1
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Hicks KG, Cluntun AA, Schubert HL, Hackett SR, Berg JA, Leonard PG, Ajalla Aleixo MA, Zhou Y, Bott AJ, Salvatore SR, Chang F, Blevins A, Barta P, Tilley S, Leifer A, Guzman A, Arok A, Fogarty S, Winter JM, Ahn HC, Allen KN, Block S, Cardoso IA, Ding J, Dreveny I, Gasper WC, Ho Q, Matsuura A, Palladino MJ, Prajapati S, Sun P, Tittmann K, Tolan DR, Unterlass J, VanDemark AP, Vander Heiden MG, Webb BA, Yun CH, Zhao P, Wang B, Schopfer FJ, Hill CP, Nonato MC, Muller FL, Cox JE, Rutter J. Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase. Science 2023; 379:996-1003. [PMID: 36893255 PMCID: PMC10262665 DOI: 10.1126/science.abm3452] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/07/2023] [Indexed: 03/11/2023]
Abstract
Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates, and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl-coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment.
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Affiliation(s)
- Kevin G Hicks
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ahmad A Cluntun
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Heidi L Schubert
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Jordan A Berg
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul G Leonard
- Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mariana A Ajalla Aleixo
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Youjia Zhou
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Alex J Bott
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Sonia R Salvatore
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Fei Chang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Aubrie Blevins
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paige Barta
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Samantha Tilley
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Aaron Leifer
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrea Guzman
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ajak Arok
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Sarah Fogarty
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jacob M Winter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Hee-Chul Ahn
- Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, The Republic of Korea
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Samuel Block
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Iara A Cardoso
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Ingrid Dreveny
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | | | - Quinn Ho
- Department of Biology, Boston University, Boston, MA, USA
| | - Atsushi Matsuura
- Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, The Republic of Korea
| | - Michael J Palladino
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sabin Prajapati
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Pengkai Sun
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dean R Tolan
- Department of Biology, Boston University, Boston, MA, USA
| | - Judith Unterlass
- Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew G Vander Heiden
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bradley A Webb
- Department of Biochemistry, West Virginia University, Morgantown, WV, USA
| | - Cai-Hong Yun
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Pengkai Zhao
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Bei Wang
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Francisco J Schopfer
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, Pittsburgh, PA, USA
- Center for Metabolism and Mitochondrial Medicine, Pittsburgh, PA, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Florian L Muller
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James E Cox
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
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2
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Chen J, Gu Z, Xu Y, Deng M, Lai L, Pei J. QuoteTarget: A sequence-based transformer protein language model to identify potentially druggable protein targets. Protein Sci 2023; 32:e4555. [PMID: 36564866 PMCID: PMC9878469 DOI: 10.1002/pro.4555] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
The development of efficient computational methods for drug target protein identification can compensate for the high cost of experiments and is therefore of great significance for drug development. However, existing structure-based drug target protein-identification algorithms are limited by the insufficient number of proteins with experimentally resolved structures. Moreover, sequence-based algorithms cannot effectively extract information from protein sequences and thus display insufficient accuracy. Here, we combined the sequence-based self-supervised pretraining protein language model ESM1b with a graph convolutional neural network classifier to develop an improved, sequence-based drug target protein identification method. This complete model, named QuoteTarget, efficiently encodes proteins based on sequence information alone and achieves an accuracy of 95% with the nonredundant drug target and nondrug target datasets constructed for this study. When applied to all proteins from Homo sapiens, QuoteTarget identified 1213 potential undeveloped drug target proteins. We further inferred residue-binding weights from the well-trained network using the gradient-weighted class activation mapping (Grad-Cam) algorithm. Notably, we found that without any binding site information input, significant residues inferred by the model closely match the experimentally confirmed drug molecule-binding sites. Thus, our work provides a highly effective sequence-based identifier for drug target proteins, as well to yield new insights into recognizing drug molecule-binding sites. The entire model is available at https://github.com/Chenjxjx/drug-target-prediction.
