-7322. [PMID: 30543165 DOI: 10.2174/0929867326666181213092652] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/26/2018] [Accepted: 11/06/2018] [Indexed: 12/24/2022]
Abstract
Glycolysis is a tightly regulated process in which several enzymes, such as Hexokinases (HKs), play crucial roles. Cancer cells are characterized by specific expression levels of several isoenzymes in different metabolic pathways and these features offer possibilities for therapeutic interventions. Overexpression of HKs (mostly of the HK2 isoform) have been consistently reported in numerous types of cancer. Moreover, deletion of HK2 has been shown to decrease cancer cell proliferation without explicit side effects in animal models, which suggests that targeting HK2 is a viable strategy for cancer therapy. HK2 inhibition causes a substantial decrease of glycolysis that affects multiple pathways of central metabolism and also destabilizes the mitochondrial outer membrane, ultimately enhancing cell death. Although glycolysis inhibition has met limited success, partly due to low selectivity for specific isoforms and excessive side effects of the reported HK inhibitors, there is ample ground for progress. The current review is focused on HK2 inhibition, envisaging the development of potent and selective anticancer agents. The information on function, expression, and activity of HKs is presented, along with their structures, known inhibitors, and reported effects of HK2 ablation/inhibition. The structural features of the different isozymes are discussed, aiming to stimulate a more rational approach to the design of selective HK2 inhibitors with appropriate drug-like properties. Particular attention is dedicated to a structural and sequence comparison of the structurally similar HK1 and HK2 isoforms, aiming to unveil differences that could be explored therapeutically. Finally, several additional catalytic- and non-catalytic roles on different pathways and diseases, recently attributed to HK2, are reviewed and their implications briefly discussed.
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Affiliation(s)
- Sara N Garcia
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal.,iMed.ULisboa, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Rita C Guedes
- iMed.ULisboa, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - M Matilde Marques
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
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10
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Tomimoto K, Osafune Y, Kakizono D, Han J, Mukai N. Isolation methods of high glycosidase-producing mutants of Aspergillus luchuensis and its mutated genes. Biosci Biotechnol Biochem 2019; 84:198-207. [PMID: 31566090 DOI: 10.1080/09168451.2019.1671788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
High glycosidase-producing strains of Aspergillus luchuensis were isolated from 2-deoxyglucose (2-DG) resistant mutants. α-Amylase, exo-α-1,4-glucosidase, β-glucosidase and β-xylosidase activity in the mutants was ~3, ~2, ~4 and ~2.5 times higher than the parental strain RIB2604 on koji-making conditions, respectively. Citric acid production and mycelia growth of the mutants, however, approximately halved to that of the parent. Compared to the parent, the alcohol yield from rice and sweet potato shochu mash of the mutant increased ~5.7% and 3.0%, respectively. The mutant strains showed significantly low glucose assimilability despite the fructose one was almost normal, and they had a single missense or nonsense mutation in the glucokinase gene glkA. The recombinant strain that was introduced at one of the mutations, glkA Q300K, demonstrated similar but not identical phenotypes to the mutant strain. This result indicates that glkA Q300K is one of the major mutations in 2-DG resistant strains.
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Affiliation(s)
- Kazuya Tomimoto
- Brewing Microbiology Division, National Research Institute of Brewing, Higashi-hiroshima, Japan
| | - Yukio Osafune
- Brewing Technology Division, National Research Institute of Brewing, Higashi-hiroshima, Japan
| | - Dararat Kakizono
- Brewing Technology Division, National Research Institute of Brewing, Higashi-hiroshima, Japan
| | - Jinshun Han
- Brewing Technology Division, National Research Institute of Brewing, Higashi-hiroshima, Japan
| | - Nobuhiko Mukai
- Brewing Technology Division, National Research Institute of Brewing, Higashi-hiroshima, Japan
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11
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Defenouillère Q, Verraes A, Laussel C, Friedrich A, Schacherer J, Léon S. The induction of HAD-like phosphatases by multiple signaling pathways confers resistance to the metabolic inhibitor 2-deoxyglucose. Sci Signal 2019; 12:12/597/eaaw8000. [PMID: 31481524 DOI: 10.1126/scisignal.aaw8000] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Anti-cancer strategies that target the glycolytic metabolism of tumors have been proposed. The glucose analog 2-deoxyglucose (2DG) is imported into cells and, after phosphorylation, becomes 2DG-6-phosphate, a toxic by-product that inhibits glycolysis. Using yeast as a model, we performed an unbiased mass spectrometry-based approach to probe the cellular effects of 2DG on the proteome and study resistance mechanisms to 2DG. We found that two phosphatases that target 2DG-6-phosphate were induced upon exposure to 2DG and participated in 2DG detoxification. Dog1 and Dog2 are HAD (haloacid dehalogenase)-like phosphatases, which are evolutionarily conserved. 2DG induced Dog2 by activating several signaling pathways, such as the stress response pathway mediated by the p38 MAPK ortholog Hog1, the unfolded protein response (UPR) triggered by 2DG-induced ER stress, and the cell wall integrity (CWI) pathway mediated by the MAPK Slt2. Loss of the UPR or CWI pathways led to 2DG hypersensitivity. In contrast, mutants impaired in the glucose-mediated repression of genes were 2DG resistant because glucose availability transcriptionally repressed DOG2 by inhibiting signaling mediated by the AMPK ortholog Snf1. The characterization and genome resequencing of spontaneous 2DG-resistant mutants revealed that DOG2 overexpression was a common strategy underlying 2DG resistance. The human Dog2 homolog HDHD1 displayed phosphatase activity toward 2DG-6-phosphate in vitro and its overexpression conferred 2DG resistance in HeLa cells, suggesting that this 2DG phosphatase could interfere with 2DG-based chemotherapies. These results show that HAD-like phosphatases are evolutionarily conserved regulators of 2DG resistance.
