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Chen XR, Zhou T, Zhou ZD, Fang ZH, Wang KB, Zhang C, Kong LY, Yang MH. The discovery of an anti-Candida xanthone with selective inhibition of Candida albicans GAPDH. Int J Antimicrob Agents 2024; 63:107172. [PMID: 38608845 DOI: 10.1016/j.ijantimicag.2024.107172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/26/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024]
Abstract
OBJECTIVES This study aimed to discover novel antifungals targeting Candida albicans glyceraldehyde-3-phosphate dehydrogenase (CaGAPDH), have an insight into inhibitory mode, and provide evidence supporting CaGAPDH as a target for new antifungals. METHODS Virtual screening was utilized to discover inhibitors of CaGAPDH. The inhibitory effect on cellular GAPDH was evaluated by determining the levels of ATP, NAD, NADH, etc., as well as examining GAPDH mRNA and protein expression. The role of GAPDH inhibition in C. albicans was supported by drug affinity responsive target stability and overexpression experiments. The mechanism of CaGAPDH inhibition was elucidated by Michaelis-Menten enzyme kinetics and site-specific mutagenesis based on docking. Chemical synthesis was used to produce an improved candidate. Different sources of GAPDH were used to evaluate inhibitory selectivity across species. In vitro and in vivo antifungal tests, along with anti-biofilm activity, were carried out to evaluate antifungal potential of GAPDH inhibitors. RESULTS A natural xanthone was identified as the first competitive inhibitor of CaGAPDH. It demonstrated in vitro anti-C. albicans potential but also caused hemolysis. XP-W, a synthetic side-chain-optimized xanthone, demonstrated a better safety profile, exhibiting a 50-fold selectivity for CaGAPDH over human GAPDH. XP-W also exhibited potent anti-biofilm activity and displayed broad-spectrum anti-Candida activities in vitro and in vivo, including multi-azole-resistant C. albicans. CONCLUSIONS These results demonstrate for the first time that CaGAPDH is a valuable target for antifungal drug discovery, and XP-W provides a promising lead.
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Affiliation(s)
- Xing-Ru Chen
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Tao Zhou
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Zhuo-Da Zhou
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Zhan-Hong Fang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Kai-Bo Wang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Chao Zhang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Ling-Yi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, China.
| | - Ming-Hua Yang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, China.
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2
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Guner-Yılmaz OZ, Kurkcuoglu O, Akten ED. Tunnel-like region observed as a potential allosteric site in Staphylococcus aureus Glyceraldehyde-3-phosphate dehydrogenase. Arch Biochem Biophys 2024; 752:109875. [PMID: 38158117 DOI: 10.1016/j.abb.2023.109875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/14/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyzing the sixth step of glycolysis has been investigated for allosteric features that might be used as potential target for specific inhibition of Staphylococcus aureus (S.aureus). X-ray structure of bacterial enzyme for which a tunnel-like opening passing through the center previously proposed as an allosteric site has been subjected to six independent 500 ns long Molecular Dynamics simulations. Harmonic bond restraints were employed at key residues to underline the allosteric feature of this region. A noticeable reduction was observed in the mobility of NAD+ binding domains when restrictions were applied. Also, a substantial decrease in cross-correlations between distant Cα fluctuations was detected throughout the structure. Mutual information (MI) analysis revealed a similar decrease in the degree of correspondence in positional fluctuations in all directions everywhere in the receptor. MI between backbone and side-chain torsional variations changed its distribution profile and decreased considerably around the catalytic sites when restraints were employed. Principal component analysis clearly showed that the restrained state sampled a narrower range of conformations than apo state, especially in the first principal mode due to restriction in the conformational flexibility of NAD+ binding domain. Clustering the trajectory based on catalytic site residues displayed a smaller repertoire of conformations for restrained state compared to apo. Representative snapshots subjected to k-shortest pathway analysis revealed the impact of bond restraints on the allosteric communication which displayed distinct optimal and suboptimal pathways for two states, where observed frequencies of critical residues Gln51 and Val283 at the proposed site changed considerably.
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Affiliation(s)
| | - Ozge Kurkcuoglu
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Ebru Demet Akten
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey.
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3
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Galbiati A, Bova S, Pacchiana R, Borsari C, Persico M, Zana A, Bruno S, Donadelli M, Fattorusso C, Conti P. Discovery of a spirocyclic 3-bromo-4,5-dihydroisoxazole covalent inhibitor of hGAPDH with antiproliferative activity against pancreatic cancer cells. Eur J Med Chem 2023; 254:115286. [PMID: 37058971 DOI: 10.1016/j.ejmech.2023.115286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 04/16/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a key glycolytic enzyme, plays a crucial role in the energy metabolism of cancer cells and has been proposed as a valuable target for the development of anticancer agents. Among a series of 5-substituted 3-bromo-4,5-dihydroisoxazole (BDHI) derivatives, we identified the spirocyclic compound 11, which is able to covalently inactivate recombinant human GAPDH (hGAPDH) with a faster reactivity than koningic acid, one of the most potent hGAPDH inhibitors known to date. Computational studies confirmed that conformational rigidification is crucial to stabilize the interaction of the inhibitor with the binding site, thus favoring the subsequent covalent bond formation. Investigation of intrinsic warhead reactivity at different pH disclosed the negligible reactivity of 11 with free thiols, highlighting its ability to selectively react with the activated cysteine of hGAPDH with respect to other sulfhydryl groups. Compound 11 strongly reduced cancer cell growth in four different pancreatic cancer cell lines and its antiproliferative activity correlated well with the intracellular inhibition of hGAPDH. Overall, our results qualify 11 as a potent hGAPDH covalent inhibitor with a moderate drug-like reactivity that could be further exploited to develop anticancer agents.
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Affiliation(s)
- Andrea Galbiati
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133, Milano, Italy
| | - Stefania Bova
- Department of Medicine and Surgery, University of Parma, 43125, Parma, Italy
| | - Raffaella Pacchiana
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, 37134, Verona, Italy
| | - Chiara Borsari
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133, Milano, Italy; Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058, Basel, Switzerland
| | - Marco Persico
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Napoli, Italy
| | - Aureliano Zana
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133, Milano, Italy
| | - Stefano Bruno
- Food and Drug Department, University of Parma, 43124, Parma, Italy
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, 37134, Verona, Italy
| | - Caterina Fattorusso
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Napoli, Italy
| | - Paola Conti
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133, Milano, Italy.
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4
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Chen PC, Hsieh MH, Kuo WS, Wu LSH, Kao HF, Liu LF, Liu ZG, Jeng WY, Wang JY. Moonlighting glyceraldehyde-3-phosphate dehydrogenase (GAPDH) protein of Lactobacillus gasseri attenuates allergic asthma via immunometabolic change in macrophages. J Biomed Sci 2022; 29:75. [PMID: 36175886 PMCID: PMC9520948 DOI: 10.1186/s12929-022-00861-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The extra-intestinal effects of probiotics for preventing allergic diseases are well known. However, the probiotic components that interact with host target molecules and have a beneficial effect on allergic asthma remain unknown. Lactobacillus gasseri attenuates allergic airway inflammation through the activation of peroxisome proliferator- activated receptor γ (PPARγ) in dendritic cells. Therefore, we aimed to isolate and investigate the immunomodulatory effect of the PPARγ activation component from L. gasseri. METHODS Culture supernatants of L. gasseri were fractionated and screened for the active component for allergic asthma. The isolated component was subjected to in vitro functional assays and then cloned. The crystal structure of this component protein was determined using X-ray crystallography. Intrarectal inoculation of the active component-overexpressing Clear coli (lipopolysaccharide-free Escherichia coli) and intraperitoneal injection of recombinant component protein were used in a house dust mite (HDM)-induced allergic asthma mouse model to investigate the protective effect. Recombinant mutant component proteins were assayed, and their structures were superimposed to identify the detailed mechanism of alleviating allergic inflammation. RESULTS A moonlighting protein, glycolytic glyceraldehyde 3-phosphate dehydrogenase (GAPDH), LGp40, that has multifunctional effects was purified from cultured L. gasseri, and the crystal structure was determined. Both intrarectal inoculation of LGp40-overexpressing Clear coli and intraperitoneal administration of recombinant LGp40 protein attenuated allergic inflammation in a mouse model of allergic asthma. However, CDp40, GAPDH isolated from Clostridium difficile did not possess this anti-asthma effect. LGp40 redirected allergic M2 macrophages toward the M1 phenotype and impeded M2-prompted Th2 cell activation through glycolytic activity that induced immunometabolic changes. Recombinant mutant LGp40, without enzyme activity, showed no protective effect against HDM-induced airway inflammation. CONCLUSIONS We found a novel mechanism of moonlighting LGp40 in the reversal of M2-prompted Th2 cell activation through glycolytic activity, which has an important immunoregulatory role in preventing allergic asthma. Our results provide a new strategy for probiotics application in alleviating allergic asthma.
