1
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Liu Y, Jang H, Nussinov R. SHP2-EGFR States in Dephosphorylation Can Inform Selective SHP2 Inhibitors, Dampening RasGAP Action. J Phys Chem B 2024; 128:5175-5187. [PMID: 38747619 DOI: 10.1021/acs.jpcb.4c00873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
SHP2 is a positive regulator of the EGFR-dependent Ras/MAPK pathway. It dephosphorylates a regulatory phosphorylation site in EGFR that serves as the binding site to RasGAP (RASA1 or p120RasGAP). RASA1 is activated by binding to the EGFR phosphate group. Active RASA1 deactivates Ras by hydrolyzing Ras-bound GTP to GDP. Thus, SHP2 dephosphorylation of EGFR effectively prevents RASA1-mediated deactivation of Ras, thereby stimulating proliferation. Despite knowledge of this vital regulation in cell life, mechanistic in-depth structural understanding of the involvement of SHP2, EGFR, and RASA1 in the Ras/MAPK pathway has largely remained elusive. Here we elucidate the interactions, the factors influencing EGFR's recruitment of RASA1, and SHP2's recognition of the substrate site in EGFR. We reveal that RASA1 specifically interacts with the DEpY992LIP motif in EGFR featuring a proline residue at the +3 position C-terminal to pY primarily through its nSH2 domain. This interaction is strengthened by the robust attraction of two acidic residues, E991 and D990, of EGFR to two basic residues in the BC-loop near the pY-binding pocket of RASA1's nSH2. In the stable precatalytic state of SHP2 with EGFR (DADEpY992LIPQ), the E-loop of SHP2's active site favors the interaction with the (-2)-position D990 and (-4)-position D988 N-terminal to pY992 in EGFR, while the pY-loop constrains the (+4)-position Q996 C-terminal to pY992. These specific interactions not only provide a structural basis for identifying negative regulatory sites in other RTKs but can inform selective, high-affinity active-site SHP2 inhibitors tailored for SHP2 mutants.
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Affiliation(s)
- Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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2
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Bremer HJ, Pflum MKH. Kinase-Catalyzed Biotinylation to Identify Phosphatase Substrates (K-BIPS). Methods Mol Biol 2024; 2743:135-152. [PMID: 38147213 DOI: 10.1007/978-1-0716-3569-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Phosphorylation is a reversible post-translational modification that alters the functions of proteins to govern various cellular events, including cell signaling. Kinases catalyze the transfer of a phosphoryl group onto the hydroxyl residue of serine, threonine, and tyrosine, while phosphatases catalyze the removal. Unregulated kinase and phosphatase activity have been observed in various cancers and neurodegenerative diseases. Despite their importance in cell biology, the role of phosphatases in cellular events has yet to be fully characterized, partly due to the lack of tools to identify phosphatase-substrate pairs in a biological context. The method called kinase-catalyzed biotinylation to identify phosphatase substrates (K-BIPS) was developed to remedy the lack of information surrounding phosphatase biology, particularly focused on substrate identification. In the K-BIPS method, the γ-phosphoryl modified adenosine 5'-triphosphate (ATP) analog, ATP-biotin, is used by kinases to biotin-label phosphoproteins. Because phosphatases must initially remove a phosphoryl group for subsequent biotinylation by ATP-biotin, phosphatase substrates are identified in K-BIPS by comparing biotinylated proteins in the presence and absence of active phosphatases. K-BIPS has been used to discover novel substrates of both serine/threonine and tyrosine phosphatases. This chapter describes the K-BIPS method to enable the identification of substrates to any phosphatases of interest, which will augment studies of phosphatase biology.
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Affiliation(s)
- Hannah J Bremer
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, Detroit, MI, USA.
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3
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Villamar-Cruz O, Loza-Mejía MA, Vivar-Sierra A, Saldivar-Cerón HI, Patiño-López G, Olguín JE, Terrazas LI, Armas-López L, Ávila-Moreno F, Saha S, Chernoff J, Camacho-Arroyo I, Arias-Romero LE. A PTP1B-Cdk3 Signaling Axis Promotes Cell Cycle Progression of Human Glioblastoma Cells through an Rb-E2F Dependent Pathway. Mol Cell Biol 2023; 43:631-649. [PMID: 38014992 PMCID: PMC10761042 DOI: 10.1080/10985549.2023.2273193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 09/11/2023] [Indexed: 11/29/2023] Open
Abstract
PTP1B plays a key role in developing different types of cancer. However, the molecular mechanism underlying this effect is unclear. To identify molecular targets of PTP1B that mediate its role in tumorigenesis, we undertook a SILAC-based phosphoproteomic approach, which allowed us to identify Cdk3 as a novel PTP1B substrate. Substrate trapping experiments and docking studies revealed stable interactions between the PTP1B catalytic domain and Cdk3. In addition, we observed that PTP1B dephosphorylates Cdk3 at tyrosine residue 15 in vitro and interacts with it in human glioblastoma cells. Next, we found that pharmacological inhibition of PTP1B or its depletion with siRNA leads to cell cycle arrest with diminished activity of Cdk3, hypophosphorylation of Rb, and the downregulation of E2F target genes Cdk1, Cyclin A, and Cyclin E1. Finally, we observed that the expression of a constitutively active Cdk3 mutant bypasses the requirement of PTP1B for cell cycle progression and expression of E2F target genes. These data delineate a novel signaling pathway from PTP1B to Cdk3 required for efficient cell cycle progression in an Rb-E2F dependent manner in human GB cells.
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Affiliation(s)
- Olga Villamar-Cruz
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Marco Antonio Loza-Mejía
- Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Chemical Sciences School, Universidad La Salle-México, Mexico City, Mexico
| | - Alonso Vivar-Sierra
- Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Chemical Sciences School, Universidad La Salle-México, Mexico City, Mexico
| | | | - Genaro Patiño-López
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de Mexico Federico Gómez, Mexico City, Mexico
| | - Jonadab Efraín Olguín
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
- Laboratorio Nacional en Salud FES-Iztacala, Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
| | - Luis Ignacio Terrazas
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
- Laboratorio Nacional en Salud FES-Iztacala, Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
| | - Leonel Armas-López
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
| | - Federico Ávila-Moreno
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
- Unidad de Investigación, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Sayanti Saha
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Jonathan Chernoff
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Ignacio Camacho-Arroyo
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Luis Enrique Arias-Romero
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
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EswarKumar N, Yang CH, Tewary S, Peng WH, Chen GC, Yeh YQ, Yang HC, Ho MC. An integrative approach unveils a distal encounter site for rPTPε and phospho-Src complex formation. Structure 2023; 31:1567-1577.e5. [PMID: 37794594 DOI: 10.1016/j.str.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/10/2023] [Accepted: 09/07/2023] [Indexed: 10/06/2023]
Abstract
The structure determination of protein tyrosine phosphatase (PTP): phospho-protein complexes, which is essential to understand how specificity is achieved at the amino acid level, remains a significant challenge for protein crystallography and cryoEM due to the transient nature of binding interactions. Using rPTPεD1 and phospho-SrcKD as a model system, we have established an integrative workflow to address this problem, by means of which we generate a protein:phospho-protein complex model using predetermined protein structures, SAXS and pTyr-tailored MD simulations. Our model reveals transient protein-protein interactions between rPTPεD1 and phospho-SrcKD and is supported by three independent experimental validations. Measurements of the association rate between rPTPεD1 and phospho-SrcKD showed that mutations on the rPTPεD1: SrcKD complex interface disrupts these transient interactions, resulting in a reduction in protein-protein association rate and, eventually, phosphatase activity. This integrative approach is applicable to other PTP: phospho-protein complexes and the characterization of transient protein-protein interface interactions.
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Affiliation(s)
- Nadendla EswarKumar
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan
| | - Sunilkumar Tewary
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wen-Hsin Peng
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Guang-Chao Chen
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, Hsin-Chu 300, Taiwan
| | - Hsiao-Ching Yang
- Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan.
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.
