1
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Zheng S, Zheng C, Chen S, Guo J, Huang L, Huang Z, Xu S, Wu Y, Li S, Lin J, You Y, Hu F. Structural and biochemical characterization of active sites mutant in human inorganic pyrophosphatase. Biochim Biophys Acta Gen Subj 2024; 1868:130594. [PMID: 38428647 DOI: 10.1016/j.bbagen.2024.130594] [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: 09/27/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Inorganic pyrophosphatases (PPases) are enzymes that catalyze the conversion of inorganic pyrophosphate (PPi) into phosphate (Pi). Human inorganic pyrophosphatase 1 (Hu-PPase) exhibits high expression levels in a variety of tumors and plays roles in cell proliferation, apoptosis, invasion and metastasis, making it a promising prognostic biomarker and a target for cancer therapy. Despite its widespread presence, the catalytic mechanism of Hu-PPase in humans remains inadequately understood. The signature motif amino acid sequence (DXDPXD) within the active sites of PPases is preserved across different species. In this research, an enzymatic activity assay revealed that mutations led to a notable reduction in enzymatic function, although the impact of the four amino acids on the activity of the pocket varied. To investigate the influence of these residues on the substrate binding and enzymatic function of PPase, the crystal structure of the Hu-PPase-ED quadruple mutant (D116A/D118A/P119A/D121A) was determined at 1.69 Å resolution. The resulting structure maintained a barrel-like shape similar to that of the wild-type, albeit lacking Mg2+ ions. Molecular docking analysis demonstrated a decreased ability of Hu-PPase-ED to bind to PPi. Further, molecular dynamics simulation analysis indicated that the mutation rendered the loop of Mg2+ ion-binding residues less stable. Therefore, the effect on enzyme activity did not result from a change in the gross protein structure but rather from a mutation that abolished the Mg2+-coordinating groups, thereby eliminating Mg2+ binding and leading to the loss of enzyme activity.
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Affiliation(s)
- Shuping Zheng
- Public Technology Service Center, Fujian Medical University, Fuzhou, China
| | - Chenhua Zheng
- Experiment Teaching Center of Basic Medical Sciences, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Sishi Chen
- Public Technology Service Center, Fujian Medical University, Fuzhou, China
| | - Jianpeng Guo
- Department of Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, China; Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, Fujian Medical University, Fuzhou, China
| | - Lirui Huang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Zhenhong Huang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Sunting Xu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yihan Wu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Shunfa Li
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Junjin Lin
- Public Technology Service Center, Fujian Medical University, Fuzhou, China
| | - Yiqing You
- Key Laboratory of Diagnostic Medicine Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Fen Hu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
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2
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Zhang N, Zhao L, He M, Luo P, Tan L. Assay of inorganic pyrophosphatase activity based on a fluorescence "turn-off" strategy using carbon quantum dots@Cu-MOF nanotubes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 284:121771. [PMID: 36027790 DOI: 10.1016/j.saa.2022.121771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/06/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
A highly sensitive and selective sensor for the quantitative assay of inorganic pyrophosphatase (PPase) activity was developed based on a fluorescence "turn-off" strategy. Carbon quantum dots@Cu(II)-based metal-organic framework nanotubes (CQDs@Cu-MOF) with length less than 300 nm and width less than 20 nm were synthesized. CQDs in the nanotubes exhibited weak fluorescence owing to static quenching. The coordination reaction between pyrophosphate ion (PPi) and Cu(II) decomposed CQDs@Cu-MOF and led to the release of CQDs, of which the fluorescence recovered. In the presence of PPase, the hydrolysis of PPi generated phosphate ion (Pi). CQDs@Cu-MOF remained their structural stability and the fluorescence turned off. The fluorescence intensity difference of the mixture of CQDs@Cu-MOF and PPi in the absence and presence of PPase (-ΔF) was proportional to the PPase concentration from 0.1 to 5 mU mL-1 and that from 5 to 50 mU mL-1, and a limit of detection at 0.03 mU mL-1 was obtained. PPase activity in human serum was analyzed using the proposed fluorescence sensor and the recovery values were found to vary from 95.0% to 104 %.
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Affiliation(s)
- Ningning Zhang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Lixin Zhao
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Mengting He
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Peng Luo
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Liang Tan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China.
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3
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Oliver EB, Friesen JD, Walker JA, Peters SJ, Weitzel CS, Friesen JA. Characterization of an archaeal inorganic pyrophosphatase from Sulfolobus islandicus using a [ 31P]-NMR-based assay. Biochem Biophys Res Commun 2021; 585:8-14. [PMID: 34781059 DOI: 10.1016/j.bbrc.2021.11.019] [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: 09/15/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022]
Abstract
Inorganic pyrophosphatase catalyzes the conversion of pyrophosphate to phosphate and is often critical for driving reactions forward in cellular processes such as nucleic acid and protein synthesis. Commonly used methods for quantifying pyrophosphatase enzyme activity employ reacting liberated phosphate with a second molecule to produce absorbance changes or employing a second enzyme in coupled reactions to produce a product with a detectable absorbance. In this investigation, a novel [31P]-NMR spectroscopy-based assay was used to quantitatively measure the formation of phosphate and evaluate the activity of inorganic pyrophosphatase from the thermoacidophilic Crenarchaeota Sulfolobus islandicus. The enzymatic activity was directly measured via integration of the [31P] resonance associated with the phosphate product (δ = 2.1 ppm). Sulfolobus islandicus inorganic pyrophosphatase preferentially utilized Mg2+ as divalent cation and had pH and temperature optimums of 6.0 of 50 °C, respectively. The Vmax value was 850 μmol/min/mg and the Km for pyrophosphate was 1.02 mM. Sequence analysis indicates the enzyme is a Family I pyrophosphatase. Sulfolobus islandicus inorganic pyrophosphatase was shown to be inhibited by sodium fluoride with a IC50 of 2.26 mM, compared to a IC50 of 0.066 mM for yeast inorganic pyrophosphatase. These studies reveal that a [31P]-NMR spectroscopy-based assay is an effective method for analyzing catalysis by phosphate-producing enzymes.
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Affiliation(s)
- Ethan B Oliver
- Department of Chemistry, Illinois State University, Normal, IL, 61790, USA
| | - Joshua D Friesen
- Department of Chemistry, Illinois State University, Normal, IL, 61790, USA
| | - Jacob A Walker
- Department of Chemistry, Illinois State University, Normal, IL, 61790, USA
| | - Steven J Peters
- Department of Chemistry, Illinois State University, Normal, IL, 61790, USA
| | | | - Jon A Friesen
- Department of Chemistry, Illinois State University, Normal, IL, 61790, USA.