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Affiliation(s)
- Pei-Chi Chen
- Center for Allergy, Immunology, and Microbiome (A.I.M.), China Medical University Hospital, No. 2, Yuh-Der Road, Taichung City, 404, Taiwan.,Department of Nursing, National Tainan Junior College of Nursing, Tainan, Taiwan
| | - Miao-Hsi Hsieh
- Center for Allergy, Immunology, and Microbiome (A.I.M.), China Medical University Hospital, No. 2, Yuh-Der Road, Taichung City, 404, Taiwan
| | - Wen-Shuo Kuo
- Center for Allergy, Immunology, and Microbiome (A.I.M.), China Medical University Hospital, No. 2, Yuh-Der Road, Taichung City, 404, Taiwan.,School of Chemistry and Materials Science, Nanjing University of Information Science and Technology, Nanjing, China
| | - Lawrence Shih-Hsin Wu
- Center for Allergy, Immunology, and Microbiome (A.I.M.), China Medical University Hospital, No. 2, Yuh-Der Road, Taichung City, 404, Taiwan.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Hui-Fang Kao
- Department of Nursing, National Tainan Junior College of Nursing, Tainan, Taiwan
| | - Li-Fan Liu
- Institute of Gerontology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Zhi-Gang Liu
- Department of Respirology and Allergy, Third Affiliated Hospital of Shengzhen University, Shengzhen, China
| | - Wen-Yih Jeng
- University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan. .,Department of Biochemistry and Molecular Biology, National Cheng Kung University, No. 1, University Road, Tainan City, 701, Taiwan.
| | - Jiu-Yao Wang
- Center for Allergy, Immunology, and Microbiome (A.I.M.), China Medical University Hospital, No. 2, Yuh-Der Road, Taichung City, 404, Taiwan. .,Children's Hospital, China Medical University, Taichung, Taiwan.
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5
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Lei J, Yang Y, Lu Z, Pan H, Fang J, Jing B, Chen Y, Yin L. Taming metabolic competition via glycolysis inhibition for safe and potent tumor immunotherapy. Biochem Pharmacol 2022; 202:115153. [PMID: 35750199 DOI: 10.1016/j.bcp.2022.115153] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 11/02/2022]
Abstract
Metabolic competition between tumors and T cells is fierce in the tumor microenvironment (TME). Tumors usually exhaust glucose and accumulate lactic acid in TME. Nutrient deprivation and lactic acid accumulation in TME blunt T cell functions and antitumor immune responses. Here, we reported that glycolysis-related genes were upregulated in melanoma patients with weak immune responses and T cell poorly infiltrated tumors of BRCA and COAD patients. Dimethyl fumarate (DMF), a GAPDH inhibitor, which is FDA proved to treat autoimmune diseases was identified to promote oxidative pentose phosphate pathway through glucose-6-phosphate dehydrogenase (G6PD) but to suppress aerobic glycolysis and oxidative phosphorylation in tumor cells. Additionally, DMF normalized metabolic competition between tumors and T cells, thus potentiate antitumor responses of tumor infiltrating CD8+ T lymphocytes (TILs). Moreover, DMF optimized the efficiency of immune checkpoint therapy and interleukin-2 (IL-2) therapy while eliminating severe toxicity induced by IL-2 therapy. This study indicates a novel clinically feasible therapy strategy aiming shared metabolic pathway of tumors and T cells for effective and less toxic tumor immunotherapy.
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Affiliation(s)
- Jun Lei
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yi Yang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhaoliang Lu
- The School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Haiyan Pan
- The School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jialing Fang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Baowei Jing
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yongshun Chen
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| | - Lei Yin
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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6
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Celebi M, Inan T, Kurkcuoglu O, Akten ED. Potential allosteric sites captured in glycolytic enzymes via residue-based network models: Phosphofructokinase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase. Biophys Chem 2021; 280:106701. [PMID: 34736071 DOI: 10.1016/j.bpc.2021.106701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 01/05/2023]
Abstract
Likelihood of new allosteric sites for glycolytic enzymes, phosphofructokinase (PFK), glyceraldehyde-3-phosphate dehydrogenase (GADPH) and pyruvate kinase (PK) was evaluated for bacterial, parasitic and human species. Allosteric effect of a ligand binding at a site was revealed on the basis of low-frequency normal modes via Cα-harmonic residue network model. In bacterial PFK, perturbation of the proposed allosteric site outperformed the known allosteric one, producing a high amount of stabilization or reduced dynamics, on all catalytic regions. Another proposed allosteric spot at the dimer interface in parasitic PFK exhibited major stabilization effect on catalytic regions. In parasitic GADPH, the most desired allosteric response was observed upon perturbation of its tunnel region which incorporated key residues for functional regulation. Proposed allosteric site in bacterial PK produced a satisfactory allosteric response on all catalytic regions, whereas in human and parasitic PKs, a partial inhibition was observed. Residue network model based solely on contact topology identified the 'hub residues' with high betweenness tracing plausible allosteric communication pathways between distant functional sites. For both bacterial PFK and PK, proposed sites accommodated hub residues twice as much as the known allosteric site. Tunnel region in parasitic GADPH with the strongest allosteric effect among species, incorporated the highest number of hub residues. These results clearly suggest a one-to-one correspondence between the degree of allosteric effect and the number of hub residues in that perturbation site, which increases the likelihood of its allosteric nature.
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Affiliation(s)
- Metehan Celebi
- Graduate Program of Computational Biology and Bioinformatics, Graduate School of Science and Engineering, Kadir Has University, Istanbul, Turkey
| | - Tugce Inan
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Ozge Kurkcuoglu
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Ebru Demet Akten
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey.
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7
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Zhang L, Liu M, Bao L, Boström KI, Yao Y, Li J, Gu S, Ji C. Novel Structures of Type 1 Glyceraldehyde-3-phosphate Dehydrogenase from Escherichia coli Provide New Insights into the Mechanism of Generation of 1,3-Bisphosphoglyceric Acid. Biomolecules 2021; 11:1565. [PMID: 34827563 PMCID: PMC8615399 DOI: 10.3390/biom11111565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 11/18/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a highly conserved enzyme involved in the ubiquitous process of glycolysis and presents a loop (residues 208-215 of Escherichia coli GAPDH) in two alternative conformations (I and II). It is uncertain what triggers this loop rearrangement, as well as which is the precise site from which phosphate attacks the thioacyl intermediate precursor of 1,3-bisphosphoglycerate (BPG). To clarify these uncertainties, we determined the crystal structures of complexes of wild-type GAPDH (WT) with NAD and phosphate or G3P, and of essentially inactive GAPDH mutants (C150S, H177A), trapping crystal structures for the thioacyl intermediate or for ternary complexes with NAD and either phosphate, BPG, or G3P. Analysis of these structures reported here lead us to propose that phosphate is located in the "new Pi site" attacks the thioester bond of the thioacyl intermediate to generate 1,3-bisphosphoglyceric acid (BPG). In the structure of the thioacyl intermediate, the mobile loop is in conformation II in subunits O, P, and R, while both conformations coexist in subunit Q. Moreover, only the Q subunit hosts bound NADH. In the R subunit, only the pyrophosphate part of NADH is well defined, and NADH is totally absent from the O and P subunits. Thus, the change in loop conformation appears to occur after NADH is produced, before NADH is released. In addition, two new D-glyceraldehyde-3-phosphate (G3P) binding forms are observed in WT.NAD.G3P and C150A+H177A.NAD.G3P. In summary, this paper improves our understanding of the GAPDH catalytic mechanism, particularly regarding BPG formation.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.Z.); (M.L.); (L.B.); (J.L.); (S.G.)
| | - Meiruo Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.Z.); (M.L.); (L.B.); (J.L.); (S.G.)
| | - Luyao Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.Z.); (M.L.); (L.B.); (J.L.); (S.G.)
| | - Kristina I. Boström
- Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1679, USA; (K.I.B.); (Y.Y.)
| | - Yucheng Yao
- Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1679, USA; (K.I.B.); (Y.Y.)
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.Z.); (M.L.); (L.B.); (J.L.); (S.G.)
| | - Shaohua Gu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.Z.); (M.L.); (L.B.); (J.L.); (S.G.)
| | - Chaoneng Ji
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (L.Z.); (M.L.); (L.B.); (J.L.); (S.G.)
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China
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Zheng J, Shang Y, Wu Y, Wu J, Chen J, Wang Z, Sun X, Xu G, Deng Q, Qu D, Yu Z. Diclazuril Inhibits Biofilm Formation and Hemolysis of Staphylococcus aureus. ACS Infect Dis 2021; 7:1690-1701. [PMID: 34019393 DOI: 10.1021/acsinfecdis.1c00030] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biofilm formation and hemolysis induced by Staphylococcus aureus are closely related to pathogenicity. However, no drugs exist to inhibit biofilm formation or hemolysis induced by S. aureus in clinical practice. This study found diclazuril had antibacterial action against S. aureus with minimum inhibitory concentrations (MICs) at 50 μM for both methicillin-sensitive S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA). Diclazuril (at 1/4× or 1/8× MICs) significantly inhibited biofilm formation of S. aureus under static or flow-based conditions and also inhibited hemolysis induced by S. aureus. The RNA levels of transcriptional regulatory genes (agrA, agrC, luxS, sarA, sigB, saeR, saeS), biofilm formation-related genes (aur, bap, ccpA, cidA, clfA, clfB, fnbA, fnbB, icaA, icaB, sasG), and virulence-related genes (hla, hlb, hld, hlg, lukDE, lukpvl-S, spa, sbi, alpha-3 PSM, beta PSM, coa) of S. aureus were decreased when treated by diclazuril (at 1/4× MIC) for 4 h. The diclazuril nonsensitive clones of S. aureus were selected in vitro by induction of wildtype strains for about 90 days under the pressure of diclazuril. Mutations in the possible target genes of diclazuril against S. aureus were detected by whole-genome sequencing. This study indicated that there were three amino acid mutations in the diclazuril nonsensitive clone of S. aureus, two of which were located in genes with known function (SMC-Scp complex subunit ScpB and glyceraldehyde-3-phosphate dehydrogenase 1, respectively) and one in a gene with unknown function (hypothetical protein). Diclazuril showed a strong inhibition effect on planktonic cells and biofilm formation of S. aureus with the overexpression of the scpB gene.