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5
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Apley KD, Griffith AS, Downes GM, Ross P, Farrell MP, Kendall P, Berkland CJ. CD22L Conjugation to Insulin Attenuates Insulin-Specific B Cell Activation. Bioconjug Chem 2023; 34:2077-2088. [PMID: 37883211 PMCID: PMC11034786 DOI: 10.1021/acs.bioconjchem.3c00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Pancreatic islet-reactive B lymphocytes promote Type 1 diabetes (T1D) by presenting an antigen to islet-destructive T cells. Teplizumab, an anti-CD3 monoclonal, delays T1D onset in patients at risk, but additional therapies are needed to prevent the disease entirely. Therefore, bifunctional molecules were designed to selectively inhibit T1D-promoting anti-insulin B cells by conjugating a ligand for the B cell inhibitory receptor CD22 (i.e., CD22L) to insulin, which permit these molecules to concomitantly bind to anti-insulin B cell receptors (BCRs) and CD22. Two prototypes were synthesized: 2:2 insulin-CD22L conjugate on a 4-arm PEG backbone, and 1:1 insulin-CD22L direct conjugate. Transgenic mice (125TgSD) expressing anti-insulin BCRs provided cells for in vitro testing. Cells were cultured with constructs for 3 days, then assessed by flow cytometry. Duplicate wells with anti-CD40 simulated T cell help. A 2-insulin 4-arm PEG control caused robust proliferation and activation-induced CD86 upregulation. Anti-CD40 further boosted these effects. This may indicate that BCR-cross-linking occurs when antigens are tethered by the PEG backbone as soluble insulin alone has no effect. Addition of CD22L via the 2:2 insulin-CD22L conjugate restored B cell properties to that of controls without an additional beneficial effect. In contrast, the 1:1 insulin-CD22L direct conjugate significantly reduced anti-insulin B cell proliferation in the presence of anti-CD40. CD22L alone had no effect, and the constructs did not affect the WT B cells. Thus, multivalent antigen constructs tend to activate anti-insulin B cells, while monomeric antigen-CD22L conjugates reduce B cell activation in response to simulated T cell help and reduce pathogenic B cell numbers without harming normal cells. Therefore, monomeric antigen-CD22L conjugates warrant futher study and may be promising candidates for preclinical trials to prevent T1D without inducing immunodeficiency.
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Affiliation(s)
- Kyle D Apley
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Amber S Griffith
- Department of Medicine, Division of Allergy and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Grant M Downes
- Bioengineering Graduate Program, University of Kansas, Lawrence, Kansas 66045, United States
| | - Patrick Ross
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Mark P Farrell
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Peggy Kendall
- Department of Medicine, Division of Allergy and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Cory J Berkland
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
- Bioengineering Graduate Program, University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemical and Petroleum Engineering, University of Kansas, Lawrence, Kansas 66045, United States
- Department of Biomedical Engineering, Washington University, St. Louis, Missouri 63130, United States
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
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6
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Tsubata T. The ligand interactions of B cell Siglecs are involved in the prevention of autoimmunity to sialylated self-antigens and in the quality control of signaling-competent B cells. Int Immunol 2023; 35:461-473. [PMID: 37504378 DOI: 10.1093/intimm/dxad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023] Open
Abstract
Sialic acid-binding immunoglobulin-like lectins (Siglecs) are a family of membrane molecules that recognize sialic acid. Most of them are inhibitory receptors that inhibit immune-cell activation by recognizing sialic acid as a self-motif. Human B cells express CD22 (also known as Siglec-2), Siglec-5, Siglec-6 and Siglec-10 whereas mouse B cells express CD22 and Siglec-G (ortholog of human Siglec-10). Siglecs recognize both sialylated molecules expressed on the same cell (cis-ligands) and those expressed by other cells (trans-ligands). In Guillain-Barré syndrome (GBS), antibody production to gangliosides (which are sialic acid-containing glycolipids) expressed by neurons plays a pathogenic role. A Siglec-10 variant deficient in recognition of gangliosides is genetically associated with GBS, suggesting that Siglec-10 induces self-tolerance to gangliosides by recognizing gangliosides as trans-ligands. Recognition of the BCR as a cis-ligand by Siglec-G and CD22 suppresses BCR signaling in B-1 cells and conventional B cells, respectively. This signal suppression prevents excess expansion of B-1 cells and is involved in the quality control of signaling-competent B cells by setting a threshold for tonic signaling during B cell development. CD22 recognizes other cis-ligands including CD22 and β7 integrin. Interaction of CD22 with other CD22 molecules induces CD22 clustering that suppresses CD22-mediated signal inhibition upon BCR ligation, and interaction with β7 integrin maintains its function in the gut-homing of B cells. Taken together, interactions of B cell Siglecs with multiple trans- and cis-ligands play important roles in B cell homeostasis and immune responses.
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Affiliation(s)
- Takeshi Tsubata
- Department of Pathology, Nihon University School of Dentistry, 1-8-13 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan
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Fürst A, Shahzadi I, Akkuş-Dağdeviren ZB, Schöpf AM, Gust R, Bernkop-Schnürch A. Zeta potential shifting nanoemulsions comprising single and gemini tyrosine-based surfactants. Eur J Pharm Sci 2023; 189:106538. [PMID: 37495057 DOI: 10.1016/j.ejps.2023.106538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/16/2023] [Accepted: 07/23/2023] [Indexed: 07/28/2023]
Abstract
AIM This study aims to design and evaluate zeta potential shifting nanoemulsions comprising single and gemini type tyrosine-based surfactants for specific cleavage by tyrosine phosphatase. METHODS Tyrosine-based surfactants, either single 4-(2-amino-3-(dodecylamino)-3-oxopropyl)phenyl dihydrogen phosphate (AF1) or gemini 4-(2-amino-3-((1-(dodecylamino)-3-(4-hydroxyphenyl)-1-oxopropan-2-yl)amino)-3-oxopropyl)phenyl dihydrogen phosphate (AF2) type were synthesized via amide bond formation of tyrosine with dodecylamine followed by phosphorylation. These surfactants were incorporated into nanoemulsions. Nanoemulsions were monitored by incubation with isolated tyrosine phosphatase as well as secreted tyrosine phosphatase of Escherichia coli in terms of phosphate release and zeta potential change. RESULTS Via isolated tyrosine phosphatase, and mediated by E. coli, phosphate groups of either single or gemini tyrosine-based surfactants could be cleaved by secreted tyrosine phosphatase. Nanoemulsions comprising a single tyrosine-based surfactant resulted in a charge shift from - 13.46 mV to - 4.41 mV employing isolated tyrosine phosphatase whilst nanoemulsions consisting of a gemini tyrosine-based surfactant showed a shift in zeta potential from - 15.92 mV to - 5.86 mV, respectively. CONCLUSION Nanoemulsions containing tyrosine-based surfactants represent promising zeta potential shifting nanocarrier systems targeting tyrosine phosphatase secreting bacteria.
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Affiliation(s)
- Andrea Fürst
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Iram Shahzadi
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Zeynep Burcu Akkuş-Dağdeviren
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Anna Maria Schöpf
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Chemistry, Institute of Pharmacy, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Ronald Gust
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Chemistry, Institute of Pharmacy, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Andreas Bernkop-Schnürch
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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8
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Tsubata T. Siglec cis-ligands and their roles in the immune system. Glycobiology 2023; 33:532-544. [PMID: 37154567 DOI: 10.1093/glycob/cwad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Sialic acid-binding immunoglobulin-like lectins are a family of membrane molecules primarily expressed in immune cells. Most of them are inhibitory receptors containing immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic tail. On the cell surface, sialic acid-binding immunoglobulin-like lectins are mostly bound by sialylated glycans on membrane molecules expressed in the same cell (cis-ligands). Although ligands of sialic acid-binding immunoglobulin-like lectins are not efficiently identified by conventional methods such as immunoprecipitation, in situ labeling including proximity labeling is useful in identifying both cis-ligands and the sialylated ligands expressed by other cells (trans-ligands) of sialic acid-binding immunoglobulin-like lectins. Interaction of the inhibitory sialic acid-binding immunoglobulin-like lectins with cis-ligands including both those with and without signaling function modulates the inhibitory activity of sialic acid-binding immunoglobulin-like lectins by multiple different ways. This interaction also modulates signaling function of the cis-ligands. So far, little is known about the role of the interaction between sialic acid-binding immunoglobulin-like lectins and the cis-ligands. Nonetheless, recent studies showed that the inhibitory activity of CD22 (also known as Siglec-2) is regulated by endogenous ligands, most likely cis-ligands, differentially in resting B cells and those in which B-cell antigen receptor is ligated. This differential regulation plays a role in quality control of signaling-competent B cells and also partial restoration of B-cell antigen receptor signaling in immunodeficient B cells.