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Affiliation(s)
- Jiaxiao Chen
- Center for Quantitative BiologyAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Zhonghui Gu
- Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Youjun Xu
- Infinite Intelligence PharmaBeijingChina
| | - Minghua Deng
- Center for Quantitative BiologyAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
- School of Mathematical SciencesPeking UniversityBeijingChina
- Center for Statistical SciencePeking UniversityBeijingChina
| | - Luhua Lai
- Center for Quantitative BiologyAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
- Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
- BNLMS, College of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
- Research Unit of Drug Design MethodChinese Academy of Medical SciencesBeijingChina
| | - Jianfeng Pei
- Center for Quantitative BiologyAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
- Research Unit of Drug Design MethodChinese Academy of Medical SciencesBeijingChina
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3
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Human cytomegalovirus induces neuronal enolase to support virally mediated metabolic remodeling. Proc Natl Acad Sci U S A 2022; 119:e2205789119. [PMID: 36459650 PMCID: PMC9894225 DOI: 10.1073/pnas.2205789119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Viruses depend on cellular metabolic resources to supply the energy and biomolecular building blocks necessary for their replication. Human cytomegalovirus (HCMV), a leading cause of birth defects and morbidity in immunosuppressed individuals, induces numerous metabolic activities that are important for productive infection. However, many of the mechanisms through which these metabolic activities are induced and how they contribute to infection are unclear. We find that HCMV infection of fibroblasts induces a neuronal gene signature as well as the expression of several metabolic enzyme isoforms that are typically expressed in other tissue types. Of these, the most substantially induced glycolytic gene was the neuron-specific isoform of enolase 2 (ENO2). Induction of ENO2 expression is important for HCMV-mediated glycolytic activation as well as for the virally induced remodeling of pyrimidine-sugar metabolism, which provides the glycosyl subunits necessary for protein glycosylation. Inhibition of ENO2 expression or activity reduced uridine diphosphate (UDP)-sugar pools, attenuated the accumulation of viral glycoproteins, and induced the accumulation of noninfectious viral particles. In addition, our data indicate that the induction of ENO2 expression depends on the HCMV UL38 protein. Collectively, our data indicate that HCMV infection induces a tissue atypical neuronal glycolytic enzyme to activate glycolysis and UDP-sugar metabolism, increase the accumulation of glycosyl building blocks, and enable the expression of an essential viral glycoprotein and the production of infectious virions.
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4
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GDPD5 Related to Lipid Metabolism Is a Potential Prognostic Biomarker in Neuroblastoma. Int J Mol Sci 2022; 23:ijms232213740. [PMID: 36430219 PMCID: PMC9695425 DOI: 10.3390/ijms232213740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
Neuroblastoma (NB) is an extracranial solid tumor in children with poor prognosis in high-risk patients and its pathogenesis and prognostic markers urgently need to be explored. This study aimed to explore potential biomarkers related to NB from the aspect of lipid metabolism. Fifty-eight lipid metabolism-related differentially expressed genes between high-risk NB and non-high-risk NB in the GSE49710 dataset were analyzed using bioinformatics, including 45 down-regulated genes and 13 up-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified steroid hormone biosynthesis as an abnormal metabolic pathway in high-risk NB. Survival analysis established a three-gene prognostic model, including ACHE, GDPD5 and PIK3R1. In the test data, the AUCs of the established prognostic models used to predict patient survival at 1, 3 and 5 years were 0.84, 0.90 and 0.91, respectively. Finally, in the SH-SY5Y cell line, it was verified that overexpression of GDPD5 can inhibit cell proliferation and migration, as well as affect the lipid metabolism of SH-SY5Y, but not the sugar metabolism. hsa-miR-592 was predicted to be a potential target miRNA of GDPD5 by bioinformatics. In conclusion, this study develops a lipid-metabolism-related gene-based prognostic model for NB and demonstrates that GDPD5 inhibits SH-SY5Y proliferation and migration and may be targeted by hsa-miR-592 and inhibit SH-SY5Y fat synthesis.
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5
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Yan VC, Pham CD, Ballato ES, Yang KL, Arthur K, Khadka S, Barekatain Y, Shrestha P, Tran T, Poral AH, Washington M, Raghavan S, Czako B, Pisaneschi F, Lin YH, Satani N, Hammoudi N, Ackroyd JJ, Georgiou DK, Millward SW, Muller FL. Prodrugs of a 1-Hydroxy-2-oxopiperidin-3-yl Phosphonate Enolase Inhibitor for the Treatment of ENO1-Deleted Cancers. J Med Chem 2022; 65:13813-13832. [PMID: 36251833 PMCID: PMC9620261 DOI: 10.1021/acs.jmedchem.2c01039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cancers harboring homozygous deletion of the glycolytic enzyme enolase 1 (ENO1) are selectively vulnerable to inhibition of the paralogous isoform, enolase 2 (ENO2). A previous work described the sustained tumor regression activities of a substrate-competitive phosphonate inhibitor of ENO2, 1-hydroxy-2-oxopiperidin-3-yl phosphonate (HEX) (5), and its bis-pivaloyoxymethyl prodrug, POMHEX (6), in an ENO1-deleted intracranial orthotopic xenograft model of glioblastoma [Nature Metabolism 2020, 2, 1423-1426]. Due to poor pharmacokinetics of bis-ester prodrugs, this study was undertaken to identify potential non-esterase prodrugs for further development. Whereas phosphonoamidate esters were efficiently bioactivated in ENO1-deleted glioma cells, McGuigan prodrugs were not. Other strategies, including cycloSal and lipid prodrugs of 5, exhibited low micromolar IC50 values in ENO1-deleted glioma cells and improved stability in human serum over 6. The activity of select prodrugs was also probed using the NCI-60 cell line screen, supporting its use to examine the relationship between prodrugs and cell line-dependent bioactivation.