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4
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Wu QF, Wang WS, Chen SB, Xu B, Li YD, Chen JH. Crystal Structure of Inorganic Pyrophosphatase From Schistosoma japonicum Reveals the Mechanism of Chemicals and Substrate Inhibition. Front Cell Dev Biol 2021; 9:712328. [PMID: 34458268 PMCID: PMC8386120 DOI: 10.3389/fcell.2021.712328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/15/2021] [Indexed: 11/13/2022] Open
Abstract
Soluble inorganic pyrophosphatases (PPases) are essential for facilitating the growth and development of organisms, making them attractive functional proteins. To provide insight into the molecular basis of PPases in Schistosoma japonicum (SjPPase), we expressed the recombinant SjPPase, analyzed the hydrolysis mechanism of inorganic pyrophosphate (PPi), and measured its activity. Moreover, we solved the crystal structure of SjPPase in complex with orthophosphate (Pi) and performed PPi and methylene diphosphonic acid (MDP) docking into the active site. Our results suggest that the SjPPase possesses PPi hydrolysis activity, and the activity declines with increased MDP or NaF concentration. However, the enzyme shows unexpected substrate inhibition properties. Through PPi metabolic pathway analysis, the physiological action of substrate inhibition might be energy saving, adaptably cytoprotective, and biosynthetic rate regulating. Furthermore, the structure of apo-SjPPase and SjPPase with Pi has been solved at 2.6 and 2.3 Å, respectively. The docking of PPi into the active site of the SjPPase-Pi complex revealed that substrate inhibition might result from blocking Pi exit due to excess PPi in the SjPPase-Pi complex of the catalytic cycle. Our results revealed the structural features of apo-SjPPase and the SjPPase-Pi complex by X-ray crystallography, providing novel insights into the physiological functions of PPase in S. japonicum without the PPi transporter and the mechanism of its substrate inhibition.
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Affiliation(s)
- Qun-Feng Wu
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,NHC Key Laboratory of Parasite and Vector Biology, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China.,Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, China
| | - Wei-Si Wang
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,NHC Key Laboratory of Parasite and Vector Biology, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,NHC Key Laboratory of Parasite and Vector Biology, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,NHC Key Laboratory of Parasite and Vector Biology, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Yong-Dong Li
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,NHC Key Laboratory of Parasite and Vector Biology, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China.,Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,NHC Key Laboratory of Parasite and Vector Biology, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Shanghai, China.,The School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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5
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Niu H, Zhu J, Qu Q, Zhou X, Huang X, Du Z. Crystallographic and modeling study of the human inorganic pyrophosphatase 1: A potential anti-cancer drug target. Proteins 2021; 89:853-865. [PMID: 33583053 DOI: 10.1002/prot.26064] [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: 08/11/2020] [Revised: 11/09/2020] [Accepted: 01/31/2021] [Indexed: 11/10/2022]
Abstract
Inorganic pyrophosphatases (PPases) catalyze the hydrolysis of pyrophosphate to phosphates. PPases play essential roles in growth and development, and are found in all kingdoms of life. Human possess two PPases, PPA1 and PPA2. PPA1 is present in all tissues, acting largely as a housekeeping enzyme. Besides pyrophosphate hydrolysis, PPA1 can also directly dephosphorylate phosphorylated c-Jun N-terminal kinases 1 (JNK1). Upregulated expression of PPA1 has been linked to many human malignant tumors. PPA1 knockdown induces apoptosis and decreases proliferation. PPA1 is emerging as a potential prognostic biomarker and target for anti-cancer drug development. In spite of the biological and physiopathological importance of PPA1, there is no detailed study on the structure and catalytic mechanisms of mammalian origin PPases. Here we report the crystal structure of human PPA1 at a resolution of 2.4 Å. We also carried out modeling studies of PPA1 in complex with JNK1 derived phosphor-peptides. The monomeric protein fold of PPA1 is similar to those found in other family I PPases. PPA1 forms a dimeric structure that should be conserved in animal and fungal PPases. Analysis of the PPA1 structure and comparison with available structures of PPases from lower organisms suggest that PPA1 has a largely pre-organized and relatively rigid active site for pyrophosphate hydrolysis. Results from the modeling study indicate the active site of PPA1 has the potential to accommodate double-phosphorylated peptides from JNK1. In short, results from the study provides new insights into the mechanisms of human PPA1 and basis for structure-based anti-cancer drug developments using PPA1 as the target.
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Affiliation(s)
- Haiying Niu
- Department of Gynecology and Obstetrics, Tianjin First Central Hospital, Tianjin, China.,Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Jiang Zhu
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College 16802, Pennsylvania, USA
| | - Quanxin Qu
- Department of Gynecology and Obstetrics, Tianjin First Central Hospital, Tianjin, China
| | - Xia Zhou
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Xiaolan Huang
- Department of Computer Science, Southern Illinois University, Carbondale, Illinois, USA
| | - Zhihua Du
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
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6
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Huang X, Jia J, Lin Y, Qiu B, Lin Z, Chen H. A Highly Sensitive Electrochemiluminescence Biosensor for Pyrophosphatase Detection Based on Click Chemistry-Triggered Hybridization Chain Reaction in Homogeneous Solution. ACS APPLIED MATERIALS & INTERFACES 2020; 12:34716-34722. [PMID: 32643920 DOI: 10.1021/acsami.0c10542] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The abnormal expression of pyrophosphatase (PPase) is closely related to many diseases and malignant tumors, so the detection for PPase is of great significance in clinical diagnosis, disease monitoring, and other biomedical aspects. In this study, a sensitive and specific electrochemiluminescence (ECL) biosensor combined highly specific Cu+-catalyzed azide-alkyne cycloaddition (CuAAC) with high efficiency of hybridization chain reaction (HCR) for the purpose of detecting pyrophosphatase has been designed. Highly efficient hybridization chain reaction amplification processed in homogeneous solution and the amplification products were connected to the electrode surface in one step, which solved the problem of low DNA amplification efficiency on the electrode surface because of the steric hindrance. Ru(phen)32+ was embedded into the dsDNA and functioned as ECL probes; the enhanced ECL intensity of the system had a linear relationship with the logarithm of PPase concentration in the range of 0.025-50 mU with a detection limit of 8 μU. The method was proved to be of good specificity, repeatability, and stability that could be used for screening and quantitatively determining pyrophosphatase inhibitor sodium fluoride. The practicability of this method in clinical application has been proved through the detection of serum from the clinical arthritis patients. Moreover, the method can be used to monitor PPase activity of arthritis patients before and after administration to provide reference for the effect of drug treatment.
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Affiliation(s)
- Xiaocui Huang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Jinpeng Jia
- Department of Orthopaedics, General Hospital of Chinese People's Liberation Army, 28 Fuxing Road, Beijing 100853, China
| | - Yue Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Huixing Chen
- Department of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian 350000, China
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7
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Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study. Biophys J 2020; 119:142-150. [PMID: 32533942 DOI: 10.1016/j.bpj.2020.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/06/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023] Open
Abstract
The mesophilic inorganic pyrophosphatase from Escherichia coli (EcPPase) retains function at 353 K, the physiological temperature of hyperthermophilic Thermococcus thioreducens, whereas the homolog protein (TtPPase) from this hyperthermophilic organism cannot function at room temperature. To explain this asymmetric behavior, we examined structural and dynamical properties of the two proteins using molecular dynamics simulations. The global flexibility of TtPPase is significantly higher than its mesophilic homolog at all tested temperature/pressure conditions. However, at 353 K, EcPPase reduces its solvent-exposed surface area and increases subunit compaction while maintaining flexibility in its catalytic pocket. In contrast, TtPPase lacks this adaptability and has increased rigidity and reduced protein/water interactions in its catalytic pocket at room temperature, providing a plausible explanation for its inactivity near room temperature.
