1
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Shen R, Crean RM, Olsen KJ, Corbella M, Calixto AR, Richan T, Brandão TAS, Berry RD, Tolman A, Loria JP, Johnson SJ, Kamerlin SCL, Hengge AC. Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases. Chem Sci 2022; 13:13524-13540. [PMID: 36507179 PMCID: PMC9682893 DOI: 10.1039/d2sc04135a] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) possess a conserved mobile catalytic loop, the WPD-loop, which brings an aspartic acid into the active site where it acts as an acid/base catalyst. Prior experimental and computational studies, focused on the human enzyme PTP1B and the PTP from Yersinia pestis, YopH, suggested that loop conformational dynamics are important in regulating both catalysis and evolvability. We have generated a chimeric protein in which the WPD-loop of YopH is transposed into PTP1B, and eight chimeras that systematically restored the loop sequence back to native PTP1B. Of these, four chimeras were soluble and were subjected to detailed biochemical and structural characterization, and a computational analysis of their WPD-loop dynamics. The chimeras maintain backbone structural integrity, with somewhat slower rates than either wild-type parent, and show differences in the pH dependency of catalysis, and changes in the effect of Mg2+. The chimeric proteins' WPD-loops differ significantly in their relative stability and rigidity. The time required for interconversion, coupled with electrostatic effects revealed by simulations, likely accounts for the activity differences between chimeras, and relative to the native enzymes. Our results further the understanding of connections between enzyme activity and the dynamics of catalytically important groups, particularly the effects of non-catalytic residues on key conformational equilibria.
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Affiliation(s)
- Ruidan Shen
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Rory M. Crean
- Science for Life Laboratory, Department of Chemistry – BMC, Uppsala University, BMCBox 576S-751 23 UppsalaSweden
| | - Keith J. Olsen
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Marina Corbella
- Science for Life Laboratory, Department of Chemistry – BMC, Uppsala University, BMCBox 576S-751 23 UppsalaSweden
| | - Ana R. Calixto
- Science for Life Laboratory, Department of Chemistry – BMC, Uppsala University, BMCBox 576S-751 23 UppsalaSweden
| | - Teisha Richan
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Tiago A. S. Brandão
- Departamento de Química, ICEX, Universidade Federal de Minas GeraisBelo HorizonteMinas Gerais31270-901Brazil
| | - Ryan D. Berry
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Alex Tolman
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - J. Patrick Loria
- Department of Chemistry, Yale University225 Prospect StreetNew HavenCT 06520USA,Department of Molecular Biophysics and Biochemistry, Yale University266 Whitney AvenueNew HavenCT 06520USA
| | - Sean J. Johnson
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Shina C. L. Kamerlin
- Science for Life Laboratory, Department of Chemistry – BMC, Uppsala University, BMCBox 576S-751 23 UppsalaSweden,School of Chemistry and Biochemistry, Georgia Institute of Technology901 Atlantic Drive NWAtlanta, GA 30332-0400USA
| | - Alvan C. Hengge
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
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Ma Y, Ding TT, Liu YY, Zheng ZH, Sun SX, Zhang LS, Zhang H, Lu XH, Cheng XC, Wang RL. Design, synthesis, biological evaluation and molecular dynamics simulation studies of imidazolidine-2,4-dione derivatives as novel PTP1B inhibitors. Biochem Biophys Res Commun 2021; 579:40-46. [PMID: 34583194 DOI: 10.1016/j.bbrc.2021.09.047] [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: 08/15/2021] [Revised: 09/10/2021] [Accepted: 09/19/2021] [Indexed: 12/14/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a member of the phosphotyrosine phosphatase family and plays an important role in the signal transduction of diabetes. Inhibition of PTP1B activity can increase insulin sensitivity and reduce blood sugar levels. Therefore, it is urgent to find compounds with novel structures that can inhibit PTP1B. This study designed imidazolidine-2,4-dione derivatives through the computer-aided drug design (CADD) strategy, and the Comp#10 showed outstanding inhibitory ability. (IC50 = 2.07 μM) and selectivity. The inhibitory mechanism at molecular level of Comp#10 on PTP1B was studied by molecular dynamics simulation. The results show that the catalytic region of PTP1B protein is more stable, which makes the catalytic sites unsuitable for exposure. Interestingly, the most obvious changes in the interaction between residues in the P-loop region (such as: His214, Cys215, and Ser216). In short, this study reported for the first time that imidazolidine-2,4-dione derivatives as novel PTP1B inhibitors had good inhibitory activity and selectivity, providing new ideas for the development of small molecule PTP1B inhibitors.