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Affiliation(s)
- Takeshi Tsubata
- Department of Pathology, Nihon University School of Dentistry, Tokyo 101-8310, Japan
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DeMarco AG, Hall MC. Phosphoproteomic Approaches for Identifying Phosphatase and Kinase Substrates. Molecules 2023; 28:3675. [PMID: 37175085 PMCID: PMC10180314 DOI: 10.3390/molecules28093675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Protein phosphorylation is a ubiquitous post-translational modification controlled by the opposing activities of protein kinases and phosphatases, which regulate diverse biological processes in all kingdoms of life. One of the key challenges to a complete understanding of phosphoregulatory networks is the unambiguous identification of kinase and phosphatase substrates. Liquid chromatography-coupled mass spectrometry (LC-MS/MS) and associated phosphoproteomic tools enable global surveys of phosphoproteome changes in response to signaling events or perturbation of phosphoregulatory network components. Despite the power of LC-MS/MS, it is still challenging to directly link kinases and phosphatases to specific substrate phosphorylation sites in many experiments. Here, we survey common LC-MS/MS-based phosphoproteomic workflows for identifying protein kinase and phosphatase substrates, noting key advantages and limitations of each. We conclude by discussing the value of inducible degradation technologies coupled with phosphoproteomics as a new approach that overcomes some limitations of current methods for substrate identification of kinases, phosphatases, and other regulatory enzymes.
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Affiliation(s)
- Andrew G. DeMarco
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C. Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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10
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Chen S, Ji X, Dedkova LM, Potuganti GR, Hecht SM. Site-Selective Tyrosine Phosphorylation in the Activation of the p50 Subunit of NF-κB for DNA Binding and Transcription. ACS Chem Biol 2023; 18:59-69. [PMID: 36534507 PMCID: PMC10026595 DOI: 10.1021/acschembio.2c00678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The family of NF-κB transcriptional activators controls the expression of many genes, including those involved in cell survival and development. The family consists of homo- and heterodimers constituted by combinations of five subunits. Subunit p50 includes 13 tyrosine residues, but the relationship between specific tyrosine phosphorylations and p50 function is not well understood. Subunits of p50 and p65 prepared in vitro formed a heterodimer, but this NF-κB would not bind to the interleukin-2 (IL-2) promoter DNA. Treatment of p50 with guanosine triphosphate (GTP) and a lysate from activated Jurkat cells, effected rapid p50 phosphorylation, and, in the presence of wild-type subunit p65, was accompanied on the same time scale by IL-2 promoter DNA binding. Modified p50s containing one of seven stoichiometrically phosphorylated tyrosines in NF-κB p50/p65 heterodimers, included three that facilitated binding to the IL-2 DNA promoter region to a greater extent than the wild type. One of these three stoichiometrically phosphorylated p50/p65 heterodimers of NF-κB, containing pTyr60 in the p50 subunit, was treated with a lysate from activated Jurkat cells + GTP and shown to be phosphorylated on the same time scale as wild-type p50. This modified NF-κB also developed IL-2 promoter DNA binding activity on the same time scale as the wild type but exhibited greater binding to the IL-2 DNA promoters than the wild type. The nature of this enhanced binding was studied in greater detail using a metabolically stable pTyr derivative at position 60 of p50 and cellular phosphatases. We suggest that enhanced DNA binding of modified NF-κB containing pTyr60 in the p50 subunit may reflect stoichiometric NF-κB phosphorylation at a site that is not normally fully phosphorylated, or not phosphorylated at all, and is relatively resistant to the effects of Jurkat cell tyrosine phosphatase activity. This conclusion was reinforced by demonstrating that modification of Tyr60 of p50 with a metabolically stable methylenephosphonate moiety further increased the stability of the formed NF-κB p50/p65 heterodimer against the action of activated Jurkat cell phosphatases.
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Affiliation(s)
- Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xun Ji
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Gal Reddy Potuganti
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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11
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Zhu P, Wu X, Zhang RY, Hsu CC, Zhang ZY, Tao WA. An Integrated Proteomic Strategy to Identify SHP2 Substrates. J Proteome Res 2022; 21:2515-2525. [PMID: 36103635 PMCID: PMC9597472 DOI: 10.1021/acs.jproteome.2c00481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein phosphatases play an essential role in normal cell physiology and the development of diseases such as cancer. The innate challenges associated with studying protein phosphatases have limited our understanding of their substrates, molecular mechanisms, and unique functions within highly coordinated networks. Here, we introduce a novel strategy using substrate-trapping mutants coupled with quantitative proteomics methods to identify physiological substrates of Src homology 2 containing protein tyrosine phosphatase 2 (SHP2) in a high-throughput manner. The technique integrates three parallel mass spectrometry-based proteomics experiments, including affinity isolation of substrate-trapping mutant complex using wild-type and SHP2 KO cells, in vivo global quantitative phosphoproteomics, and in vitro phosphatase reaction. We confidently identified 18 direct substrates of SHP2 in the epidermal growth factor receptor signaling pathways, including both known and novel SHP2 substrates. Docking protein 1 was further validated using biochemical assays as a novel SHP2 substrate, providing a mechanism for SHP2-mediated Ras activation. This advanced workflow improves the systemic identification of direct substrates of protein phosphatases, facilitating our understanding of the equally important roles of protein phosphatases in cellular signaling.
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Affiliation(s)
- Peipei Zhu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ruo-Yu Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chuan-Chih Hsu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhong-Yin Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - W Andy Tao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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12
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Huang CF, Gottardi CJ, Mrksich M. Tyrosine phosphatase activity is restricted by basic charge substituting mutation of substrates. Sci Rep 2022; 12:15095. [PMID: 36064958 PMCID: PMC9445012 DOI: 10.1038/s41598-022-19133-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Phosphorylation controls important cellular signals and its dysregulation leads to disease. While most phospho-regulation studies are focused on kinases, phosphatases are comparatively overlooked. Combining peptide arrays with SAMDI mass spectrometry, we show that tyrosine phosphatase activity is restricted by basic amino acids adjacent to phosphotyrosines. We validate this model using two β-catenin mutants associated with cancer (T653R/K) and a mouse model for intellectual disability (T653K). These mutants introduce a basic residue next to Y654, an established phosphorylation site where modification shifts β-catenin from cell-cell adhesions and towards its essential nuclear role as Wnt-signaling effector. We show that T653-basic mutant β-catenins are less efficiently dephosphorylated by phosphatases, leading to sustained Y654 phosphorylation and elevated Wnt signals, similar to those observed for Y654E phospho-mimic mutant mice. This model rationalizes how basic mutations proximal to phosphotyrosines can restrict counter-regulation by phosphatases, providing new mechanismistic and treatment insights for 6000+ potentially relevant cancer mutations.
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Affiliation(s)
- Che-Fan Huang
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Cara J Gottardi
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, 60611, USA.
| | - Milan Mrksich
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA.
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Department of Cell & Developmental Biology, Northwestern University, Chicago, IL, 60611, USA.
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13
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Computational Methods in Cooperation with Experimental Approaches to Design Protein Tyrosine Phosphatase 1B Inhibitors in Type 2 Diabetes Drug Design: A Review of the Achievements of This Century. Pharmaceuticals (Basel) 2022; 15:ph15070866. [PMID: 35890163 PMCID: PMC9322956 DOI: 10.3390/ph15070866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 02/04/2023] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B) dephosphorylates phosphotyrosine residues and is an important regulator of several signaling pathways, such as insulin, leptin, and the ErbB signaling network, among others. Therefore, this enzyme is considered an attractive target to design new drugs against type 2 diabetes, obesity, and cancer. To date, a wide variety of PTP1B inhibitors that have been developed by experimental and computational approaches. In this review, we summarize the achievements with respect to PTP1B inhibitors discovered by applying computer-assisted drug design methodologies (virtual screening, molecular docking, pharmacophore modeling, and quantitative structure–activity relationships (QSAR)) as the principal strategy, in cooperation with experimental approaches, covering articles published from the beginning of the century until the time this review was submitted, with a focus on studies conducted with the aim of discovering new drugs against type 2 diabetes. This review encourages the use of computational techniques and includes helpful information that increases the knowledge generated to date about PTP1B inhibition, with a positive impact on the route toward obtaining a new drug against type 2 diabetes with PTP1B as a molecular target.
