1
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Di X, Ortega-Alarcon D, Kakumanu R, Iglesias-Fernandez J, Diaz L, Baidoo EEK, Velazquez-Campoy A, Rodríguez-Concepción M, Perez-Gil J. MEP pathway products allosterically promote monomerization of deoxy-D-xylulose-5-phosphate synthase to feedback-regulate their supply. PLANT COMMUNICATIONS 2023; 4:100512. [PMID: 36575800 DOI: 10.1016/j.xplc.2022.100512] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/11/2022] [Accepted: 12/22/2022] [Indexed: 05/11/2023]
Abstract
Isoprenoids are a very large and diverse family of metabolites required by all living organisms. All isoprenoids derive from the double-bond isomers isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are produced by the methylerythritol 4-phosphate (MEP) pathway in bacteria and plant plastids. It has been reported that IPP and DMAPP feedback-regulate the activity of deoxyxylulose 5-phosphate synthase (DXS), a dimeric enzyme that catalyzes the main flux-controlling step of the MEP pathway. Here we provide experimental insights into the underlying mechanism. Isothermal titration calorimetry and dynamic light scattering approaches showed that IPP and DMAPP can allosterically bind to DXS in vitro, causing a size shift. In silico ligand binding site analysis and docking calculations identified a potential allosteric site in the contact region between the two monomers of the active DXS dimer. Modulation of IPP and DMAPP contents in vivo followed by immunoblot analyses confirmed that high IPP/DMAPP levels resulted in monomerization and eventual aggregation of the enzyme in bacterial and plant cells. Loss of the enzymatically active dimeric conformation allows a fast and reversible reduction of DXS activity in response to a sudden increase or decrease in IPP/DMAPP supply, whereas aggregation and subsequent removal of monomers that would otherwise be available for dimerization appears to be a more drastic response in the case of persistent IPP/DMAPP overabundance (e.g., by a blockage in their conversion to downstream isoprenoids). Our results represent an important step toward understanding the regulation of the MEP pathway and rational design of biotechnological endeavors aimed at increasing isoprenoid contents in microbial and plant systems.
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Affiliation(s)
- Xueni Di
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de València, 46022 Valencia, Spain; Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain
| | - David Ortega-Alarcon
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ramu Kakumanu
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Lucia Diaz
- Nostrum Biodiscovery SL, 08029 Barcelona, Spain
| | - Edward E K Baidoo
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Adrian Velazquez-Campoy
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Manuel Rodríguez-Concepción
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de València, 46022 Valencia, Spain; Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain.
| | - Jordi Perez-Gil
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain.
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2
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Dimitrova YN, Gutierrez JA, Huard K. It's ok to be outnumbered - sub-stoichiometric modulation of homomeric protein complexes. RSC Med Chem 2023; 14:22-46. [PMID: 36760737 PMCID: PMC9890894 DOI: 10.1039/d2md00212d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
An arsenal of molecular tools with increasingly diversified mechanisms of action is being developed by the scientific community to enable biological interrogation and pharmaceutical modulation of targets and pathways of ever increasing complexity. While most small molecules interact with the target of interest in a 1 : 1 relationship, a noteworthy number of recent examples were reported to bind in a sub-stoichiometric manner to a homomeric protein complex. This approach requires molecular understanding of the physiologically relevant protein assemblies and in-depth characterization of the compound's mechanism of action. The recent literature examples summarized here were selected to illustrate methods used to identify and characterize molecules with such mechanisms. The concept of one small molecule targeting a homomeric protein assembly is not new but the subject deserves renewed inspection in light of emerging technologies and increasingly diverse target biology, to ensure relevant in vitro systems are used and valuable compounds with potentially novel sub-stoichiometric mechanisms of action aren't overlooked.