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8
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Wang H, Rao H, Xue X, An P, Gao M, Luo M, Liu X, Xue Z. Target-mediated surface chemistry of gold nanorods for breaking the low color resolution limitation of monocolorimetric sensor. Anal Chim Acta 2020; 1097:222-229. [DOI: 10.1016/j.aca.2019.11.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/01/2019] [Accepted: 11/06/2019] [Indexed: 12/20/2022]
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9
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In situ formation of fluorescent polydopamine catalyzed by peroxidase-mimicking FeCo-LDH for pyrophosphate ion and pyrophosphatase activity detection. Anal Chim Acta 2019; 1053:89-97. [DOI: 10.1016/j.aca.2018.12.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/28/2018] [Accepted: 12/03/2018] [Indexed: 11/24/2022]
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10
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Tian Y, Hao L, Wang C, Yang X, Liu S. Quantum Dot Doping-Induced Photoluminescence for Facile, Label-Free, and Sensitive Pyrophosphatase Activity Assay and Inhibitor Screening. NANOMATERIALS 2019; 9:nano9010111. [PMID: 30669286 PMCID: PMC6359004 DOI: 10.3390/nano9010111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 12/19/2022]
Abstract
Development of simple, convenient, and sensitive assay methods for pyrophosphatase (PPase) activity is of importance, for disease diagnosis and drug discovery. Herein, a simple, rapid, label-free, and sensitive fluorescence sensor for PPase activity assay is developed, using Cu2+ doping-induced quantum dot (QD) photoluminescence as a signal reporter. The Cu2+ doping of ZnSe QD can induce a dopant-dependent emission response, which will be inhibited after the premixing of Cu2+ with pyrophosphate (PPi), to form a Cu2+-PPi complex. Then, the hydrolysis of PPi into phosphate (Pi), specifically catalyzed by PPase, liberates the free Cu2+ to regain the QD doping for the fluorescence response, which is highly dependent on the PPase activity. The PPase can be sensitively and selectively assayed, with a detection limit of 0.1 mU/mL. The developed sensing strategy can be also employed for the PPase inhibitor screening. Thus, the current QD doping-based sensing strategy offers an efficient and promising avenue for Cu2+, PPi, or PPase-related target analysis, and might hold great potential for the further applications in the clinical disease diagnosis.
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Affiliation(s)
- Yishen Tian
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Lijie Hao
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Chao Wang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Xiaoyan Yang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Shufeng Liu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
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11
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Zhao H, Ma C, Chen M. A novel fluorometric method for inorganic pyrophosphatase detection based on G-quadruplex-thioflavin T. Mol Cell Probes 2018; 43:29-33. [PMID: 30572018 DOI: 10.1016/j.mcp.2018.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/29/2018] [Accepted: 12/16/2018] [Indexed: 10/27/2022]
Abstract
In this paper, we propose a fluorometric approach for the highly sensitive detection of inorganic pyrophosphatase (PPase) based on G-quadruplex-thioflavin T (ThT). In the absence of PPase, Cu2+ can coordinate with pyrophosphate (PPi) to generate a Cu2+/PPi complex. Then the G-rich sequence folds into the G-quadruplex structure, which can combine with ThT to generate a remarkable fluorescent signal. In the presence of PPase, the coordinated compound can be destroyed by the PPase catalyzed hydrolysis of PPi into inorganic phosphate (Pi). The subsequent release of Cu2+ can compete with ThT to induce a tighter G-quadruplex structure, causing the release of ThT and a sharp fluorescence decrease. Based on this mechanism, a facile and quantitative strategy for PPase detection was developed. The fluorescence intensity of the system shows a linear relationship with the PPase activities in the range of 0.5-30 U/L with a detection limit as low as 0.48 U/L. The proposed strategy for fluorescence spectrometric PPase detection is convenient, cost effective, and sensitive. This can be utilized to evaluate the inhibition effect of NaF on PPase as well as diagnose PPase-related diseases.
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Affiliation(s)
- Han Zhao
- School of Life Sciences, Central South University, Changsha, 410013, China
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha, 410013, China.
| | - Mingjian Chen
- School of Life Sciences, Central South University, Changsha, 410013, China
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12
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Oh J, Hong JI. Cation Effect on Fluorescent Sensing of Pyrophosphate by a Bis(Zn-DPA) Probe. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jinrok Oh
- Department of Chemistry; Seoul National University; Seoul 08826 South Korea
| | - Jong-In Hong
- Department of Chemistry; Seoul National University; Seoul 08826 South Korea
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13
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Gutiérrez-Luna FM, Hernández-Domínguez EE, Valencia-Turcotte LG, Rodríguez-Sotres R. Review: "Pyrophosphate and pyrophosphatases in plants, their involvement in stress responses and their possible relationship to secondary metabolism". PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 267:11-19. [PMID: 29362089 DOI: 10.1016/j.plantsci.2017.10.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 10/19/2017] [Accepted: 10/26/2017] [Indexed: 05/14/2023]
Abstract
Pyrophosphate (PPi) is produced as byproduct of biosynthesis in the cytoplasm, nucleus, mitochondria and chloroplast, or in the tonoplast and Golgi by membrane-bound H+-pumping pyrophosphatases (PPv). Inorganic pyrophosphatases (E.C. 3.6.1.1; GO:0004427) impulse various biosynthetic reactions by recycling PPi and are essential to living cells. Soluble and membrane-bound enzymes of high specificity have evolved in different protein families and multiple pyrophosphatases are encoded in all plant genomes known to date. The soluble proteins are present in cytoplasm, extracellular space, inside chloroplasts, and perhaps inside mitochondria, nucleus or vacuoles. The cytoplasmic isoforms may compete for PPi with the PPv enzymes and how PPv and soluble activities are controlled is currently unknown, yet the cytoplasmic PPi concentration is high and fairly constant. Manipulation of the PPi metabolism impacts primary metabolism and vice versa, indicating a tight link between PPi levels and carbohydrate metabolism. These enzymes appear to play a role in germination, development and stress adaptive responses. In addition, the transgenic overexpression of PPv has been used to enhance plant tolerance to abiotic stress, but the reasons behind this tolerance are not completely understood. Finally, the relationship of PPi to stress suggest a currently unexplored link between PPi and secondary metabolism.
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Affiliation(s)
- Francisca Morayna Gutiérrez-Luna
- FACULTAD DE QUÍMICA, UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO, Ave. Universidad 3000, Cd. Universitaria, Del. Coyoacán, P.C. 04510, Mexico City, Mexico.
| | | | - Lilián Gabriela Valencia-Turcotte
- FACULTAD DE QUÍMICA, UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO, Ave. Universidad 3000, Cd. Universitaria, Del. Coyoacán, P.C. 04510, Mexico City, Mexico.
| | - Rogelio Rodríguez-Sotres
- FACULTAD DE QUÍMICA, UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO, Ave. Universidad 3000, Cd. Universitaria, Del. Coyoacán, P.C. 04510, Mexico City, Mexico.