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Affiliation(s)
- Jinxin Zheng
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People’s Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518052, China
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yongpeng Shang
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People’s Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518052, China
| | - Yang Wu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jianfeng Wu
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Junwen Chen
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People’s Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518052, China
| | - Zhanwen Wang
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People’s Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518052, China
| | - Xiang Sun
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People’s Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518052, China
| | - Guangjian Xu
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People’s Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518052, China
| | - Qiwen Deng
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People’s Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518052, China
| | - Di Qu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Science and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zhijian Yu
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, Shenzhen Nanshan People’s Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518052, China
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9
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Perez AM, Wolfe JA, Schermerhorn JT, Qian Y, Cela BA, Kalinowski CR, Largoza GE, Fields PA, Brandt GS. Thermal stability and structure of glyceraldehyde-3-phosphate dehydrogenase from the coral Acropora millepora. RSC Adv 2021; 11:10364-10374. [PMID: 35423531 PMCID: PMC8695597 DOI: 10.1039/d0ra10119b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/03/2021] [Indexed: 11/21/2022] Open
Abstract
Corals are vulnerable to increasing ocean temperatures. It is known that elevated temperatures lead to the breakdown of an essential mutualistic relationship with photosynthetic algae. The molecular mechanisms of this temperature-dependent loss of symbiosis are less well understood. Here, the thermal stability of a critical metabolic enzyme, glyceraldehyde-3-phosphate dehydrogenase, from the stony coral Acropora millepora was found to increase significantly in the presence of its cofactor NAD+. Determination of the structure of the cofactor-enzyme complex (PDB ID 6PX2) revealed variable NAD+ occupancy across the four monomers of the tetrameric enzyme. The structure of the fully occupied monomers was compared to those with partial cofactor occupancy, identifying regions of difference that may account for the increased thermal stability.
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Affiliation(s)
- Astrid M Perez
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
| | - Jacob A Wolfe
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
| | - Janse T Schermerhorn
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Yiwen Qian
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
| | - Bekim A Cela
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Cody R Kalinowski
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Garrett E Largoza
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Peter A Fields
- Department of Biology, Franklin & Marshall College Lancaster PA 17604 USA
| | - Gabriel S Brandt
- Department of Chemistry, Franklin & Marshall College Lancaster PA 17604 USA +1 717 358 4846 +1 717 358 4846
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10
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Zhang L, Liu MR, Yao YC, Bostrom IK, Wang YD, Chen AQ, Li JX, Gu SH, Ji CN. Characterization and structure of glyceraldehyde-3-phosphate dehydrogenase type 1 from Escherichia coli. Acta Crystallogr F Struct Biol Commun 2020; 76:406-413. [PMID: 32880588 PMCID: PMC7470045 DOI: 10.1107/s2053230x20010067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/21/2020] [Indexed: 11/10/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key enzyme in the glycolytic pathway that catalyzes the conversion of D-glyceraldehyde 3-phosphate to 1,3-diphosphoglycerate. Here, the full-length GAPDH type 1 from Escherichia coli (EcGAPDH1) was cloned and overexpressed, and the protein was purified. Biochemical analyses found that the optimum reaction temperature and pH of EcGAPDH1 were 55°C and 10.0, respectively. The protein has a certain amount of thermostability. Crystals of EcGAPDH1 were obtained using the sitting-drop vapor-diffusion technique and X-ray diffraction data were collected to 1.88 Å resolution. Characterization of the crystals showed that they belonged to space group P41212, with unit-cell parameters a = b = 89.651, c = 341.007 Å, α = β = γ = 90°. The structure of EcGAPDH1 contains four subunits, each of which includes an N-terminal NAD+-binding domain and a C-terminal catalytic domain. Analysis of the NAD+-bound form showed some differences between the structures of EcGAPDH1 and human GAPDH. As EcGAPDH1 shares 100% identity with GAPDH from Shigella sonnei, its structure may help in finding a drug for the treatment of shigellosis.
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Affiliation(s)
- L. Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - M. R. Liu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - Y. C. Yao
- Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1679, USA
| | - I. K. Bostrom
- Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1679, USA
| | - Y. D. Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - A. Q. Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - J. X. Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - S. H. Gu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
| | - C. N. Ji
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
- Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of China
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11
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Ayyildiz M, Celiker S, Ozhelvaci F, Akten ED. Identification of Alternative Allosteric Sites in Glycolytic Enzymes for Potential Use as Species-Specific Drug Targets. Front Mol Biosci 2020; 7:88. [PMID: 32478093 PMCID: PMC7240002 DOI: 10.3389/fmolb.2020.00088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/16/2020] [Indexed: 12/22/2022] Open
Abstract
Three allosteric glycolytic enzymes, phosphofructokinase, glyceraldehyde-3 phosphate dehydrogenase and pyruvate kinase, associated with bacterial, parasitic and human species, were explored to identify potential allosteric sites that would be used as prime targets for species-specific drug design purposes using a newly developed approach which incorporates solvent mapping, elastic network modeling, sequence and structural alignments. The majority of binding sites detected by solvent mapping overlapped with the interface regions connecting the subunits, thus appeared as promising target sites for allosteric regulation. Each binding site was then evaluated by its ability to alter the global dynamics of the receptor defined by the percentage change in the frequencies of the lowest-frequency modes most significantly and as anticipated, the most effective ones were detected in the vicinity of the well-reported catalytic and allosteric sites. Furthermore, some of our proposed regions intersected with experimentally resolved sites which are known to be critical for activity regulation, which further validated our approach. Despite the high degree of structural conservation encountered between bacterial/parasitic and human glycolytic enzymes, the majority of the newly presented allosteric sites exhibited a low degree of sequence conservation which further increased their likelihood to be used as species-specific target regions for drug design studies.
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Affiliation(s)
- Merve Ayyildiz
- Graduate Program of Computational Biology and Bioinformatics, Graduate School of Science and Engineering, Kadir Has University, Istanbul, Turkey
| | - Serkan Celiker
- Graduate Program of Computational Biology and Bioinformatics, Graduate School of Science and Engineering, Kadir Has University, Istanbul, Turkey
| | - Fatih Ozhelvaci
- Graduate Program of Computational Science and Engineering, Graduate School of Science and Engineering, Bogazici University, Istanbul, Turkey
| | - E. Demet Akten
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
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12
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Barrett KF, Dranow DM, Phan IQ, Michaels SA, Shaheen S, Navaluna ED, Craig JK, Tillery LM, Choi R, Edwards TE, Conrady DG, Abendroth J, Horanyi PS, Lorimer DD, Van Voorhis WC, Zhang Z, Barrett LK, Subramanian S, Staker B, Fan E, Myler PJ, Soge OO, Hybiske K, Ojo KK. Structures of glyceraldehyde 3-phosphate dehydrogenase in Neisseria gonorrhoeae and Chlamydia trachomatis. Protein Sci 2020; 29:768-778. [PMID: 31930578 DOI: 10.1002/pro.3824] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/05/2020] [Accepted: 01/08/2020] [Indexed: 12/12/2022]
Abstract
Neisseria gonorrhoeae (Ng) and Chlamydia trachomatis (Ct) are the most commonly reported sexually transmitted bacteria worldwide and usually present as co-infections. Increasing resistance of Ng to currently recommended dual therapy of azithromycin and ceftriaxone presents therapeutic challenges for syndromic management of Ng-Ct co-infections. Development of a safe, effective, and inexpensive dual therapy for Ng-Ct co-infections is an effective strategy for the global control and prevention of these two most prevalent bacterial sexually transmitted infections. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a validated drug target with two approved drugs for indications other than antibacterials. Nonetheless, any new drugs targeting GAPDH in Ng and Ct must be specific inhibitors of bacterial GAPDH that do not inhibit human GAPDH, and structural information of Ng and Ct GAPDH will aid in finding such selective inhibitors. Here, we report the X-ray crystal structures of Ng and Ct GAPDH. Analysis of the structures demonstrates significant differences in amino acid residues in the active sites of human GAPDH from those of the two bacterial enzymes suggesting design of compounds to selectively inhibit Ng and Ct is possible. We also describe an efficient in vitro assay of recombinant GAPDH enzyme activity amenable to high-throughput drug screening to aid in identifying inhibitory compounds and begin to address selectivity.