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Affiliation(s)
| | | | - Kim Huard
- Genentech 1 DNA Way South San Francisco CA 94080 USA
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3
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Bai Y, Jiao W, Vörster J, Parker EJ. Conformational interdomain flexibility in a bacterial α-isopropylmalate synthase is necessary for leucine biosynthesis. J Biol Chem 2022; 299:102789. [PMID: 36509144 PMCID: PMC9860122 DOI: 10.1016/j.jbc.2022.102789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
α-Isopropylmalate synthase (IPMS) catalyzes the first step in leucine (Leu) biosynthesis and is allosterically regulated by the pathway end product, Leu. IPMS is a dimeric enzyme with each chain consisting of catalytic, accessory, and regulatory domains, with the accessory and regulatory domains of each chain sitting adjacent to the catalytic domain of the other chain. The IPMS crystal structure shows significant asymmetry because of different relative domain conformations in each chain. Owing to the challenges posed by the dynamic and asymmetric structures of IPMS enzymes, the molecular details of their catalytic and allosteric mechanisms are not fully understood. In this study, we have investigated the allosteric feedback mechanism of the IPMS enzyme from the bacterium that causes meningitis, Neisseria meningitidis (NmeIPMS). By combining molecular dynamics simulations with small-angle X-ray scattering, mutagenesis, and heterodimer generation, we demonstrate that Leu-bound NmeIPMS is in a rigid conformational state stabilized by asymmetric interdomain polar interactions. Furthermore, we found removing these polar interactions by mutagenesis impaired the allosteric response without compromising Leu binding. Our results suggest that the allosteric inhibition of NmeIPMS is achieved by restricting the flexibility of the accessory and regulatory domains, demonstrating that significant conformational flexibility is required for catalysis.
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Affiliation(s)
- Yu Bai
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Wanting Jiao
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Jan Vörster
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Emily J. Parker
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand,For correspondence: Emily J. Parker
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4
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PRPS2 mutations drive acute lymphoblastic leukemia relapse through influencing PRPS1/2 hexamer stability. BLOOD SCIENCE 2022; 5:39-50. [PMID: 36742181 PMCID: PMC9891442 DOI: 10.1097/bs9.0000000000000139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Tumor relapse is the major cause of treatment failure in childhood acute lymphoblastic leukemia (ALL), yet the underlying mechanisms are still elusive. Here, we demonstrate that phosphoribosyl pyrophosphate synthetase 2 (PRPS2) mutations drive ALL relapse through influencing PRPS1/2 hexamer stability. Ultra-deep sequencing was performed to identify PRPS2 mutations in ALL samples. The effects of PRPS2 mutations on cell survival, cell apoptosis, and drug resistance were evaluated. In vitro PRPS2 enzyme activity and ADP/GDP feedback inhibition of PRPS enzyme activity were assessed. Purine metabolites were analyzed by ultra-performance liquid-chromatography tandem mass spectrometry (UPLC-MS/MS). Integrating sequencing data with clinical information, we identified PRPS2 mutations only in relapsed childhood ALL with thiopurine therapy. Functional PRPS2 mutations mediated purine metabolism specifically on thiopurine treatment by influencing PRPS1/2 hexamer stability, leading to reduced nucleotide feedback inhibition of PRPS activity and enhanced thiopurine resistance. The 3-amino acid V103-G104-E105, the key difference between PRPS1 and PRPS2, insertion in PRPS2 caused severe steric clash to the interface of PRPS hexamer, leading to its low enzyme activity. In addition, we demonstrated that PRPS2 P173R increased thiopurine resistance in xenograft models. Our work describes a novel mechanism by which PRPS2 mutants drive childhood ALL relapse and highlights PRPS2 mutations as biomarkers for relapsed childhood ALL.
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5
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Allostery Modulates Interactions between Proteasome Core Particles and Regulatory Particles. Biomolecules 2022; 12:biom12060764. [PMID: 35740889 PMCID: PMC9221237 DOI: 10.3390/biom12060764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 01/27/2023] Open
Abstract
Allostery-regulation at distant sites is a key concept in biology. The proteasome exhibits multiple forms of allosteric regulation. This regulatory communication can span a distance exceeding 100 Ångstroms and can modulate interactions between the two major proteasome modules: its core particle and regulatory complexes. Allostery can further influence the assembly of the core particle with regulatory particles. In this focused review, known and postulated interactions between these proteasome modules are described. Allostery may explain how cells build and maintain diverse populations of proteasome assemblies and can provide opportunities for therapeutic interventions.
