1
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Structural insights into the pSer/pThr dependent regulation of the SHP2 tyrosine phosphatase in insulin and CD28 signaling. Nat Commun 2022; 13:5439. [PMID: 36114179 PMCID: PMC9481563 DOI: 10.1038/s41467-022-32918-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 08/23/2022] [Indexed: 11/09/2022] Open
Abstract
Serine/threonine phosphorylation of insulin receptor substrate (IRS) proteins is well known to modulate insulin signaling. However, the molecular details of this process have mostly been elusive. While exploring the role of phosphoserines, we have detected a direct link between Tyr-flanking Ser/Thr phosphorylation sites and regulation of specific phosphotyrosine phosphatases. Here we present a concise structural study on how the activity of SHP2 phosphatase is controlled by an asymmetric, dual phosphorylation of its substrates. The structure of SHP2 has been determined with three different substrate peptides, unveiling the versatile and highly dynamic nature of substrate recruitment. What is more, the relatively stable pre-catalytic state of SHP2 could potentially be useful for inhibitor design. Our findings not only show an unusual dependence of SHP2 catalytic activity on Ser/Thr phosphorylation sites in IRS1 and CD28, but also suggest a negative regulatory mechanism that may also apply to other tyrosine kinase pathways as well. SHP2 is an important human tyrosine phosphatase with key roles in cancer, immune responses and insulin signaling. Here, the authors explore its substrate recognition mechanism in molecular detail and uncover a complex regulatory mechanism for this enzyme that marks specific target sites for dephosphorylation.
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2
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A New Paradigm for KIM-PTP Drug Discovery: Identification of Allosteric Sites with Potential for Selective Inhibition Using Virtual Screening and LEI Analysis. Int J Mol Sci 2021; 22:ijms222212206. [PMID: 34830087 PMCID: PMC8624330 DOI: 10.3390/ijms222212206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 02/04/2023] Open
Abstract
The kinase interaction motif protein tyrosine phosphatases (KIM-PTPs), HePTP, PTPSL and STEP, are involved in the negative regulation of mitogen-activated protein kinase (MAPK) signalling pathways and are important therapeutic targets for a number of diseases. We have used VSpipe, a virtual screening pipeline, to identify a ligand cluster distribution that is unique to this subfamily of PTPs. Several clusters map onto KIM-PTP specific sequence motifs in contrast to the cluster distribution obtained for PTP1B, a classic PTP that mapped to general PTP motifs. Importantly, the ligand clusters coincide with previously reported functional and substrate binding sites in KIM-PTPs. Assessment of the KIM-PTP specific clusters, using ligand efficiency index (LEI) plots generated by the VSpipe, ascertained that the binders in these clusters reside in a more drug-like chemical-biological space than those at the active site. LEI analysis showed differences between clusters across all KIM-PTPs, highlighting a distinct and specific profile for each phosphatase. The most druggable cluster sites are unexplored allosteric functional sites unique to each target. Exploiting these sites may facilitate the delivery of inhibitors with improved drug-like properties, with selectivity amongst the KIM-PTPs and over other classical PTPs.
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3
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Kumar GS, Page R, Peti W. The interaction of p38 with its upstream kinase MKK6. Protein Sci 2021; 30:908-913. [PMID: 33554397 DOI: 10.1002/pro.4039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 02/06/2023]
Abstract
Mitogen-activated protein kinase (MAPK; p38, ERK, and JNK) cascades are evolutionarily conserved signaling pathways that regulate the cellular response to a variety of extracellular stimuli, such as growth factors and interleukins. The MAPK p38 is activated by its specific upstream MAPK kinases, MKK6 and MKK3. However, a comprehensive molecular understanding of how these cognate upstream kinases bind and activate p38 is still missing. Here, we combine NMR spectroscopy and isothermal titration calorimetry to define the binding interface between full-length MKK6 and p38. It was shown that p38 engages MKK6 not only via its hydrophobic docking groove, but also influences helix αF, a secondary structural element that plays a key role in organizing the kinase core. It was also shown that, unlike MAPK phosphatases, the p38 conserved docking (CD) site is much less affected by MKK6 binding. Finally, it was demonstrated that these interactions with p38 are conserved independent of the MKK6 activation state. Together, the results revealed differences between specificity markers of p38 regulation by upstream kinases, which do not effectively engage the CD site, and downstream phosphatases, which require the CD site for productive binding.