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Affiliation(s)
- Quentin Defenouillère
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75205, Paris Cedex 13, France
| | - Agathe Verraes
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75205, Paris Cedex 13, France
| | - Clotilde Laussel
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75205, Paris Cedex 13, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, 67000 Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, 67000 Strasbourg, France
| | - Sébastien Léon
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75205, Paris Cedex 13, France.
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12
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He C, Chen J, Wang H, Wan Y, Zhou J, Dan Z, Zeng Y, Xu W, Zhu Y, Huang W, Yin L. Crystal structures of rice hexokinase 6 with a series of substrates shed light on its enzymatic mechanism. Biochem Biophys Res Commun 2019; 515:614-620. [PMID: 31176485 DOI: 10.1016/j.bbrc.2019.05.139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/22/2019] [Indexed: 11/29/2022]
Abstract
Hexokinases (HXKs) have determined to be multifaceted proteins, and they are the only ones able to phosphorylate glucose in plants. However, the binding mode for ATP to plant HXKs remains unclear. Here, we report the crystal structures of rice hexokinase 6 (OsHXK6) in four different forms: (i) apo-form, (ii) binary complex with D-Glc, (iii) quaternary complex with ADP, PO4 and Mg2+, and (iv) pentanary complex with D-Glc, ADP, PO4, and Mg2+. The apo form is in the open state conformation, and the three others are in the closed state, indicating that glucose and ADP-PO4 binding induces a large conformational change by domain rearrangement. The quaternary complex is a novel intermediate during the catalytic reaction we trapped for the first time, which provides a new evidence for the enzymatic mechanism of HXKs. In addition, the latter two complexes reveal the binding mode for ADP-PO4 to plant HXKs, which provide the structural explanation for the dual-function of OsHXK6. In addition, we identified that residues Gly112, Thr261, Gly262, and Gly450 are essential to the binding between ADP-PO4 and OsHXK6 by a series of single mutations and enzymatic assays. Our study provide structural basis for the other functional studies of OsHXK6 in rice.
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Affiliation(s)
- Chunlan He
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Ministry of Agriculture, Wuhan University, Wuhan, 430072, China
| | - Juan Chen
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Ministry of Agriculture, Wuhan University, Wuhan, 430072, China
| | - Hongjian Wang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yibin Wan
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jin Zhou
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhiwu Dan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Ministry of Agriculture, Wuhan University, Wuhan, 430072, China
| | - Yafei Zeng
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Ministry of Agriculture, Wuhan University, Wuhan, 430072, China
| | - Wuwu Xu
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Ministry of Agriculture, Wuhan University, Wuhan, 430072, China
| | - Yingguo Zhu
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Ministry of Agriculture, Wuhan University, Wuhan, 430072, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, The Ministry of Agriculture, Wuhan University, Wuhan, 430072, China.