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Affiliation(s)
- Victoria C. Yan
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States,. Twitter: @victoriacyanide
| | - Cong-Dat Pham
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Elliot S. Ballato
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Kristine L. Yang
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Kenisha Arthur
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Sunada Khadka
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States,Department
of Cancer Biology, University of Texas MD
Anderson Cancer Center, Houston, Texas 77054, United States
| | - Yasaman Barekatain
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States,Department
of Cancer Biology, University of Texas MD
Anderson Cancer Center, Houston, Texas 77054, United States
| | - Prakriti Shrestha
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Theresa Tran
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Anton H. Poral
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Mykia Washington
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Sudhir Raghavan
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Barbara Czako
- Institute
of Applied Cancer Science, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Federica Pisaneschi
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Yu-Hsi Lin
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Nikunj Satani
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Naima Hammoudi
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Jeffrey J. Ackroyd
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Dimitra K. Georgiou
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Steven W. Millward
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Florian L. Muller
- Department
of Cancer Systems Imaging, University of
Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
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6
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Sariyer E, Kocer S, Danis O, Turgut-Balik D. In vitro inhibition studies of coumarin derivatives on Bos taurus enolase and elucidating their interaction by molecular docking, molecular dynamics simulations and MMGB(PB)SA binding energy calculation. Bioorg Chem 2021; 110:104796. [PMID: 33799179 DOI: 10.1016/j.bioorg.2021.104796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/24/2021] [Accepted: 03/02/2021] [Indexed: 11/19/2022]
Abstract
Tropical theileriosis is among the most common vector-borne diseases and caused by Theileria parasites. Theileria annulata is an obligate intracellular protozoan parasite and transmitted to especially Bos taurus and Bos indicus by Hyalomma tick vectors. C8 ([4-(3,4-dimethoxyphenyl)-6,7-dihydroxy-2H-chromen-2-one); C9 (4-(3,4-dihydroxyphenyl)-7,8 dihydroxy-2H-chromen-2-one); C21 (4-(3,4-dihydroxyphenyl)-6,7-dihydroxy-2H-chromen-2 one) were identified as potent Theileria annulata enolase (TaEno) inhibitors in our previous studies. An ideal drug compound must inhibit the target parasite enzyme without inhibiting its homolog in the host. In this study, the inhibitory effect of the compounds previously evaluated on TaEno were tested on the host Bos taurus enolase (BtEno3) by in vitro studies. The interactions of enzyme-coumarin and enzyme-coumarin-substrate by in silico studies were also performed. All of the coumarin derivatives tested showed very low inhibitory effects on B. taurus enolase; 36,87% inhibition at 100 μM concentration for C8, 8,13% inhibition at 100 μM concentration for C9 and 77,69 μM of IC50 value for C21. In addition, these three coumarin derivatives and substrate 2PG were docked into the BtEno3 using molecular docking methods. Molecular interactions between enolase-coumarin and enolase-coumarin-substrate complexes were analyzed using molecular dynamics simulation methods for 100 ns. Estimated free energy of bindings of the substrate 2PG and coumarin derivatives to the BtEno3 were calculated by MM-GB(PB)SA methods. In comparison to the inhibition studies performed on TaEno, C8 and C9 coumarin derivatives remain the possible inhibitor candidates as they inhibit the host enolase at very high concentrations. These two promising compounds will be further analyzed by in vitro and in vivo studies towards developing an alternative drug against tropical theileriosis.
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Affiliation(s)
- Emrah Sariyer
- Yıldız Technical University, Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Davutpasa campus, 34210, Istanbul, Turkey; Artvin Coruh University, Vocational School of Health Services, Medical Laboratory Techniques, 08000, Artvin, Turkey
| | - Sinem Kocer
- İstanbul Yeni Yüzyıl University, Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, 34010, Istanbul, Turkey
| | - Ozkan Danis
- Marmara University, Faculty of Arts and Sciences, Department of Chemistry, 34722, Istanbul, Turkey
| | - Dilek Turgut-Balik
- Yıldız Technical University, Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Davutpasa campus, 34210, Istanbul, Turkey.