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Affiliation(s)
- Ganesan Senthil Kumar
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Rebecca Page
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
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4
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Omerbašić D, Smith ESJ, Moroni M, Homfeld J, Eigenbrod O, Bennett NC, Reznick J, Faulkes CG, Selbach M, Lewin GR. Hypofunctional TrkA Accounts for the Absence of Pain Sensitization in the African Naked Mole-Rat. Cell Rep 2017; 17:748-758. [PMID: 27732851 PMCID: PMC5081396 DOI: 10.1016/j.celrep.2016.09.035] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 06/23/2016] [Accepted: 09/13/2016] [Indexed: 12/21/2022] Open
Abstract
The naked mole-rat is a subterranean rodent lacking several pain behaviors found in humans, rats, and mice. For example, nerve growth factor (NGF), an important mediator of pain sensitization, fails to produce thermal hyperalgesia in naked mole-rats. The sensitization of capsaicin-sensitive TRPV1 ion channels is necessary for NGF-induced hyperalgesia, but naked mole-rats have fully functional TRPV1 channels. We show that exposing isolated naked mole-rat nociceptors to NGF does not sensitize TRPV1. However, the naked mole-rat NGF receptor TrkA displays a reduced ability to engage signal transduction pathways that sensitize TRPV1. Between one- and three-amino-acid substitutions in the kinase domain of the naked mole-rat TrkA are sufficient to render the receptor hypofunctional, and this is associated with the absence of heat hyperalgesia. Our data suggest that evolution has selected for a TrkA variant that abolishes a robust nociceptive behavior in this species but is still compatible with species fitness. TRPV1 ion channels in naked mole-rat nociceptors are not sensitized by NGF Naked mole-rat TRPV1 channels are sensitized by NGF in mouse nociceptors NGF activation of naked mole-rat TrkA receptors does not sensitize TRPV1 One to three amino acids in the naked mole-rat TrkA receptors may render it hypofunctional
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Affiliation(s)
- Damir Omerbašić
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; Proteome Dynamics Group, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Ewan St J Smith
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| | - Mirko Moroni
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Johanna Homfeld
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Ole Eigenbrod
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Nigel C Bennett
- Department of Zoology and Entomology, University of Pretoria, Pretoria, Hatfield 0028, Republic of South Africa
| | - Jane Reznick
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Chris G Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Matthias Selbach
- Proteome Dynamics Group, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Gary R Lewin
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; Excellence Cluster Neurocure, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
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5
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Keyes JD, Parsonage D, Yammani RD, Rogers LC, Kesty C, Furdui CM, Nelson KJ, Poole LB. Endogenous, regulatory cysteine sulfenylation of ERK kinases in response to proliferative signals. Free Radic Biol Med 2017; 112:534-543. [PMID: 28843779 PMCID: PMC5623068 DOI: 10.1016/j.freeradbiomed.2017.08.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/11/2017] [Accepted: 08/22/2017] [Indexed: 01/04/2023]
Abstract
ERK-dependent signaling is key to many pathways through which extracellular signals are transduced into cell-fate decisions. One conundrum is the way in which disparate signals induce specific responses through a common, ERK-dependent kinase cascade. While studies have revealed intricate ways of controlling ERK signaling through spatiotemporal localization and phosphorylation dynamics, additional modes of ERK regulation undoubtedly remain to be discovered. We hypothesized that fine-tuning of ERK signaling could occur by cysteine oxidation. We report that ERK is actively and directly oxidized by signal-generated H2O2 during proliferative signaling, and that ERK oxidation occurs downstream of a variety of receptor classes tested in four cell lines. Furthermore, within the tested cell lines and proliferative signals, we observed that both activation loop-phosphorylated and non-phosphorylated ERK undergo sulfenylation in cells and that dynamics of ERK sulfenylation is dependent on the cell growth conditions prior to stimulation. We also tested the effect of endogenous ERK oxidation on kinase activity and report that phosphotransfer reactions are reversibly inhibited by oxidation by as much as 80-90%, underscoring the importance of considering this additional modification when assessing ERK activation in response to extracellular signals.
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Affiliation(s)
- Jeremiah D Keyes
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Molecular Signaling, Wake Forest University, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, USA
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, USA
| | - Rama D Yammani
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, USA
| | - LeAnn C Rogers
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Molecular Signaling, Wake Forest University, USA
| | - Chelsea Kesty
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Molecular Signaling, Wake Forest University, USA
| | - Cristina M Furdui
- Center for Molecular Signaling, Wake Forest University, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, USA; Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Kimberly J Nelson
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Molecular Signaling, Wake Forest University, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, USA
| | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Molecular Signaling, Wake Forest University, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, USA.
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6
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Palma A, Tinti M, Paoluzi S, Santonico E, Brandt BW, Hooft van Huijsduijnen R, Masch A, Heringa J, Schutkowski M, Castagnoli L, Cesareni G. Both Intrinsic Substrate Preference and Network Context Contribute to Substrate Selection of Classical Tyrosine Phosphatases. J Biol Chem 2017; 292:4942-4952. [PMID: 28159843 DOI: 10.1074/jbc.m116.757518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/31/2017] [Indexed: 01/19/2023] Open
Abstract
Reversible tyrosine phosphorylation is a widespread post-translational modification mechanism underlying cell physiology. Thus, understanding the mechanisms responsible for substrate selection by kinases and phosphatases is central to our ability to model signal transduction at a system level. Classical protein-tyrosine phosphatases can exhibit substrate specificity in vivo by combining intrinsic enzymatic specificity with the network of protein-protein interactions, which positions the enzymes in close proximity to their substrates. Here we use a high throughput approach, based on high density phosphopeptide chips, to determine the in vitro substrate preference of 16 members of the protein-tyrosine phosphatase family. This approach helped identify one residue in the substrate binding pocket of the phosphatase domain that confers specificity for phosphopeptides in a specific sequence context. We also present a Bayesian model that combines intrinsic enzymatic specificity and interaction information in the context of the human protein interaction network to infer new phosphatase substrates at the proteome level.