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6
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Inhibitory feedback control of NF-κB signalling in health and disease. Biochem J 2021; 478:2619-2664. [PMID: 34269817 PMCID: PMC8286839 DOI: 10.1042/bcj20210139] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 12/14/2022]
Abstract
Cells must adapt to changes in their environment to maintain cell, tissue and organismal integrity in the face of mechanical, chemical or microbiological stress. Nuclear factor-κB (NF-κB) is one of the most important transcription factors that controls inducible gene expression as cells attempt to restore homeostasis. It plays critical roles in the immune system, from acute inflammation to the development of secondary lymphoid organs, and also has roles in cell survival, proliferation and differentiation. Given its role in such critical processes, NF-κB signalling must be subject to strict spatiotemporal control to ensure measured and context-specific cellular responses. Indeed, deregulation of NF-κB signalling can result in debilitating and even lethal inflammation and also underpins some forms of cancer. In this review, we describe the homeostatic feedback mechanisms that limit and ‘re-set’ inducible activation of NF-κB. We first describe the key components of the signalling pathways leading to activation of NF-κB, including the prominent role of protein phosphorylation and protein ubiquitylation, before briefly introducing the key features of feedback control mechanisms. We then describe the array of negative feedback loops targeting different components of the NF-κB signalling cascade including controls at the receptor level, post-receptor signalosome complexes, direct regulation of the critical ‘inhibitor of κB kinases’ (IKKs) and inhibitory feedforward regulation of NF-κB-dependent transcriptional responses. We also review post-transcriptional feedback controls affecting RNA stability and translation. Finally, we describe the deregulation of these feedback controls in human disease and consider how feedback may be a challenge to the efficacy of inhibitors.
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7
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Biddle JW, Martinez-Corral R, Wong F, Gunawardena J. Allosteric conformational ensembles have unlimited capacity for integrating information. eLife 2021; 10:65498. [PMID: 34106049 PMCID: PMC8189718 DOI: 10.7554/elife.65498] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 04/30/2021] [Indexed: 12/24/2022] Open
Abstract
Integration of binding information by macromolecular entities is fundamental to cellular functionality. Recent work has shown that such integration cannot be explained by pairwise cooperativities, in which binding is modulated by binding at another site. Higher-order cooperativities (HOCs), in which binding is collectively modulated by multiple other binding events, appear to be necessary but an appropriate mechanism has been lacking. We show here that HOCs arise through allostery, in which effective cooperativity emerges indirectly from an ensemble of dynamically interchanging conformations. Conformational ensembles play important roles in many cellular processes but their integrative capabilities remain poorly understood. We show that sufficiently complex ensembles can implement any form of information integration achievable without energy expenditure, including all patterns of HOCs. Our results provide a rigorous biophysical foundation for analysing the integration of binding information through allostery. We discuss the implications for eukaryotic gene regulation, where complex conformational dynamics accompanies widespread information integration.
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Affiliation(s)
- John W Biddle
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | | | - Felix Wong
- Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, Boston, United States
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8
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Wang Y, Wang G, Moitessier N, Mittermaier AK. Enzyme Kinetics by Isothermal Titration Calorimetry: Allostery, Inhibition, and Dynamics. Front Mol Biosci 2020; 7:583826. [PMID: 33195429 PMCID: PMC7604385 DOI: 10.3389/fmolb.2020.583826] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
Isothermal titration calorimetry (ITC) involves accurately measuring the heat that is released or absorbed in real time when one solution is titrated into another. This technique is usually used to measure the thermodynamics of binding reactions. However, there is mounting interest in using it to measure reaction kinetics, particularly enzymatic catalysis. This application of ITC has been steadily growing for the past two decades, and the method is proving to be sensitive, generally applicable, and capable of providing information on enzyme activity that is difficult to obtain using traditional biochemical assays. This review aims to give a broad overview of the use of ITC to measure enzyme kinetics. It describes several different classes of ITC experiment, their strengths and weaknesses, and recent methodological advancements. A summary of applications in the literature is given and several examples where ITC has been used to investigate challenging aspects of enzyme behavior are presented in more detail. These include examples of allostery, where small-molecule binding outside the active site modulates activity. We describe the use of ITC to measure the strength, mode (i.e., competitive, uncompetitive, or mixed), and association and dissociation kinetics of enzyme inhibitors. Further, we provide examples of ITC applied to complex, heterogeneous mixtures, such as insoluble substrates and live cells. These studies exemplify the wide range of problems where ITC can provide answers, and illustrate the versatility of the technique and potential for future development and applications.