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14
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Fauser J, Huyot V, Matsche J, Szynal BN, Alexeev Y, Kota P, Karginov AV. Dissecting protein tyrosine phosphatase signaling by engineered chemogenetic control of its activity. J Cell Biol 2022; 221:213352. [PMID: 35829702 PMCID: PMC9284425 DOI: 10.1083/jcb.202111066] [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: 11/17/2021] [Revised: 05/06/2022] [Accepted: 06/22/2022] [Indexed: 01/16/2023] Open
Abstract
Protein tyrosine phosphatases (PTPases) are critical mediators of dynamic cell signaling. A tool capable of identifying transient signaling events downstream of PTPases is essential to understand phosphatase function on a physiological time scale. We report a broadly applicable protein engineering method for allosteric regulation of PTPases. This method enables dissection of transient events and reconstruction of individual signaling pathways. Implementation of this approach for Shp2 phosphatase revealed parallel MAPK and ROCK II dependent pathways downstream of Shp2, mediating transient cell spreading and migration. Furthermore, we show that the N-SH2 domain of Shp2 regulates MAPK-independent, ROCK II-dependent cell migration. Engineered targeting of Shp2 activity to different protein complexes revealed that Shp2-FAK signaling induces cell spreading whereas Shp2-Gab1 or Shp2-Gab2 mediates cell migration. We identified specific transient morphodynamic processes induced by Shp2 and determined the role of individual signaling pathways downstream of Shp2 in regulating these events. Broad application of this approach is demonstrated by regulating PTP1B and PTP-PEST phosphatases.
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Affiliation(s)
- Jordan Fauser
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL
| | - Vincent Huyot
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL
| | - Jacob Matsche
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL
| | - Barbara N. Szynal
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL
| | | | - Pradeep Kota
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Andrei V. Karginov
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL,Correspondence to Andrei V. Karginov:
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15
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Hongdusit A, Liechty ET, Fox JM. Analysis of Three Architectures for Controlling PTP1B with Light. ACS Synth Biol 2022; 11:61-68. [PMID: 34898189 DOI: 10.1021/acssynbio.1c00398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Photosensory domains are powerful tools for placing proteins under optical control, but their integration into light-sensitive chimeras is often challenging. Many designs require structural iterations, and direct comparisons of alternative approaches are rare. This study uses protein tyrosine phosphatase 1B (PTP1B), an influential regulatory enzyme, to compare three architectures for controlling PTPs with light: a protein fusion, an insertion chimera, and a split construct. All three designs permitted optical control of PTP1B activity in vitro (i.e., kinetic assays of purified enzyme) and in mammalian cells; photoresponses measured under both conditions, while different in magnitude, were linearly correlated. The fusion- and insertion-based architectures exhibited the highest dynamic range and maintained native localization patterns in mammalian cells. A single insertion architecture enabled optical control of both PTP1B and TCPTP, but not SHP2, where the analogous chimera was active but not photoswitchable. Findings suggest that PTPs are highly tolerant of domain insertions and support the use of in vitro screens to evaluate different optogenetic designs.
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Affiliation(s)
- Akarawin Hongdusit
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, Colorado 80303, United States
| | - Evan T. Liechty
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, Colorado 80303, United States
| | - Jerome M. Fox
- Department of Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, Colorado 80303, United States
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16
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Szedlacsek HS, Bajusz D, Badea RA, Pop A, Bică CC, Ravasz L, Mittli D, Mátyás D, Necula-Petrăreanu G, Munteanu CVA, Papp I, Juhász G, Hritcu L, Keserű GM, Szedlacsek SE. Designed Peptide Inhibitors of STEP Phosphatase-GluA2 AMPA Receptor Interaction Enhance the Cognitive Performance in Rats. J Med Chem 2021; 65:217-233. [PMID: 34962802 DOI: 10.1021/acs.jmedchem.1c01303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cognitive impairment and learning ability of the brain are directly linked to synaptic plasticity as measured in changes of long-term potentiation (LTP) and long-term depression (LTD) in animal models of brain diseases. LTD reflects a sustained reduction of the synaptic AMPA receptor content based on targeted clathrin-mediated endocytosis. AMPA receptor endocytosis is initiated by dephosphorylation of Tyr876 on the C-terminus of the AMPAR subunit GluA2. The brain-specific striatal-enriched protein tyrosine phosphatase (STEP) is responsible for this process. To identify new, highly effective inhibitors of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) internalization, we performed structure-based design of peptides able to inhibit STEP-GluA2-CT complex formation. Two short peptide derivatives were found as efficient in vitro inhibitors. Our in vivo experiments evidenced that both peptides restore the memory deficits and display anxiolytic and antidepressant effects in a scopolamine-treated rat model. The interference peptides identified and characterized here represent promising lead compounds for novel cognitive enhancers and/or behavioral modulators.
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Affiliation(s)
- Horea Stefan Szedlacsek
- Department of Enzymology, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Rodica Aura Badea
- Department of Enzymology, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Andreea Pop
- Department of Enzymology, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Constantin Cătălin Bică
- Department of Enzymology, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Lilla Ravasz
- CRU Hungary Kft, Thököly utca 15, 2131 Göd, Hungary
| | | | | | - Georgiana Necula-Petrăreanu
- Department of Enzymology, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Cristian V A Munteanu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Ildikó Papp
- CRU Hungary Kft, Thököly utca 15, 2131 Göd, Hungary
| | - Gábor Juhász
- CRU Hungary Kft, Thököly utca 15, 2131 Göd, Hungary
| | - Lucian Hritcu
- Department of Biology, Faculty of Biology, Alexandru Ioan Cuza University of Iasi, Bd. Carol I, No. 11, 700505 Iasi, Romania
| | - György Miklós Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Stefan Eugen Szedlacsek
- Department of Enzymology, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
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17
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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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18
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Suter EC, Schmid EM, Harris AR, Voets E, Francica B, Fletcher DA. Antibody:CD47 ratio regulates macrophage phagocytosis through competitive receptor phosphorylation. Cell Rep 2021; 36:109587. [PMID: 34433055 PMCID: PMC8477956 DOI: 10.1016/j.celrep.2021.109587] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 04/19/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023] Open
Abstract
Cancer immunotherapies often modulate macrophage effector function by introducing either targeting antibodies that activate Fcγ receptors (FcγRs) or blocking antibodies that disrupt inhibitory SIRPα-CD47 engagement. However, how these competing signals are integrated is poorly understood, raising questions about how to effectively titrate immune responses. Here, we find that macrophage phagocytic decisions are regulated by the ratio of activating ligand to inhibitory ligand over a broad range of absolute molecular densities. Using both endogenous and chimeric receptors, we show that activating:inhibitory ligand ratios of at least 10:1 are required to promote phagocytosis of model antibody-opsonized CD47-inhibited targets and that lowering that ratio reduces FcγR phosphorylation because of inhibitory phosphatases recruited to CD47-bound SIRPα. We demonstrate that ratiometric signaling is critical for phagocytosis of tumor cells and can be modified by blocking SIRPα, indicating that balancing targeting and blocking antibodies may be important for controlling macrophage phagocytosis in cancer immunotherapy.