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Affiliation(s)
- Anita Palma
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Michele Tinti
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Serena Paoluzi
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Elena Santonico
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Bernd Willem Brandt
- the Centre for Integrative Bioinformatics, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands, and
| | | | - Antonia Masch
- the Institut für Biochemie & Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06108 Halle, Germany
| | - Jaap Heringa
- the Centre for Integrative Bioinformatics, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands, and
| | - Mike Schutkowski
- the Institut für Biochemie & Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06108 Halle, Germany
| | - Luisa Castagnoli
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Gianni Cesareni
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy,
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7
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Zhou YH, Chen LQ, Tao J, Shen JL, Gong DY, Yun RR, Cheng Y. Effective cleavage of phosphodiester promoted by the zinc(II) and copper(II) inclusion complexes of β-cyclodextrin. J Inorg Biochem 2016; 163:176-184. [DOI: 10.1016/j.jinorgbio.2016.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 07/06/2016] [Accepted: 07/13/2016] [Indexed: 12/23/2022]
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8
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de Oliveira PSL, Ferraz FAN, Pena DA, Pramio DT, Morais FA, Schechtman D. Revisiting protein kinase-substrate interactions: Toward therapeutic development. Sci Signal 2016; 9:re3. [PMID: 27016527 DOI: 10.1126/scisignal.aad4016] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite the efforts of pharmaceutical companies to develop specific kinase modulators, few drugs targeting kinases have been completely successful in the clinic. This is primarily due to the conserved nature of kinases, especially in the catalytic domains. Consequently, many currently available inhibitors lack sufficient selectivity for effective clinical application. Kinases phosphorylate their substrates to modulate their activity. One of the important steps in the catalytic reaction of protein phosphorylation is the correct positioning of the target residue within the catalytic site. This positioning is mediated by several regions in the substrate binding site, which is typically a shallow crevice that has critical subpockets that anchor and orient the substrate. The structural characterization of this protein-protein interaction can aid in the elucidation of the roles of distinct kinases in different cellular processes, the identification of substrates, and the development of specific inhibitors. Because the region of the substrate that is recognized by the kinase can be part of a linear consensus motif or a nonlinear motif, advances in technology beyond simple linear sequence scanning for consensus motifs were needed. Cost-effective bioinformatics tools are already frequently used to predict kinase-substrate interactions for linear consensus motifs, and new tools based on the structural data of these interactions improve the accuracy of these predictions and enable the identification of phosphorylation sites within nonlinear motifs. In this Review, we revisit kinase-substrate interactions and discuss the various approaches that can be used to identify them and analyze their binding structures for targeted drug development.
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Affiliation(s)
- Paulo Sérgio L de Oliveira
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-970, Brazil
| | - Felipe Augusto N Ferraz
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-970, Brazil
| | - Darlene A Pena
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Dimitrius T Pramio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Felipe A Morais
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Deborah Schechtman
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil.
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9
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Chen KE, Li MY, Chou CC, Ho MR, Chen GC, Meng TC, Wang AJ. Substrate Specificity and Plasticity of FERM-Containing Protein Tyrosine Phosphatases. Structure 2015; 23:653-64. [DOI: 10.1016/j.str.2015.01.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 01/18/2015] [Accepted: 01/24/2015] [Indexed: 10/23/2022]
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10
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Li J, Liu X, Chu H, Fu X, Li T, Hu L, Xing S, Li G, Gu J, Zhao ZJ. Specific dephosphorylation of Janus Kinase 2 by protein tyrosine phosphatases. Proteomics 2014; 15:68-76. [PMID: 25354842 DOI: 10.1002/pmic.201400146] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 09/19/2014] [Accepted: 10/23/2014] [Indexed: 01/06/2023]
Abstract
Many protein kinases are activated through phosphorylation of an activation loop thereby turning on downstream signaling pathways. Activation of JAK2, a nonreceptor tyrosine kinase with an important role in growth factor and cytokine signaling, requires phosphorylation of the 1007 and 1008 tyrosyl residues. Dephosphorylation of these two sites by phosphatases presumably inactivates the enzyme, but the underlying mechanism is not known. In this study, we employed MALDI-TOF/TOF and triple quadrupole mass spectrometers to analyze qualitatively and quantitatively the dephosphorylation process by using synthetic peptides derived from the tandem autophosphorylation sites (Y1007 and Y1008) of human JAK2. We found that tyrosine phosphatases catalyzed the dephosphorylation reaction sequentially, but different enzymes exhibited different selectivity. Protein tyrosine phosphatase 1B caused rapid dephosphorylation of Y1008 followed by Y1007, while SHP1 and SHP2 selectively dephosphorylated Y1008 only, and yet HePTP randomly removed a single phosphate from either Y1007 or Y1008, leaving behind mono-phosphorylated peptides. The specificity of dephosphorylation was further confirmed by molecular modeling. The data reveal multiple modes of JAK2 regulation by tyrosine phosphatases, reflecting a complex, and intricate interplay between protein phosphorylation and dephosphorylation.