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14
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Electrochemical strategy for pyrophosphatase detection Based on the peroxidase-like activity of G-quadruplex-Cu2+ DNAzyme. Talanta 2018; 178:491-497. [DOI: 10.1016/j.talanta.2017.09.069] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/23/2017] [Accepted: 09/26/2017] [Indexed: 12/13/2022]
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15
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He R, Yu G, Han X, Han J, Li W, Wang B, Huang S, Cheng X. ThPP1 gene, encodes an inorganic pyrophosphatase in Thellungiella halophila, enhanced the tolerance of the transgenic rice to alkali stress. PLANT CELL REPORTS 2017; 36:1929-1942. [PMID: 29030650 DOI: 10.1007/s00299-017-2208-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 09/12/2017] [Indexed: 05/14/2023]
Abstract
An inorganic pyrophosphorylase gene, ThPP1 , modulated the accumulations of phosphate and osmolytes by up-regulating the differentially expression genes, thus enhancing the tolerance of the transgenic rice to alkali stress (AS). Inorganic pyrophosphorylase is essential in catalyzing the hydrolysis of pyrophosphate to inorganic phosphate during plant growth. Here, we report the changes of physiological osmolytes and differentially expression genes in the transgenic rice overexpressing a soluble inorganic pyrophosphatase gene ThPP1 of Thellungiella halophila in response to AS. Analyses showed that the ThPP1 gene was a PPase family I member which is located to the cytoplasm. Data showed that the transgenic lines revealed an enhanced tolerance to AS compared to the wild type, and effectively increased the accumulations of inorganic phosphate and organic small molecules starch, sucrose, proline and chlorophyll, and maintained the balance of osmotic potential by modulating the ratio of Na+/K+ in plant cells. Under AS, total 379 of differentially expression genes were up-regulated in the leaves of the transgenic line compared with control, and the enhanced tolerance of the transgenic rice to the AS seemed to be associated with the up-regulations of the osmotic stress-related genes such as the L-type lectin-domain containing receptor kinase (L-type LecRK), the cation/H+ antiporter gene and the vacuolar cation/proton exchanger 1 gene (CAX1), which conferred the involvements in the biosynthesis and metabolic pathways. Protein interaction showed that the ThPP1 protein specifically interacted with a 16# target partner of the photosystem II light-harvesting-Chl-binding protein. This study suggested that the ThPP1 gene plays an important regulatory role in conferring the tolerance of the transgenic rice to AS, and is an effective candidate in molecular breeding for crop cultivation of the alkali tolerance.
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Affiliation(s)
- Rui He
- College of Land and Environment, Shenyang Agricultural University, No. 120 Dongling Road, Shenyang, 110866, Liaoning, People's Republic of China
- Key Lab of Plant Nutrition and Fertilizers, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 South Street, Zhongguancun, Beijing, 100081, People's Republic of China
| | - Guohong Yu
- Key Lab of Plant Nutrition and Fertilizers, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 South Street, Zhongguancun, Beijing, 100081, People's Republic of China
| | - Xiaori Han
- College of Land and Environment, Shenyang Agricultural University, No. 120 Dongling Road, Shenyang, 110866, Liaoning, People's Republic of China
| | - Jiao Han
- Key Lab of Plant Nutrition and Fertilizers, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 South Street, Zhongguancun, Beijing, 100081, People's Republic of China
- College of Life Science, Shanxi Normal University, No. 1 Gongyue Street, Yaodu Area, Linfen, 0410004, Shanxi, People's Republic of China
| | - Wei Li
- Key Lab of Plant Nutrition and Fertilizers, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 South Street, Zhongguancun, Beijing, 100081, People's Republic of China
| | - Bing Wang
- Key Lab of Plant Nutrition and Fertilizers, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 South Street, Zhongguancun, Beijing, 100081, People's Republic of China
| | - Shengcai Huang
- Key Lab of Plant Nutrition and Fertilizers, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 South Street, Zhongguancun, Beijing, 100081, People's Republic of China
| | - Xianguo Cheng
- Key Lab of Plant Nutrition and Fertilizers, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 South Street, Zhongguancun, Beijing, 100081, People's Republic of China.
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16
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Jamwal A, Yogavel M, Abdin MZ, Jain SK, Sharma A. Structural and Biochemical Characterization of Apicomplexan Inorganic Pyrophosphatases. Sci Rep 2017; 7:5255. [PMID: 28701714 PMCID: PMC5507929 DOI: 10.1038/s41598-017-05234-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/25/2017] [Indexed: 11/17/2022] Open
Abstract
Inorganic pyrophosphatases (PPase) participate in energy cycling and they are essential for growth and survival of organisms. Here we report extensive structural and functional characterization of soluble PPases from the human parasites Plasmodium falciparum (PfPPase) and Toxoplasma gondii (TgPPase). Our results show that PfPPase is a cytosolic enzyme whose gene expression is upregulated during parasite asexual stages. Cambialistic PfPPase actively hydrolyzes linear short chain polyphosphates like PPi, polyP3 and ATP in the presence of Zn2+. A remarkable new feature of PfPPase is the low complexity asparagine-rich N-terminal region that mediates its dimerization. Deletion of N-region has an unexpected and substantial effect on the stability of PfPPase domain, resulting in aggregation and significant loss of enzyme activity. Significantly, the crystal structures of PfPPase and TgPPase reveal unusual and unprecedented dimeric organizations and provide new fundamental insights into the variety of oligomeric assemblies possible in eukaryotic inorganic PPases.
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Affiliation(s)
- Abhishek Jamwal
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.,Department of Biotechnology, Jamia Hamdard, New Delhi, 110063, India
| | - Manickam Yogavel
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Malik Z Abdin
- Department of Biotechnology, Jamia Hamdard, New Delhi, 110063, India
| | - Swatantra K Jain
- Department of Biotechnology, Jamia Hamdard, New Delhi, 110063, India.,Department of Biochemistry, Hamdard Institute of Medical Sciences, 110063, New Delhi, India
| | - Amit Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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17
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He Q, Kelliher M, Bähring S, Lynch VM, Sessler JL. A Bis-calix[4]pyrrole Enzyme Mimic That Constrains Two Oxoanions in Close Proximity. J Am Chem Soc 2017; 139:7140-7143. [PMID: 28493689 DOI: 10.1021/jacs.7b02329] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Herein we describe a large capsule-like bis-calix[4]pyrrole 1, which is able to host concurrently two dihydrogen phosphate anions within a relatively large internal cavity. Evidence for the concurrent, dual recognition of the encapsulated anions came from 1H NMR and UV-vis spectroscopies and ITC titrations carried out in CD2Cl2/CD3OD (9/1, v/v) or dichloroethane (DCE), as well as single crystal X-ray diffraction analyses. Receptor 1 was also found to bind two dianionic sulfate anions bridged by two water molecules in the solid state. The resulting sulfate dimer was retained in DCE solution, as evidenced by spectroscopic analyses. Finally, receptor 1 was found capable of accommodating two trianionic pyrophosphate anions in the cavity. The present experimental findings are supported by DFT calculations along with 1H NMR and UV-vis spectroscopies, ITC studies, and single crystal X-ray diffraction analyses.