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7
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Pietkiewicz J, Danielewicz R, Wandzel C, Beznosiuk J, Szuba A, Samsel-Czekała M, Gamian A. Influence of Water Polarization Caused by Phonon Resonance on Catalytic Activity of Enolase. ACS OMEGA 2021; 6:4255-4261. [PMID: 33644547 PMCID: PMC7906585 DOI: 10.1021/acsomega.0c05199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
Enolase is a conservative protein. Its cellular enzymatic activity catalyzes the conversion of 2-phospho-d-glycerate (2-PGA) to a phosphoenolpyruvate (PEP) product in the glycolysis pathway. This enzyme also has a multifunctional nature participating in several biological processes. This work aims to determine the effect of water polarization on the catalytic activity of enolase. The experiments have been set based on the concept that water, a polar dielectric, may undergo the phenomenon of electric polarization, decreasing its configurational and vibrational entropy. Prior to the reaction, the 2-PGA substrate was incubated for 5 h in the glass cuvette with an attached chip-inductor. The latter device was designed to transfer quantum information about a given quantum state from the quantum state generator to water by a phonon resonance. Then, such substrate samples preincubated with the chip-inductor were removed every hour in a separate quartz cuvette with the enzyme to determine its catalytic activity. The influence of the chip-inductor on the preincubated substrate resulted in an increase in the catalytic activity of enolase by 30% compared to the control substrate, not preincubated with the chip-inductor. This suggests that the catalytic activity of the enzyme is augmented when the substrate was primed by chip-inductors. In another kind of experiment, wherein enolase was exposed to methylglyoxal modification, the catalytic activity of the enzyme dropped to 71.7%, while the same enzyme glycated with methylglyoxal primed by chip-inductors restored its activity by 8.4%. This shows the protective effect of chip-inductors on enolase activity despite the harmful effect of methylglyoxal on the protein.
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Affiliation(s)
- Jadwiga Pietkiewicz
- Department
of Biochemistry, Wroclaw Medical University, Wroclaw, Chalubinskiego 10, 50-368 Wroclaw, Poland
| | - Regina Danielewicz
- Department
of Biochemistry, Wroclaw Medical University, Wroclaw, Chalubinskiego 10, 50-368 Wroclaw, Poland
| | - Czesław Wandzel
- Metanel
Group Spółka Akcyjna, Nad Bialką 2A, 43-503 Czechowice-Dziedzice, Poland
| | - Jarosław Beznosiuk
- Metanel
Group Spółka Akcyjna, Nad Bialką 2A, 43-503 Czechowice-Dziedzice, Poland
| | - Andrzej Szuba
- Department
of Angiology, Hypertension and Diabetology, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland
| | - Małgorzata Samsel-Czekała
- Institute
of Low Temperature and Structure Research, Polish Academy of Sciences, Okólna 2, 50-422 Wroclaw, Poland
| | - Andrzej Gamian
- Department
of Biochemistry, Wroclaw Medical University, Wroclaw, Chalubinskiego 10, 50-368 Wroclaw, Poland
- Hirszfeld
Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
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8
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Functional and structural basis of E. coli enolase inhibition by SF2312: a mimic of the carbanion intermediate. Sci Rep 2019; 9:17106. [PMID: 31745118 PMCID: PMC6863902 DOI: 10.1038/s41598-019-53301-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/22/2019] [Indexed: 11/08/2022] Open
Abstract
Many years ago, the natural secondary metabolite SF2312, produced by the actinomycete Micromonospora, was reported to display broad spectrum antibacterial properties against both Gram-positive and Gram-negative bacteria. Recent studies have revealed that SF2312, a natural phosphonic acid, functions as a potent inhibitor of human enolase. The mechanism of SF2312 inhibition of bacterial enolase and its role in bacterial growth and reproduction, however, have remained elusive. In this work, we detail a structural analysis of E. coli enolase bound to both SF2312 and its oxidized imide-form. Our studies support a model in which SF2312 acts as an analog of a high energy intermediate formed during the catalytic process. Biochemical, biophysical, computational and kinetic characterization of these compounds confirm that altering features characteristic of a putative carbanion (enolate) intermediate significantly reduces the potency of enzyme inhibition. When SF2312 is combined with fosfomycin in the presence of glucose-6 phosphate, significant synergy is observed. This suggests the two agents could be used as a potent combination, targeting distinct cellular mechanism for the treatment of bacterial infections. Together, our studies rationalize the structure-activity relationships for these phosphonates and validate enolase as a promising target for antibiotic discovery.