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Affiliation(s)
- Yun Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
| | - Guanyu Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
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9
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Merdanovic M, Burston SG, Schmitz AL, Köcher S, Knapp S, Clausen T, Kaiser M, Huber R, Ehrmann M. Activation by substoichiometric inhibition. Proc Natl Acad Sci U S A 2020; 117:1414-1418. [PMID: 31907318 PMCID: PMC6983408 DOI: 10.1073/pnas.1918721117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Startling reports described the paradoxical triggering of the human mitogen-activated protein kinase pathway when a small-molecule inhibitor specifically inactivates the BRAF V600E protein kinase but not wt-BRAF. We performed a conceptual analysis of the general phenomenon "activation by inhibition" using bacterial and human HtrA proteases as models. Our data suggest a clear explanation that is based on the classic biochemical principles of allostery and cooperativity. Although substoichiometric occupancy of inhibitor binding sites results in partial inhibition, this effect is overrun by a concomitant activation of unliganded binding sites. Therefore, when an inhibitor of a cooperative enzyme does not reach saturating levels, a common scenario during drug administration, it may cause the contrary of the desired effect. The implications for drug development are discussed.
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Affiliation(s)
- Melisa Merdanovic
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117 Essen, Germany
| | - Steven G Burston
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, United Kingdom
| | - Anna Laura Schmitz
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117 Essen, Germany
| | - Steffen Köcher
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117 Essen, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Tim Clausen
- Research Institute of Molecular Pathology, 1030 Vienna, Austria
| | - Markus Kaiser
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117 Essen, Germany
| | - Robert Huber
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117 Essen, Germany;
- Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117 Essen, Germany;
- School of Biosciences, Cardiff University, Cardiff CF10 3US, United Kingdom
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10
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The Response of nor and nos Contributes to Staphylococcus aureus Virulence and Metabolism. J Bacteriol 2019; 201:JB.00107-19. [PMID: 30782631 DOI: 10.1128/jb.00107-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 12/21/2022] Open
Abstract
Staphylococcus aureus causes a wide spectrum of disease, with the site and severity of infection dependent on virulence traits encoded within genetically distinct clonal complexes (CCs) and bacterial responses to host innate immunity. The production of nitric oxide (NO) by activated phagocytes is a major host response to which S. aureus metabolically adapts through multiple strategies that are conserved in all CCs, including an S. aureus nitric oxide synthase (Nos). Previous genome analysis of CC30, a lineage associated with chronic endocardial and osteoarticular infections, revealed a putative NO reductase (Nor) not found in other CCs that potentially contributes to NO resistance and clinical outcome. Here, we demonstrate that Nor has true nitric oxide reductase activity, with nor expression enhanced by NO stress and anaerobic growth. Furthermore, we demonstrate that nor is regulated by MgrA and SrrAB, which modulate S. aureus virulence and hypoxic response. Transcriptome analysis of the S. aureus UAMS-1, UAMS-1 Δnor, and UAMS-1 Δnos strains under NO stress and anaerobic growth demonstrates that Nor contributes to nucleotide metabolism and Nos to glycolysis. We demonstrate that Nor and Nos contribute to enhanced survival in the presence of human human polymorphonuclear cells and have organ-specific seeding in a tail vein infection model. Nor contributes to abscess formation in an osteological implant model. We also demonstrate that Nor has a role in S. aureus metabolism and virulence. The regulation overlap between Nor and Nos points to an intriguing link between regulation of intracellular NO, metabolic adaptation, and persistence in the CC30 lineage.IMPORTANCE Staphylococcus aureus can cause disease at most body sites, and illness spans asymptomatic infection to death. The variety of clinical presentations is due to the diversity of strains, which are grouped into distinct clonal complexes (CCs) based on genetic differences. The ability of S. aureus CC30 to cause chronic infections relies on its ability to evade the oxidative/nitrosative defenses of the immune system and survive under different environmental conditions, including differences in oxygen and nitric oxide concentrations. The significance of this work is the exploration of unique genes involved in resisting NO stress and anoxia. A better understanding of the functions that control the response of S. aureus CC30 to NO and oxygen will guide the treatment of severe disease presentations.