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Affiliation(s)
- Emily C Suter
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA
| | - Eva M Schmid
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, ON, Canada
| | - Erik Voets
- Aduro Biotech Europe, Oss, the Netherlands
| | | | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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19
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Kanegasaki S, Tsuchiya T. A possible way to prevent the progression of bone lesions in multiple myeloma via Src-homology-region-2-domain-containing-phosphatase-1 activation. J Cell Biochem 2021; 122:1313-1325. [PMID: 33969922 DOI: 10.1002/jcb.29949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/01/2021] [Accepted: 04/26/2021] [Indexed: 11/08/2022]
Abstract
On the basis of our recent findings, in which multiple receptor-mediated mast cell functions are regulated via a common signaling cascade, we posit that the formation and functioning of osteoclasts are also controlled by a similar common mechanism. These cells are derived from the same granulocyte/monocyte progenitors and share multiple receptors except those that are cell-specific. In both types of cells, all known receptors reside in lipid rafts, form multiprotein complexes with recruited signaling molecules, and are internalized upon receptor engagement. Signal transduction proceeds in a chain of protein phosphorylations, where adaptor protein LAT (linker-for-activation-of-T-cells) plays a central role. The key kinase that associates LAT phosphorylation and lipid raft internalization is Syk (spleen-tyrosine-kinase) and/or an Src-family-kinase, most probably Lck (lymphocyte-specific-protein-tyrosine-kinase). Dephosphorylation of phosphorylated Syk and Lck by activated SHP-1 (Src-homology-region-2-domain-containing-phosphatase-1) terminates the signal transduction and endocytosis of receptors, resulting in inhibition of osteoclast differentiation and other functions. In malignant plasma cells (MM cells) too, SHP-1 plays a similar indispensable role in controlling signal transduction required for survival and proliferation, though BLNK (B-cell-linker-protein), a functional equivalent of LAT and SLP-76 (SH2-domain-containing-leukocyte-protein-of-76-kDa) in B cells, is used instead of LAT. In both osteoclasts and MM cells, therefore, activated SHP-1 acts negatively in receptor-mediated cellular functions. In osteoblasts, however, activated SHP-1 promotes differentiation, osteocalcin generation, and mineralization by preventing both downregulation of transcription factors, such as Ostrix and Runx2, and degradation of β-catenin required for activation of the transcription factors. SHP-1 is activated by tyrosine phosphorylation and micromolar doses (M-dose) of CCRI-ligand-induced SHP-1 activation. Small molecular compounds, such as A770041, Sorafenib, Nitedanib, and Dovitinib, relieve the autoinhibitory conformation. Activation of SHP-1 by M-dose CCRI ligands or the compounds described may prevent the progression of bone lesions in MM.
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Affiliation(s)
- Shiro Kanegasaki
- Department of Lipid Signaling, Research Institute National Center for Global Health and Medicine, Tokyo, Japan
| | - Tomoko Tsuchiya
- Department of Molecular Immunology and Inflammation, Research Institute National Center for Global Health and Medicine, Tokyo, Japan
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20
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Nagata S, Segawa K. Sensing and clearance of apoptotic cells. Curr Opin Immunol 2020; 68:1-8. [PMID: 32853880 DOI: 10.1016/j.coi.2020.07.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/07/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022]
Abstract
Macrophages specifically engulf apoptotic cells but not healthy cells. Phosphatidylserine (PtdSer) is localized at the inner leaflet of plasma membranes as a result of the action of flippases (ATP11A and 11C). When cells undergo apoptosis, caspase 3 cleaves and inactivates the flippases, while simultaneously cleaving XKR8 to activate its phospholipid scramblase activity. PtdSer is thus swiftly and irreversibly exposed to the cell surface as an 'eat me' signal. Tissue resident macrophages recognize the apoptotic cells using a PtdSer-receptor TIM4 and engulf them with TAM tyrosine-kinase receptors, and integrins. The PtdSer 'eat me' signal appears to override 'don't eat me' signals in most cases.
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Affiliation(s)
- Shigekazu Nagata
- Laboratory of Biochemistry & Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan.
| | - Katsumori Segawa
- Laboratory of Biochemistry & Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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21
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A Fish Leukocyte Immune-Type Receptor Uses a Novel Intracytoplasmic Tail Networking Mechanism to Cross-Inhibit the Phagocytic Response. Int J Mol Sci 2020; 21:ijms21145146. [PMID: 32708174 PMCID: PMC7404264 DOI: 10.3390/ijms21145146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 02/04/2023] Open
Abstract
Channel catfish (Ictalurus punctatus) leukocyte immune-type receptors (IpLITRs) are a family of immunoregulatory proteins shown to regulate several innate immune cell effector responses, including phagocytosis. The precise mechanisms of IpLITR-mediated regulation of the phagocytic process are not entirely understood, but we have previously shown that different IpLITR-types use classical as well as novel pathways for controlling immune cell-mediated target engulfment. To date, all functional assessments of IpLITR-mediated regulatory actions have focused on the independent characterization of select IpLITR-types in transfected cells. As members of the immunoglobulin superfamily, many IpLITRs share similar extracellular Ig-like domains, thus it is possible that various IpLITR actions are influenced by cross-talk mechanisms between different IpLITR-types; analogous to the paired innate receptor paradigm in mammals. Here, we describe in detail the co-expression of different IpLITR-types in the human embryonic AD293 cell line and examination of their receptor cross-talk mechanisms during the regulation of the phagocytic response using imaging flow cytometry, confocal microscopy, and immunoprecipitation protocols. Overall, our data provides interesting new insights into the integrated control of phagocytosis via the antagonistic networking of independent IpLITR-types that requires the selective recruitment of inhibitory signaling molecules for the initiation and sustained cross-inhibition of phagocytosis.
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22
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Martinelli S, Pannone L, Lissewski C, Brinkmann J, Flex E, Schanze D, Calligari P, Anselmi M, Pantaleoni F, Canale VC, Radio FC, Ioannides A, Rahner N, Schanze I, Josifova D, Bocchinfuso G, Ryten M, Stella L, Tartaglia M, Zenker M. Pathogenic PTPN11 variants involving the poly-glutamine Gln 255 -Gln 256 -Gln 257 stretch highlight the relevance of helix B in SHP2's functional regulation. Hum Mutat 2020; 41:1171-1182. [PMID: 32112654 DOI: 10.1002/humu.24007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/14/2020] [Accepted: 02/27/2020] [Indexed: 01/28/2023]
Abstract
Germline PTPN11 mutations cause Noonan syndrome (NS), the most common disorder among RASopathies. PTPN11 encodes SHP2, a protein tyrosine-phosphatase controlling signaling through the RAS-MAPK and PI3K-AKT pathways. Generally, NS-causing PTPN11 mutations are missense changes destabilizing the inactive conformation of the protein or enhancing its binding to signaling partners. Here, we report on two PTPN11 variants resulting in the deletion or duplication of one of three adjacent glutamine residues (Gln255 -to-Gln257 ). While p.(Gln257dup) caused a typical NS phenotype in carriers of a first family, p.(Gln257del) had incomplete penetrance in a second family. Missense mutations involving Gln256 had previously been reported in NS. This poly-glutamine stretch is located on helix B of the PTP domain, a region involved in stabilizing SHP2 in its autoinhibited state. Molecular dynamics simulations predicted that changes affecting this motif perturb the SHP2's catalytically inactive conformation and/or substrate recognition. Biochemical data showed that duplication and deletion of Gln257 variably enhance SHP2's catalytic activity, while missense changes involving Gln256 affect substrate specificity. Expression of mutants in HEK293T cells documented their activating role on MAPK signaling, uncoupling catalytic activity and modulation of intracellular signaling. These findings further document the relevance of helix B in the regulation of SHP2's function.
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Affiliation(s)
- Simone Martinelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Luca Pannone
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy.,Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Christina Lissewski
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
| | - Julia Brinkmann
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
| | - Elisabetta Flex
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Denny Schanze
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
| | - Paolo Calligari
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Massimiliano Anselmi
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Viviana Claudia Canale
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | | | - Adonis Ioannides
- Clinical Genetics, University of Nicosia Medical School, Nicosia, Cyprus.,South East Thames Regional Genetics Service, Guy's Hospital, London, UK
| | - Nils Rahner
- Medical Faculty, Institute of Human Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Ina Schanze
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
| | - Dragana Josifova
- South East Thames Regional Genetics Service, Guy's Hospital, London, UK
| | - Gianfranco Bocchinfuso
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Mina Ryten
- South East Thames Regional Genetics Service, Guy's Hospital, London, UK
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Martin Zenker
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
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23
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Hartman Z, Geldenhuys WJ, Agazie YM. A specific amino acid context in EGFR and HER2 phosphorylation sites enables selective binding to the active site of Src homology phosphatase 2 (SHP2). J Biol Chem 2020; 295:3563-3575. [PMID: 32024694 DOI: 10.1074/jbc.ra119.011422] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/22/2020] [Indexed: 11/06/2022] Open
Abstract
The Src homology phosphatase 2 (SHP2) is a cytoplasmic enzyme that mediates signaling induced by multiple receptor tyrosine kinases, including signaling by the epidermal growth factor receptor (EGFR) family (EGFR1-4 or the human homologs HER1-4). In EGFR (HER1) and EGFR2 (HER2) signaling, SHP2 increases the half-life of activated Ras by blocking recruitment of Ras GTPase-activating protein (RasGAP) to the plasma membrane through dephosphorylation of docking sites on the receptors. However, it is unclear how SHP2 selectively recognizes RasGAP-binding sites on EGFR and HER2. In this report, we show that SHP2-targeted pTyr residues exist in a specific amino acid context that allows selective binding. More specifically, we show that acidic residues N-terminal to the substrate pTyr in EGFR and HER2 mediate specific binding by the SHP2 active site, leading to blockade of RasGAP binding and optimal signaling by the two receptors. Molecular modeling studies revealed that a peptide derived from the region of pTyr992-EGFR packs well and makes stronger interactions with the SHP2 active site than with the SHP1 active site, suggesting a built-in mechanism that enables selective substrate recognition by SHP2. A phosphorylated form of this peptide inhibits SHP2 activity in vitro and EGFR and HER2 signaling in cells, suggesting inhibition of SHP2 protein tyrosine phosphatase activity by this peptide. Although we do not expect this peptide to be a strong inhibitor by itself, we foresee that the insights into SHP2 selectivity described here will be useful in future development of active-site small molecule-based inhibitors.