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Affiliation(s)
- Jianzhuo Li
- Key Laboratory Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, China; Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, China
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11
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Chen KE, Lin SY, Wu MJ, Ho MR, Santhanam A, Chou CC, Meng TC, Wang AHJ. Reciprocal allosteric regulation of p38γ and PTPN3 involves a PDZ domain-modulated complex formation. Sci Signal 2014; 7:ra98. [PMID: 25314968 DOI: 10.1126/scisignal.2005722] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The mitogen-activated protein kinase p38γ (also known as MAPK12) and its specific phosphatase PTPN3 (also known as PTPH1) cooperate to promote Ras-induced oncogenesis. We determined the architecture of the PTPN3-p38γ complex by a hybrid method combining x-ray crystallography, small-angle x-ray scattering, and chemical cross-linking coupled to mass spectrometry. A unique feature of the glutamic acid-containing loop (E-loop) of the phosphatase domain defined the substrate specificity of PTPN3 toward fully activated p38γ. The solution structure revealed the formation of an active-state complex between p38γ and the phosphatase domain of PTPN3. The PDZ domain of PTPN3 stabilized the active-state complex through an interaction with the PDZ-binding motif of p38γ. This interaction alleviated autoinhibition of PTPN3, enabling efficient tyrosine dephosphorylation of p38γ. Our findings may enable structure-based drug design targeting the PTPN3-p38γ interaction as an anticancer therapeutic.
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Affiliation(s)
- Kai-En Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 11581, Taiwan
| | - Shu-Yu Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 11581, Taiwan
| | - Mei-Ju Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11581, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei 11581, Taiwan
| | - Abirami Santhanam
- Institute of Biological Chemistry, Academia Sinica, Taipei 11581, Taiwan
| | - Chia-Cheng Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei 11581, Taiwan. National Core Facility for Protein Structural Analysis, Academia Sinica, Taipei 11581, Taiwan
| | - Tzu-Ching Meng
- Institute of Biological Chemistry, Academia Sinica, Taipei 11581, Taiwan. Institute of Biochemical Sciences, National Taiwan University, Taipei 10717, Taiwan.
| | - Andrew H J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11581, Taiwan. National Core Facility for Protein Structural Analysis, Academia Sinica, Taipei 11581, Taiwan. Institute of Biochemical Sciences, National Taiwan University, Taipei 10717, Taiwan. Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11047, Taiwan.
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12
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Stanford SM, Ahmed V, Barrios AM, Bottini N. Cellular biochemistry methods for investigating protein tyrosine phosphatases. Antioxid Redox Signal 2014; 20:2160-78. [PMID: 24294920 PMCID: PMC3995294 DOI: 10.1089/ars.2013.5731] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SIGNIFICANCE The protein tyrosine phosphatases (PTPs) are a family of proteins that play critical roles in cellular signaling and influence many aspects of human health and disease. Although a wealth of information has been collected about PTPs since their discovery, many questions regarding their regulation and function still remain. CRITICAL ISSUES Of particular importance are the elucidation of the biological substrates of individual PTPs and understanding of the chemical and biological basis for temporal and spatial resolution of PTP activity within a cell. RECENT ADVANCES Drawing from recent advances in both biology and chemistry, innovative approaches have been developed to study the intracellular biochemistry and physiology of PTPs. We provide a summary of PTP-tailored techniques and approaches, emphasizing methodologies to study PTP activity within a cellular context. We first provide a discussion of methods for identifying PTP substrates, including substrate-trapping mutants and synthetic peptide libraries for substrate selectivity profiling. We next provide an overview of approaches for monitoring intracellular PTP activity, including a discussion of mechanistic-based probes, gel-based assays, substrates that can be used intracellularly, and assays tied to cell growth. Finally, we review approaches used for monitoring PTP oxidation, a key regulatory pathway for these enzymes, discussing the biotin switch method and variants of this approach, along with affinity trapping techniques and probes designed to detect PTP oxidation. FUTURE DIRECTIONS Further development of approaches to investigate the intracellular PTP activity and functions will provide specific insight into their mechanisms of action and control of diverse signaling pathways.