| | - Lei Yin
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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13
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Aguilera-Alvarado GP, Guevara-García ÁA, Estrada-Antolín SA, Sánchez-Nieto S. Biochemical properties and subcellular localization of six members of the HXK family in maize and its metabolic contribution to embryo germination. BMC PLANT BIOLOGY 2019; 19:27. [PMID: 30646852 PMCID: PMC6332545 DOI: 10.1186/s12870-018-1605-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/17/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND Seed germination is a crucial process in the plant life cycle when a dramatic variation of type and sugar content occurs just as the seed is hydrated. The production of hexose 6 phosphate is a key node in different pathways that are required for a successful germination. Hexokinase (HXK) is the only plant enzyme that phosphorylates glucose (Glc), so it is key to fueling several metabolic pathways depending on their substrate specificity, metabolite regulatory responses and subcellular localization. In maize, the HXK family is composed of nine genes, but only six of them (ZmHXK4-9) putatively encode catalytically active enzymes. Here, we cloned and functionally characterized putative catalytic enzymes to analyze their metabolic contribution during germination process. RESULTS From the six HXKs analyzed here, only ZmHXK9 has minimal hexose phosphorylating activity even though enzymatic function of all isoforms (ZmHXK4-9) was confirmed using a yeast complementation approach. The kinetic parameters of recombinant proteins showed that ZmHXK4-7 have high catalytic efficiency for Glc, fructose (Fru) and mannose (Man), ZmHXK7 has a lower Km for ATP, and together with ZmHXK8 they have lower sensitivity to inhibition by ADP, G6P and N-acetylglucosamine than ZmHXK4-6 and ZmHXK9. Additionally, we demonstrated that ZmHXK4-6 and ZmHXK9 are located in the mitochondria and their location relies on the first 30 amino acids of the N-terminal domain. Otherwise, ZmHXK7-8 are constitutively located in the cytosol. HXK activity was detected in cytosolic and mitochondrial fractions and high Glc and Fru phosphorylating activities were found in imbibed embryos. CONCLUSIONS Considering the biochemical characteristics, location and the expression of ZmHXK4 at onset of germination, we suggest that it is the main contributor to mitochondrial activity at early germination times, at 24 h other ZmHXKs also contribute to the total activity. While in the cytosol, ZmHXK7 could be responsible for the activity at the onset of germination, although later, ZmHXK8 also contributes to the total HXK activity. Our observations suggest that the HXKs may be redundant proteins with specific roles depending on carbon and ATP availability, metabolic needs, or sensor requirements. Further investigation is necessary to understand their specific or redundant physiological roles.
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Affiliation(s)
| | - Ángel Arturo Guevara-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Sobeida Sánchez-Nieto
- Departamento de Bioquímica, Facultad de Química, Conjunto E., Universidad Nacional Autónoma de México, CDMX, Mexico
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14
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Günther JP, Börsch M, Fischer P. Diffusion Measurements of Swimming Enzymes with Fluorescence Correlation Spectroscopy. Acc Chem Res 2018; 51:1911-1920. [PMID: 30160941 DOI: 10.1021/acs.accounts.8b00276] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Self-propelled chemical motors are chemically powered micro- or nanosized swimmers. The energy required for these motors' active motion derives from catalytic chemical reactions and the transformation of a fuel dissolved in the solution. While self-propulsion is now well established for larger particles, it is still unclear if enzymes, nature's nanometer-sized catalysts, are potentially also self-powered nanomotors. Because of its small size, any increase in an enzyme's diffusion due to active self-propulsion must be observed on top of the enzyme's passive Brownian motion, which dominates at this scale. Fluorescence correlation spectroscopy (FCS) is a sensitive method to quantify the diffusion properties of single fluorescently labeled molecules in solution. FCS experiments have shown a general increase in the diffusion constant of a number of enzymes when the enzyme is catalytically active. Diffusion enhancements after addition of the enzyme's substrate (and sometimes its inhibitor) of up to 80% have been reported, which is at least 1 order of magnitude higher than what theory would predict. However, many factors contribute to the FCS signal and in particular the shape of the autocorrelation function, which underlies diffusion measurements by fluorescence correlation spectroscopy. These effects need to be considered to establish if and by how much the catalytic activity changes an enzyme's diffusion. We carefully review phenomena that can play a role in FCS experiments and the determination of enzyme diffusion, including the dissociation of enzyme oligomers upon interaction with the substrate, surface binding of the enzyme to glass during the experiment, conformational changes upon binding, and quenching of the fluorophore. We show that these effects can cause changes in the FCS signal that behave similar to an increase in diffusion. However, in the case of the enzymes F1-ATPase and alkaline phosphatase, we demonstrate that there is no measurable increase in enzyme diffusion. Rather, dissociation and conformational changes account for the changes in the FCS signal in the former and fluorophore quenching in the latter. Within the experimental accuracy of our FCS measurements, we do not observe any change in diffusion due to activity for the enzymes we have investigated. We suggest useful control experiments and additional tests for future FCS experiments that should help establish if the observed diffusion enhancement is real or if it is due to an experimental or data analysis artifact. We show that fluorescence lifetime and mean intensity measurements are essential in order to identify the nature of the observed changes in the autocorrelation function. While it is clear from theory that chemically active enzymes should also act as self-propelled nanomotors, our FCS measurements show that the associated increase in diffusion is much smaller than previously reported. Further experiments are needed to quantify the contribution of the enzymes' catalytic activity to their self-propulsion. We hope that our findings help to establish a useful protocol for future FCS studies in this field and help establish by how much the diffusion of an enzyme is enhanced through catalytic activity.