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Affiliation(s)
- Kayleigh F Barrett
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Samantha A Michaels
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Shareef Shaheen
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Edelmar D Navaluna
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Justin K Craig
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Logan M Tillery
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Ryan Choi
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Deborah G Conrady
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bedford, Massachusetts
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Peter S Horanyi
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bedford, Massachusetts
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Wesley C Van Voorhis
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
| | - Zhongsheng Zhang
- Department of Biochemistry, University of Washington, Seattle, Washington
| | - Lynn K Barrett
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Bart Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, Washington
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington.,Department of Biomedical Informatics & Medical Education
| | - Olusegun O Soge
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
| | - Kevin Hybiske
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
| | - Kayode K Ojo
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
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13
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Sanabria-Ríos DJ, Morales-Guzmán C, Mooney J, Medina S, Pereles-De-León T, Rivera-Román A, Ocasio-Malavé C, Díaz D, Chorna N, Carballeira NM. Antibacterial Activity of Hexadecynoic Acid Isomers toward Clinical Isolates of Multidrug-Resistant Staphylococcus aureus. Lipids 2020; 55:101-116. [PMID: 31975430 DOI: 10.1002/lipd.12213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/16/2019] [Accepted: 01/06/2020] [Indexed: 11/07/2022]
Abstract
In the present study, the structural characteristics that impart antibacterial activity to C16 alkynoic fatty acids (aFA) were further investigated. The syntheses of hexadecynoic acids (HDA) containing triple bonds at C-3, C-6, C-8, C-9, C-10, and C-12 were carried out in four steps and with an overall yield of 34-78%. In addition, HDA analogs containing a sulfur atom at either C-4 or C-5 were also prepared in 69-77% overall yields, respectively. Results from this study revealed that the triple bond at C-2 is pivotal for the antibacterial activity displayed by 2-HDA, while the farther the position of the triple bond from the carbonyl group, the lower its bactericidal activity against gram-positive bacteria, including clinical isolates of methicillin-resistant Staphylococcus aureus (CIMRSA) strains. The potential of 2-HDA as an antibacterial agent was also assessed in five CIMRSA strains that were resistant to Ciprofloxacin (Cipro) demonstrating that 2-HDA was the most effective treatment in inhibiting their growth when compared with either Cipro alone or equimolar combinations of Cipro and 2-HDA. Moreover, it was proved that the inhibition of S. aureus DNA gyrase can be linked to the antibacterial activity displayed by 2-HDA. Finally, it was determined that the ability of HDA analogs to form micelles can be linked to their decreased activity against gram-positive bacteria, since critical micellar concentrations (CMC) between 50 and 300 μg/mL were obtained.
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Affiliation(s)
- David J Sanabria-Ríos
- Faculty of Science and Technology, Inter American University of Puerto Rico, Metropolitan Campus, PO Box 191293, San Juan, PR, 00919, USA
| | - Christian Morales-Guzmán
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, 17 Ave Universidad STE 1701, San Juan, PR, 00925, USA
| | - Joseph Mooney
- Faculty of Science and Technology, Inter American University of Puerto Rico, Metropolitan Campus, PO Box 191293, San Juan, PR, 00919, USA
| | - Solymar Medina
- Faculty of Science and Technology, Inter American University of Puerto Rico, Metropolitan Campus, PO Box 191293, San Juan, PR, 00919, USA
| | - Tomás Pereles-De-León
- Faculty of Science and Technology, Inter American University of Puerto Rico, Metropolitan Campus, PO Box 191293, San Juan, PR, 00919, USA
| | - Ashley Rivera-Román
- Faculty of Science and Technology, Inter American University of Puerto Rico, Metropolitan Campus, PO Box 191293, San Juan, PR, 00919, USA
| | - Carlimar Ocasio-Malavé
- Faculty of Science and Technology, Inter American University of Puerto Rico, Metropolitan Campus, PO Box 191293, San Juan, PR, 00919, USA
| | - Damarith Díaz
- Faculty of Science and Technology, Inter American University of Puerto Rico, Metropolitan Campus, PO Box 191293, San Juan, PR, 00919, USA
| | - Nataliya Chorna
- Department of Biochemistry, University of Puerto Rico, Medical Sciences, Campus, PO Box 365067, San Juan, PR, 00936, USA
| | - Néstor M Carballeira
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, 17 Ave Universidad STE 1701, San Juan, PR, 00925, USA
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14
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Zanon PRA, Lewald L, Hacker SM. Isotopically Labeled Desthiobiotin Azide (isoDTB) Tags Enable Global Profiling of the Bacterial Cysteinome. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201912075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Patrick R. A. Zanon
- Department of ChemistryTechnical University of Munich Lichtenbergstrasse 4 85748 Garching Germany
| | - Lisa Lewald
- Department of ChemistryTechnical University of Munich Lichtenbergstrasse 4 85748 Garching Germany
| | - Stephan M. Hacker
- Department of ChemistryTechnical University of Munich Lichtenbergstrasse 4 85748 Garching Germany
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15
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Zanon PRA, Lewald L, Hacker SM. Isotopically Labeled Desthiobiotin Azide (isoDTB) Tags Enable Global Profiling of the Bacterial Cysteinome. Angew Chem Int Ed Engl 2020; 59:2829-2836. [PMID: 31782878 PMCID: PMC7027453 DOI: 10.1002/anie.201912075] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Indexed: 12/20/2022]
Abstract
Rapid development of bacterial resistance has led to an urgent need to find new druggable targets for antibiotics. In this context, residue-specific chemoproteomic approaches enable proteome-wide identification of binding sites for covalent inhibitors. Described here are easily synthesized isotopically labeled desthiobiotin azide (isoDTB) tags that shortened the chemoproteomic workflow and allowed an increased coverage of cysteines in bacterial systems. They were used to quantify 59 % of all cysteines in essential proteins in Staphylococcus aureus and enabled the discovery of 88 cysteines that showed high reactivity, which correlates with functional importance. Furthermore, 268 cysteines that are engaged by covalent ligands were identified. Inhibition of HMG-CoA synthase was verified and will allow addressing the bacterial mevalonate pathway through a new target. Overall, a broad map of the bacterial cysteinome was obtained, which will facilitate the development of antibiotics with novel modes-of-action.
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Affiliation(s)
- Patrick R A Zanon
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Lisa Lewald
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Stephan M Hacker
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
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16
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Li R, Liang C, Jiang L, Yuan C, Huang M. Structural determination of group A Streptococcal surface dehydrogenase and characterization of its interaction with urokinase-type plasminogen activator receptor. Biochem Biophys Res Commun 2019; 510:539-544. [PMID: 30737033 DOI: 10.1016/j.bbrc.2019.01.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 01/23/2019] [Indexed: 10/27/2022]
Abstract
Streptococcus pyogenes (group A Streptococcus, GAS) has caused a wide variety of human diseases. Its multifunctional surface dehydrogenase (SDH) is crucial for GAS life cycle. Furthermore, GAS infection into human pharyngeal cells has been previously shown to be mediated by the interaction between SDH and host urokinase-type plasminogen activator receptor (uPAR). However, the structural information of SDH remains to be elucidated and there are few detailed studies to characterize its interaction with uPAR. In-depth research on these issues will provide potential targets and strategies for combating GAS. Here, we prepared recombinant SDH tetramer in Escherichia coli BL21 (DE3) cells. After purification and crystallization, we determined its crystal structure at 1.74 Å. The unique characteristics might be potentially explored as drug targets or vaccine immunogen. We subsequently performed gel filtration chromatography, native-polyacrylamide gel electrophoresis (PAGE) and in vitro pull-down analyses. The results showed that their interaction was too weak to form stable complexes and the role of uPAR involved in GAS infection needs further demonstration. Altogether the current work provides the first view of SDH and deepens the knowledge of GAS infection.
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Affiliation(s)
- Rui Li
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
| | - Chenghui Liang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, Fujian, China.
| | - Longguang Jiang
- College of Chemistry, Fuzhou University, Fuzhou, 350116, Fujian, China.
| | - Cai Yuan
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, Fujian, China.
| | - Mingdong Huang
- College of Chemistry, Fuzhou University, Fuzhou, 350116, Fujian, China.
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17
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Gómez S, Querol-García J, Sánchez-Barrón G, Subias M, González-Alsina À, Franco-Hidalgo V, Albertí S, Rodríguez de Córdoba S, Fernández FJ, Vega MC. The Antimicrobials Anacardic Acid and Curcumin Are Not-Competitive Inhibitors of Gram-Positive Bacterial Pathogenic Glyceraldehyde-3-Phosphate Dehydrogenase by a Mechanism Unrelated to Human C5a Anaphylatoxin Binding. Front Microbiol 2019; 10:326. [PMID: 30863383 PMCID: PMC6400076 DOI: 10.3389/fmicb.2019.00326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/07/2019] [Indexed: 12/12/2022] Open
Abstract
The ubiquitous and highly abundant glycolytic enzyme D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is pivotal for the energy and carbon metabolism of most organisms, including human pathogenic bacteria. For bacteria that depend mostly on glycolysis for survival, GAPDH is an attractive target for inhibitor discovery. The availability of high-resolution structures of GAPDH from various pathogenic bacteria is central to the discovery of new antibacterial compounds. We have determined the X-ray crystal structures of two new GAPDH enzymes from Gram-positive bacterial pathogens, Streptococcus pyogenes and Clostridium perfringens. These two structures, and the recent structure of Atopobium vaginae GAPDH, reveal details in the active site that can be exploited for the design of novel inhibitors based on naturally occurring molecules. Two such molecules, anacardic acid and curcumin, have been found to counter bacterial infection in clinical settings, although the cellular targets responsible for their antimicrobial properties remain unknown. We show that both anacardic acid and curcumin inhibit GAPDH from two bacterial pathogens through uncompetitive and non-competitive mechanisms, suggesting GAPDH as a relevant pharmaceutical target for antibacterial development. Inhibition of GAPDH by anacardic acid and curcumin seems to be unrelated to the immune evasion function of pathogenic bacterial GAPDH, since neither natural compound interfere with binding to the human C5a anaphylatoxin.