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Affiliation(s)
- Yangchun Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China; Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, 250012, China
| | - Ting-Ting Ding
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Zhi-Hui Zheng
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, Shijiazhuang, 050015, Hebei, China
| | - Su-Xia Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Li-Song Zhang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Hao Zhang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Xin-Hua Lu
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, Shijiazhuang, 050015, Hebei, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
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3
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Design, synthesis, kinetic, molecular dynamics, and hypoglycemic effect characterization of new and potential selective benzimidazole derivatives as Protein Tyrosine Phosphatase 1B inhibitors. Bioorg Med Chem 2021; 48:116418. [PMID: 34563877 DOI: 10.1016/j.bmc.2021.116418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/27/2021] [Accepted: 09/13/2021] [Indexed: 11/21/2022]
Abstract
Protein-tyrosine phosphatase 1B (PTP1B) is a negative regulator of insulin signaling pathway and has been validated as a therapeutic target for type 2 diabetes. A wide variety of scaffolds have been included in the structure of PTP1B inhibitors, one of them is the benzimidazole nucleus. Here, we report the design and synthesis of a new series of di- and tri- substituted benzimidazole derivatives including their kinetic and structural characterization as PTP1B inhibitors and hypoglycemic activity. Results show that compounds 43, 44, 45, and 46 are complete mixed type inhibitors with a Ki of 12.6 μM for the most potent (46). SAR type analysis indicates that a chloro substituent at position 6(5), a β-naphthyloxy at position 5(6), and a p-benzoic acid attached to the linker 2-thioacetamido at position 2 of the benzimidazole nucleus, was the best combination for PTP1B inhibition and hypoglycemic activity. In addition, molecular dynamics studies suggest that these compounds could be potential selective inhibitors from other PTPs such as its closest homologous TCPTP, SHP-1, SHP-2 and CDC25B. Therefore, the compounds reported here are good hits that provide structural, kinetic, and biological information that can be used to develop novel and selective PTP1B inhibitors based on benzimidazole scaffold.
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4
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Yang X, Zhao Y, Sun Q, Yang Y, Gao Y, Ge W, Liu J, Xu X, Weng D, Wang S, Zhang J. Adenine nucleotide-mediated regulation of hepatic PTP1B activity in mouse models of type 2 diabetes. Diabetologia 2019; 62:2106-2117. [PMID: 31410531 DOI: 10.1007/s00125-019-04971-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/24/2019] [Indexed: 12/18/2022]
Abstract
AIMS/HYPOTHESIS Plasma 5'-AMP (pAMP) is elevated in mouse models of type 2 diabetes. However, the metabolic regulatory role of adenine nucleotides in type 2 diabetes remains unclear. METHODS Adenine nucleotides and their metabolites in plasma and liver were examined by HPLC. 1H NMR-based metabolomics analysis was performed to explore the changes of metabolites in mouse models of type 2 diabetes. Na+/K+ ATPase and Na+/H+ exchanger activity were measured in response to adenine nucleotide metabolites. Human recombinant protein tyrosine phosphatase 1B (PTP1B) was used for enzyme kinetic assays. Protein binding assays were performed with microscale thermophoresis. The intracellular pH of hepatocyte AML12 cell lines was measured using the BCECF-AM method. We also analysed pAMP levels in participants with type 2 diabetes. RESULTS Elevation of pAMP was a universal phenomenon in all mouse models of type 2 diabetes including db/db vs lean mice (13.9 ± 2.3 μmol/l vs 3.7 ± 0.9 μmol/l; p < 0.01), ob/ob vs lean mice (9.1 ± 2.0 μmol/l vs 3.9 ± 1.2 μmol/l; p < 0.01) and high-fat diet/streptozotocin-induced vs wild-type mice (6.6 ± 1.5 μmol/l vs 4.1 ± 0.9 μmol/l; p < 0.05); this elevation was required for the occurrence of hyperglycaemia in obese mice. 1H NMR-based metabolomics study following HPLC analysis revealed that the metabolite profile in wild-type mice treated with 5'-AMP was similar to that in db/db diabetic mice, especially the accumulation of a large quantity of ATP and its metabolites. The glucose-lowering drug metformin reduced the severity of hyperglycaemia both in 5'-AMP-induced wild-type mice and db/db mice. Metformin decreased the accumulation of liver ATP but not its metabolites in these hyperglycaemic mice. ATP and metformin reciprocally change cellular pH homeostasis in liver, causing opposite shifts in liver activity of PTP1B, a key negative regulator of insulin signalling. Furthermore, pAMP levels were also elevated in individuals with type 2 diabetes (45.2 ± 22.7 nmol/l vs 3.1 ± 1.9 nmol/l; p < 0.01). CONCLUSIONS/INTERPRETATION These results reveal an emerging role for adenine nucleotide in the regulation of hyperglycaemia and provide a potential therapeutic target in obesity and type 2 diabetes.