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11
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Hodges M, Barahona M, Yaliraki SN. Allostery and cooperativity in multimeric proteins: bond-to-bond propensities in ATCase. Sci Rep 2018; 8:11079. [PMID: 30038211 PMCID: PMC6056424 DOI: 10.1038/s41598-018-27992-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/13/2018] [Indexed: 11/08/2022] Open
Abstract
Aspartate carbamoyltransferase (ATCase) is a large dodecameric enzyme with six active sites that exhibits allostery: its catalytic rate is modulated by the binding of various substrates at distal points from the active sites. A recently developed method, bond-to-bond propensity analysis, has proven capable of predicting allosteric sites in a wide range of proteins using an energy-weighted atomistic graph obtained from the protein structure and given knowledge only of the location of the active site. Bond-to-bond propensity establishes if energy fluctuations at given bonds have significant effects on any other bond in the protein, by considering their propagation through the protein graph. In this work, we use bond-to-bond propensity analysis to study different aspects of ATCase activity using three different protein structures and sources of fluctuations. First, we predict key residues and bonds involved in the transition between inactive (T) and active (R) states of ATCase by analysing allosteric substrate binding as a source of energy perturbations in the protein graph. Our computational results also indicate that the effect of multiple allosteric binding is non linear: a switching effect is observed after a particular number and arrangement of substrates is bound suggesting a form of long range communication between the distantly arranged allosteric sites. Second, cooperativity is explored by considering a bisubstrate analogue as the source of energy fluctuations at the active site, also leading to the identification of highly significant residues to the T ↔ R transition that enhance cooperativity across active sites. Finally, the inactive (T) structure is shown to exhibit a strong, non linear communication between the allosteric sites and the interface between catalytic subunits, rather than the active site. Bond-to-bond propensity thus offers an alternative route to explain allosteric and cooperative effects in terms of detailed atomistic changes to individual bonds within the protein, rather than through phenomenological, global thermodynamic arguments.
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Affiliation(s)
- Maxwell Hodges
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
- Institute of Chemical Biology, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
- Institute of Chemical Biology, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Sophia N Yaliraki
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom.
- Institute of Chemical Biology, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom.
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12
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Schamel WWA, Alarcon B, Höfer T, Minguet S. The Allostery Model of TCR Regulation. THE JOURNAL OF IMMUNOLOGY 2017; 198:47-52. [PMID: 27994168 DOI: 10.4049/jimmunol.1601661] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022]
Abstract
The activity of the αβ TCR is controlled by conformational switches. In the resting conformation, the TCR is not phosphorylated and is inactive. Binding of multivalent peptide-MHC to the TCR stabilizes the active conformation, leading to TCR signaling. These two conformations allow the TCRs to be allosterically regulated. We review recent data on heterotropic allostery where peptide-MHC and membrane cholesterol serve opposing functions as positive and negative allosteric regulators, respectively. In resting T cells cholesterol keeps TCRs in the resting conformation that otherwise would become spontaneously active. This regulation is well described by the classical Monod-Wyman-Changeux model of allostery. Moreover, the observation that TCRs assemble into nanoclusters might allow for homotropic allostery, in which individual TCRs could positively cooperate and thus enhance the sensitivity of T cell activation. This new view of TCR regulation will contribute to a better understanding of TCR functioning.