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Affiliation(s)
- Stephanie M Stanford
- 1 Division of Cellular Biology, La Jolla Institute for Allergy and Immunology , La Jolla, California
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13
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Selner NG, Luechapanichkul R, Chen X, Neel BG, Zhang ZY, Knapp S, Bell CE, Pei D. Diverse levels of sequence selectivity and catalytic efficiency of protein-tyrosine phosphatases. Biochemistry 2014; 53:397-412. [PMID: 24359314 PMCID: PMC3954597 DOI: 10.1021/bi401223r] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The sequence selectivity of 14 classical protein-tyrosine phosphatases (PTPs) (PTPRA, PTPRB, PTPRC, PTPRD, PTPRO, PTP1B, SHP-1, SHP-2, HePTP, PTP-PEST, TCPTP, PTPH1, PTPD1, and PTPD2) was systematically profiled by screening their catalytic domains against combinatorial peptide libraries. All of the PTPs exhibit similar preference for pY peptides rich in acidic amino acids and disfavor positively charged sequences but differ vastly in their degrees of preference/disfavor. Some PTPs (PTP-PEST, SHP-1, and SHP-2) are highly selective for acidic over basic (or neutral) peptides (by >10(5)-fold), whereas others (PTPRA and PTPRD) show no to little sequence selectivity. PTPs also have diverse intrinsic catalytic efficiencies (kcat/KM values against optimal substrates), which differ by >10(5)-fold due to different kcat and/or KM values. Moreover, PTPs show little positional preference for the acidic residues relative to the pY residue. Mutation of Arg47 of PTP1B, which is located near the pY-1 and pY-2 residues of a bound substrate, decreased the enzymatic activity by 3-18-fold toward all pY substrates containing acidic residues anywhere within the pY-6 to pY+5 region. Similarly, mutation of Arg24, which is situated near the C-terminus of a bound substrate, adversely affected the kinetic activity of all acidic substrates. A cocrystal structure of PTP1B bound with a nephrin pY(1193) peptide suggests that Arg24 engages in electrostatic interactions with acidic residues at the pY+1, pY+2, and likely other positions. These results suggest that long-range electrostatic interactions between positively charged residues near the PTP active site and acidic residues on pY substrates allow a PTP to bind acidic substrates with similar affinities, and the varying levels of preference for acidic sequences by different PTPs are likely caused by the different electrostatic potentials near their active sites. The implications of the varying sequence selectivity and intrinsic catalytic activities with respect to PTP in vivo substrate specificity and biological functions are discussed.
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Affiliation(s)
- Nicholas G. Selner
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, USA
| | - Rinrada Luechapanichkul
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, USA
| | - Xianwen Chen
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, USA
| | - Benjamin G. Neel
- Princess Margaret Cancer Center, University Health Network, and Department of Medical Biophysics, University of Toronto, 610 University Avenue, Room 7-504, Toronto, ON M5G 2M9, Canada
| | - Zhong-Yin Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Stefan Knapp
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Charles E. Bell
- Department of Molecular and Cellular Biochemistry, The Ohio State University, 1645 Neil Avenue, Columbus, OH 43210
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, USA
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14
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Gulerez IE, Gehring K. X-ray crystallography and NMR as tools for the study of protein tyrosine phosphatases. Methods 2014; 65:175-83. [DOI: 10.1016/j.ymeth.2013.07.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/19/2013] [Accepted: 07/23/2013] [Indexed: 10/26/2022] Open
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15
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Seo H, Lee IS, Park JE, Park SG, Lee DH, Park BC, Cho S. Role of protein tyrosine phosphatase non-receptor type 7 in the regulation of TNF-α production in RAW 264.7 macrophages. PLoS One 2013; 8:e78776. [PMID: 24265715 PMCID: PMC3827119 DOI: 10.1371/journal.pone.0078776] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 09/23/2013] [Indexed: 11/19/2022] Open
Abstract
Protein tyrosine phosphatases play key roles in a diverse range of cellular processes such as differentiation, cell proliferation, apoptosis, immunological signaling, and cytoskeletal function. Protein tyrosine phosphatase non-receptor type 7 (PTPN7), a member of the phosphatase family, specifically inactivates mitogen-activated protein kinases (MAPKs). Here, we report that PTPN7 acts as a regulator of pro-inflammatory TNF-α production in RAW 264.7 cells that are stimulated with lipopolysaccharide (LPS) that acts as an endotoxin and elicits strong immune responses in animals. Stimulation of RAW 264.7 cells with LPS leads to a transient decrease in the levels of PTPN7 mRNA and protein. The overexpression of PTPN7 inhibits LPS-stimulated production of TNF-α. In addition, small interfering RNA (siRNA) analysis showed that knock-down of PTPN7 in RAW 264.7 cells increased TNF-α production. PTPN7 has a negative regulatory function to extracellular signal regulated kinase 1/2 (ERK1/2) and p38 that increase LPS-induced TNF-α production in macrophages. Thus, our data presents PTPN7 as a negative regulator of TNF-α expression and the inflammatory response in macrophages.