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Affiliation(s)
- Xiao Yang
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Yang Zhao
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Qi Sun
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Yunxia Yang
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Yan Gao
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Wenhao Ge
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Junhao Liu
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Xi Xu
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Dan Weng
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Shiming Wang
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei, Nanjing, 210094, China
| | - Jianfa Zhang
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei, Nanjing, 210094, China.
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5
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Fujikawa A, Chow JPH, Matsumoto M, Suzuki R, Kuboyama K, Yamamoto N, Noda M. Identification of novel splicing variants of protein tyrosine phosphatase receptor type Z. J Biochem 2017; 162:381-390. [PMID: 28992190 DOI: 10.1093/jb/mvx042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/14/2017] [Indexed: 11/13/2022] Open
Abstract
Protein tyrosine phosphatase receptor type Z (PTPRZ, also known as PTPζ or RPTPβ) is preferentially expressed in the central nervous system (CNS). PTPRZ plays important roles during development and adulthood in CNS myelination, learning and memory. Three splicing isoforms for PTPRZ have been identified to date: two receptor type isoforms, PTPRZ-A and PTPRZ-B, and one secretory isoform, PTPRZ-S. We herein identified novel PTPRZ receptor sub-isoforms without a seven-amino acid sequence encoded by exon 16. This sequence forms a part of the helix-turn-helix segment called the 'wedge' structure, which is located at the N-terminal region in the membrane-proximal protein tyrosine phosphatase domain. In contrast to conventional receptor isoforms with uniform expression, the deleted isoforms were expressed in the brain, but not in the retina, indicating the tissue-specific splicing of exon 16. Biochemical analyses of PTPRZ intracellular regions revealed differences in the characteristics of the deleted form, namely, stronger binding activity to postsynaptic density protein 95 (PSD95) and greater enrichment in the postsynaptic density fraction than the full-length form. Furthermore, the exon 16-deleted form exhibited higher catalytic efficiency in vitro. These results suggest that sub-isoforms of PTPRZ have different functions because of variations in the wedge structure.
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Affiliation(s)
- Akihiro Fujikawa
- Division of Molecular Neurobiology, National Institute for Basic Biology
| | - Jeremy Pak Hong Chow
- Division of Molecular Neurobiology, National Institute for Basic Biology.,School of Life Science, Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Masahito Matsumoto
- Division of Molecular Neurobiology, National Institute for Basic Biology
| | - Ryoko Suzuki
- Division of Molecular Neurobiology, National Institute for Basic Biology
| | - Kazuya Kuboyama
- Division of Molecular Neurobiology, National Institute for Basic Biology
| | - Naoki Yamamoto
- Laboratory of Molecular Biology & Histochemistry, Fujita Health University, 1-98, Toyoake, Aichi 470-1192, Japan
| | - Masaharu Noda
- Division of Molecular Neurobiology, National Institute for Basic Biology.,School of Life Science, Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
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6
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Du W, Goldstein R, Jiang Y, Aly O, Cerchietti L, Melnick A, Elemento O. Effective Combination Therapies for B-cell Lymphoma Predicted by a Virtual Disease Model. Cancer Res 2017; 77:1818-1830. [PMID: 28130226 DOI: 10.1158/0008-5472.can-16-0476] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 12/10/2016] [Accepted: 01/23/2017] [Indexed: 12/15/2022]
Abstract
The complexity of cancer signaling networks limits the efficacy of most single-agent treatments and brings about challenges in identifying effective combinatorial therapies. In this study, we used chronic active B-cell receptor (BCR) signaling in diffuse large B-cell lymphoma as a model system to establish a computational framework to optimize combinatorial therapy in silico We constructed a detailed kinetic model of the BCR signaling network, which captured the known complex cross-talk between the NFκB, ERK, and AKT pathways and multiple feedback loops. Combining this signaling model with a data-derived tumor growth model, we predicted viability responses of many single drug and drug combinations in agreement with experimental data. Under this framework, we exhaustively predicted and ranked the efficacy and synergism of all possible combinatorial inhibitions of eleven currently targetable kinases in the BCR signaling network. Ultimately, our work establishes a detailed kinetic model of the core BCR signaling network and provides the means to explore the large space of possible drug combinations. Cancer Res; 77(8); 1818-30. ©2017 AACR.