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Affiliation(s)
- Wolfgang W A Schamel
- Department of Immunology, Institute for Biology III, Faculty of Biology, University of Freiburg, 79108 Freiburg, Germany; .,BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Balbino Alarcon
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, 69120 Heidelberg, Germany; and.,BioQuant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Susana Minguet
- Department of Immunology, Institute for Biology III, Faculty of Biology, University of Freiburg, 79108 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
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13
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Sebastián M, Serrano A, Velázquez-Campoy A, Medina M. Kinetics and thermodynamics of the protein-ligand interactions in the riboflavin kinase activity of the FAD synthetase from Corynebacterium ammoniagenes. Sci Rep 2017; 7:7281. [PMID: 28779158 PMCID: PMC5544777 DOI: 10.1038/s41598-017-07875-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/04/2017] [Indexed: 01/20/2023] Open
Abstract
Enzymes known as bifunctional and bimodular prokaryotic type-I FAD synthetase (FADS) exhibit ATP:riboflavin kinase (RFK) and FMN:ATP adenylyltransferase (FMNAT) activities in their C-terminal and N-terminal modules, respectively, and produce flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). These act as cofactors of a plethora of flavoproteins in all organisms. Therefore, regulation of their production maintains the cellular flavoproteome homeostasis. Here, we focus on regulation of the FMN synthesis in Corynebacterium ammoniagenes (Ca) by the inhibition of its RFK activity by substrates and products of the reaction. We use a truncated CaFADS variant consisting in the isolated C-terminal RFK module, whose RFK activity is similar to that of the full-length enzyme. Inhibition of the RFK activity by the RF substrate is independent of the FMNAT module, and FMN production, in addition to being inhibited by an excess of RF, is also inhibited by both of the reaction products. Pre-steady-state kinetic and thermodynamic studies reveal key aspects to the substrates induced fit to produce the catalytically competent complex. Among them, the role of Mg2+ in the concerted allocation of substrates for catalysis and the ensemble of non-competent complexes that contribute to the regulated inhibition of the RFK activity are particularly relevant.
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Affiliation(s)
- María Sebastián
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain
| | - Ana Serrano
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain.,Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, Madrid, Spain
| | - Adrián Velázquez-Campoy
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain.,ARAID Foundation, Diputación General de Aragón, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Milagros Medina
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain.
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14
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Einav T, Phillips R. Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants. J Phys Chem B 2017; 121:3813-3824. [PMID: 28134524 DOI: 10.1021/acs.jpcb.6b12672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a framework for computing the gating properties of ligand-gated ion channel mutants using the Monod-Wyman-Changeux (MWC) model of allostery. We derive simple analytic formulas for key functional properties such as the leakiness, dynamic range, half-maximal effective concentration ([EC50]), and effective Hill coefficient, and explore the full spectrum of phenotypes that are accessible through mutations. Specifically, we consider mutations in the channel pore of nicotinic acetylcholine receptor (nAChR) and the ligand binding domain of a cyclic nucleotide-gated (CNG) ion channel, demonstrating how each mutation can be characterized as only affecting a subset of the biophysical parameters. In addition, we show how the unifying perspective offered by the MWC model allows us, perhaps surprisingly, to collapse the plethora of dose-response data from different classes of ion channels into a universal family of curves.
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Affiliation(s)
- Tal Einav
- Department of Physics, California Institute of Technology , Pasadena, California 91125, United States
| | - Rob Phillips
- Department of Applied Physics and Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States
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15
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Costa IM, Schultz L, de Araujo Bianchi Pedra B, Leite MSM, Farsky SHP, de Oliveira MA, Pessoa A, Monteiro G. Recombinant L-asparaginase 1 from Saccharomyces cerevisiae: an allosteric enzyme with antineoplastic activity. Sci Rep 2016; 6:36239. [PMID: 27824095 PMCID: PMC5099943 DOI: 10.1038/srep36239] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 10/12/2016] [Indexed: 01/16/2023] Open
Abstract
L-asparaginase (L-ASNase) (EC 3.5.1.1) is an important enzyme for the treatment of acute lymphoblastic leukaemia. Currently, the enzyme is obtained from bacteria, Escherichia coli and Erwinia chrysanthemi. The bacterial enzymes family is subdivided in type I and type II; nevertheless, only type II have been employed in therapeutic proceedings. However, bacterial enzymes are susceptible to induce immune responses, leading to a high incidence of adverse effects compromising the effectiveness of the treatment. Therefore, alternative sources of L-ASNase may be useful to reduce toxicity and enhance efficacy. The yeast Saccharomyces cerevisiae has the ASP1 gene responsible for encoding L-asparaginase 1 (ScASNase1), an enzyme predicted as type II, like bacterial therapeutic isoforms, but it has been poorly studied. Here we characterised ScASNase1 using a recombinant enzyme purified by affinity chromatography. ScASNase1 has specific activity of 196.2 U/mg and allosteric behaviour, like type I enzymes, but with a low K0.5 = 75 μM like therapeutic type II. We showed through site-directed mutagenesis that the T64-Y78-T141-K215 residues are involved in catalysis. Furthermore, ScASNase1 showed cytotoxicity for the MOLT-4 leukemic cell lineage. Our data show that ScASNase1 has characteristics described for the two subfamilies of l-asparaginase, types I and II, and may have promising antineoplastic properties.