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Affiliation(s)
- Sara Gómez
- Center for Biological Research, Spanish National Research Council, Madrid, Spain
| | - Javier Querol-García
- Center for Biological Research, Spanish National Research Council, Madrid, Spain
| | - Gara Sánchez-Barrón
- Center for Biological Research, Spanish National Research Council, Madrid, Spain
| | - Marta Subias
- Center for Biological Research, Spanish National Research Council, Madrid, Spain.,CIBER de Enfermedades Raras, Madrid, Spain
| | - Àlex González-Alsina
- Institut Universitari d'Investigació en Ciències de la Salut, University of the Balearic Islands, Mallorca, Spain
| | | | - Sebastián Albertí
- Institut Universitari d'Investigació en Ciències de la Salut, University of the Balearic Islands, Mallorca, Spain
| | - Santiago Rodríguez de Córdoba
- Center for Biological Research, Spanish National Research Council, Madrid, Spain.,CIBER de Enfermedades Raras, Madrid, Spain
| | | | - M Cristina Vega
- Center for Biological Research, Spanish National Research Council, Madrid, Spain
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18
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Corregido MC, Asención Diez MD, Iglesias AÁ, Piattoni CV. New pieces to the carbon metabolism puzzle of Nitrosomonas europaea: Kinetic characterization of glyceraldehyde-3 phosphate and succinate semialdehyde dehydrogenases. Biochimie 2019; 158:238-245. [PMID: 30690134 DOI: 10.1016/j.biochi.2019.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/19/2019] [Indexed: 02/02/2023]
Abstract
Nitrosomonas europaea is a chemolithotroph that obtains energy through the oxidation of ammonia to hydroxylamine while assimilates atmospheric CO2 to cover the cell carbon demands for growth. This microorganism plays a relevant role in the nitrogen biogeochemical cycle on Earth but its carbon metabolism remains poorly characterized. Based on sequence homology, we identified two genes (cbbG and gabD) coding for redox enzymes in N. europaea. Cloning and expression of the genes in Escherichia coli, allowed the production of recombinant enzymes purified to determine their biochemical properties. The protein CbbG is a glyceraldehyde-3-phosphate (Ga3P) dehydrogenase (Ga3PDHase) catalyzing the reversible oxidation of Ga3P to 1,3-bis-phospho-glycerate (1,3bisPGA), using specifically NAD+/NADH as cofactor. CbbG showed ∼6-fold higher Km value for 1,3bisPGA but ∼5-fold higher kcat for the oxidation of Ga3P. The protein GabD irreversibly oxidizes Ga3P to 3Pglycerate using NAD+ or NADP+, thus resembling a non-phosphorylating Ga3PDHase. However, the enzyme showed ∼6-fold higher Km value and three orders of magnitude higher catalytic efficiency with succinate semialdehyde (SSA) and NADP+. Indeed, the GabD protein identity corresponds to an SSA dehydrogenase (SSADHase). CbbG seems to be the only Ga3PDHase present in N. europaea; which would be involved in reducing triose-P during autotrophic carbon fixation. Otherwise, in cells grown under conditions deprived of ammonia and oxygen, the enzyme could catalyze the glycolytic step of Ga3P oxidation producing NADH. As an SSADHase, GabD would physiologically act producing succinate and preferentially NADPH over NADH; thus being part of an alternative pathway of the tricarboxylic acid cycle converting α-ketoglutarate to succinate. The properties determined for these enzymes contribute to better identify metabolic steps in CO2 assimilation, glycolysis and the tricarboxylic acid cycle in N. europaea. Results are discussed in the framework of metabolic pathways that launch biosynthetic intermediates relevant in the microorganism to develop and fulfill its role in nature.
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Affiliation(s)
- María Cecilia Corregido
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (IAL, CONICET-UNL) & FBCB, Centro Científico Tecnológico CONICET Santa Fe, Santa Fe, Argentina
| | - Matías Damián Asención Diez
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (IAL, CONICET-UNL) & FBCB, Centro Científico Tecnológico CONICET Santa Fe, Santa Fe, Argentina
| | - Alberto Álvaro Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (IAL, CONICET-UNL) & FBCB, Centro Científico Tecnológico CONICET Santa Fe, Santa Fe, Argentina.
| | - Claudia Vanesa Piattoni
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (IAL, CONICET-UNL) & FBCB, Centro Científico Tecnológico CONICET Santa Fe, Santa Fe, Argentina; Instituto Pasteur de Montevideo, Montevideo, Uruguay.
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19
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Imber M, Pietrzyk-Brzezinska AJ, Antelmann H. Redox regulation by reversible protein S-thiolation in Gram-positive bacteria. Redox Biol 2018; 20:130-145. [PMID: 30308476 PMCID: PMC6178380 DOI: 10.1016/j.redox.2018.08.017] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/09/2018] [Accepted: 08/23/2018] [Indexed: 12/21/2022] Open
Abstract
Low molecular weight (LMW) thiols play an important role as thiol-cofactors for many enzymes and are crucial to maintain the reduced state of the cytoplasm. Most Gram-negative bacteria utilize glutathione (GSH) as major LMW thiol. However, in Gram-positive Actinomycetes and Firmicutes alternative LMW thiols, such as mycothiol (MSH) and bacillithiol (BSH) play related roles as GSH surrogates, respectively. Under conditions of hypochlorite stress, MSH and BSH are known to form mixed disulfides with protein thiols, termed as S-mycothiolation or S-bacillithiolation that function in thiol-protection and redox regulation. Protein S-thiolations are widespread redox-modifications discovered in different Gram-positive bacteria, such as Bacillus and Staphylococcus species, Mycobacterium smegmatis, Corynebacterium glutamicum and Corynebacterium diphtheriae. S-thiolated proteins are mainly involved in cellular metabolism, protein translation, redox regulation and antioxidant functions with some conserved targets across bacteria. The reduction of protein S-mycothiolations and S-bacillithiolations requires glutaredoxin-related mycoredoxin and bacilliredoxin pathways to regenerate protein functions. In this review, we present an overview of the functions of mycothiol and bacillithiol and their physiological roles in protein S-bacillithiolations and S-mycothiolations in Gram-positive bacteria. Significant progress has been made to characterize the role of protein S-thiolation in redox-regulation and thiol protection of main metabolic and antioxidant enzymes. However, the physiological roles of the pathways for regeneration are only beginning to emerge as well as their interactions with other cellular redox systems. Future studies should be also directed to explore the roles of protein S-thiolations and their redox pathways in pathogenic bacteria under infection conditions to discover new drug targets and treatment options against multiple antibiotic resistant bacteria. Bacillithiol and mycothiol are major LMW thiols in many Gram-positive bacteria. HOCl leads to widespread protein S-mycothiolation and S-bacillithiolation which function in thiol-protection and redox regulation. Redox-sensitive metabolic and antioxidant enzymes are main targets for S-mycothiolation or S-bacillithiolation. Mycoredoxin and bacilliredoxin pathways mediate reduction of S-thiolations.
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Affiliation(s)
- Marcel Imber
- Freie Universität Berlin, Institute for Biology-Microbiology, Königin-Luise-Strasse 12-16, D-14195 Berlin, Germany
| | - Agnieszka J Pietrzyk-Brzezinska
- Freie Universität Berlin, Laboratory of Structural Biochemistry, D-14195 Berlin, Germany; Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz 90-924, Poland
| | - Haike Antelmann
- Freie Universität Berlin, Institute for Biology-Microbiology, Königin-Luise-Strasse 12-16, D-14195 Berlin, Germany.
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20
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Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells. Biochem J 2018; 475:1909-1937. [PMID: 29626155 PMCID: PMC5989533 DOI: 10.1042/bcj20180043] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/29/2018] [Accepted: 04/03/2018] [Indexed: 02/07/2023]
Abstract
In all living organisms, coenzyme A (CoA) is an essential cofactor with a unique design allowing it to function as an acyl group carrier and a carbonyl-activating group in diverse biochemical reactions. It is synthesized in a highly conserved process in prokaryotes and eukaryotes that requires pantothenic acid (vitamin B5), cysteine and ATP. CoA and its thioester derivatives are involved in major metabolic pathways, allosteric interactions and the regulation of gene expression. A novel unconventional function of CoA in redox regulation has been recently discovered in mammalian cells and termed protein CoAlation. Here, we report for the first time that protein CoAlation occurs at a background level in exponentially growing bacteria and is strongly induced in response to oxidizing agents and metabolic stress. Over 12% of Staphylococcus aureus gene products were shown to be CoAlated in response to diamide-induced stress. In vitro CoAlation of S. aureus glyceraldehyde-3-phosphate dehydrogenase was found to inhibit its enzymatic activity and to protect the catalytic cysteine 151 from overoxidation by hydrogen peroxide. These findings suggest that in exponentially growing bacteria, CoA functions to generate metabolically active thioesters, while it also has the potential to act as a low-molecular-weight antioxidant in response to oxidative and metabolic stress.
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21
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Kim YJ. A cryoprotectant induces conformational change in glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallogr F Struct Biol Commun 2018; 74:277-282. [PMID: 29717994 PMCID: PMC5931139 DOI: 10.1107/s2053230x18004557] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/19/2018] [Indexed: 12/28/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme, catalyses the conversion of D-glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate. While mammalian and yeast GAPDHs are multifunctional proteins that have additional functions beyond those involved in glycolysis, including reactions related to nuclear RNA transport, DNA replication/repair, membrane fusion and cellular apoptosis, Escherichia coli GAPDH (ecGAPDH) has only been reported to function in glycolysis. The S-loop of GAPDH is required for interaction with its cofactor and with other proteins. In this study, the three-dimensional crystal structure of GAPDH treated with trehalose is reported at 2.0 Å resolution. Trehalose was used as a cryoprotectant for the GAPDH crystals. The structure of trehalose-bound ecGAPDH was compared with the structures of both NAD+-free and NAD+-bound ecGAPDH. At the S-loop, the bound trehalose in the GAPDH structure induces a 2.4° rotation compared with the NAD+-free ecGAPDH structure and a 3.1° rotation compared with the NAD+-bound ecGAPDH structure.