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Affiliation(s)
- Wei Du
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Rebecca Goldstein
- Hematology/Oncology Division, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Yanwen Jiang
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York.,Hematology/Oncology Division, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Omar Aly
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Leandro Cerchietti
- Hematology/Oncology Division, Department of Medicine, Weill Cornell Medicine, New York, New York.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Ari Melnick
- Hematology/Oncology Division, Department of Medicine, Weill Cornell Medicine, New York, New York.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York. .,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York.,Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
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7
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Birtwistle MR. Analytical reduction of combinatorial complexity arising from multiple protein modification sites. J R Soc Interface 2015; 12:rsif.2014.1215. [PMID: 25519995 DOI: 10.1098/rsif.2014.1215] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Combinatorial complexity is a major obstacle to ordinary differential equation (ODE) modelling of biochemical networks. For example, a protein with 10 sites that can each be unphosphorylated, phosphorylated or bound to adaptor protein requires 3(10) ODEs. This problem is often dealt with by making ad hoc assumptions which have unclear validity and disallow modelling of site-specific dynamics. Such site-specific dynamics, however, are important in many biological systems. We show here that for a common biological situation where adaptors bind modified sites, binding is slow relative to modification/demodification, and binding to one modified site hinders binding to other sites, for a protein with n modification sites and m adaptor proteins the number of ODEs needed to simulate the site-specific dynamics of biologically relevant, lumped bound adaptor states is independent of the number of modification sites and equal to m + 1, giving a significant reduction in system size. These considerations can be relaxed considerably while retaining reasonably accurate descriptions of the true system dynamics. We apply the theory to model, using only 11 ODEs, the dynamics of ligand-induced phosphorylation of nine tyrosines on epidermal growth factor receptor (EGFR) and primary recruitment of six signalling proteins (Grb2, PI3K, PLCγ1, SHP2, RasA1 and Shc1). The model quantitatively accounts for experimentally determined site-specific phosphorylation and dephosphorylation rates, differential affinities of binding proteins for the phosphorylated sites and binding protein expression levels. Analysis suggests that local concentration of site-specific phosphatases such as SHP2 in membrane subdomains by a factor of approximately 10(7) is critical for effective site-specific regulation. We further show how our framework can be extended with minimal effort to consider binding cooperativity between Grb2 and c-Cbl, which is important for receptor trafficking. Our theory has potentially broad application to reduce combinatorial complexity and allow practical simulation of a variety ODE models relevant to systems biology and pharmacology applications to allow exploration of key aspects of complexity that control signal flux.
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Affiliation(s)
- Marc R Birtwistle
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
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8
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Kobzar OL, Shevchuk MV, Lyashenko AN, Tanchuk VY, Romanenko VD, Kobelev SM, Averin AD, Beletskaya IP, Vovk AI, Kukhar VP. Phosphonate derivatives of tetraazamacrocycles as new inhibitors of protein tyrosine phosphatases. Org Biomol Chem 2015; 13:7437-44. [DOI: 10.1039/c5ob00713e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α,α-Difluoro-β-ketophosphonate derivatives of tetraazamacrocycles were synthesized and found to be potential inhibitors of protein tyrosine phosphatases.