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Affiliation(s)
- Qing He
- Department of Chemistry, The University of Texas at Austin , 105 East 24th Street-A5300, Austin, Texas 78712-1224, United States
| | - Michael Kelliher
- Department of Chemistry, The University of Texas at Austin , 105 East 24th Street-A5300, Austin, Texas 78712-1224, United States
| | - Steffen Bähring
- Department of Chemistry, The University of Texas at Austin , 105 East 24th Street-A5300, Austin, Texas 78712-1224, United States.,Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Vincent M Lynch
- Department of Chemistry, The University of Texas at Austin , 105 East 24th Street-A5300, Austin, Texas 78712-1224, United States
| | - Jonathan L Sessler
- Department of Chemistry, The University of Texas at Austin , 105 East 24th Street-A5300, Austin, Texas 78712-1224, United States
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18
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Xu S, Feng X, Gao T, Wang R, Mao Y, Lin J, Yu X, Luo X. A novel dual-functional biosensor for fluorometric detection of inorganic pyrophosphate and pyrophosphatase activity based on globulin stabilized gold nanoclusters. Anal Chim Acta 2016; 958:22-29. [PMID: 28110681 DOI: 10.1016/j.aca.2016.12.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 11/03/2016] [Accepted: 12/19/2016] [Indexed: 12/27/2022]
Abstract
A novel ultrasensitive dual-functional biosensor for highly sensitive detection of inorganic pyrophosphate (PPi) and pyrophosphatase (PPase) activity was developed based on the fluorescent variation of globulin protected gold nanoclusters (Glo@Au NCs) with the assistance of Cu2+. Glo@Au NCs and PPi were used as the fluorescent indicator and substrate for PPase activity evaluation, respectively. In the presence of Cu2+, the fluorescence of the Glo@Au NCs will be quenched owing to the formation of Cu2+-Glo@Au NCs complex, while PPi can restore the fluorescence of the Cu2+-Glo@Au NCs complex because of its higher binding affinity with Cu2+. As PPase can catalyze the hydrolysis of PPi, it will lead to the release of Cu2+ and re-quench the fluorescence of the Glo@Au NCs. Based on this mechanism, quantitative evaluation of the PPi and PPase activity can be achieved ranging from 0.05 μM to 218.125 μM for PPi and from 0.1 to 8 mU for PPase, with detection limits of 0.02 μM and 0.04 mU, respectively, which is much lower than that of other PPi and PPase assay methods. More importantly, this ultrasensitive dual-functional biosensor can also be successfully applied to evaluate the PPase activity in human serum, showing great promise for practical diagnostic applications.
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Affiliation(s)
- Shenghao Xu
- Key Laboratory of Sensor Analysis of Tumor Marker Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Xiuying Feng
- Key Laboratory of Sensor Analysis of Tumor Marker Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Teng Gao
- Key Laboratory of Sensor Analysis of Tumor Marker Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Ruizhi Wang
- Key Laboratory of Sensor Analysis of Tumor Marker Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China; College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Yaning Mao
- Key Laboratory of Sensor Analysis of Tumor Marker Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Jiehua Lin
- Key Laboratory of Sensor Analysis of Tumor Marker Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Xijuan Yu
- Key Laboratory of Sensor Analysis of Tumor Marker Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Xiliang Luo
- Key Laboratory of Sensor Analysis of Tumor Marker Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China.
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19
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Zhang Y, Guo Y, Zhao M, Lin C, Lin Z, Luo F, Chen G. Fluorescence biosensor for inorganic pyrophosphatase activity. Anal Bioanal Chem 2016; 409:999-1005. [DOI: 10.1007/s00216-016-0014-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/26/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
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20
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Chen C, Zhao D, Sun J, Yang X. Colorimetric Logic Gate for Pyrophosphate and Pyrophosphatase via Regulating the Catalytic Capability of Horseradish Peroxidase. ACS APPLIED MATERIALS & INTERFACES 2016; 8:29529-29535. [PMID: 27714993 DOI: 10.1021/acsami.6b10712] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
By regulating the catalytic capability of horseradish peroxidase (HRP), an artful colorimetric assay platform for pyrophosphate (PPi) and pyrophosphatase (PPase) was unprecedentedly designed. In this work, Cu(I), generated by reducing Cu(II) in the presence of ascorbate, could inhibit HRP's catalytic capability of transforming colorless 3,3',5,5'-tetramethylbenzidine (TMB) into blue oxidized TMB (oxTMB). The robust coordination between PPi and Cu(II) is able to discourage the reduction of Cu(II) to Cu(I) effectively, thus restoring the original catalytic capability of HRP and regenerating blue-colored oxTMB. Upon PPase introduction, PPi would be hydrolyzed into orthophosphate, which could release Cu(II) free from the Cu(II)-PPi complex, and thus in turn allows the catalytic capability of HRP to be inhibited by Cu(I). HRP was activated or deactivated to different degrees depending on PPi or PPase levels, which could be indicated by using HRP-triggered catalytic system as a signal amplifier, thus paving a way for PPi and PPase sensing. Based on the colorimetric sensor for PPi and PPase, an "INH" logic gate was rationally constructed. With the merits of high sensitivity and selectivity, cost-effectiveness, and simplification, our proposed analytical system has also been verified to have potential to be utilized for enzyme inhibitor screening and diagnosis of PPase-related diseases.
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Affiliation(s)
- Chuanxia Chen
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Dan Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Jian Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
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21
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Zhao L, Zhao L, Miao Y, Liu C, Zhang C. Construction of a Turn Off-On-Off Fluorescent System Based on Competitive Coordination of Cu 2+ between 6,7-Dihydroxycoumarin and Pyrophosphate Ion for Sensitive Assay of Pyrophosphatase Activity. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2016; 2016:4306838. [PMID: 27766179 PMCID: PMC5059578 DOI: 10.1155/2016/4306838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 08/25/2016] [Accepted: 09/05/2016] [Indexed: 06/06/2023]
Abstract
The detection of pyrophosphatase (PPase) activity is of great significance in diagnosing diseases and understanding the function of PPase-related biological events. This study constructed a turn off-on-off fluorescent system for PPase activity assay based on PPase-regulated competitive coordination of Cu2+ between a water-soluble fluorescent probe 6,7-dihydroxycoumarin (DHC) and pyrophosphate (PPi). The probe DHC can coordinate with Cu2+ and consequently display on-off type fluorescence response. Furthermore, the in situ formed nonfluorescent Cu2+-DHC complex can act as an effective off-on type fluorescent probe for sensing PPi due to the higher coordination reactivity between Cu2+ and PPi than that between Cu2+ and DHC. The subsequent addition of PPase to the mixture containing Cu2+, DHC, and PPi leads to the fluorescence requenching of the system again (an off state) because PPase catalyzes the hydrolysis of PPi into orthophosphate in the reaction system. Under the optimum conditions, the decrease of the fluorescence intensity of DHC-Cu2+-PPi system was linear with the increase of the PPase activity in the range from 0.1 to 0.3 U. The detection limit was down to 0.028 U PPase (S/N = 3). Moreover, the as-established system was also applied to evaluate PPase inhibitor. This study offers a simple yet effective method for the detection of PPase activity.