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9
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Didiasova M, Schaefer L, Wygrecka M. When Place Matters: Shuttling of Enolase-1 Across Cellular Compartments. Front Cell Dev Biol 2019; 7:61. [PMID: 31106201 PMCID: PMC6498095 DOI: 10.3389/fcell.2019.00061] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/05/2019] [Indexed: 12/22/2022] Open
Abstract
Enolase is a glycolytic enzyme, which catalyzes the inter-conversion of 2-phosphoglycerate to phosphoenolpyruvate. Altered expression of this enzyme is frequently observed in cancer and accounts for the Warburg effect, an adaptive response of tumor cells to hypoxia. In addition to its catalytic function, ENO-1 exhibits other activities, which strongly depend on its cellular and extracellular localization. For example, the association of ENO-1 with mitochondria membrane was found to be important for the stability of the mitochondrial membrane, and ENO-1 sequestration on the cell surface was crucial for plasmin-mediated pericellular proteolysis. The latter activity of ENO-1 enables many pathogens but also immune and cancer cells to invade the tissue, leading further to infection, inflammation or metastasis formation. The ability of ENO-1 to conduct so many diverse processes is reflected by its contribution to a high number of pathologies, including type 2 diabetes, cardiovascular hypertrophy, fungal and bacterial infections, cancer, systemic lupus erythematosus, hepatic fibrosis, Alzheimer's disease, rheumatoid arthritis, and systemic sclerosis. These unexpected non-catalytic functions of ENO-1 and their contributions to diseases are the subjects of this review.
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Affiliation(s)
- Miroslava Didiasova
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Giessen, Germany
| | - Liliana Schaefer
- Institute of Pharmacology and Toxicology, Goethe University Frankfurt, Frankfurt, Germany
| | - Malgorzata Wygrecka
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Giessen, Germany.,Member of the German Center for Lung Research, Giessen, Germany
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10
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Zheng X, Gao Y, Li W, Wang S. iTRAQ-based quantitative proteomic analysis identified Eno1 as a cadmium stress response gene in Propsilocerus akamusi (Tokunaga) hemolymph. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 165:126-135. [PMID: 30195204 DOI: 10.1016/j.ecoenv.2018.08.086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/16/2018] [Accepted: 08/23/2018] [Indexed: 06/08/2023]
Abstract
Propsilocerus akamusi (Tokunaga) is a common species of midge in Siberia, Japan, and China and an important prey species for fish and aquatic birds. Furthermore, this species has been shown to have an extraordinary capacity to resist cadmium (Cd) toxicity. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) coupled liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to analyze relative changes in the P. akamusi hemolymph proteome following exposure to a sublethal concentration of Cd2+. The results showed that Cd2+ stress affects energy metabolism in P. akamusi. After examining the differentially expressed proteins (DEPs), only one up-regulated protein associated with metabolism, α-enolase (Eno1) was identified and further isolated and characterized. Sequence alignments showed that the deduced P. akamusi Eno1 amino acid sequence is highly conserved, with similarities of 77-95% noted when compared to other Dipteran Eno1 sequences. Furthermore, prolonged Cd2+ exposure impacted Eno1 transcription, protein expression and enzyme activity levels. These results suggest that Eno1 may play a role in the response to Cd2+ stress in P. akamusi.
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Affiliation(s)
- Xianyun Zheng
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, PR China.
| | - Ye Gao
- School of Physical Exercise and Education, Shanxi University, Taiyuan 030006, PR China
| | - Wanghong Li
- School of Physical Exercise and Education, Shanxi University, Taiyuan 030006, PR China
| | - Shu Wang
- School of Physical Exercise and Education, Shanxi University, Taiyuan 030006, PR China
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11
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Sariyer E, Yakarsonmez S, Danis O, Turgut-Balik D. A study of Bos taurus muscle specific enolase; biochemical characterization, homology modelling and investigation of molecular interaction using molecular docking and dynamics simulations. Int J Biol Macromol 2018; 120:2346-2353. [DOI: 10.1016/j.ijbiomac.2018.08.184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 08/28/2018] [Accepted: 08/30/2018] [Indexed: 01/09/2023]
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12
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Aguayo-Ortiz R, Meza-Cervantez P, Castillo R, Hernández-Campos A, Dominguez L, Yépez-Mulia L. Insights into the Giardia intestinalis enolase and human plasminogen interaction. MOLECULAR BIOSYSTEMS 2018; 13:2015-2023. [PMID: 28770921 DOI: 10.1039/c7mb00252a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Giardia intestinalis is an intestinal parasite that causes diarrhea in humans and animals worldwide. The enolase of G. intestinalis (GiENO) participates in its glycolysis pathway and is abundantly expressed in the parasite cytosol; however, its localization on the surface of trophozoites and cysts has been demonstrated. Enolases from bacteria and parasites can have different functions and are considered moonlighting proteins, for example, as a cell surface plasminogen receptor. In relation to GiENO, no studies have been performed about its possible participation as a plasminogen receptor. In this work, we employed molecular docking and multiscale molecular dynamics (MD) simulations to explore the possible interactions of human plasminogen (HsPLG) with the open and closed GiENO conformations. Our proposed GiENO plasminogen binding site (PLGBs) was identified at Lys266 based on the sequence comparison with bacterial enolase known to act as a plasminogen receptor. Our docking results performed with multiple MD snapshots of the closed GiENO conformation showed that Lys266 preferentially binds to the K5 domain of HsPLG. On the other hand, open GiENO conformations from all-atom and coarse-grained simulations indicated a high preference of the HsPLG K4 domain for lysine residues 186 and 188. Furthermore, we identified a potential N-glycosylation site of GiENO which suggests a possible explanation for the parasite cell surface localization or host mucin oligosaccharide adhesion mechanism. Our study constitutes the first multiscale computational study to explore the plasminogen receptor function of GiENO for its further consideration as a potential therapeutic target for giardiasis treatment.