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Affiliation(s)
- Jan-Philipp Günther
- Max Planck Institute for Intelligent Systems, 70569 Stuttgart, Germany
- Institute of Physical Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Michael Börsch
- Jena University Hospital, Friedrich-Schiller University Jena, 07743 Jena, Germany
| | - Peer Fischer
- Max Planck Institute for Intelligent Systems, 70569 Stuttgart, Germany
- Institute of Physical Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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15
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Cross M, Biberacher S, Park S, Rajan S, Korhonen P, Gasser RB, Kim J, Coster MJ, Hofmann A. Trehalose 6‐phosphate phosphatases of
Pseudomonas aeruginosa. FASEB J 2018; 32:5470-5482. [DOI: 10.1096/fj.201800500r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Megan Cross
- Griffith Institute for Drug Discovery, Griffith UniversityNathan QueenslandAustralia
| | - Sonja Biberacher
- Griffith Institute for Drug Discovery, Griffith UniversityNathan QueenslandAustralia
- Department of BiologyFriedrich‐Alexander University, Erlangen‐NurembergErlangenGermany
| | - Suk‐Youl Park
- Pohang Accelerator Laboratory, Pohang University of Science and TechnologyPohang GyeongbukSouth Korea
| | - Siji Rajan
- Griffith Institute for Drug Discovery, Griffith UniversityNathan QueenslandAustralia
| | - Pasi Korhonen
- Department of Veterinary BiosciencesMelbourne Veterinary School, The University of MelbourneParkville VictoriaAustralia
| | - Robin B. Gasser
- Department of Veterinary BiosciencesMelbourne Veterinary School, The University of MelbourneParkville VictoriaAustralia
| | - Jeong‐Sun Kim
- Department of ChemistryChonnam National UniversityGwangjuSouth Korea
| | - Mark J. Coster
- Griffith Institute for Drug Discovery, Griffith UniversityNathan QueenslandAustralia
| | - Andreas Hofmann
- Griffith Institute for Drug Discovery, Griffith UniversityNathan QueenslandAustralia
- Department of Veterinary BiosciencesMelbourne Veterinary School, The University of MelbourneParkville VictoriaAustralia
- Queensland Tropical Health AllianceSmithfield QueenslandAustralia
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16
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Barradas-Bautista D, Rosell M, Pallara C, Fernández-Recio J. Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems. PROTEIN-PROTEIN INTERACTIONS IN HUMAN DISEASE, PART A 2018; 110:203-249. [DOI: 10.1016/bs.apcsb.2017.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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17
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Conformational Characteristics of Rice Hexokinase OsHXK7 as a Moonlighting Protein involved in Sugar Signalling and Metabolism. Protein J 2017; 36:249-256. [PMID: 28555318 DOI: 10.1007/s10930-017-9718-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Hexokinase (HXK) as a moonlighting protein involves in glucose metabolism and signalling to regulate growth and development in plants. Therefore, the clarification for the structural properties of OsHXK7 (Oryza sativa Hexokinase 7) is essential to understand its role mechanism associated with the Glc signalling and metabolism. In this study, the structural characteristics of OsHXK7 (Oryza sativa Hexokinase 7) were identified. In the fluorescence spectrum, the Trp peak representing OsHXK7 binding to D-glucose (D-Glc) and 2-deoxyglucose (2-dG) showed an obvious blue shift. The distinct change in the secondary structure of OsHXK7 after binding to Glc was also detected in circular dichroism spectra. Using superimposed modelling, OsHXK7 showed a Glc-induced structural change, in which the 76th glycine, 148th serine and 256th tryptophan were contained within the pocket region. It was further shown by site-directed mutagenesis that the 76th glycine and the 256th tryptophan, but not the 148th serine, are the pivotal sites of OsHXK7 that maintain its catalytic activity and intrinsic blue shift fluorescence. These results suggest that OsHXK7 binding to Glc leads to a conformational change, that is likely essential for the function of OsHXK7 in Glc signalling and metabolism during plant growth and development.