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Affiliation(s)
- Zachary Hartman
- Department of Biochemistry, School of Medicine West Virginia University, Morgantown, West Virginia 26506
| | - Werner J Geldenhuys
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia 26506
| | - Yehenew M Agazie
- Department of Biochemistry, School of Medicine West Virginia University, Morgantown, West Virginia 26506; WVU Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia 26506.
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24
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Szymczak LC, Sykora DJ, Mrksich M. Using Peptide Arrays to Profile Phosphatase Activity in Cell Lysates. Chemistry 2020; 26:165-170. [PMID: 31691395 DOI: 10.1002/chem.201904364] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/31/2019] [Indexed: 12/30/2022]
Abstract
Phosphorylation is an important post-translational modification on proteins involved in many cellular processes; however, understanding of the regulation and mechanisms of global phosphorylation remains limited. Herein, we utilize self-assembled monolayers on gold for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI-MS) with three phosphorylated peptide arrays to profile global phosphatase activity in cell lysates derived from five mammalian cell lines. Our results reveal significant differences in the activities of protein phosphatases on phospho- serine, threonine, and tyrosine substrates and suggest that phosphatases play a much larger role in the regulation of global phosphorylation on proteins than previously understood.
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Affiliation(s)
- Lindsey C Szymczak
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Daniel J Sykora
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Milan Mrksich
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.,Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
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25
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Huang CF, Mrksich M. Profiling Protein Tyrosine Phosphatase Specificity with Self-Assembled Monolayers for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry and Peptide Arrays. ACS COMBINATORIAL SCIENCE 2019; 21:760-769. [PMID: 31553163 PMCID: PMC6848775 DOI: 10.1021/acscombsci.9b00152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The opposing activities of phosphatases and kinases determine the phosphorylation status of proteins, yet kinases have received disproportionate attention in studies of cellular processes, with the roles of phosphatases remaining less understood. This Research Article describes the use of phosphotyrosine-containing peptide arrays together with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to directly profile phosphatase substrate selectivities. Twenty-two protein tyrosine phosphatases were characterized with the arrays to give a profile of their specificities. An analysis of the data revealed that certain residues in the substrates had a conserved effect on activity for all enzymes tested, including the general rule that inclusion of a basic lysine or arginine residue on either side of the phosphotyrosine decreased activity. This insight also provides a new perspective on the role of a R1152Q mutant in the insulin receptor, which is known to exhibit a lower phosphorylation level and which this work suggests may be due to an increased activity toward phosphatase enzymes. The use of self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI-MS) to provide a rapid and quantitative assay of phosphatase enzymes will be important to gaining a more complete understanding of the biochemistry and biology of this important enzyme class.
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Affiliation(s)
- Che-Fan Huang
- Department of Chemistry, Northwestern University, Evanston, IL 60208, United States
| | - Milan Mrksich
- Department of Chemistry, Northwestern University, Evanston, IL 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, United States
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26
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Rodenfels J, Neugebauer KM, Howard J. Heat Oscillations Driven by the Embryonic Cell Cycle Reveal the Energetic Costs of Signaling. Dev Cell 2019; 48:646-658.e6. [PMID: 30713074 DOI: 10.1016/j.devcel.2018.12.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 10/31/2018] [Accepted: 12/28/2018] [Indexed: 12/18/2022]
Abstract
All living systems function out of equilibrium and exchange energy in the form of heat with their environment. Thus, heat flow can inform on the energetic costs of cellular processes, which are largely unknown. Here, we have repurposed an isothermal calorimeter to measure heat flow between developing zebrafish embryos and the surrounding medium. Heat flow increased over time with cell number. Unexpectedly, a prominent oscillatory component of the heat flow, with periods matching the synchronous early reductive cleavage divisions, persisted even when DNA synthesis and mitosis were blocked by inhibitors. Instead, the heat flow oscillations were driven by the phosphorylation and dephosphorylation reactions catalyzed by the cell-cycle oscillator, the biochemical network controlling mitotic entry and exit. We propose that the high energetic cost of cell-cycle signaling reflects the significant thermodynamic burden of imposing accurate and robust timing on cell proliferation during development.
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Affiliation(s)
- Jonathan Rodenfels
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Jonathon Howard
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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27
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Trease AJ, Li H, Spagnol G, Zheng L, Stauch KL, Sorgen PL. Regulation of Connexin32 by ephrin receptors and T-cell protein-tyrosine phosphatase. J Biol Chem 2019; 294:341-350. [PMID: 30401746 PMCID: PMC6322898 DOI: 10.1074/jbc.ra118.003883] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 10/25/2018] [Indexed: 11/06/2022] Open
Abstract
Gap junctions are intercellular conduits that permit the passage of ions, small metabolites, and signaling molecules between cells. Connexin32 (Cx32) is a major gap junction protein in the liver and brain. Phosphorylation is integral to regulating connexin assembly, degradation, and electrical and metabolic coupling, as well as to interactions with molecular partners. Cx32 contains two intracellular tyrosine residues, and tyrosine phosphorylation of Cx32 has been detected after activation of the epidermal growth factor receptor; however, the specific tyrosine residue and the functional implication of this phosphorylation remain unknown. To address the limited available information on Cx32 regulation by tyrosine kinases, here we used the Cx32 C-terminal (CT) domain in an in vitro kinase-screening assay, which identified ephrin (Eph) receptor family members as tyrosine kinases that phosphorylate Cx32. We found that EphB1 and EphA1 phosphorylate the Cx32CT domain residue Tyr243 Unlike for Cx43, the tyrosine phosphorylation of the Cx32CT increased gap junction intercellular communication. We also demonstrated that T-cell protein-tyrosine phosphatase dephosphorylates pTyr243 The data presented above along with additional examples throughout the literature of gap junction regulation by kinases, indicate that one cannot extrapolate the effect of a kinase on one connexin to another.
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Affiliation(s)
| | - Hanjun Li
- Department of Biochemistry and Molecular Biology; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | | | - Li Zheng
- Department of Biochemistry and Molecular Biology
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28
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Campbell H, Heidema C, Pilarczyk DG, DeMali KA. SHP-2 is activated in response to force on E-cadherin and dephosphorylates vinculin Y822. J Cell Sci 2018; 131:jcs.216648. [PMID: 30478196 DOI: 10.1242/jcs.216648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 11/16/2018] [Indexed: 11/20/2022] Open
Abstract
The response of cells to mechanical inputs is a key determinant of cell behavior. In response to external forces, E-cadherin initiates signal transduction cascades that allow the cell to modulate its contractility to withstand the force. Much attention has focused on identifying the E-cadherin signaling pathways that promote contractility, but the negative regulators remain undefined. In this study, we identify SHP-2 as a force-activated phosphatase that negatively regulates E-cadherin force transmission by dephosphorylating vinculin Y822. To specifically probe a role for SHP-2 in E-cadherin mechanotransduction, we mutated vinculin so that it retains its phosphorylation but cannot be dephosphorylated. Cells expressing the mutant vinculin have increased contractility. This work provides a mechanism for inactivating E-cadherin mechanotransduction and provides a new method for specifically targeting the action of phosphatases in cells.