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Affiliation(s)
- Iris Munhoz Costa
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo/SP 05508-000, Brazil
| | - Leonardo Schultz
- Biosciences Institute, São Paulo State University - UNESP, Coastal Campus, São Vicente/SP 11330-900, Brazil
| | - Beatriz de Araujo Bianchi Pedra
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo/SP 05508-000, Brazil
| | - Mariana Silva Moreira Leite
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo/SP 05508-000, Brazil
| | - Sandra H P Farsky
- Department of Clinical and Toxicological Analysis School of Pharmaceutical Sciences, University of São Paulo, São Paulo/SP 05508-000, Brazil
| | - Marcos Antonio de Oliveira
- Biosciences Institute, São Paulo State University - UNESP, Coastal Campus, São Vicente/SP 11330-900, Brazil
| | - Adalberto Pessoa
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo/SP 05508-000, Brazil
| | - Gisele Monteiro
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo/SP 05508-000, Brazil
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16
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Lunev S, Bosch SS, Batista FDA, Wrenger C, Groves MR. Crystal structure of truncated aspartate transcarbamoylase from Plasmodium falciparum. Acta Crystallogr F Struct Biol Commun 2016; 72:523-33. [PMID: 27380369 PMCID: PMC4933002 DOI: 10.1107/s2053230x16008475] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/25/2016] [Indexed: 11/10/2022] Open
Abstract
The de novo pyrimidine-biosynthesis pathway of Plasmodium falciparum is a promising target for antimalarial drug discovery. The parasite requires a supply of purines and pyrimidines for growth and proliferation and is unable to take up pyrimidines from the host. Direct (or indirect) inhibition of de novo pyrimidine biosynthesis via dihydroorotate dehydrogenase (PfDHODH), the fourth enzyme of the pathway, has already been shown to be lethal to the parasite. In the second step of the plasmodial pyrimidine-synthesis pathway, aspartate and carbamoyl phosphate are condensed to N-carbamoyl-L-aspartate and inorganic phosphate by aspartate transcarbamoylase (PfATC). In this paper, the 2.5 Å resolution crystal structure of PfATC is reported. The space group of the PfATC crystals was determined to be monoclinic P21, with unit-cell parameters a = 87.0, b = 103.8, c = 87.1 Å, α = 90.0, β = 117.7, γ = 90.0°. The presented PfATC model shares a high degree of homology with the catalytic domain of Escherichia coli ATC. There is as yet no evidence of the existence of a regulatory domain in PfATC. Similarly to E. coli ATC, PfATC was modelled as a homotrimer in which each of the three active sites is formed at the oligomeric interface. Each active site comprises residues from two adjacent subunits in the trimer with a high degree of evolutional conservation. Here, the activity loss owing to mutagenesis of the key active-site residues is also described.
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Affiliation(s)
- Sergey Lunev
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Soraya S. Bosch
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
| | - Fernando de Assis Batista
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
| | - Matthew R. Groves
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
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17
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Abstract
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic processes, yet a simple and unified treatment of the effects of allostery in enzymes has been lacking. In this work, we take a step toward this goal by modeling allosteric enzymes and their interaction with two key molecular players-allosteric regulators and competitive inhibitors. We then apply this model to characterize existing data on enzyme activity, comment on how enzyme parameters (such as substrate binding affinity) can be experimentally tuned, and make novel predictions on how to control phenomena such as substrate inhibition.
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Affiliation(s)
- Tal Einav
- Department of Physics, California Institute of Technology , Pasadena, California 91125, United States
| | - Linas Mazutis
- Institute of Biotechnology, Vilnius University , Vilnius, 02241 Lithuania
| | - Rob Phillips
- Department of Applied Physics and Division of Biology, California Institute of Technology , Pasadena, California 91125, United States
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18
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Abstract
During the 20th century great progress was made in genetics and biochemistry, and these were combined into a molecular biological understanding of functions of macromolecules. Further great discoveries will be made about bioregulations, applicable to scientific problems such as cell development and evolution, and to illnesses including heart disease through defective control of cholesterol production, and to neurological cell-based diseases. The "War Against Cancer" is still far from won. The present generation of scientists can develop clinical applications from recent basic science discoveries.