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Affiliation(s)
- Lingzhi Zhao
- Department of Pharmacy, Xi'an Medical College, Xi'an 710021, China
- Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Liu Zhao
- Beijing Research Center of Agricultural Standards and Testing, Beijing 100097, China
| | - Yanqing Miao
- Department of Pharmacy, Xi'an Medical College, Xi'an 710021, China
| | - Chunye Liu
- Department of Pharmacy, Xi'an Medical College, Xi'an 710021, China
| | - Chenxiao Zhang
- Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
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22
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Zhou Q, Lin Y, Xu M, Gao Z, Yang H, Tang D. Facile Synthesis of Enhanced Fluorescent Gold–Silver Bimetallic Nanocluster and Its Application for Highly Sensitive Detection of Inorganic Pyrophosphatase Activity. Anal Chem 2016; 88:8886-92. [DOI: 10.1021/acs.analchem.6b02543] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Qian Zhou
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Youxiu Lin
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Mingdi Xu
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Zhuangqiang Gao
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Huanghao Yang
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Dianping Tang
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
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23
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Lin Y, Zhou Q, Li J, Shu J, Qiu Z, Lin Y, Tang D. Magnetic Graphene Nanosheet-Based Microfluidic Device for Homogeneous Real-Time Electronic Monitoring of Pyrophosphatase Activity Using Enzymatic Hydrolysate-Induced Release of Copper Ion. Anal Chem 2015; 88:1030-8. [DOI: 10.1021/acs.analchem.5b04005] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Youxiu Lin
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Qian Zhou
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Juan Li
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Jian Shu
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Zhenli Qiu
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Yuping Lin
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
| | - Dianping Tang
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou 350108, People’s Republic of China
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24
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Archaeal Inorganic Pyrophosphatase Displays Robust Activity under High-Salt Conditions and in Organic Solvents. Appl Environ Microbiol 2015; 82:538-48. [PMID: 26546423 DOI: 10.1128/aem.03055-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/02/2015] [Indexed: 11/20/2022] Open
Abstract
Soluble inorganic pyrophosphatases (PPAs) that hydrolyze inorganic pyrophosphate (PPi) to orthophosphate (Pi) are commonly used to accelerate and detect biosynthetic reactions that generate PPi as a by-product. Current PPAs are inactivated by high salt concentrations and organic solvents, which limits the extent of their use. Here we report a class A type PPA of the haloarchaeon Haloferax volcanii (HvPPA) that is thermostable and displays robust PPi-hydrolyzing activity under conditions of 25% (vol/vol) organic solvent and salt concentrations from 25 mM to 3 M. HvPPA was purified to homogeneity as a homohexamer by a rapid two-step method and was found to display non-Michaelis-Menten kinetics with a Vmax of 465 U · mg(-1) for PPi hydrolysis (optimal at 42°C and pH 8.5) and Hill coefficients that indicated cooperative binding to PPi and Mg(2+). Similarly to other class A type PPAs, HvPPA was inhibited by sodium fluoride; however, hierarchical clustering and three-dimensional (3D) homology modeling revealed HvPPA to be distinct in structure from characterized PPAs. In particular, HvPPA was highly negative in surface charge, which explained its extreme resistance to organic solvents. To demonstrate that HvPPA could drive thermodynamically unfavorable reactions to completion under conditions of reduced water activity, a novel coupled assay was developed; HvPPA hydrolyzed the PPi by-product generated in 2 M NaCl by UbaA (a "salt-loving" noncanonical E1 enzyme that adenylates ubiquitin-like proteins in the presence of ATP). Overall, we demonstrate HvPPA to be useful for hydrolyzing PPi under conditions of reduced water activity that are a hurdle to current PPA-based technologies.
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25
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Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis. J Struct Biol 2015; 192:76-87. [DOI: 10.1016/j.jsb.2015.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/04/2015] [Accepted: 08/17/2015] [Indexed: 02/01/2023]
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26
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Zhang L, Li M, Qin Y, Chu Z, Zhao S. A convenient label free colorimetric assay for pyrophosphatase activity based on a pyrophosphate-inhibited Cu2+–ABTS–H2O2reaction. Analyst 2014; 139:6298-303. [DOI: 10.1039/c4an01415d] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Galizzi M, Bustamante JM, Fang J, Miranda K, Soares Medeiros LC, Tarleton RL, Docampo R. Evidence for the role of vacuolar soluble pyrophosphatase and inorganic polyphosphate in Trypanosoma cruzi persistence. Mol Microbiol 2013; 90:699-715. [PMID: 24033456 DOI: 10.1111/mmi.12392] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2013] [Indexed: 11/30/2022]
Abstract
Trypanosoma cruzi infection leads to development of a chronic disease but the mechanisms that the parasite utilizes to establish a persistent infection despite activation of a potent immune response by the host are currently unknown. Unusual characteristics of T. cruzi are that it possesses cellular levels of pyrophosphate (PPi ) at least 10 times higher than those of ATP and molar levels of inorganic polyphosphate (polyP) within acidocalcisomes. We characterized an inorganic soluble EF-hand containing pyrophosphatase from T. cruzi (TcVSP) that, depending on the pH and cofactors, can hydrolyse either pyrophosphate (PPi ) or polyphosphate (polyP). The enzyme is localized to both acidocalcisomes and cytosol. Overexpression of TcVSP (TcVSP-OE) resulted in a significant decrease in cytosolic PPi , and short and long-chain polyP levels. Additionally, the TcVSP-OE parasites showed a significant growth defect in fibroblasts, less responsiveness to hyperosmotic stress, and reduced persistence in tissues of mice, suggesting that PPi and polyP are essential for the parasite to resist the stressful conditions in the host and to maintain a persistent infection.
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Affiliation(s)
- Melina Galizzi
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
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28
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Deng J, Jiang Q, Wang Y, Yang L, Yu P, Mao L. Real-Time Colorimetric Assay of Inorganic Pyrophosphatase Activity Based on Reversibly Competitive Coordination of Cu2+ between Cysteine and Pyrophosphate Ion. Anal Chem 2013; 85:9409-15. [DOI: 10.1021/ac402524e] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jingjing Deng
- Beijing
National Laboratory
for Molecular Sciences, Key Laboratory of Analytical Chemistry for
Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, China
| | - Qin Jiang
- Beijing
National Laboratory
for Molecular Sciences, Key Laboratory of Analytical Chemistry for
Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, China
| | - Yuexiang Wang
- Beijing
National Laboratory
for Molecular Sciences, Key Laboratory of Analytical Chemistry for
Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, China
| | - Lifen Yang
- Beijing
National Laboratory
for Molecular Sciences, Key Laboratory of Analytical Chemistry for
Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, China
| | - Ping Yu
- Beijing
National Laboratory
for Molecular Sciences, Key Laboratory of Analytical Chemistry for
Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, China
| | - Lanqun Mao
- Beijing
National Laboratory
for Molecular Sciences, Key Laboratory of Analytical Chemistry for
Living Biosystems, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, China
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29
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Kajander T, Kellosalo J, Goldman A. Inorganic pyrophosphatases: one substrate, three mechanisms. FEBS Lett 2013; 587:1863-9. [PMID: 23684653 DOI: 10.1016/j.febslet.2013.05.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 10/26/2022]
Abstract
Soluble inorganic pyrophosphatases (PPases) catalyse an essential reaction, the hydrolysis of pyrophosphate to inorganic phosphate. In addition, an evolutionarily ancient family of membrane-integral pyrophosphatases couple this hydrolysis to Na(+) and/or H(+) pumping, and so recycle some of the free energy from the pyrophosphate. The structures of the H(+)-pumping mung bean PPase and the Na(+)-pumping Thermotoga maritima PPase solved last year revealed an entirely novel membrane protein containing 16 transmembrane helices. The hydrolytic centre, well above the membrane, is linked by a charged "coupling funnel" to the ionic gate about 20Å away. By comparing the active sites, fluoride inhibition data and the various models for ion transport, we conclude that membrane-integral PPases probably use binding of pyrophosphate to drive pumping.