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18
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Schwarz RJ, Richert C. A four-helix bundle DNA nanostructure with binding pockets for pyrimidine nucleotides. NANOSCALE 2017; 9:7047-7054. [PMID: 28327725 DOI: 10.1039/c7nr00094d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Designed DNA nanostructures of impressive size have been described, but designed structures of the size of protein enzymes that bind organic ligands with high specificity are rare. Here we report a four-helix motif consisting of three synthetic strands with 65 base pairs and 165 nucleotides in total that folds well. Furthermore, we show that in the interior of this small folded DNA nanostructure, cavities can be set up that bind pyrimidine nucleotides with micromolar affinity. Base-specific binding for both thymidine and cytidine derivatives is demonstrated. The binding affinity depends on the position in the structure, as expected for recognition beyond simple base pairing. The folding motif reported here can help to expand DNA nanotechnology into the realm of selective molecular recognition that is currently dominated by protein-based enzymes and receptors.
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Affiliation(s)
- Rainer Joachim Schwarz
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany.
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19
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Wiredu Boakye D, Jaroenlak P, Prachumwat A, Williams TA, Bateman KS, Itsathitphaisarn O, Sritunyalucksana K, Paszkiewicz KH, Moore KA, Stentiford GD, Williams BAP. Decay of the glycolytic pathway and adaptation to intranuclear parasitism within Enterocytozoonidae microsporidia. Environ Microbiol 2017; 19:2077-2089. [DOI: 10.1111/1462-2920.13734] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/24/2017] [Accepted: 03/05/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Dominic Wiredu Boakye
- Biosciences; College of Life and Environmental Sciences, University of Exeter; EX4 4QD UK
| | - Pattana Jaroenlak
- Department of Biochemistry, Faculty of Science; Mahidol University; Rama VI Rd Bangkok 10400 Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science; Mahidol University; Rama VI Rd Bangkok 10400 Thailand
| | - Anuphap Prachumwat
- Shrimp-Virus Interaction Laboratory (ASVI); National Center for Genetic Engineering and Biotechnology (BIOTEC); Rama VI Rd Bangkok 10400 Thailand
| | | | - Kelly S. Bateman
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment Fisheries and Aquaculture Science, Weymouth Laboratory; Weymouth Dorset DT4 8UB UK
| | - Ornchuma Itsathitphaisarn
- Department of Biochemistry, Faculty of Science; Mahidol University; Rama VI Rd Bangkok 10400 Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science; Mahidol University; Rama VI Rd Bangkok 10400 Thailand
| | - Kallaya Sritunyalucksana
- Shrimp-Virus Interaction Laboratory (ASVI); National Center for Genetic Engineering and Biotechnology (BIOTEC); Rama VI Rd Bangkok 10400 Thailand
| | - Konrad H. Paszkiewicz
- Biosciences; College of Life and Environmental Sciences, University of Exeter; EX4 4QD UK
| | - Karen A. Moore
- Biosciences; College of Life and Environmental Sciences, University of Exeter; EX4 4QD UK
| | - Grant D. Stentiford
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment Fisheries and Aquaculture Science, Weymouth Laboratory; Weymouth Dorset DT4 8UB UK
| | - Bryony A. P. Williams
- Biosciences; College of Life and Environmental Sciences, University of Exeter; EX4 4QD UK
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20
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Feng J, Zhao S, Chen X, Wang W, Dong W, Chen J, Shen JR, Liu L, Kuang T. Biochemical and structural study of Arabidopsis hexokinase 1. ACTA ACUST UNITED AC 2015; 71:367-75. [PMID: 25664748 DOI: 10.1107/s1399004714026091] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/27/2014] [Indexed: 01/11/2023]
Abstract
Hexokinase 1 from Arabidopsis thaliana (AtHXK1) plays a dual role in glycolysis and sugar sensing for vital metabolic and physiological processes. The uncoupling of glucose signalling from glucose metabolism was demonstrated by the analysis of two mutants (AtHXK1(G104D) and AtHXK1(S177A)) that are catalytically inactive but still functional in signalling. In this study, substrate-binding experiments indicate that the two catalytically inactive mutants have a high affinity for glucose, and an ordered substrate-binding mechanism has been observed for wild-type AtHXK1. The structure of AtHXK1 was determined both in its inactive unliganded form and in its active glucose-bound form at resolutions of 1.8 and 2.0 Å, respectively. These structures reveal a domain rearrangement of AtHXK1 upon glucose binding. The 2.1 Å resolution structure of AtHXK1(S177A) in the glucose-bound form shows similar glucose-binding interactions as the wild type. A glucose-sensing network has been proposed based on these structures. Taken together, the results provide a structural explanation for the dual functions of AtHXK1.