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Affiliation(s)
- Huiyun Seo
- College of Pharmacy, Chung-Ang University, Seoul, Korea
| | - In-Seon Lee
- College of Pharmacy, Chung-Ang University, Seoul, Korea
| | - Jae Eun Park
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sung Goo Park
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Do Hee Lee
- Department of Biotechnology, College of Natural Sciences, Seoul Women’s University, Seoul, Korea
| | - Byoung Chul Park
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sayeon Cho
- College of Pharmacy, Chung-Ang University, Seoul, Korea
- * E-mail:
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16
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Li R, Xie DD, Dong JH, Li H, Li KS, Su J, Chen LZ, Xu YF, Wang HM, Gong Z, Cui GY, Yu X, Wang K, Yao W, Xin T, Li MY, Xiao KH, An XF, Huo Y, Xu ZG, Sun JP, Pang Q. Molecular mechanism of ERK dephosphorylation by striatal-enriched protein tyrosine phosphatase. J Neurochem 2013; 128:315-329. [PMID: 24117863 DOI: 10.1111/jnc.12463] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 09/20/2013] [Accepted: 09/23/2013] [Indexed: 12/26/2022]
Abstract
Striatal-enriched tyrosine phosphatase (STEP) is an important regulator of neuronal synaptic plasticity, and its abnormal level or activity contributes to cognitive disorders. One crucial downstream effector and direct substrate of STEP is extracellular signal-regulated protein kinase (ERK), which has important functions in spine stabilisation and action potential transmission. The inhibition of STEP activity toward phospho-ERK has the potential to treat neuronal diseases, but the detailed mechanism underlying the dephosphorylation of phospho-ERK by STEP is not known. Therefore, we examined STEP activity toward para-nitrophenyl phosphate, phospho-tyrosine-containing peptides, and the full-length phospho-ERK protein using STEP mutants with different structural features. STEP was found to be a highly efficient ERK tyrosine phosphatase that required both its N-terminal regulatory region and key residues in its active site. Specifically, both kinase interaction motif (KIM) and kinase-specific sequence of STEP were required for ERK interaction. In addition to the N-terminal kinase-specific sequence region, S245, hydrophobic residues L249/L251, and basic residues R242/R243 located in the KIM region were important in controlling STEP activity toward phospho-ERK. Further kinetic experiments revealed subtle structural differences between STEP and HePTP that affected the interactions of their KIMs with ERK. Moreover, STEP recognised specific positions of a phospho-ERK peptide sequence through its active site, and the contact of STEP F311 with phospho-ERK V205 and T207 were crucial interactions. Taken together, our results not only provide the information for interactions between ERK and STEP, but will also help in the development of specific strategies to target STEP-ERK recognition, which could serve as a potential therapy for neurological disorders. Regulation of phospho-ERK by STEP underlies important neuronal activities. A detailed enzymologic characterisation and cellular studies of STEP revealed that specific residues in KIM and active site mediated ERK recognition. Structural differences between the KIM-ERK interfaces and the active site among different ERK phosphatases could be targeted to develop specific STEP inhibitor, which has therapeutic potential for neurological disorders. PKA, protein kinase A & NGF, nerve growth factor.
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Affiliation(s)
- Rong Li
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Di-Dong Xie
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Provincial Hospital affiliated to Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Jun-Hong Dong
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China.,Weifang Medical University,Weifang, Shandong, 261042, China
| | - Hui Li
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Kang-Shuai Li
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Jing Su
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Lai-Zhong Chen
- School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, 250012, China
| | - Yun-Fei Xu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Hong-Mei Wang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Zheng Gong
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Weihai campus, Shandong University, Weihai, Shandong, 264209, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Guo-Ying Cui
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Kai Wang
- Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Wei Yao
- Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Tao Xin
- Provincial Hospital affiliated to Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Min-Yong Li
- School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, 250012, China
| | - Kun-Hong Xiao
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiao-Fei An
- Drug Discovery Center, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, 518055
| | - Yuqing Huo
- Vascular Biology Center, Department of Cellular Biology and Anatomy, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912
| | - Zhi-Gang Xu
- Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China.,Shandong University, School of Life Sciences, Jinan, Shandong, 250021, China
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Provincial Hospital affiliated to Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Qi Pang
- Provincial Hospital affiliated to Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
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17
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Peti W, Page R. Molecular basis of MAP kinase regulation. Protein Sci 2013; 22:1698-710. [PMID: 24115095 DOI: 10.1002/pro.2374] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 12/11/2022]
Abstract
Mitogen-activated protein kinases (MAPKs; ERK1/2, p38, JNK, and ERK5) have evolved to transduce environmental and developmental signals (growth factors, stress) into adaptive and programmed responses (differentiation, inflammation, apoptosis). Almost 20 years ago, it was discovered that MAPKs contain a docking site in the C-terminal lobe that binds a conserved 13-16 amino acid sequence known as the D- or KIM-motif (kinase interaction motif). Recent crystal structures of MAPK:KIM-peptide complexes are leading to a precise understanding of how KIM sequences contribute to MAPK selectivity. In addition, new crystal and especially NMR studies are revealing how residues outside the canonical KIM motif interact with specific MAPKs and contribute further to MAPK selectivity and signaling pathway fidelity. In this review, we focus on these recent studies, with an emphasis on the use of NMR spectroscopy, isothermal titration calorimetry and small angle X-ray scattering to investigate these processes.