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Affiliation(s)
- Yong Ju Kim
- Department of Herbal Medicine Resources, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Republic of Korea
- Department of Lifestyle, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Republic of Korea
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22
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Zhou K, Fan X, Li Y, Zhang C, Jin T. High-resolution crystal structure of Streptococcus agalactiae glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallogr F Struct Biol Commun 2018; 74:236-244. [PMID: 29633972 PMCID: PMC5894109 DOI: 10.1107/s2053230x18003801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 03/05/2018] [Indexed: 12/28/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a multifunctional enzyme that plays critical roles in bacterial pathogenesis in some pathogenic bacteria. In this study, the crystal structure of group B streptococcus GAPDH was determined at 1.36 Å resolution. The structure contained an asymmetric mixed holo tetramer, with two NAD ligands bound to two protomers. Further structural analysis identified interesting phosphate ion-binding sites, which shed light on its catalytic mechanism.
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Affiliation(s)
- Kang Zhou
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Xiaojiao Fan
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Yuelong Li
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Caiying Zhang
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
| | - Tengchuan Jin
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, People’s Republic of China
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23
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Imber M, Huyen NTT, Pietrzyk-Brzezinska AJ, Loi VV, Hillion M, Bernhardt J, Thärichen L, Kolšek K, Saleh M, Hamilton CJ, Adrian L, Gräter F, Wahl MC, Antelmann H. Protein S-Bacillithiolation Functions in Thiol Protection and Redox Regulation of the Glyceraldehyde-3-Phosphate Dehydrogenase Gap in Staphylococcus aureus Under Hypochlorite Stress. Antioxid Redox Signal 2018; 28:410-430. [PMID: 27967218 PMCID: PMC5791933 DOI: 10.1089/ars.2016.6897] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
AIMS Bacillithiol (BSH) is the major low-molecular-weight thiol of the human pathogen Staphylococcus aureus. In this study, we used OxICAT and Voronoi redox treemaps to quantify hypochlorite-sensitive protein thiols in S. aureus USA300 and analyzed the role of BSH in protein S-bacillithiolation. RESULTS The OxICAT analyses enabled the quantification of 228 Cys residues in the redox proteome of S. aureus USA300. Hypochlorite stress resulted in >10% increased oxidation of 58 Cys residues (25.4%) in the thiol redox proteome. Among the highly oxidized sodium hypochlorite (NaOCl)-sensitive proteins are five S-bacillithiolated proteins (Gap, AldA, GuaB, RpmJ, and PpaC). The glyceraldehyde-3-phosphate (G3P) dehydrogenase Gap represents the most abundant S-bacillithiolated protein contributing 4% to the total Cys proteome. The active site Cys151 of Gap was very sensitive to overoxidation and irreversible inactivation by hydrogen peroxide (H2O2) or NaOCl in vitro. Treatment with H2O2 or NaOCl in the presence of BSH resulted in reversible Gap inactivation due to S-bacillithiolation, which could be regenerated by the bacilliredoxin Brx (SAUSA300_1321) in vitro. Molecular docking was used to model the S-bacillithiolated Gap active site, suggesting that formation of the BSH mixed disulfide does not require major structural changes. Conclusion and Innovation: Using OxICAT analyses, we identified 58 novel NaOCl-sensitive proteins in the pathogen S. aureus that could play protective roles against the host immune defense and include the glycolytic Gap as major target for S-bacillithiolation. S-bacillithiolation of Gap did not require structural changes, but efficiently functions in redox regulation and protection of the active site against irreversible overoxidation in S. aureus. Antioxid. Redox Signal. 28, 410-430.
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Affiliation(s)
- Marcel Imber
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
| | - Nguyen Thi Thu Huyen
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
| | | | - Vu Van Loi
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
| | - Melanie Hillion
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
| | - Jörg Bernhardt
- 3 Institute for Microbiology , Ernst-Moritz-Arndt-Universität of Greifswald, Greifswald, Germany
| | - Lena Thärichen
- 4 Molecular Biomechanics, Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University , Heidelberg, Germany .,5 Heidelberg Institute of Theoretical Studies , Heidelberg, Germany
| | - Katra Kolšek
- 5 Heidelberg Institute of Theoretical Studies , Heidelberg, Germany
| | - Malek Saleh
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
| | - Chris J Hamilton
- 6 School of Pharmacy, University of East Anglia , Norwich Research Park, Norwich, United Kingdom
| | - Lorenz Adrian
- 7 Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ , Leipzig, Germany
| | - Frauke Gräter
- 4 Molecular Biomechanics, Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University , Heidelberg, Germany .,5 Heidelberg Institute of Theoretical Studies , Heidelberg, Germany
| | - Markus C Wahl
- 2 Laboratory of Structural Biochemistry, Freie Universität Berlin , Berlin, Germany
| | - Haike Antelmann
- 1 Institute for Biology-Microbiology, Freie Universität Berlin , Berlin, Germany
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24
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Wang M, Zhai L, Yu W, Wei Y, Wang L, Liu S, Li W, Li X, Yu S, Chen X, Zhang H, Chen J, Feng Z, Yu L, Cui Y. Identification of a protective B-cell epitope of the Staphylococcus aureus GapC protein by screening a phage-displayed random peptide library. PLoS One 2018; 13:e0190452. [PMID: 29304128 PMCID: PMC5755776 DOI: 10.1371/journal.pone.0190452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/14/2017] [Indexed: 01/16/2023] Open
Abstract
The impact of epidemic Staphylococcus aureus (S. aureus) on public health is increasing. Because of the abuse of antibiotics, the antibiotic resistance of S. aureus is increasing. Thus, there is an urgent need to develop new immunotherapies and immunoprophylaxes. Previous studies showed that the GapC protein of S. aureus, which is a surface protein with high glyceraldehyde 3-phosphate dehydrogenase activity, transferrin binding activity, and other biological activities, is highly conserved. GapC induces an effective humoral immune response in vivo. However, the B-cell epitopes of S. aureus GapC have not been well identified. Here we used the bioinformatics tools to analyze the sequence of GapC, and we generated protective anti-GapC monoclonal antibodies (mAbs). A protective mAb (1F4) showed strong specificity to GapC and the ability to induce macrophages to phagocytose S. aureus. We screened the motif 272GYTEDEIVSSD282, which was recognized by mAb 1F4, using a phage display system. Then, we used site-directed mutagenesis to identify key amino acids in the motif. Residues G272 D276 E277 I278 and V279 formed the core of the 272GYTEDEIVSSD282 motif. In addition, we showed that this epitope peptide induced a protective humoral immune response against S. aureus infection in immunized mice. Our results will be useful for the further study of epitope-based vaccines against S. aureus infection.
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Affiliation(s)
- Mengyao Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Lu Zhai
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Wei Yu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Yuhua Wei
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Lizi Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Shuo Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Wanyu Li
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Xiaoting Li
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Simiao Yu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Xiaoting Chen
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Hua Zhang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Jing Chen
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Zhenyue Feng
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Liquan Yu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
| | - Yudong Cui
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, P.R. China
- * E-mail:
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25
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Querol-García J, Fernández FJ, Marin AV, Gómez S, Fullà D, Melchor-Tafur C, Franco-Hidalgo V, Albertí S, Juanhuix J, Rodríguez de Córdoba S, Regueiro JR, Vega MC. Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen A. vaginae, an Immunoevasive Factor that Interacts with the Human C5a Anaphylatoxin. Front Microbiol 2017; 8:541. [PMID: 28443070 PMCID: PMC5385343 DOI: 10.3389/fmicb.2017.00541] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 03/14/2017] [Indexed: 01/05/2023] Open
Abstract
The Gram-positive anaerobic human pathogenic bacterium Atopobium vaginae causes most diagnosed cases of bacterial vaginosis as well as opportunistic infections in immunocompromised patients. In addition to its well-established role in carbohydrate metabolism, D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Streptococcus pyogenes and S. pneumoniae have been reported to act as extracellular virulence factors during streptococcal infections. Here, we report the crystal structure of GAPDH from A. vaginae (AvGAPDH) at 2.19 Å resolution. The refined model has a crystallographic Rfree of 22.6%. AvGAPDH is a homotetramer wherein each subunit is bound to a nicotinamide adenine dinucleotide (NAD+) molecule. The AvGAPDH enzyme fulfills essential glycolytic as well as moonlight (non-glycolytic) functions, both of which might be targets of chemotherapeutic intervention. We report that AvGAPDH interacts in vitro with the human C5a anaphylatoxin and inhibits C5a-specific granulocyte chemotaxis, thereby suggesting the participation of AvGAPDH in complement-targeted immunoevasion in a context of infection. The availability of high-quality structures of AvGAPDH and other homologous virulence factors from Gram-positive pathogens is critical for drug discovery programs. In this study, sequence and structural differences between AvGAPDH and related bacterial and eukaryotic GAPDH enzymes are reported in an effort to understand how to subvert the immunoevasive properties of GAPDH and evaluate the potential of AvGAPDH as a druggable target.