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Affiliation(s)
- Oleksandr L. Kobzar
- Institute of Bioorganic Chemistry and Petrochemistry
- National Academy of Sciences of Ukraine
- Kyiv-94
- Ukraine
| | - Michael V. Shevchuk
- Institute of Bioorganic Chemistry and Petrochemistry
- National Academy of Sciences of Ukraine
- Kyiv-94
- Ukraine
| | - Alesya N. Lyashenko
- Institute of Bioorganic Chemistry and Petrochemistry
- National Academy of Sciences of Ukraine
- Kyiv-94
- Ukraine
| | - Vsevolod Yu. Tanchuk
- Institute of Bioorganic Chemistry and Petrochemistry
- National Academy of Sciences of Ukraine
- Kyiv-94
- Ukraine
| | - Vadim D. Romanenko
- Institute of Bioorganic Chemistry and Petrochemistry
- National Academy of Sciences of Ukraine
- Kyiv-94
- Ukraine
| | - Sergei M. Kobelev
- Lomonosov Moscow State University
- Department of Chemistry
- Moscow 119991
- Russian Federation
| | - Alexei D. Averin
- Lomonosov Moscow State University
- Department of Chemistry
- Moscow 119991
- Russian Federation
| | - Irina P. Beletskaya
- Lomonosov Moscow State University
- Department of Chemistry
- Moscow 119991
- Russian Federation
| | - Andriy I. Vovk
- Institute of Bioorganic Chemistry and Petrochemistry
- National Academy of Sciences of Ukraine
- Kyiv-94
- Ukraine
| | - Valery P. Kukhar
- Institute of Bioorganic Chemistry and Petrochemistry
- National Academy of Sciences of Ukraine
- Kyiv-94
- Ukraine
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9
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Bellomo E, Massarotti A, Hogstrand C, Maret W. Zinc ions modulate protein tyrosine phosphatase 1B activity. Metallomics 2014; 6:1229-39. [DOI: 10.1039/c4mt00086b] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A novel mechanism by which Zn2+ modulates PTP1B activity encompasses the binding to the closed and phospho-intermediate forms only.
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Affiliation(s)
- Elisa Bellomo
- King's College London
- Metal Metabolism Group
- Division of Diabetes and Nutritional Sciences
- School of Medicine
- London, UK
| | - Alberto Massarotti
- Dipartimento di Scienze del Farmaco
- Universitá degli Studi del Piemonte Orientale “A. Avogadro”
- 28100 Novara, Italy
| | - Christer Hogstrand
- King's College London
- Metal Metabolism Group
- Division of Diabetes and Nutritional Sciences
- School of Medicine
- London, UK
| | - Wolfgang Maret
- King's College London
- Metal Metabolism Group
- Division of Diabetes and Nutritional Sciences
- School of Medicine
- London, UK
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10
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Liu B, Fan J, Zhang Y, Mu P, Wang P, Su J, Lai H, Li S, Feng D, Wang J, Wang H. OsPFA-DSP1, a rice protein tyrosine phosphatase, negatively regulates drought stress responses in transgenic tobacco and rice plants. PLANT CELL REPORTS 2012; 31:1021-32. [PMID: 22218675 DOI: 10.1007/s00299-011-1220-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Revised: 12/22/2011] [Accepted: 12/24/2011] [Indexed: 05/31/2023]
Abstract
Dephosphorylation plays a pivotal role in regulating plant growth, development and abiotic/biotic stress responses. Here, we characterized a plant and fungi atypical dual-specificity phosphatase (PFA-DSP) subfamily member, OsPFA-DSP1, from rice. OsPFA-DSP1 was determined to be a functional protein tyrosine phosphatase (PTP) in vitro using phosphatase activity assays. Quantitative real-time PCR and GENEVESTIGATOR analysis showed that OsPFA-DSP1 mRNA was induced by drought stress. Transfection of rice protoplasts showed that OsPFA-DSP1 accumulated in both the cytoplasm and nucleus. Ectopic overexpression of OsPFA-DSP1 in tobacco increased sensitivity to drought stress and insensitivity to ABA-induced stomatal closure and inhibition of stomatal opening. Furthermore, overexpression of OsPFA-DSP1 in rice also increased sensitivity to drought stress. These results indicated that OsPFA-DSP1 is a functional PTP and may act as a negative regulator in drought stress responses.
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Affiliation(s)
- Bing Liu
- Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, People's Republic of China
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11
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Castanheira P, Moreira S, Gama M, Faro C. Escherichia coli expression, refolding and characterization of human laforin. Protein Expr Purif 2010; 71:195-9. [PMID: 20152902 DOI: 10.1016/j.pep.2010.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 02/08/2010] [Accepted: 02/08/2010] [Indexed: 11/26/2022]
Abstract
Laforin is a unique human dual-specificity phosphatase as it contains an amino terminal carbohydrate binding module (CBM). Laforin gene mutations lead to Lafora disease, a progressive myoclonus epilepsy with an early fatal issue. Previous attempts to produce recombinant laforin faced various difficulties, namely the appearance of protein inclusion bodies, the contamination with bacterial proteins and a high tendency of the protein to aggregate, despite the use of fusion tags to improve solubility and ease the purification process. In this work, we have expressed human laforin in Escherichia coli in the form of inclusion bodies devoid of any fusion tags. After a rapid dilution refolding step, the protein was purified by two chromatographic steps, yielding 5-7mg of purified protein per liter of bacterial culture. The purified protein was shown to have the kinetic characteristics of a dual-specificity phosphatase, and a functional carbohydrate binding module. With this protocol, we were able for the first time, to produce and purify laforin without fusion tags in the amounts traditionally needed for the crystallographic structural studies paving the way to the understanding of the molecular mechanisms of laforin activity and to the development of novel therapies for Lafora disease.