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Affiliation(s)
- R Aguayo-Ortiz
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, CDMX, México 04510, Mexico.
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13
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Sun C, Xu B, Liu X, Zhang Z, Su Z. Crystal structure of enolase from Drosophila melanogaster. Acta Crystallogr F Struct Biol Commun 2017; 73:228-234. [PMID: 28368282 PMCID: PMC5379173 DOI: 10.1107/s2053230x17004022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 03/13/2017] [Indexed: 11/10/2022] Open
Abstract
Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase from Drosophila melanogaster (DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space group R32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and evolutionary studies of enolase.
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Affiliation(s)
- Congcong Sun
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, People’s Republic of China
| | - Baokui Xu
- Jianghuai College, Anhui University, Hefei, Anhui 230039, People’s Republic of China
| | - Xueyan Liu
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, People’s Republic of China
| | - Zhen Zhang
- Laboratory for TCM Immunopharmacology and Molecular Biology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, 18877 Jingshi Road, Jinan, Shandong 250062, People’s Republic of China
| | - Zhongliang Su
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, People’s Republic of China
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Bearne SL. The interdigitating loop of the enolase superfamily as a specificity binding determinant or 'flying buttress'. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:619-630. [PMID: 28179138 DOI: 10.1016/j.bbapap.2017.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/21/2016] [Accepted: 02/03/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND Enzymes of the enolase superfamily (ENS) are mechanistically diverse, yet share a common partial reaction (abstraction of the α-proton from a carboxylate substrate). While the catalytic machinery responsible for the deprotonation reaction has been conserved, divergent evolution has led to numerous ENS members that catalyze different overall reactions. This rich functional diversity has made the ENS an excellent model system for developing the approaches necessary to validate enzyme function. However, enzymes of the ENS also share a common bidomain structure ((β/α)7β-barrel domain and α+β capping domain) which makes validation of function from structural information challenging. SCOPE OF THE REVIEW This review presents a comparative survey of the structural data obtained over the past decade for enzymes from all seven subgroups that comprise the ENS. MAJOR CONCLUSIONS Of the seven ENS subgroups (enolase, mandelate racemase (MR), muconate lactonizing enzyme, β-methylaspartate ammonia lyase, d-glucarate dehydratase, d-mannonate dehydratase (ManD), and galactarate dehydratase 2), only enzymes of the MR and ManD subgroups exhibit an additional feature of structural complexity-an interdigitating loop. This loop emanates from one protomer of a homodimeric pair and penetrates into the adjacent, symmetry-related protomer to either contribute a binding determinant to the active site of the adjacent protomer, or act as a 'flying buttress' to support residues of the active site. GENERAL SIGNIFICANCE The analysis presented in this review suggests that the interdigitating loop is the only gross structural element that permits functional distinction between ENS subgroups at the tertiary level of protein structure.