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19
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Buc H. A faith in the coherence of the living world. C R Biol 2015; 338:372-9. [DOI: 10.1016/j.crvi.2015.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Costantini A, Rantsiou K, Majumder A, Jacobsen S, Pessione E, Svensson B, Garcia-Moruno E, Cocolin L. Complementing DIGE proteomics and DNA subarray analyses to shed light on Oenococcus oeni adaptation to ethanol in wine-simulated conditions. J Proteomics 2015; 123:114-27. [DOI: 10.1016/j.jprot.2015.04.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 01/27/2023]
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21
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Li B, Li H, Bai Y, Kirschner-Schwabe R, Yang JJ, Chen Y, Lu G, Tzoneva G, Ma X, Wu T, Li W, Lu H, Ding L, Liang H, Huang X, Yang M, Jin L, Kang H, Chen S, Du A, Shen S, Ding J, Chen H, Chen J, von Stackelberg A, Gu L, Zhang J, Ferrando A, Tang J, Wang S, Zhou BBS. Negative feedback-defective PRPS1 mutants drive thiopurine resistance in relapsed childhood ALL. Nat Med 2015; 21:563-71. [PMID: 25962120 DOI: 10.1038/nm.3840] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/17/2015] [Indexed: 01/08/2023]
Abstract
Relapse is the leading cause of mortality in children with acute lymphoblastic leukemia (ALL). Among chemotherapeutics, thiopurines are key drugs in ALL combination therapy. Using whole-exome sequencing, we identified relapse-specific mutations in the phosphoribosyl pyrophosphate synthetase 1 gene (PRPS1), which encodes a rate-limiting purine biosynthesis enzyme, in 24/358 (6.7%) relapsed childhood B cell ALL (B-ALL) cases. All individuals who harbored PRPS1 mutations relapsed early during treatment, and mutated ALL clones expanded exponentially before clinical relapse. Our functional analyses of PRPS1 mutants uncovered a new chemotherapy-resistance mechanism involving reduced feedback inhibition of de novo purine biosynthesis and competitive inhibition of thiopurine activation. Notably, the de novo purine synthesis inhibitor lometrexol effectively abrogated PRPS1 mutant-driven drug resistance. These results highlight the importance of constitutive activation of the de novo purine synthesis pathway in thiopurine resistance, and they offer therapeutic strategies for the treatment of relapsed and thiopurine-resistant ALL.
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Affiliation(s)
- Benshang Li
- 1] Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [2] Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China. [3] Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Li
- 1] Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [2] Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [3] Department of Pharmacology, School of Basic Medicine and Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Bai
- Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Renate Kirschner-Schwabe
- 1] Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany. [2] German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Jun J Yang
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yao Chen
- 1] Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [2] Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Gang Lu
- Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Gannie Tzoneva
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Xiaotu Ma
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Tongmin Wu
- 1] Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [2] Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [3] Department of Pharmacology, School of Basic Medicine and Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjing Li
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | | | - Lixia Ding
- 1] Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [2] Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huanhuan Liang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohang Huang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minjun Yang
- Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Lei Jin
- Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Hui Kang
- Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Shuting Chen
- Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | | | - Shuhong Shen
- 1] Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [2] Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianping Ding
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Hongzhuan Chen
- 1] Department of Pharmacology, School of Basic Medicine and Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [2] Collaborative Innovation Center of Systems Biomedicine, National Research Center for Translational Medicine, Shanghai, China
| | - Jing Chen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Arend von Stackelberg
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Longjun Gu
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinghui Zhang
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Jingyan Tang
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shengyue Wang
- 1] Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China. [2] Collaborative Innovation Center of Systems Biomedicine, National Research Center for Translational Medicine, Shanghai, China
| | - Bin-Bing S Zhou
- 1] Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [2] Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [3] Department of Pharmacology, School of Basic Medicine and Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [4] Collaborative Innovation Center of Systems Biomedicine, National Research Center for Translational Medicine, Shanghai, China
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22
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Changeux JP. 50 years of allosteric interactions: the twists and turns of the models. Nat Rev Mol Cell Biol 2013; 14:819-29. [DOI: 10.1038/nrm3695] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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