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Affiliation(s)
- Hannah Campbell
- Department of Biochemistry and the Interdisciplinary Program in Molecular and Cellular Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Christy Heidema
- Department of Biochemistry and the Interdisciplinary Program in Molecular and Cellular Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Daisy G Pilarczyk
- Department of Biochemistry and the Interdisciplinary Program in Molecular and Cellular Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Kris A DeMali
- Department of Biochemistry and the Interdisciplinary Program in Molecular and Cellular Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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29
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Tang H, Dai Z, Qin X, Cai W, Hu L, Huang Y, Cao W, Yang F, Wang C, Liu T. Proteomic Identification of Protein Tyrosine Phosphatase and Substrate Interactions in Living Mammalian Cells by Genetic Encoding of Irreversible Enzyme Inhibitors. J Am Chem Soc 2018; 140:13253-13259. [PMID: 30247891 DOI: 10.1021/jacs.8b06922] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein tyrosine phosphatases (PTPs) play critical roles in cell signaling pathways, but identification of unknown PTPs for a given substrate in live cells remain technically challenging. Here, we synthesized a series of tyrosine-based irreversible PTP inhibitors and characterized by site-specific encoding on substrate proteins in cells with an expanded genetic code. By fine-tuning the chemical reactivity, we identified optimal active amino acid probes to covalently cross-link a PTP and its substrate both in vitro and in mammalian cells. Using HER2 as an example, we provide first direct evidence of HER2 Y1023 and SHP2 cross-linking in situ in living human cells. Moreover, proteomic analysis using our approach identified PTP1B as a novel phosphatase for HER2 that specifically dephosphorylated pY1221 position, which may shed light on the puzzle of PTP1B's role in HER2 positive breast cancer. This novel method provides a useful tool for dissecting tyrosine phosphoregulation in living cells.
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Affiliation(s)
- Hongting Tang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Zhen Dai
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China.,College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry , Nankai University , Tianjin 300071 , China
| | - Xuewen Qin
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Wenkang Cai
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Liming Hu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Yujia Huang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
| | - Wenbing Cao
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China.,College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry , Nankai University , Tianjin 300071 , China
| | - Fan Yang
- College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Chu Wang
- College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences , Peking University , 38 Xueyuan Road , Haidian District, Beijing 100191 , China
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30
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Komnatnyy VV, Nielsen TE, Qvortrup K. Bead-based screening in chemical biology and drug discovery. Chem Commun (Camb) 2018; 54:6759-6771. [PMID: 29888365 DOI: 10.1039/c8cc02486c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High-throughput screening is an important component of the drug discovery process. The screening of libraries containing hundreds of thousands of compounds requires assays amenable to miniaturisation and automization. Combinatorial chemistry holds a unique promise to deliver structurally diverse libraries for early drug discovery. Among the various library forms, the one-bead-one-compound (OBOC) library, where each bead carries many copies of a single compound, holds the greatest potential for the rapid identification of novel hits against emerging drug targets. However, this potential has not yet been fully realized due to a number of technical obstacles. In this feature article, we review the progress that has been made in bead-based library screening and its application to the discovery of bioactive compounds. We identify the key challenges of this approach and highlight key steps needed for making a greater impact in the field.
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Affiliation(s)
- Vitaly V Komnatnyy
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark.
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31
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Gao M, Huang ZL, Tao K, Xiao Q, Wang X, Cao WX, Xu M, Hu J, Feng WL. Depression of oncogenecity by dephosphorylating and degrading BCR-ABL. Oncotarget 2018; 8:3304-3314. [PMID: 27926512 PMCID: PMC5356883 DOI: 10.18632/oncotarget.13754] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 11/21/2016] [Indexed: 11/25/2022] Open
Abstract
Aberrant phosphorylation and overexpression of BCR-ABL fusion protein are responsible for the main pathogenesis in chronic myeloid leukemia (CML). Phosphorylated BCR-ABL Y177 recruits GRB2 adaptor and triggers leukemic RAS-MAPK and PI3K-AKT signals. In this study, we engineered a SPOA system to dephosphorylate and degrade BCR-ABL by targeting BCR-ABL Y177. We tested its effect on BCR-ABL phosphorylation and expression, as well as cell proliferation and apoptosis in CML cells. We found that SPOA remarkably dephosphorylated BCR-ABL Y177, prevented GRB2 recruitment, and uncoupled RAS-MAPK and PI3K-AKT signals. Meanwhile, SPOA degraded BCR-ABL oncoprotein in ubiquitin-independent manner and depressed the signal transduction of STAT5 and CRKL by BCR-ABL. Furthermore, SPOA inhibited proliferation and induced apoptosis in CML cells and depressed the oncogenecity of K562 cells in mice. These results provide evidence that dephosphorylating and degrading oncogenic BCR-ABL offer an alternative CML therapy.
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Affiliation(s)
- Miao Gao
- Department of Clinical Hematology, Key Laboratory of Laboratory Medical Diagnostics Designated by The Ministry of Education, Chongqing Medical University, Chongqing, People's Republic of China
| | - Zheng-Lan Huang
- Department of Clinical Hematology, Key Laboratory of Laboratory Medical Diagnostics Designated by The Ministry of Education, Chongqing Medical University, Chongqing, People's Republic of China
| | - Kun Tao
- Department of Immunology, Molecular Medicine and Cancer Research, Chongqing Medical University, Chongqing, People's Republic of China
| | - Qing Xiao
- Department of Hematology, The First Affiliated Hospital, Chongqing Medical University, Chongqing, People's Republic of China
| | - Xin Wang
- Department of Hematology, The First Affiliated Hospital, Chongqing Medical University, Chongqing, People's Republic of China
| | - Wei-Xi Cao
- Department of Clinical Hematology, Key Laboratory of Laboratory Medical Diagnostics Designated by The Ministry of Education, Chongqing Medical University, Chongqing, People's Republic of China
| | - Min Xu
- Department of Clinical Hematology, Key Laboratory of Laboratory Medical Diagnostics Designated by The Ministry of Education, Chongqing Medical University, Chongqing, People's Republic of China
| | - Jing Hu
- Department of Clinical Hematology, Key Laboratory of Laboratory Medical Diagnostics Designated by The Ministry of Education, Chongqing Medical University, Chongqing, People's Republic of China
| | - Wen-Li Feng
- Department of Clinical Hematology, Key Laboratory of Laboratory Medical Diagnostics Designated by The Ministry of Education, Chongqing Medical University, Chongqing, People's Republic of China
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32
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Dedigama-Arachchige PM, Acharige NPN, Pflum MKH. Identification of PP1-Gadd34 substrates involved in the unfolded protein response using K-BIPS, a method for phosphatase substrate identification. Mol Omics 2018; 14:121-133. [PMID: 29623310 DOI: 10.1039/c7mo00064b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphorylation is a key post-translational modification in cell signaling, which is regulated by the equilibrium activities of kinases and phosphatases. The biological significance of many phosphorylation events remains poorly characterized due to the scarcity of tools to discover phosphatases substrates. In prior work, we established kinase-catalyzed biotinylation where kinases accept the γ-modified ATP analog, ATP-biotin, to label phosphoproteins. Here, we developed a novel method to study substrates of phosphatases using kinase-catalyzed biotinylation termed K-BIPS (Kinase-catalyzed Biotinylation to Identify Phosphatase Substrates). In a proof-of-concept experiment, K-BIPS was initially used to explore the substrates of phosphatases inhibited by okadaic acid. Many known phosphatase substrates were observed, confirming K-BIPS as a valid phosphatase substrate identification tool. Then, as a further application, K-BIPS was used to discover the substrates of the PP1-Gadd34 phosphatase complex in the context of unfolded protein response (UPR). In addition to the known substrate eIF2α, K-BIPS revealed several novel substrates, suggesting a more prominent role for the PP1-Gadd34 complex in UPR than previously appreciated. Overall, the two studies establish K-BIPS as a powerful tool to discover the cellular substrates of phosphatases.