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Affiliation(s)
- Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada; Department of Chemistry, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
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15
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Martínez-Betancur V, Martínez-Gutierrez M. Proteomic profile of human monocytic cells infected with dengue virus. Asian Pac J Trop Biomed 2016. [DOI: 10.1016/j.apjtb.2016.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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16
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Leonard PG, Satani N, Maxwell D, Lin YH, Hammoudi N, Peng Z, Pisaneschi F, Link TM, Lee GR, Sun D, Prasad BAB, Di Francesco ME, Czako B, Asara JM, Wang YA, Bornmann W, DePinho RA, Muller FL. SF2312 is a natural phosphonate inhibitor of enolase. Nat Chem Biol 2016; 12:1053-1058. [PMID: 27723749 PMCID: PMC5110371 DOI: 10.1038/nchembio.2195] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/02/2016] [Indexed: 12/28/2022]
Abstract
Despite being critical for energy generation in most forms of life, few if any microbial antibiotics specifically inhibit glycolysis. To develop a specific inhibitor of the glycolytic enzyme Enolase 2 for the treatment of cancers with deletion of Enolase 1, we modeled the synthetic tool compound inhibitor, Phosphonoacetohydroxamate (PhAH) into the active site of human ENO2. A ring-stabilized analogue of PhAH, with the hydroxamic nitrogen linked to the alpha-carbon by an ethylene bridge, was predicted to increase binding affinity by stabilizing the inhibitor in a bound conformation. Unexpectedly, a structure based search revealed that our hypothesized back-bone-stabilized PhAH bears strong similarity to SF2312, a phosphonate antibiotic of unknown mode of action produced by the actinomycete Micromonospora, which is active under anaerobic conditions. Here, we present multiple lines of evidence, including a novel X-ray structure, that SF2312 is a highly potent, low nM inhibitor of Enolase.
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Affiliation(s)
- Paul G Leonard
- Department of Genomic Medicine and Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX 77054
| | - Nikunj Satani
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX 77054
| | - David Maxwell
- Department of Clinical Analytics & Informatics, Houston, TX 77054-3403
| | - Yu-Hsi Lin
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX 77054
| | - Naima Hammoudi
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX 77054
| | | | - Federica Pisaneschi
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX 77054
| | - Todd M Link
- Department of Genomic Medicine and Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX 77054
| | - Gilbert R Lee
- Department of Genomic Medicine and Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX 77054
| | - Duoli Sun
- Department of Genomic Medicine and Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX 77054
| | - Basvoju A Bhanu Prasad
- Department of Genomic Medicine and Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX 77054
| | - Maria Emilia Di Francesco
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX 77054
| | - Barbara Czako
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX 77054
| | - John M Asara
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115
| | - Y Alan Wang
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA University of Texas MD Anderson Cancer Center, Houston, TX 77054 USA
| | | | - Ronald A DePinho
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA University of Texas MD Anderson Cancer Center, Houston, TX 77054 USA
| | - Florian L Muller
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX 77054
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17
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Mutlu O, Yakarsonmez S, Sariyer E, Danis O, Yuce-Dursun B, Topuzogullari M, Akbulut E, Turgut-Balik D. Comprehensive structural analysis of the open and closed conformations of Theileria annulata enolase by molecular modelling and docking. Comput Biol Chem 2016; 64:134-144. [DOI: 10.1016/j.compbiolchem.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/19/2016] [Accepted: 06/06/2016] [Indexed: 01/15/2023]
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18
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Wu Y, Wang C, Lin S, Wu M, Han L, Tian C, Zhang X, Zang J. Octameric structure of Staphylococcus aureus enolase in complex with phosphoenolpyruvate. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2457-70. [PMID: 26627653 PMCID: PMC4667285 DOI: 10.1107/s1399004715018830] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/07/2015] [Indexed: 12/31/2022]
Abstract
Staphylococcus aureus is a Gram-positive bacterium with strong pathogenicity that causes a wide range of infections and diseases. Enolase is an evolutionarily conserved enzyme that plays a key role in energy production through glycolysis. Additionally, enolase is located on the surface of S. aureus and is involved in processes leading to infection. Here, crystal structures of Sa_enolase with and without bound phosphoenolpyruvate (PEP) are presented at 1.6 and 2.45 Å resolution, respectively. The structure reveals an octameric arrangement; however, both dimeric and octameric conformations were observed in solution. Furthermore, enzyme-activity assays show that only the octameric variant is catalytically active. Biochemical and structural studies indicate that the octameric form of Sa_enolase is enzymatically active in vitro and likely also in vivo, while the dimeric form is catalytically inactive and may be involved in other biological processes.