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Affiliation(s)
- Javier Querol-García
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - Francisco J Fernández
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain.,Department of Immunology, Complutense University School of MedicineMadrid, Spain.,Hospital 12 de Octubre Health Research InstituteMadrid, Spain.,Abvance Biotech srlMadrid, Spain
| | - Ana V Marin
- Department of Immunology, Complutense University School of MedicineMadrid, Spain.,Hospital 12 de Octubre Health Research InstituteMadrid, Spain
| | - Sara Gómez
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - Daniel Fullà
- ALBA Synchrotron, Cerdanyola del VallèsCatalonia, Spain
| | - Cecilia Melchor-Tafur
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - Virginia Franco-Hidalgo
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | | | | | - Santiago Rodríguez de Córdoba
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - José R Regueiro
- Department of Immunology, Complutense University School of MedicineMadrid, Spain.,Hospital 12 de Octubre Health Research InstituteMadrid, Spain
| | - M Cristina Vega
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
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26
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Schormann N, Ayres CA, Fry A, Green TJ, Banerjee S, Ulett GC, Chattopadhyay D. Crystal Structures of Group B Streptococcus Glyceraldehyde-3-Phosphate Dehydrogenase: Apo-Form, Binary and Ternary Complexes. PLoS One 2016; 11:e0165917. [PMID: 27875551 PMCID: PMC5119734 DOI: 10.1371/journal.pone.0165917] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 10/19/2016] [Indexed: 01/07/2023] Open
Abstract
Glyceraldehyde 3-phosphate dehydrogenase or GAPDH is an evolutionarily conserved glycolytic enzyme. It catalyzes the two step oxidative phosphorylation of D-glyceraldehyde 3-phosphate into 1,3-bisphosphoglycerate using inorganic phosphate and NAD+ as cofactor. GAPDH of Group B Streptococcus is a major virulence factor and a potential vaccine candidate. Moreover, since GAPDH activity is essential for bacterial growth it may serve as a possible drug target. Crystal structures of Group B Streptococcus GAPDH in the apo-form, two different binary complexes and the ternary complex are described here. The two binary complexes contained NAD+ bound to 2 (mixed-holo) or 4 (holo) subunits of the tetrameric protein. The structure of the mixed-holo complex reveals the effects of NAD+ binding on the conformation of the protein. In the ternary complex, the phosphate group of the substrate was bound to the new Pi site in all four subunits. Comparison with the structure of human GAPDH showed several differences near the adenosyl binding pocket in Group B Streptococcus GAPDH. The structures also reveal at least three surface-exposed areas that differ in amino acid sequence compared to the corresponding areas of human GAPDH.
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Affiliation(s)
- Norbert Schormann
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Chapelle A. Ayres
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Alexandra Fry
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Todd J. Green
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Surajit Banerjee
- North-Eastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne, Illinois 60439, United States of America
| | - Glen C. Ulett
- School of Medical Science, and Menzies Health Institute Queensland, Griffith University, Parklands 4222, Australia
| | - Debasish Chattopadhyay
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
- * E-mail:
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27
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Shimizu T, Tomita T, Kuzuyama T, Nishiyama M. Crystal Structure of the LysY·LysW Complex from Thermus thermophilus. J Biol Chem 2016; 291:9948-59. [PMID: 26966182 DOI: 10.1074/jbc.m115.707034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 11/06/2022] Open
Abstract
Several bacteria and archaea utilize the amino group-carrier protein, LysW, for lysine biosynthesis, in which an isopeptide bond is formed between the C-terminal Glu of LysW and an amino group of α-aminoadipate (AAA). The resulting LysW-γ-AAA is phosphorylated by LysZ to form LysW-γ-AAA phosphate, which is subsequently reduced to LysW-γ-aminoadipic semialdehyde (LysW-γ-AASA) through a reaction catalyzed by LysY. In this study, we determined the crystal structures of LysY from Thermus thermophilus HB27 (TtLysY) complexed with TtLysW-γ-AASA and TtLysW-γ-AAA, respectively. In both structures, the globular domain of TtLysW was recognized by positively charged residues on helix α9 and the β11-α10 loop of TtLysY through conformational changes. A mutational analysis confirmed that the interactions observed between TtLysY and TtLysW are important for the function of TtLysY. The extended LysW recognition loop and conserved arginine residue were identified as signatures to discriminate LysY from ArgC, which is involved in arginine biosynthesis. Combined with the previously determined TtLysZ·TtLysW complex structure, TtLysW may simultaneously bind TtLysZ and TtLysY. These structural insights suggest the formation of a TtLysWZY ternary complex, in which the flexible C-terminal extension of TtLysW promotes the efficient transfer of the labile intermediate from the active site of TtLysZ to that of TtLysY during the sequential reactions catalyzed by TtLysZY.
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Affiliation(s)
- Tetsu Shimizu
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takeo Tomita
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Makoto Nishiyama
- From the Biotechnology Research Center, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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28
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Mukherjee S, Ura M, Hoey RJ, Kossiakoff AA. A New Versatile Immobilization Tag Based on the Ultra High Affinity and Reversibility of the Calmodulin-Calmodulin Binding Peptide Interaction. J Mol Biol 2015; 427:2707-25. [PMID: 26159704 DOI: 10.1016/j.jmb.2015.06.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/25/2015] [Accepted: 06/28/2015] [Indexed: 01/09/2023]
Abstract
Reversible, high-affinity immobilization tags are critical tools for myriad biological applications. However, inherent issues are associated with a number of the current methods of immobilization. Particularly, a critical element in phage display sorting is functional immobilization of target proteins. To circumvent these problems, we have used a mutant (N5A) of calmodulin binding peptide (CBP) as an immobilization tag in phage display sorting. The immobilization relies on the ultra high affinity of calmodulin to N5A mutant CBP (RWKKNFIAVSAANRFKKIS) in presence of calcium (KD~2 pM), which can be reversed by EDTA allowing controlled "capture and release" of the specific binders. To evaluate the capabilities of this system, we chose eight targets, some of which were difficult to overexpress and purify with other tags and some had failed in sorting experiments. In all cases, specific binders were generated using a Fab phage display library with CBP-fused constructs. KD values of the Fabs were in subnanomolar to low nanomolar (nM) ranges and were successfully used to selectively recognize antigens in cell-based experiments. Some of these targets were problematic even without any tag; thus, the fact that all led to successful selection endpoints means that borderline cases can be worked on with a high probability of a positive outcome. Taken together with examples of successful case specific, high-level applications like generation of conformation-, epitope- and domain-specific Fabs, we feel that the CBP tag embodies all the attributes of covalent immobilization tags but does not suffer from some of their well-documented drawbacks.
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Affiliation(s)
- Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Marcin Ura
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Robert J Hoey
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
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Roychowdhury A, Kundu A, Bose M, Gujar A, Mukherjee S, Das AK. Complete catalytic cycle of cofactor-independent phosphoglycerate mutase involves a spring-loaded mechanism. FEBS J 2015; 282:1097-110. [DOI: 10.1111/febs.13205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/13/2015] [Accepted: 01/16/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Amlan Roychowdhury
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Anirban Kundu
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Madhuparna Bose
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Akanksha Gujar
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Somnath Mukherjee
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Amit Kumar Das
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
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Peralta D, Bronowska AK, Morgan B, Dóka É, Van Laer K, Nagy P, Gräter F, Dick TP. A proton relay enhances H2O2 sensitivity of GAPDH to facilitate metabolic adaptation. Nat Chem Biol 2015; 11:156-63. [PMID: 25580853 DOI: 10.1038/nchembio.1720] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 11/06/2014] [Indexed: 12/12/2022]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is sensitive to reversible oxidative inactivation by hydrogen peroxide (H2O2). Here we show that H2O2 reactivity of the active site thiolate (C152) is catalyzed by a previously unrecognized mechanism based on a dedicated proton relay promoting leaving group departure. Disruption of the peroxidatic reaction mechanism does not affect the glycolytic activity of GAPDH. Therefore, specific and separate mechanisms mediate the reactivity of the same thiolate nucleophile toward H2O2 and glyceraldehyde 3-phosphate, respectively. The generation of mutants in which the glycolytic and peroxidatic activities of GAPDH are comprehensively uncoupled allowed for a direct assessment of the physiological relevance of GAPDH H2O2 sensitivity. Using yeast strains in which wild-type GAPDH was replaced with H2O2-insensitive mutants retaining full glycolytic activity, we demonstrate that H2O2 sensitivity of GAPDH is a key component of the cellular adaptive response to increased H2O2 levels.
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Affiliation(s)
- David Peralta
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Agnieszka K Bronowska
- 1] Molecular Biomechanics, Heidelberg Institute of Theoretical Studies, Heidelberg, Germany. [2] Faculty of Chemistry, University of Heidelberg, Heidelberg, Germany
| | - Bruce Morgan
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Éva Dóka
- 1] Department of Molecular Immunology and Toxicology, National Institute of Oncology, Budapest, Hungary. [2] Department of Inorganic and Analytical Chemistry, University of Debrecen, Debrecen, Hungary
| | - Koen Van Laer
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Péter Nagy
- Department of Molecular Immunology and Toxicology, National Institute of Oncology, Budapest, Hungary
| | - Frauke Gräter
- Molecular Biomechanics, Heidelberg Institute of Theoretical Studies, Heidelberg, Germany
| | - Tobias P Dick
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Roth AJK, Tretbar M, Stark CBW. Mimicking the active site of aldehyde dehydrogenases: stabilization of carbonyl hydrates through hydrogen bonds. Chem Commun (Camb) 2015; 51:14175-8. [DOI: 10.1039/c5cc02831k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-Oxides have been identified as reagents stabilizing aldehyde hydrates in solution and in the solid state.