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Affiliation(s)
- Tommi Kajander
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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30
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Pharmacogenomics and Personalized Medicine for Infectious Diseases. OMICS FOR PERSONALIZED MEDICINE 2013. [PMCID: PMC7122342 DOI: 10.1007/978-81-322-1184-6_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Humans have been plagued by the scourge of invasion by pathogens leading to infectious diseases from the time in memoriam and are still the cause of morbidity and mortality among millions of individuals. Trying to understand the disease mechanisms and finding the remedial measures have been the quest of humankind. The susceptibility to disease of an individual in a given population is determined by ones genetic buildup. Response to treatment and the disease prognosis also depends upon individual’s genetic predisposition. The environmental stress induces mutations and is leading to the emergence of ever-increasing more dreaded infectious pathogens, and now we are in the era of increasing antibiotic resistance that has thrown up a challenge to find new treatment regimes. Discoveries in the science of high-throughput sequencing and array technologies have shown new hope and are bringing a revolution in human health. The information gained from sequencing of both human and pathogen genomes is a way forward in deciphering host-pathogen interactions. Deciphering the pathogen virulence factors, host susceptibility genes, and the molecular programs involved in the pathogenesis of disease has paved the way for discovery of new molecular targets for drugs, diagnostic markers, and vaccines. The genomic diversity in the human population leads to differences in host responses to drugs and vaccines and is the cause of poor response to treatment as well as adverse reactions. The study of pharmacogenomics of infectious diseases is still at an early stage of development, and many intricacies of the host-pathogen interaction are yet to be understood in full measure. However, progress has been made over the decades of research in some of the important infectious diseases revealing how the host genetic polymorphisms of drug-metabolizing enzymes and transporters affect the bioavailability of the drugs which further determine the efficacy and toxicology of the drugs used for treatment. Further, the field of structural biology and chemistry has intertwined to give rise to medical structural genomics leading the way to the discovery of new drug targets against infectious diseases. This chapter explores how the advent of “omics” technologies is making a beginning in bringing about a change in the prevention, diagnosis, and treatments of the infectious diseases and hence paving way for personalized medicine.
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31
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Hughes RC, Coates L, Blakeley MP, Tomanicek SJ, Langan P, Kovalevsky AY, García-Ruiz JM, Ng JD. Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012. [PMID: 23192028 DOI: 10.1107/s1744309112032447] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Inorganic pyrophosphatase (IPPase) from the archaeon Thermococcus thioreducens was cloned, overexpressed in Escherichia coli, purified and crystallized in restricted geometry, resulting in large crystal volumes exceeding 5 mm3. IPPase is thermally stable and is able to resist denaturation at temperatures above 348 K. Owing to the high temperature tolerance of the enzyme, the protein was amenable to room-temperature manipulation at the level of protein preparation, crystallization and X-ray and neutron diffraction analyses. A complete synchrotron X-ray diffraction data set to 1.85 Å resolution was collected at room temperature from a single crystal of IPPase (monoclinic space group C2, unit-cell parameters a=106.11, b=95.46, c=113.68 Å, α=γ=90.0, β=98.12°). As large-volume crystals of IPPase can be obtained, preliminary neutron diffraction tests were undertaken. Consequently, Laue diffraction images were obtained, with reflections observed to 2.1 Å resolution with I/σ(I) greater than 2.5. The preliminary crystallographic results reported here set in place future structure-function and mechanism studies of IPPase.
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Affiliation(s)
- Ronny C Hughes
- Department of Biological Sciences and Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA
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32
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Sell H, Gehl A, Sönnichsen FD, Herges R. Thermodynamic and kinetic stabilization of divanadate in the monovanadate/divanadate equilibrium using a Zn-cyclene derivative: Towards a simple ATP synthase model. Beilstein J Org Chem 2012; 8:81-9. [PMID: 22423274 PMCID: PMC3302101 DOI: 10.3762/bjoc.8.8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 12/21/2011] [Indexed: 01/12/2023] Open
Abstract
For the condensation of anions such as phosphate and ADP to form ATP and water, nature employs sophisticated supramolecular systems to overcome coulomb repulsion and activation barriers. For an attempt to create a simple, analogous chemical system, the dimerization of vanadate is probably the simplest model. We have investigated Zn-benzylcyclene which favors the dimerization thermodynamically as shown by NMR titration. Moreover, EXSY NMR experiments reveal that the vanadate dimer is also kinetically stabilized with respect to hydrolysis by complexation with Zn-cyclene.
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Affiliation(s)
- Hanno Sell
- Otto-Diels Institut für Organische Chemie, Christian-Albrechts-Universität zu Kiel, Otto-Hahn-Platz 4, 24418 Kiel, Germany
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33
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Pace DA, Fang J, Cintron R, Docampo MD, Moreno SNJ. Overexpression of a cytosolic pyrophosphatase (TgPPase) reveals a regulatory role of PP(i) in glycolysis for Toxoplasma gondii. Biochem J 2011; 440:229-40. [PMID: 21831041 PMCID: PMC4874478 DOI: 10.1042/bj20110641] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PP(i) is a critical element of cellular metabolism as both an energy donor and as an allosteric regulator of several metabolic pathways. The apicomplexan parasite Toxoplasma gondii uses PP(i) in place of ATP as an energy donor in at least two reactions: the glycolytic PP(i)-dependent PFK (phosphofructokinase) and V-H(+)-PPase [vacuolar H(+)-translocating PPase (pyrophosphatase)]. In the present study, we report the cloning, expression and characterization of cytosolic TgPPase (T. gondii soluble PPase). Amino acid sequence alignment and phylogenetic analysis indicates that the gene encodes a family I soluble PPase. Overexpression of the enzyme in extracellular tachyzoites led to a 6-fold decrease in the cytosolic concentration of PP(i) relative to wild-type strain RH tachyzoites. Unexpectedly, this subsequent reduction in PP(i) was associated with a higher glycolytic flux in the overexpressing mutants, as evidenced by higher rates of proton and lactate extrusion. In addition to elevated glycolytic flux, TgPPase-overexpressing tachyzoites also possessed higher ATP concentrations relative to wild-type RH parasites. These results implicate PP(i) as having a significant regulatory role in glycolysis and, potentially, other downstream processes that regulate growth and cell division.
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Affiliation(s)
- Douglas A Pace
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.