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Affiliation(s)
- Pedro Castanheira
- Biocant, Molecular Biotechnology Unit, Parque Tecnológico de Cantanhede, Núcleo 4, Lote 3, Cantanhede, Portugal.
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Gingras MC, Zhang YL, Kharitidi D, Barr AJ, Knapp S, Tremblay ML, Pause A. HD-PTP is a catalytically inactive tyrosine phosphatase due to a conserved divergence in its phosphatase domain. PLoS One 2009; 4:e5105. [PMID: 19340315 PMCID: PMC2661844 DOI: 10.1371/journal.pone.0005105] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Accepted: 03/04/2009] [Indexed: 02/04/2023] Open
Abstract
Background The HD-PTP protein has been described as a tumor suppressor candidate and based on its amino acid sequence, categorized as a classical non-transmembrane protein tyrosine phosphatase (PTP). To date, no HD-PTP phosphorylated substrate has been identified and controversial results concerning its catalytic activity have been recently reported. Methodology and Results Here we report a rigorous enzymatic analysis demonstrating that the HD-PTP protein does not harbor tyrosine phosphatase or lipid phosphatase activity using the highly sensitive DiFMUP substrate and a panel of different phosphatidylinositol phosphates. We found that HD-PTP tyrosine phosphatase inactivity is caused by an evolutionary conserved amino acid divergence of a key residue located in the HD-PTP phosphatase domain since its back mutation is sufficient to restore the HD-PTP tyrosine phosphatase activity. Moreover, in agreement with a tumor suppressor activity, HD-PTP expression leads to colony growth reduction in human cancer cell lines, independently of its catalytic PTP activity status. Conclusion In summary, we demonstrate that HD-PTP is a catalytically inactive protein tyrosine phosphatase. As such, we identify one residue involved in its inactivation and show that its colony growth reduction activity is independent of its PTP activity status in human cancer cell lines.
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Affiliation(s)
- Marie-Claude Gingras
- Goodman Cancer Centre and Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Yu Ling Zhang
- Goodman Cancer Centre and Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Dmitri Kharitidi
- Goodman Cancer Centre and Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Alastair J. Barr
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Michel L. Tremblay
- Goodman Cancer Centre and Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Arnim Pause
- Goodman Cancer Centre and Department of Biochemistry, McGill University, Montréal, Québec, Canada
- * E-mail:
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Cortesio CL, Chan KT, Perrin BJ, Burton NO, Zhang S, Zhang ZY, Huttenlocher A. Calpain 2 and PTP1B function in a novel pathway with Src to regulate invadopodia dynamics and breast cancer cell invasion. ACTA ACUST UNITED AC 2008; 180:957-71. [PMID: 18332219 PMCID: PMC2265405 DOI: 10.1083/jcb.200708048] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Invasive cancer cells form dynamic adhesive structures associated with matrix degradation called invadopodia. Calpain 2 is a calcium-dependent intracellular protease that regulates adhesion turnover and disassembly through the targeting of specific substrates such as talin. Here, we describe a novel function for calpain 2 in the formation of invadopodia and in the invasive abilities of breast cancer cells through the modulation of endogenous c-Src activity. Calpain-deficient breast cancer cells show impaired invadopodia formation that is rescued by expression of a truncated fragment of protein tyrosine phosphatase 1B (PTP1B) corresponding to the calpain proteolytic fragment, which indicates that calpain modulates invadopodia through PTP1B. Moreover, PTP1B activity is required for efficient invadopodia formation and breast cancer invasion, which suggests that PTP1B may modulate breast cancer progression through its effects on invadopodia. Collectively, our experiments implicate a novel signaling pathway involving calpain 2, PTP1B, and Src in the regulation of invadopodia and breast cancer invasion.