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Affiliation(s)
- Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, 02912; Department of Chemistry, Brown University, Providence, Rhode Island, 02912
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18
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Sergienko E, Xu J, Liu WH, Dahl R, Critton DA, Su Y, Brown BT, Chan X, Yang L, Bobkova EV, Vasile S, Yuan H, Rascon J, Colayco S, Sidique S, Cosford NDP, Chung TDY, Mustelin T, Page R, Lombroso PJ, Tautz L. Inhibition of hematopoietic protein tyrosine phosphatase augments and prolongs ERK1/2 and p38 activation. ACS Chem Biol 2012; 7:367-77. [PMID: 22070201 DOI: 10.1021/cb2004274] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The hematopoietic protein tyrosine phosphatase (HePTP) is implicated in the development of blood cancers through its ability to negatively regulate the mitogen-activated protein kinases (MAPKs) ERK1/2 and p38. Small-molecule modulators of HePTP activity may become valuable in treating hematopoietic malignancies such as T cell acute lymphoblastic leukemia (T-ALL) and acute myelogenous leukemia (AML). Moreover, such compounds will further elucidate the regulation of MAPKs in hematopoietic cells. Although transient activation of MAPKs is crucial for growth and proliferation, prolonged activation of these important signaling molecules induces differentiation, cell cycle arrest, cell senescence, and apoptosis. Specific HePTP inhibitors may promote the latter and thereby may halt the growth of cancer cells. Here, we report the development of a small molecule that augments ERK1/2 and p38 activation in human T cells, specifically by inhibiting HePTP. Structure-activity relationship analysis, in silico docking studies, and mutagenesis experiments reveal how the inhibitor achieves selectivity for HePTP over related phosphatases by interacting with unique amino acid residues in the periphery of the highly conserved catalytic pocket. Importantly, we utilize this compound to show that pharmacological inhibition of HePTP not only augments but also prolongs activation of ERK1/2 and, especially, p38. Moreover, we present similar effects in leukocytes from mice intraperitoneally injected with the inhibitor at doses as low as 3 mg/kg. Our results warrant future studies with this probe compound that may establish HePTP as a new drug target for acute leukemic conditions.
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Affiliation(s)
| | | | | | | | - David A. Critton
- Department
of Molecular Biology,
Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Rebecca Page
- Department
of Molecular Biology,
Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
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19
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Francis DM, Różycki B, Koveal D, Hummer G, Page R, Peti W. Structural basis of p38α regulation by hematopoietic tyrosine phosphatase. Nat Chem Biol 2011; 7:916-24. [PMID: 22057126 DOI: 10.1038/nchembio.707] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 08/30/2011] [Indexed: 12/14/2022]
Abstract
MAP kinases regulate essential cellular events, including cell growth, differentiation and inflammation. The solution structure of a complete MAPK-MAPK-regulatory protein complex, p38α-HePTP, was determined, enabling a comprehensive investigation of the molecular basis of specificity and fidelity in MAPK regulation. Structure determination was achieved by combining NMR spectroscopy and small-angle X-ray scattering data with a new ensemble calculation-refinement procedure. We identified 25 residues outside of the HePTP kinase interaction motif necessary for p38α recognition. The complex adopts an extended conformation in solution and rarely samples the conformation necessary for kinase deactivation. Complex formation also does not affect the N-terminal lobe, the activation loop of p38α or the catalytic domain of HePTP. Together, these results show how the downstream tyrosine phosphatase HePTP regulates p38α and provide for fundamentally new insights into MAPK regulation and specificity.
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Affiliation(s)
- Dana M Francis
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, USA
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20
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Francis DM, Różycki B, Tortajada A, Hummer G, Peti W, Page R. Resting and active states of the ERK2:HePTP complex. J Am Chem Soc 2011; 133:17138-41. [PMID: 21985012 DOI: 10.1021/ja2075136] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The MAP kinase ERK2 (ERK2, extracellular signal-regulated kinase 2) is regulated by numerous phosphatases that tightly control its activity. For example, the hematopoietic tyrosine phosphatase (HePTP) negatively regulates T cell activation in lymphocytes via ERK2 dephosphorylation. However, only very limited structural information is available for these biologically important complexes. Here, we use small-angle X-ray scattering combined with EROS ensemble refinement to characterize the structures of the resting and active states of ERK2:HePTP complexes. Our data show that the resting state ERK2:HePTP complex adopts a highly extended, dynamic conformation that becomes compact and ordered in the active state complex. This work experimentally demonstrates that these complexes undergo significant dynamic structural changes in solution and provides the first structural insight into an active state MAPK complex.