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Affiliation(s)
- A. J. K. Roth
- Fachbereich Chemie
- Institut für Organische Chemie
- Universität Hamburg
- 20146 Hamburg
- Germany
| | - M. Tretbar
- Fachbereich Chemie
- Institut für Organische Chemie
- Universität Hamburg
- 20146 Hamburg
- Germany
| | - C. B. W. Stark
- Fachbereich Chemie
- Institut für Organische Chemie
- Universität Hamburg
- 20146 Hamburg
- Germany
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32
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Shen H, Wang H, Liu Q, Liu H, Teng M, Li X. Structural insights into RNA recognition properties of glyceraldehyde-3-phosphate dehydrogenase 3 fromSaccharomyces cerevisiae. IUBMB Life 2014; 66:631-8. [DOI: 10.1002/iub.1313] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/08/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Hui Shen
- School of Life Sciences; University of Science and Technology of China, Hefei; Anhui People's Republic of China
| | - Hong Wang
- School of Life Sciences; University of Science and Technology of China, Hefei; Anhui People's Republic of China
| | - Qiao Liu
- School of Life Sciences; University of Science and Technology of China, Hefei; Anhui People's Republic of China
| | - Huihui Liu
- School of Life Sciences; University of Science and Technology of China, Hefei; Anhui People's Republic of China
| | - Maikun Teng
- School of Life Sciences; University of Science and Technology of China, Hefei; Anhui People's Republic of China
| | - Xu Li
- School of Life Sciences; University of Science and Technology of China, Hefei; Anhui People's Republic of China
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Ayres CA, Schormann N, Senkovich O, Fry A, Banerjee S, Ulett GC, Chattopadhyay D. Structure of Streptococcus agalactiae glyceraldehyde-3-phosphate dehydrogenase holoenzyme reveals a novel surface. Acta Crystallogr F Struct Biol Commun 2014; 70:1333-9. [PMID: 25286935 PMCID: PMC4188075 DOI: 10.1107/s2053230x14019517] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 08/28/2014] [Indexed: 11/11/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a conserved cytosolic enzyme, which plays a key role in glycolysis. GAPDH catalyzes the oxidative phosphorylation of D-glyceraldehyde 3-phosphate using NAD or NADP as a cofactor. In addition, GAPDH localized on the surface of some bacteria is thought to be involved in macromolecular interactions and bacterial pathogenesis. GAPDH on the surface of group B streptococcus (GBS) enhances bacterial virulence and is a potential vaccine candidate. Here, the crystal structure of GBS GAPDH from Streptococcus agalactiae in complex with NAD is reported at 2.46 Å resolution. Although the overall structure of GBS GAPDH is very similar to those of other GAPDHs, the crystal structure reveals a significant difference in the area spanning residues 294-307, which appears to be more acidic. The amino-acid sequence of this region of GBS GAPDH is also distinct compared with other GAPDHs. This region therefore may be of interest as an immunogen for vaccine development.
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Affiliation(s)
- Chapelle A. Ayres
- Science and Technology Honors Program, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Norbert Schormann
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Olga Senkovich
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Alexandra Fry
- Science and Technology Honors Program, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Surajit Banerjee
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne, IL 60439, USA
| | - Glen C. Ulett
- School of Medical Science and Griffith Health Institute, Griffith University, QLD 4222, Australia
| | - Debasish Chattopadhyay
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Nagarajan R, Ponnuraj K. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of glyceraldehyde-3-phosphate dehydrogenase from Streptococcus agalactiae NEM316. Acta Crystallogr F Struct Biol Commun 2014; 70:938-41. [PMID: 25005093 PMCID: PMC4089536 DOI: 10.1107/s2053230x14011418] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/17/2014] [Indexed: 11/10/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an essential enzyme involved in glycolysis. Despite lacking the secretory signal sequence, this cytosolic enzyme has been found localized at the surface of several bacteria and fungi. As a surface protein, GAPDH exhibits various adhesive functions, thereby facilitating colonization and invasion of host tissues. Streptococcus agalactiae, also known as group B streptococcus (GBS), binds onto the host using its surface adhesins and causes sepsis and pneumonia in neonates. GAPDH is one of the surface adhesins of GBS binding to human plasminogen and is a virulent factor associated with host colonization. Although the surface-associated GAPDH has been shown to bind to a variety of host extracellular matrix (ECM) molecules in various bacteria, the molecular mechanism underlying their interaction is not fully understood. To investigate this, structural studies on GAPDH of S. agalactiae were initiated. The gapC gene of S. agalactiae NEM316 encoding GAPDH protein was cloned into pET-28a vector, overexpressed in Escherichia coli BL21(DE3) cells and purified to homogeneity. The purified protein was crystallized using the hanging-drop vapour-diffusion method. The GAPDH crystals obtained in two different crystallization conditions diffracted to 2.8 and 2.6 Å resolution, belonging to two different space groups P2₁ and P2₁2₁2₁, respectively. The structure was solved by molecular replacement and structure refinement is now in progress.
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Affiliation(s)
- Revathi Nagarajan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | - Karthe Ponnuraj
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
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Roychowdhury A, Kundu A, Gujar A, Bose M, Das AK. Expression, purification, crystallization and preliminary X-ray diffraction studies of phosphoglycerate mutase from Staphylococcus aureus NCTC8325. Acta Crystallogr F Struct Biol Commun 2014; 70:53-6. [PMID: 24419617 PMCID: PMC3943096 DOI: 10.1107/s2053230x13031476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 11/18/2013] [Indexed: 11/11/2022] Open
Abstract
Phosphoglycerate mutase (PGM) is a key enzyme in carbohydrate metabolism. It takes part in both glycolysis and gluconeogenesis. PGM from pathogenic Staphylococcus aureus (NCTC8325) was cloned in pQE30 expression vector overexpressed in Escherichia coli M15 (pREP4) cells and purified to homogeneity. The protein was crystallized from two different conditions, (i) 0.1 M HEPES pH 7.5, 20%(w/v) polyethylene glycol 10,000 and (ii) 0.2 M NaCl, 0.1 M bis-tris pH 6.5, 25%(w/v) polyethylene glycol 3350, at 25°C by the sitting-drop vapour-diffusion method. Crystals grown at pH 7.5 diffracted to 2.5 Å resolution and belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 77.0, b = 86.11, c = 94.07 Å. Crystals from the second condition at pH 6.5 diffracted to 2.00 Å resolution. These crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 73.21, b = 81.75, c = 89.18 Å. X-ray diffraction data have been collected and processed to the maximum resolution to determine the structure of PGM. The structure has been solved by molecular replacement and structure refinement is now in progress.
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Affiliation(s)
- Amlan Roychowdhury
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Anirban Kundu
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Akanksha Gujar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Madhuparna Bose
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
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Mukherjee S, Roychowdhury A, Dutta D, Das AK. Crystal structures of triosephosphate isomerase from methicillin resistant Staphylococcus aureus MRSA252 provide structural insights into novel modes of ligand binding and unique conformations of catalytic loop. Biochimie 2012; 94:2532-44. [PMID: 22813930 DOI: 10.1016/j.biochi.2012.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 07/04/2012] [Indexed: 10/28/2022]
Abstract
Staphylococcus aureus is one of the most dreaded pathogens worldwide and emergence of notorious antibiotic resistant strains have further exacerbated the present scenario. The glycolytic enzyme, triosephosphate isomerase (TIM) is one of the cell envelope proteins of the coccus and is involved in biofilm formation. It also plays an instrumental role in adherence and invasion of the bacteria into the host cell. To structurally characterize this important enzyme and analyze it's interaction with different inhibitors, substrate and transition state analogues, the present article describes several crystal structures of SaTIM alone and in complex with different ligands: glycerol-3-phosphate (G3P), glycerol-2-phosphate (G2P), 3-phosphoglyceric acid (3PG) and 2-phosphoglyceric acid (2PG). Unique conformations of the catalytic loop 6 (L6) has been observed in the different complexes. It is found to be in "almost closed" conformation in both subunits of the structure complexed to G3P. However L6 adopts the open conformation in presence of G2P and 2PG. The preference of the conformation of the catalytic loop can be correlated with the position of the phosphate group in the ligand. Novel modes of binding have been observed for G2P and 3PG for the very first time. The triose moiety is oriented away from the catalytic residues and occupies an entirely different position in some subunits. A completely new binding site for phosphate has also been identified in the complex with 2PG which differs substantially from the conventional phosphate binding site of the ligand in the crystal structures of TIM determined so far.
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Affiliation(s)
- Somnath Mukherjee
- Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302, West Bengal, India
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Roychowdhury A, Mukherjee S, Das AK. Expression, purification, crystallization and preliminary X-ray diffraction studies of phosphoglycerate kinase from methicillin-resistant Staphylococcus aureus MRSA252. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:668-71. [PMID: 21636907 PMCID: PMC3107138 DOI: 10.1107/s1744309111007391] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Accepted: 02/26/2011] [Indexed: 11/10/2022]
Abstract
Phosphoglycerate kinase (PGK) from methicillin-resistant Staphylococcus aureus MRSA252 has been cloned in pQE30 expression vector, overexpressed in Escherichia coli SG13009 (pREP4) cells and purified to homogeneity. The protein was crystallized from 0.15 M CaCl(2), 0.1 M HEPES-NaOH pH 6.8, 20%(w/v) polyethylene glycol 2000 at 298 K by the hanging-drop vapour-diffusion method. The crystals belonged to space group P2(1), with unit-cell parameters a = 45.14, b = 74.75, c = 58.67 Å, β = 95.72°. X-ray diffraction data have been collected and processed to a maximum resolution of 2.3 Å. The presence of one molecule in the asymmetric unit gives a Matthews coefficient (V(M)) of 2.26 Å(3) Da(-1) with a solvent content of 46%. The structure has been solved by molecular replacement and structure refinement is now in progress.
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Affiliation(s)
- Amlan Roychowdhury
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Somnath Mukherjee
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
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