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Affiliation(s)
- Yunfei Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Chengliang Wang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Shenglong Lin
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, People’s Republic of China
| | - Minhao Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Lu Han
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Changlin Tian
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, People’s Republic of China
| | - Xuan Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Jianye Zang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230027, People’s Republic of China
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
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Baleva M, Gowher A, Kamenski P, Tarassov I, Entelis N, Masquida B. A Moonlighting Human Protein Is Involved in Mitochondrial Import of tRNA. Int J Mol Sci 2015; 16:9354-67. [PMID: 25918939 PMCID: PMC4463592 DOI: 10.3390/ijms16059354] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/02/2015] [Accepted: 04/15/2015] [Indexed: 12/29/2022] Open
Abstract
In yeast Saccharomyces cerevisiae, ~3% of the lysine transfer RNA acceptor 1 (tRK1) pool is imported into mitochondria while the second isoacceptor, tRK2, fully remains in the cytosol. The mitochondrial function of tRK1 is suggested to boost mitochondrial translation under stress conditions. Strikingly, yeast tRK1 can also be imported into human mitochondria in vivo, and can thus be potentially used as a vector to address RNAs with therapeutic anti-replicative capacity into mitochondria of sick cells. Better understanding of the targeting mechanism in yeast and human is thus critical. Mitochondrial import of tRK1 in yeast proceeds first through a drastic conformational rearrangement of tRK1 induced by enolase 2, which carries this freight to the mitochondrial pre-lysyl-tRNA synthetase (preMSK). The latter may cross the mitochondrial membranes to reach the matrix where imported tRK1 could be used by the mitochondrial translation apparatus. This work focuses on the characterization of the complex that tRK1 forms with human enolases and their role on the interaction between tRK1 and human pre-lysyl-tRNA synthetase (preKARS2).
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Affiliation(s)
- Maria Baleva
- Department of Molecular and Cellular Genetics, UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), CNRS-Université de Strasbourg, 67084 Strasbourg, France.
- Department of Molecular Biology, Biology Faculty of Moscow State University, 119992 Moscow, Russia.
| | - Ali Gowher
- Department of Molecular and Cellular Genetics, UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), CNRS-Université de Strasbourg, 67084 Strasbourg, France.
| | - Piotr Kamenski
- Department of Molecular Biology, Biology Faculty of Moscow State University, 119992 Moscow, Russia.
| | - Ivan Tarassov
- Department of Molecular and Cellular Genetics, UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), CNRS-Université de Strasbourg, 67084 Strasbourg, France.
| | - Nina Entelis
- Department of Molecular and Cellular Genetics, UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), CNRS-Université de Strasbourg, 67084 Strasbourg, France.
| | - Benoît Masquida
- Department of Molecular and Cellular Genetics, UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), CNRS-Université de Strasbourg, 67084 Strasbourg, France.
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20
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Ruan J, Mouveaux T, Light SH, Minasov G, Anderson WF, Tomavo S, Ngô HM. The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:417-26. [PMID: 25760592 PMCID: PMC4356359 DOI: 10.1107/s1399004714026479] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 12/01/2014] [Indexed: 12/15/2022]
Abstract
In addition to catalyzing a central step in glycolysis, enolase assumes a remarkably diverse set of secondary functions in different organisms, including transcription regulation as documented for the oncogene c-Myc promoter-binding protein 1. The apicomplexan parasite Toxoplasma gondii differentially expresses two nuclear-localized, plant-like enolases: enolase 1 (TgENO1) in the latent bradyzoite cyst stage and enolase 2 (TgENO2) in the rapidly replicative tachyzoite stage. A 2.75 Å resolution crystal structure of bradyzoite enolase 1, the second structure to be reported of a bradyzoite-specific protein in Toxoplasma, captures an open conformational state and reveals that distinctive plant-like insertions are located on surface loops. The enolase 1 structure reveals that a unique residue, Glu164, in catalytic loop 2 may account for the lower activity of this cyst-stage isozyme. Recombinant TgENO1 specifically binds to a TTTTCT DNA motif present in the cyst matrix antigen 1 (TgMAG1) gene promoter as demonstrated by gel retardation. Furthermore, direct physical interactions of both nuclear TgENO1 and TgENO2 with the TgMAG1 gene promoter are demonstrated in vivo using chromatin immunoprecipitation (ChIP) assays. Structural and biochemical studies reveal that T. gondii enolase functions are multifaceted, including the coordination of gene regulation in parasitic stage development. Enolase 1 provides a potential lead in the design of drugs against Toxoplasma brain cysts.
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Affiliation(s)
- Jiapeng Ruan
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
| | - Thomas Mouveaux
- Center for Infection and Immunity of Lille, CNRS UMR 8204, INSERM U1019, Institut Pasteur de Lille, Université Lille Nord de France, France
| | - Samuel H. Light
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
| | - Stanislas Tomavo
- Center for Infection and Immunity of Lille, CNRS UMR 8204, INSERM U1019, Institut Pasteur de Lille, Université Lille Nord de France, France
| | - Huân M. Ngô
- Center for Structural Genomics of Infectious Diseases, Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611, USA
- BrainMicro LLC, 21 Pendleton Street, New Haven, CT 06511, USA
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21
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Tarasov EA, Blinov DV, Zimovina UV, Sandakova EA. Magnesium deficiency and stress: Issues of their relationship, diagnostic tests, and approaches to therapy. TERAPEVT ARKH 2015; 87:114-122. [DOI: 10.17116/terarkh2015879114-122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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