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Affiliation(s)
- Juan Feng
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, People's Republic of China
| | - Shun Zhao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, People's Republic of China
| | - Xuemin Chen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, People's Republic of China
| | - Wenda Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, People's Republic of China
| | - Wei Dong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, People's Republic of China
| | - Jinghua Chen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, People's Republic of China
| | - Jian-Ren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, People's Republic of China
| | - Lin Liu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, People's Republic of China
| | - Tingyun Kuang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, People's Republic of China
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21
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Mannige RV. Dynamic New World: Refining Our View of Protein Structure, Function and Evolution. Proteomes 2014; 2:128-153. [PMID: 28250374 PMCID: PMC5302727 DOI: 10.3390/proteomes2010128] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/12/2014] [Accepted: 02/20/2014] [Indexed: 01/06/2023] Open
Abstract
Proteins are crucial to the functioning of all lifeforms. Traditional understanding posits that a single protein occupies a single structure ("fold"), which performs a single function. This view is radically challenged with the recognition that high structural dynamism-the capacity to be extra "floppy"-is more prevalent in functional proteins than previously assumed. As reviewed here, this dynamic take on proteins affects our understanding of protein "structure", function, and evolution, and even gives us a glimpse into protein origination. Specifically, this review will discuss historical developments concerning protein structure, and important new relationships between dynamism and aspects of protein sequence, structure, binding modes, binding promiscuity, evolvability, and origination. Along the way, suggestions will be provided for how key parts of textbook definitions-that so far have excluded membership to intrinsically disordered proteins (IDPs)-could be modified to accommodate our more dynamic understanding of proteins.
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Affiliation(s)
- Ranjan V Mannige
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road,Berkeley, CA 94720, USA.
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22
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Kettner K, Kuettner EB, Otto A, Lilie H, Golbik RP, Sträter N, Kriegel TM. In vivo phosphorylation and in vitro autophosphorylation-inactivation of Kluyveromyces lactis hexokinase KlHxk1. Biochem Biophys Res Commun 2013; 435:313-8. [PMID: 23583397 DOI: 10.1016/j.bbrc.2013.03.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 03/28/2013] [Indexed: 11/16/2022]
Abstract
The bifunctional hexokinase KlHxk1 is a key component of glucose-dependent signal transduction in Kluyveromyces lactis. KlHxk1 is phosphorylated in vivo and undergoes ATP-dependent autophosphorylation-inactivation in vitro. This study identifies serine-15 as the site of in vivo phosphorylation and serine-157 as the autophosphorylation-inactivation site. X-ray crystallography of the in vivo phosphorylated enzyme indicates the existence of a ring-shaped symmetrical homodimer carrying two phosphoserine-15 residues. In contrast, small-angle X-ray scattering and equilibrium sedimentation analyses reveal the existence of monomeric phosphoserine-15 KlHxk1 in solution. While phosphorylation at serine-15 and concomitant homodimer dissociation are likely to be involved in glucose signalling, mechanism and putative physiological significance of KlHxk1 inactivation by autophosphorylation at serine-157 remain to be established.
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Affiliation(s)
- Karina Kettner
- Institute of Physiological Chemistry, Carl Gustav Carus Medical Faculty, Technische Universität Dresden, Dresden, Germany.