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34
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Huang H, Yury P, Toro R, Farelli JD, Pandya C, Almo SC, Allen KN, Dunaway-Mariano D. Divergence of structure and function in the haloacid dehalogenase enzyme superfamily: Bacteroides thetaiotaomicron BT2127 is an inorganic pyrophosphatase. Biochemistry 2011; 50:8937-49. [PMID: 21894910 PMCID: PMC3342813 DOI: 10.1021/bi201181q] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The explosion of protein sequence information requires that current strategies for function assignment evolve to complement experimental approaches with computationally based function prediction. This necessitates the development of strategies based on the identification of sequence markers in the form of specificity determinants and a more informed definition of orthologues. Herein, we have undertaken the function assignment of the unknown haloalkanoate dehalogenase superfamily member BT2127 (Uniprot accession code Q8A5 V9) from Bacteroides thetaiotaomicron using an integrated bioinformatics-structure-mechanism approach. The substrate specificity profile and steady-state rate constants of BT2127 (with a k(cat)/K(m) value for pyrophosphate of ~1 × 10(5) M(-1) s(-1)), together with the gene context, support the assigned in vivo function as an inorganic pyrophosphatase. The X-ray structural analysis of wild-type BT2127 and several variants generated by site-directed mutagenesis shows that substrate discrimination is based, in part, on active site space restrictions imposed by the cap domain (specifically by residues Tyr76 and Glu47). Structure-guided site-directed mutagenesis coupled with kinetic analysis of the mutant enzymes identified the residues required for catalysis, substrate binding, and domain-domain association. On the basis of this structure-function analysis, the catalytic residues Asp11, Asp13, Thr113, and Lys147 as well the metal binding residues Asp171, Asn172, and Glu47 were used as markers to confirm BT2127 orthologues identified via sequence searches. This bioinformatic analysis demonstrated that the biological range of BT2127 orthologue is restricted to the phylum Bacteroidetes/Chlorobi. The key structural determinants in the divergence of BT2127 and its closest homologue, β-phosphoglucomutase, control the leaving group size (phosphate vs glucose phosphate) and the position of the Asp acid/base in the open versus closed conformations. HADSF pyrophosphatases represent a third mechanistic and fold type for bacterial pyrophosphatases.
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Affiliation(s)
- Hua Huang
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Patskovsky Yury
- Department of Biochemistry, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Rafael Toro
- Department of Biochemistry, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Jeremiah D. Farelli
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215-2521
| | - Chetanya Pandya
- Bioinformatics Graduate Program, Boston University, 24 Cummington Street Boston, MA 02215-2521
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Karen N. Allen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215-2521
| | - Debra Dunaway-Mariano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131
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Oksanen E, Dauvergne F, Goldman A, Budayova-Spano M. Design of a novel Peltier-based cooling device and its use in neutron diffraction data collection of perdeuterated yeast pyrophosphatase. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889810027111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
H atoms play a central role in enzymatic mechanisms, but H-atom positions cannot generally be determined by X-ray crystallography. Neutron crystallography, on the other hand, can be used to determine H-atom positions but it is experimentally very challenging. Yeast inorganic pyrophosphatase (PPase) is an essential enzyme that has been studied extensively by X-ray crystallography, yet the details of the catalytic mechanism remain incompletely understood. The temperature instability of PPase crystals has in the past prevented the collection of a neutron diffraction data set. This paper reports how the crystal growth has been optimized in temperature-controlled conditions. To stabilize the crystals during neutron data collection a Peltier cooling device that minimizes the temperature gradient along the capillary has been developed. This device allowed the collection of a full neutron diffraction data set.
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36
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Docampo R, Ulrich P, Moreno SNJ. Evolution of acidocalcisomes and their role in polyphosphate storage and osmoregulation in eukaryotic microbes. Philos Trans R Soc Lond B Biol Sci 2010; 365:775-84. [PMID: 20124344 DOI: 10.1098/rstb.2009.0179] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Acidocalcisomes are acidic electron-dense organelles, rich in polyphosphate (poly P) complexed with calcium and other cations. While its matrix contains enzymes related to poly P metabolism, the membrane of the acidocalcisomes has a number of pumps (Ca(2+)-ATPase, V-H(+)-ATPase, H(+)-PPase), exchangers (Na(+)/H(+), Ca(2+)/H(+)), and at least one channel (aquaporin). Acidocalcisomes are present in both prokaryotes and eukaryotes and are an important storage of cations and phosphorus. They also play an important role in osmoregulation and interact with the contractile vacuole complex in a number of eukaryotic microbes. Acidocalcisomes resemble lysosome-related organelles (LRO) from mammalian cells in many of their properties. They share similar morphological characteristics, acidic properties, phosphorus contents and a system for targeting of their membrane proteins through adaptor complex-3 (AP-3). Storage of phosphate and cations may represent the ancestral physiological function of acidocalcisomes, with cation and pH homeostasis and osmoregulatory functions derived following the divergence of prokaryotes and eukaryotes.
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Affiliation(s)
- Roberto Docampo
- Department of Cellular Biology and Center for Tropical and Global Emerging Diseases, University of Georgia, Athens, GA 30602, USA.
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37
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Mukherjee P, Desai P, Zhou YD, Avery M. Targeting the BH3 Domain Mediated Protein−Protein Interaction of Bcl-xL through Virtual Screening. J Chem Inf Model 2010; 50:906-23. [DOI: 10.1021/ci1000373] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Prasenjit Mukherjee
- Department of Medicinal Chemistry and Department of Pharmacognosy, School of Pharmacy, University of Mississippi, University, Mississippi 38677
| | - Prashant Desai
- Department of Medicinal Chemistry and Department of Pharmacognosy, School of Pharmacy, University of Mississippi, University, Mississippi 38677
| | - Yu-Dong Zhou
- Department of Medicinal Chemistry and Department of Pharmacognosy, School of Pharmacy, University of Mississippi, University, Mississippi 38677
| | - Mitchell Avery
- Department of Medicinal Chemistry and Department of Pharmacognosy, School of Pharmacy, University of Mississippi, University, Mississippi 38677
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Koutsioulis D, Lyskowski A, Mäki S, Guthrie E, Feller G, Bouriotis V, Heikinheimo P. Coordination sphere of the third metal site is essential to the activity and metal selectivity of alkaline phosphatases. Protein Sci 2010; 19:75-84. [PMID: 19916164 DOI: 10.1002/pro.284] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Alkaline phosphatases (APs) are commercially applied enzymes that catalyze the hydrolysis of phosphate monoesters by a reaction involving three active site metal ions. We have previously identified H135 as the key residue for controlling activity of the psychrophilic TAB5 AP (TAP). In this article, we describe three X-ray crystallographic structures on TAP variants H135E and H135D in complex with a variety of metal ions. The structural analysis is supported by thermodynamic and kinetic data. The AP catalysis essentially requires octahedral coordination in the M3 site, but stability is adjusted with the conformational freedom of the metal ion. Comparison with the mesophilic Escherichia coli, AP shows differences in the charge transfer network in providing the chemically optimal metal combination for catalysis. Our results provide explanation why the TAB5 and E. coli APs respond in an opposite way to mutagenesis in their active sites. They provide a lesson on chemical fine tuning and the importance of the second coordination sphere in defining metal specificity in enzymes. Understanding the framework of AP catalysis is essential in the efforts to design even more powerful tools for modern biotechnology.
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40
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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