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Affiliation(s)
- Christa L Cortesio
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
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Romá-Mateo C, Ríos P, Tabernero L, Attwood TK, Pulido R. A novel phosphatase family, structurally related to dual-specificity phosphatases, that displays unique amino acid sequence and substrate specificity. J Mol Biol 2007; 374:899-909. [PMID: 17976645 DOI: 10.1016/j.jmb.2007.10.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 09/28/2007] [Accepted: 10/02/2007] [Indexed: 01/30/2023]
Abstract
Members of the superfamily of protein tyrosine phosphatases (PTPs) share the presence of an evolutionarily conserved PTP catalytic domain. Among them, the dual-specificity phosphatases (DSPs) constitute a diverse group of enzymes in terms of substrate specificity, including nonprotein substrates. In recent years, an increasing number of novel DSPs, whose functions and biological substrates are not well defined, have been discovered in a variety of organisms. In this study, we define the structural and functional properties of evolutionarily related atypical DSPs from different phyla. Sets of conserved motifs were defined that (i) uniquely segregated mammalian atypical DSPs from closely related enzymes and (ii) exclusively characterised a novel family of atypical DSPs present in plants, fungi, and kinetoplastids [plant and fungi atypical (PFA)-DSPs]; despite having different sequence "fingerprints," the PTP tertiary structure of PFA-DSPs is conserved. Analysis of the catalytic properties of PFA-DSPs suggests the existence of a unique substrate specificity for these enzymes. Our findings predict characteristic functional motifs for the diverse members of the DSP families of PTPs and provide insights into the functional properties of DSPs of unknown function.
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Affiliation(s)
- Carlos Romá-Mateo
- Centro de Investigación Príncipe Felipe, Avenida Autopista del Saler, 16-3, 46013 Valencia, Spain
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15
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Jemc J, Rebay I. The eyes absent family of phosphotyrosine phosphatases: properties and roles in developmental regulation of transcription. Annu Rev Biochem 2007; 76:513-38. [PMID: 17341163 DOI: 10.1146/annurev.biochem.76.052705.164916] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Integration of multiple signaling pathways at the level of their transcriptional effectors provides an important strategy for fine-tuning gene expression and ensuring a proper program of development. Posttranslational modifications, such as phosphorylation, play important roles in modulating transcription factor activity. The discovery that the transcription factor Eyes absent (Eya) possesses protein phosphatase activity provides an interesting new paradigm. Eya may regulate the phosphorylation state of either itself or its transcriptional cofactors, thereby directly affecting transcriptional output. The identification of a growing number of transcription factors with enzymic activity suggests that such dual-function proteins exert greater control of signaling events than previously imagined. Given the conservation of both its phosphatase and transcription factor activity across mammalian species, Eya provides an excellent model for studying how a single protein integrates these two functions under the influence of multiple signaling pathways to promote development.
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Affiliation(s)
- Jennifer Jemc
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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16
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Stuible M, Zhao L, Aubry I, Schmidt-Arras D, Böhmer FD, Li CJ, Tremblay ML. Cellular Inhibition of Protein Tyrosine Phosphatase 1B by Uncharged Thioxothiazolidinone Derivatives. Chembiochem 2007; 8:179-86. [PMID: 17191286 DOI: 10.1002/cbic.200600287] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
As important regulators of cellular signal transduction, members of the protein tyrosine phosphatase (PTP) family are considered to be promising drug targets. However, to date, the most effective in vitro PTP inhibitors have tended to be highly charged, thus limiting cellular permeability. Here, we have identified an uncharged thioxothiazolidinone derivative (compound 1), as a competitive inhibitor of a subset of PTPs. Compound 1 effectively inhibited protein tyrosine phosphatase 1B (PTP1B) in two cell-based systems: it sensitized wild-type, but not PTP1B-null fibroblasts to insulin stimulation and prevented PTP1B-dependent dephosphorylation of the FLT3-ITD receptor tyrosine kinase. We have also tested a series of derivatives in vitro against PTP1B and proposed a model of the PTP1B-inhibitor interaction. These compounds should be useful in the elucidation of cellular PTP function and could represent a starting point for development of therapeutic PTP inhibitors.