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Affiliation(s)
- Dana M Francis
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island 02912, USA
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21
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Bobkova EV, Liu WH, Colayco S, Rascon J, Vasile S, Gasior C, Critton DA, Chan X, Dahl R, Su Y, Sergienko E, Chung TDY, Mustelin T, Page R, Tautz L. Inhibition of the Hematopoietic Protein Tyrosine Phosphatase by Phenoxyacetic Acids. ACS Med Chem Lett 2011; 2:113-118. [PMID: 21503265 DOI: 10.1021/ml100103p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Protein tyrosine phosphatases (PTPs) have only recently become the focus of attention in the search for novel drug targets despite the fact that they play vital roles in numerous cellular processes and are implicated in many human diseases. The hematopoietic protein tyrosine phosphatase (HePTP) is often found dysregulated in preleukemic myelodysplastic syndrome (MDS), as well as in acute myelogenous leukemia (AML). Physiological substrates of HePTP include the mitogen-activated protein kinases (MAPKs) ERK1/2 and p38. Specific modulators of HePTP catalytic activity will be useful for elucidating mechanisms of MAPK regulation in hematopietic cells, and may also provide treatments for hematopoietic malignancies such as AML. Here we report the discovery of phenoxyacetic acids as inhibitors of HePTP. Structure-activity relationship (SAR) analysis and in silico docking studies reveal the molecular basis of HePTP inhibition by these compounds. We also show that these compounds are able to penetrate cell membranes and inhibit HePTP in human T lymphocytes.
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Affiliation(s)
| | | | | | | | | | | | - David A. Critton
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | | | | | - Ying Su
- Conrad Prebys Center for Chemical Genomics
| | | | | | | | - Rebecca Page
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Lutz Tautz
- Infectious and Inflammatory Disease Center
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22
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Critton DA, Tautz L, Page R. Visualizing active-site dynamics in single crystals of HePTP: opening of the WPD loop involves coordinated movement of the E loop. J Mol Biol 2010; 405:619-29. [PMID: 21094165 DOI: 10.1016/j.jmb.2010.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 11/09/2010] [Accepted: 11/10/2010] [Indexed: 10/18/2022]
Abstract
Phosphotyrosine hydrolysis by protein tyrosine phosphatases (PTPs) involves substrate binding by the PTP loop and closure over the active site by the WPD loop. The E loop, located immediately adjacent to the PTP and WPD loops, is conserved among human PTPs in both sequence and structure, yet the role of this loop in substrate binding and catalysis is comparatively unexplored. Hematopoietic PTP (HePTP) is a member of the kinase interaction motif (KIM) PTP family. Compared to other PTPs, KIM-PTPs have E loops that are unique in both sequence and structure. In order to understand the role of the E loop in the transition between the closed state and the open state of HePTP, we identified a novel crystal form of HePTP that allowed the closed-state-to-open-state transition to be observed within a single crystal form. These structures, which include the first structure of the HePTP open state, show that the WPD loop adopts an 'atypically open' conformation and, importantly, that ligands can be exchanged at the active site, which is critical for HePTP inhibitor development. These structures also show that tetrahedral oxyanions bind at a novel secondary site and function to coordinate the PTP, WPD, and E loops. Finally, using both structural and kinetic data, we reveal a novel role for E-loop residue Lys182 in enhancing HePTP catalytic activity through its interaction with Asp236 of the WPD loop, providing the first evidence for the coordinated dynamics of the WPD and E loops in the catalytic cycle, which, as we show, is relevant to multiple PTP families.
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Affiliation(s)
- David A Critton
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
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23
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Francis DM, Page R. Strategies to optimize protein expression in E. coli. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2010; Chapter 5:5.24.1-5.24.29. [PMID: 20814932 PMCID: PMC7162232 DOI: 10.1002/0471140864.ps0524s61] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recombinant protein expression in Escherichia coli (E. coli) is simple, fast, inexpensive, and robust, with the expressed protein comprising up to 50 percent of the total cellular protein. However, it also has disadvantages. For example, the rapidity of bacterial protein expression often results in unfolded/misfolded proteins, especially for heterologous proteins that require longer times and/or molecular chaperones to fold correctly. In addition, the highly reductive environment of the bacterial cytosol and the inability of E. coli to perform several eukaryotic post-translational modifications results in the insoluble expression of proteins that require these modifications for folding and activity. Fortunately, multiple, novel reagents and techniques have been developed that allow for the efficient, soluble production of a diverse range of heterologous proteins in E. coli. This overview describes variables at each stage of a protein expression experiment that can influence solubility and offers a summary of strategies used to optimize soluble expression in E. coli.
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