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23
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24
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Nilsson A, Olsson T, Ulfstedt M, Thelander M, Ronne H. Two novel types of hexokinases in the moss Physcomitrella patens. BMC PLANT BIOLOGY 2011; 11:32. [PMID: 21320325 PMCID: PMC3045890 DOI: 10.1186/1471-2229-11-32] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 02/14/2011] [Indexed: 05/22/2023]
Abstract
BACKGROUND Hexokinase catalyzes the phosphorylation of glucose and fructose, but it is also involved in sugar sensing in both fungi and plants. We have previously described two types of hexokinases in the moss Physcomitrella. Type A, exemplified by PpHxk1, the major hexokinase in Physcomitrella, is a soluble protein that localizes to the chloroplast stroma. Type B, exemplified by PpHxk2, has an N-terminal membrane anchor. Both types are found also in vascular plants, and localize to the chloroplast stroma and mitochondrial membranes, respectively. RESULTS We have now characterized all 11 hexokinase encoding genes in Physcomitrella. Based on their N-terminal sequences and intracellular localizations, three of the encoded proteins are type A hexokinases and four are type B hexokinases. One of the type B hexokinases has a splice variant without a membrane anchor, that localizes to the cytosol and the nucleus. However, we also found two new types of hexokinases with no obvious orthologs in vascular plants. Type C, encoded by a single gene, has neither transit peptide nor membrane anchor, and is found in the cytosol and in the nucleus. Type D hexokinases, encoded by three genes, have membrane anchors and localize to mitochondrial membranes, but their sequences differ from those of the type B hexokinases. Interestingly, all moss hexokinases are more similar to each other in overall sequence than to hexokinases from other plants, even though characteristic sequence motifs such as the membrane anchor of the type B hexokinases are highly conserved between moss and vascular plants, indicating a common origin for hexokinases of the same type. CONCLUSIONS We conclude that the hexokinase gene family is more diverse in Physcomitrella, encoding two additional types of hexokinases that are absent in vascular plants. In particular, the presence of a cytosolic and nuclear hexokinase (type C) sets Physcomitrella apart from vascular plants, and instead resembles yeast, where all hexokinases localize to the cytosol. The fact that all moss hexokinases are more similar to each other than to hexokinases from vascular plants, even though both type A and type B hexokinases are present in all plants, further suggests that the hexokinase gene family in Physcomitrella has undergone concerted evolution.
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Affiliation(s)
- Anders Nilsson
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-750 07 Uppsala, Sweden
| | - Tina Olsson
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, Box 7080, SE-750 07 Uppsala, Sweden
| | - Mikael Ulfstedt
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-750 07 Uppsala, Sweden
| | - Mattias Thelander
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, Box 7080, SE-750 07 Uppsala, Sweden
| | - Hans Ronne
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-750 07 Uppsala, Sweden
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25
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Kuettner EB, Kettner K, Keim A, Svergun DI, Volke D, Singer D, Hoffmann R, Müller EC, Otto A, Kriegel TM, Sträter N. Crystal structure of hexokinase KlHxk1 of Kluyveromyces lactis: a molecular basis for understanding the control of yeast hexokinase functions via covalent modification and oligomerization. J Biol Chem 2010; 285:41019-33. [PMID: 20943665 PMCID: PMC3003401 DOI: 10.1074/jbc.m110.185850] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Indexed: 11/06/2022] Open
Abstract
Crystal structures of the unique hexokinase KlHxk1 of the yeast Kluyveromyces lactis were determined using eight independent crystal forms. In five crystal forms, a symmetrical ring-shaped homodimer was observed, corresponding to the physiological dimer existing in solution as shown by small-angle x-ray scattering. The dimer has a head-to-tail arrangement such that the small domain of one subunit interacts with the large domain of the other subunit. Dimer formation requires favorable interactions of the 15 N-terminal amino acids that are part of the large domain with amino acids of the small domain of the opposite subunit, respectively. The head-to-tail arrangement involving both domains of the two KlHxk1 subunits is appropriate to explain the reduced activity of the homodimer as compared with the monomeric enzyme and the influence of substrates and products on dimer formation and dissociation. In particular, the structure of the symmetrical KlHxk1 dimer serves to explain why phosphorylation of conserved residue Ser-15 may cause electrostatic repulsions with nearby negatively charged residues of the adjacent subunit, thereby inducing a dissociation of the homologous dimeric hexokinases KlHxk1 and ScHxk2. Two complex structures of KlHxk1 with bound glucose provide a molecular model of substrate binding to the open conformation and the subsequent classical domain closure motion of yeast hexokinases. The entirety of the novel data extends the current concept of glucose signaling in yeast and complements the induced-fit model by integrating the events of N-terminal phosphorylation and dissociation of homodimeric yeast hexokinases.