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Affiliation(s)
- Matthew Stuible
- McGill Cancer Centre, Department of Biochemistry, McGill University, 3655 Prom. Sir William Osler, Montréal, Québec, H3G 1Y6, Canada
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17
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Girard JM, Lê KHD, Lederer F. Molecular characterization of laforin, a dual-specificity protein phosphatase implicated in Lafora disease. Biochimie 2006; 88:1961-71. [PMID: 17010495 DOI: 10.1016/j.biochi.2006.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 08/16/2006] [Indexed: 11/17/2022]
Abstract
Lafora disease is a progressive myoclonus epilepsy with an early fatal issue. Two genes were identified thus far, the mutations of which cause the disease. The first one, EPM2A, encodes the consensus sequence of a protein tyrosine phosphatase. Its product, laforin, is the object of the present work. We analysed in detail the amino acid sequence of this protein. This suggested, as also observed by others, that it could present two domains, a carbohydrate-binding domain (CBM20, known as a starch-binding domain) and the catalytic domain of a dual-specificity protein phosphatase. We produced the enzyme as two different GST-fused proteins and as an N-terminally His-tagged protein. Differences in solubility were observed between the constructs. Moreover, the N-terminal carbohydrate-binding domain contains a thrombin cleavage site, which is hidden in the simplest GST-fusion protein we produced, but was accessible after introducing a five-residue linker between the engineered cleavage site and the enzyme N-terminus. The two types of constructs hydrolyse pNPP and OMFP with kinetic parameters consistent with those of a dual-specificity phosphatase. We show in addition that the protein not only binds glycogen, but also starch, amylose and cyclodextrin. Neither binding of glycogen nor of beta-cyclodextrin appreciably affects the phosphatase activity. These results suggest that the role of the N-terminal domain is rather that of targeting the protein in the cell, probably to glycogen and the protein complexes attached to it, rather than that of directly modulating the catalytic activity.
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Affiliation(s)
- Jean-Marie Girard
- Laboratoire d'Enzymologie et Biochimie Structurales, UPR9063, Centre National de la Recherche Scientifique, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
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Yang X, Li J, Zhou Y, Shen Q, Chen J, Li J. Discovery of novel inhibitor of human leukocyte common antigen-related phosphatase. Biochim Biophys Acta Gen Subj 2005; 1726:34-41. [PMID: 16198483 DOI: 10.1016/j.bbagen.2005.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 06/23/2005] [Accepted: 07/08/2005] [Indexed: 11/18/2022]
Abstract
Human leukocyte common antigen-related phosphatase (LAR) may play a role in type 2 diabetes and cancer, and in the development of the nervous system, and it may be an attractive target for the treatment of diabetes and cancer. We identified eight hits from the random screening of LAR D1 with a high-throughput screening assay. Further validation of the eight hits showed that the meD insertion was associated with inhibition of LAR D1D2 and LAR D1Q. These data suggest that the inserted meD peptide influences the interaction of the enzyme and inhibitor, which is consistent with the kinetic catalysis constants of the substrate pNPP. Our data showed that Hit 1, the first published novel inhibitor of LAR, is a competitive inhibitor with a K(i) of 330 nM that displays obvious selectivity for LAR and mouse PTPsigma, but not for other protein tyrosine phosphatases.
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Affiliation(s)
- Xiaoning Yang
- East China Normal University, Academy of Life Science, Shanghai 200062, P. R. China
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Groen A, Lemeer S, van der Wijk T, Overvoorde J, Heck AJR, Ostman A, Barford D, Slijper M, den Hertog J. Differential Oxidation of Protein-tyrosine Phosphatases. J Biol Chem 2005; 280:10298-304. [PMID: 15623519 DOI: 10.1074/jbc.m412424200] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oxidation is emerging as an important regulatory mechanism of protein-tyrosine phosphatases (PTPs). Here we report that PTPs are differentially oxidized, and we provide evidence for the underlying mechanism. The membrane-proximal RPTPalpha-D1 was catalytically active but not readily oxidized as assessed by immunoprobing with an antibody that recognized oxidized catalytic site cysteines in PTPs (oxPTPs). In contrast, the membrane-distal RPTPalpha-D2, a poor PTP, was readily oxidized. Oxidized catalytic site cysteines in PTP immunoprobing and mass spectrometry demonstrated that mutation of two residues in the Tyr(P) loop and the WPD loop that reverse catalytic activity of RPTPalpha-D1 and RPTPalpha-D2 also reversed oxidizability, suggesting that oxidizability and catalytic activity are coupled. However, catalytically active PTP1B and LAR-D1 were readily oxidized. Oxidizability was strongly dependent on pH, indicating that the microenvironment of the catalytic cysteine has an important role. Crystal structures of PTP domains demonstrated that the orientation of the absolutely conserved PTP loop arginine correlates with oxidizability of PTPs, and consistently, RPTPmu-D1, with a similar conformation as RPTPalpha-D1, was not readily oxidized. In conclusion, PTPs are differentially oxidized at physiological pH and H(2)O(2) concentrations, and the PTP loop arginine is an important determinant for susceptibility to oxidation.
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Affiliation(s)
- Arnoud Groen
- Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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