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Affiliation(s)
- E. Bartholomeus Kuettner
- From the Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany
| | - Karina Kettner
- the Institute of Physiological Chemistry, Carl Gustav Carus Medical Faculty, Dresden University of Technology, D-01307 Dresden, Germany
| | - Antje Keim
- From the Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany
| | - Dmitri I. Svergun
- the European Molecular Biology Laboratory, Hamburg Outstation, Deutsches Elektronen-Synchrotron, D-22603 Hamburg, Germany, and
| | - Daniela Volke
- From the Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany
| | - David Singer
- From the Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany
| | - Ralf Hoffmann
- From the Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany
| | | | - Albrecht Otto
- the Max Delbrück Center for Molecular Medicine, D-13125 Berlin, Germany
| | - Thomas M. Kriegel
- the Institute of Physiological Chemistry, Carl Gustav Carus Medical Faculty, Dresden University of Technology, D-01307 Dresden, Germany
| | - Norbert Sträter
- From the Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, University of Leipzig, D-04103 Leipzig, Germany
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26
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Abstract
Hkx2 (hexokinase 2) from Saccharomyces cerevisiae was one of the first metabolic enzymes described as a multifunctional protein. Hxk2 has a double subcellular localization: it functions as a glycolytic enzyme in the cytoplasm and as a regulator of gene transcription of several Mig1-regulated genes in the nucleus. To get more insights into the structure–function relationships of the Hxk2 protein, we followed two different approaches. In the first, we deleted the last eight amino acids of Hxk2 and replaced Ser304 with phenylalanine to generate Hxk2wca. Analysis of this mutant demonstrated that these domains play an essential role in the catalytic activity of yeast Hxk2, but has no effect on the regulatory function of this protein. In the second, we analysed whether amino acids from Lys6 to Met15 of Hxk2 (Hxk2wrf) are essential for the regulatory role of Hxk2 and whether there is an effect on the hexose kinase activity of this protein. In the present paper, we report that the Hxk2wca mutant protein interacts with the Mig1 transcriptional repressor and the Snf1 protein kinase in the nucleus at the level of the SUC2–Mig1 repressor complex. We have demonstrated that Hxk2wca maintained full regulatory function because the glucose-repression signalling of the wild-type machinery is maintained. We also report that the Hxk2wrf mutant allele is incapable of glucose repression signalling because it does not interact with Mig1 at the level of the SUC2–Mig1 repressor complex. The two mutants, Hxk2wca and Hxk2wrf retain single functions, as a transcriptional factor or as an enzyme with hexose-phosphorylating activity, but have lost the original bifunctionality of Hxk2.
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Yeast hexokinase isoenzyme ScHxk2: stability of a two-domain protein with discontinuous domains. Protein Eng Des Sel 2010; 24:79-87. [DOI: 10.1093/protein/gzq098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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de C. Palmieri L, Lima LMTR, Freire JBB, Bleicher L, Polikarpov I, Almeida FCL, Foguel D. Novel Zn2+-binding sites in human transthyretin: implications for amyloidogenesis and retinol-binding protein recognition. J Biol Chem 2010; 285:31731-41. [PMID: 20659897 PMCID: PMC2951245 DOI: 10.1074/jbc.m110.157206] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Indexed: 11/06/2022] Open
Abstract
Human transthyretin (TTR) is a homotetrameric protein involved in several amyloidoses. Zn(2+) enhances TTR aggregation in vitro, and is a component of ex vivo TTR amyloid fibrils. We report the first crystal structure of human TTR in complex with Zn(2+) at pH 4.6-7.5. All four structures reveal three tetra-coordinated Zn(2+)-binding sites (ZBS 1-3) per monomer, plus a fourth site (ZBS 4) involving amino acid residues from a symmetry-related tetramer that is not visible in solution by NMR. Zn(2+) binding perturbs loop E-α-helix-loop F, the region involved in holo-retinol-binding protein (holo-RBP) recognition, mainly at acidic pH; TTR affinity for holo-RBP decreases ∼5-fold in the presence of Zn(2+). Interestingly, this same region is disrupted in the crystal structure of the amyloidogenic intermediate of TTR formed at acidic pH in the absence of Zn(2+). HNCO and HNCA experiments performed in solution at pH 7.5 revealed that upon Zn(2+) binding, although the α-helix persists, there are perturbations in the resonances of the residues that flank this region, suggesting an increase in structural flexibility. While stability of the monomer of TTR decreases in the presence of Zn(2+), which is consistent with the tertiary structural perturbation provoked by Zn(2+) binding, tetramer stability is only marginally affected by Zn(2+). These data highlight structural and functional roles of Zn(2+) in TTR-related amyloidoses, as well as in holo-RBP recognition and vitamin A homeostasis.
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Affiliation(s)
| | | | | | - Lucas Bleicher
- the Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo 13560-970, Brazil
| | - Igor Polikarpov
- the Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo 13560-970, Brazil
| | - Fabio C. L. Almeida
- From the Instituto de Bioquimica Medica, Programa de Biologia Estrutural
- Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil and
| | - Debora Foguel
- From the Instituto de Bioquimica Medica, Programa de Biologia Estrutural
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29
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Blume A, Fitzen M, Benie AJ, Peters T. Specificity of ligand binding to yeast hexokinase PII studied by STD-NMR. Carbohydr Res 2009; 344:1567-74. [DOI: 10.1016/j.carres.2009.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2008] [Revised: 12/14/2008] [Accepted: 01/06/2009] [Indexed: 11/16/2022]
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Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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