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33
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Benítez-Buelga C, Baquero JM, Vaclova T, Fernández V, Martín P, Inglada-Perez L, Urioste M, Osorio A, Benítez J. Genetic variation in the NEIL2 DNA glycosylase gene is associated with oxidative DNA damage in BRCA2 mutation carriers. Oncotarget 2017; 8:114626-114636. [PMID: 29383107 PMCID: PMC5777719 DOI: 10.18632/oncotarget.22638] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023] Open
Abstract
In this report, we have tried to gain molecular insight into a single nucleotide polymorphism (SNP) in the NEIL2 gene previously identified as "cancer risk modifier" for BRCA2 mutation carriers. To that end, we studied the role of this SNP (rs804271) on NEIL2 transcriptional regulation, oxidative DNA damage and genome instability in two independent set of samples: The first one was a series of eighty-six BRCA1 and BRCA2 mutation carriers and eighty non-carrier controls in which we evaluated the effect of the SNP on NEIL2 gene expression and oxidative DNA damage accumulation. The second was a set of twenty lymphoblastoid cell lines (LCLs), thirteen BRCA1 mutation carriers and seven non-carriers control, that were used to analyze the correlation between NEIL2 mRNA and/or protein levels, the oxidative and the double stranded break (DSB) DNA damage levels. Our results suggest that an excessive production of NEIL2 enzyme, associated with the SNP, may have a deleterious effect modifying cancer risk susceptibility in BRCA2 mutation carriers. We hypothesize that due to the SNP impact on NEIL2 transcriptional upregulation, a cascade of events may converge in the accumulation of oxidative DNA damage and its posterior conversion into DSBs for this specific group of patients.
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Affiliation(s)
| | - Juan Miguel Baquero
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Tereza Vaclova
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Victoria Fernández
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Paloma Martín
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
- Spanish Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Lucia Inglada-Perez
- Endocrine Cancer Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
- Spanish Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Miguel Urioste
- Familial Cancer Unit, Spanish National Cancer Research Center (CNIO), Madrid, Spain
- Spanish Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Ana Osorio
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
- Spanish Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
- Spanish Network on Rare Diseases (CIBERER), Madrid, Spain
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34
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Moon J, Ha J, Park SH. Identification of PTPN1 as a novel negative regulator of the JNK MAPK pathway using a synthetic screening for pathway-specific phosphatases. Sci Rep 2017; 7:12974. [PMID: 29021559 PMCID: PMC5636874 DOI: 10.1038/s41598-017-13494-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022] Open
Abstract
The mitogen activated protein kinase (MAPK) signaling cascades transmit extracellular stimulations to generate various cellular responses via the sequential and reversible phosphorylation of kinases. Since the strength and duration of kinase phosphorylation within the pathway determine the cellular response, both kinases and phosphatases play an essential role in the precise control of MAPK pathway activation and attenuation. Thus, the identification of pathway-specific phosphatases is critical for understanding the functional mechanisms by which the MAPK pathway is regulated. To identify phosphatases specific to the c-Jun N-terminal kinase (JNK) MAPK pathway, a synthetic screening approach was utilized in which phosphatases were individually tethered to the JNK pathway specific-JIP1 scaffold protein. Of 77 mammalian phosphatases tested, PTPN1 led to the inhibition of JNK pathway activation. Further analyses revealed that of three pathway member kinases, PTPN1 directly dephosphorylates JNK, the terminal kinase of the pathway, and negatively regulates the JNK MAPK pathway. Specifically, PTPN1 appears to regulate the overall signaling magnitude, rather than the adaptation timing, suggesting that PTPN1 might be involved in the control and maintenance of signaling noise. Finally, the negative regulation of the JNK MAPK pathway by PTPN1 was found to reduce the tumor necrosis factor α (TNFα)-dependent cell death response.
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Affiliation(s)
- Jiyoung Moon
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Jain Ha
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Sang-Hyun Park
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Korea.
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35
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Abram CL, Lowell CA. Shp1 function in myeloid cells. J Leukoc Biol 2017; 102:657-675. [PMID: 28606940 DOI: 10.1189/jlb.2mr0317-105r] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/01/2017] [Accepted: 05/02/2017] [Indexed: 01/28/2023] Open
Abstract
The motheaten mouse was first described in 1975 as a model of systemic inflammation and autoimmunity, as a result of immune system dysregulation. The phenotype was later ascribed to mutations in the cytoplasmic tyrosine phosphatase Shp1. This phosphatase is expressed widely throughout the hematopoietic system and has been shown to impact a multitude of cell signaling pathways. The determination of which cell types contribute to the different aspects of the phenotype caused by global Shp1 loss or mutation and which pathways within these cell types are regulated by Shp1 is important to further our understanding of immune system regulation. In this review, we focus on the role of Shp1 in myeloid cells and how its dysregulation affects immune function, which can impact human disease.
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Affiliation(s)
- Clare L Abram
- Department of Laboratory Medicine and Immunology Program, University of California, San Francisco, California, USA
| | - Clifford A Lowell
- Department of Laboratory Medicine and Immunology Program, University of California, San Francisco, California, USA
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36
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Pannone L, Bocchinfuso G, Flex E, Rossi C, Baldassarre G, Lissewski C, Pantaleoni F, Consoli F, Lepri F, Magliozzi M, Anselmi M, Delle Vigne S, Sorge G, Karaer K, Cuturilo G, Sartorio A, Tinschert S, Accadia M, Digilio MC, Zampino G, De Luca A, Cavé H, Zenker M, Gelb BD, Dallapiccola B, Stella L, Ferrero GB, Martinelli S, Tartaglia M. Structural, Functional, and Clinical Characterization of a Novel PTPN11 Mutation Cluster Underlying Noonan Syndrome. Hum Mutat 2017; 38:451-459. [PMID: 28074573 DOI: 10.1002/humu.23175] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/06/2017] [Indexed: 01/12/2023]
Abstract
Germline mutations in PTPN11, the gene encoding the Src-homology 2 (SH2) domain-containing protein tyrosine phosphatase (SHP2), cause Noonan syndrome (NS), a relatively common, clinically variable, multisystem disorder. Here, we report on the identification of five different PTPN11 missense changes affecting residues Leu261 , Leu262 , and Arg265 in 16 unrelated individuals with clinical diagnosis of NS or with features suggestive for this disorder, specifying a novel disease-causing mutation cluster. Expression of the mutant proteins in HEK293T cells documented their activating role on MAPK signaling. Structural data predicted a gain-of-function role of substitutions at residues Leu262 and Arg265 exerted by disruption of the N-SH2/PTP autoinhibitory interaction. Molecular dynamics simulations suggested a more complex behavior for changes affecting Leu261 , with possible impact on SHP2's catalytic activity/selectivity and proper interaction of the PTP domain with the regulatory SH2 domains. Consistent with that, biochemical data indicated that substitutions at codons 262 and 265 increased the catalytic activity of the phosphatase, while those affecting codon 261 were only moderately activating but impacted substrate specificity. Remarkably, these mutations underlie a relatively mild form of NS characterized by low prevalence of cardiac defects, short stature, and cognitive and behavioral issues, as well as less evident typical facial features.
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Affiliation(s)
- Luca Pannone
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy.,Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy.,Dipartimento di Medicina Sperimentale, Sapienza Università di Roma, Rome, Italy
| | - Gianfranco Bocchinfuso
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Elisabetta Flex
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy
| | - Cesare Rossi
- Genetica Medica, Policlinico S. Orsola-Malpighi, Bologna, Italy
| | | | - Christina Lissewski
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
| | - Francesca Pantaleoni
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Federica Consoli
- Ospedale Casa Sollievo della Sofferenza, IRCCS, San Giovanni Rotondo, Italy
| | - Francesca Lepri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Monia Magliozzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy.,Ospedale Casa Sollievo della Sofferenza, IRCCS, San Giovanni Rotondo, Italy
| | - Massimiliano Anselmi
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Silvia Delle Vigne
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy
| | - Giovanni Sorge
- Unità Operativa Complessa di Clinica Pediatrica, Dipartimento di Medicina Clinica e Sperimentale, Università di Catania, Catania, Italy
| | - Kadri Karaer
- Dr. Ersin Arslan Research and Training Hospital, Department of Medical Genetics, Gaziantep, Turkey
| | - Goran Cuturilo
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,University Children's Hospital, Belgrade, Serbia
| | - Alessandro Sartorio
- Istituto Auxologico Italiano, Experimental Laboratory for Auxo-Endocrinological Research, Milan and Verbania, Italy.,Istituto Auxologico Italiano, Division of Auxology, Verbania, Italy
| | - Sigrid Tinschert
- Institute of Clinical Genetics, Technical University of Dresden, Dresden, Germany
| | - Maria Accadia
- Ospedale Casa Sollievo della Sofferenza, IRCCS, San Giovanni Rotondo, Italy
| | - Maria C Digilio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Giuseppe Zampino
- Istituto di Clinica Pediatrica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alessandro De Luca
- Ospedale Casa Sollievo della Sofferenza, IRCCS, San Giovanni Rotondo, Italy
| | - Hélène Cavé
- Département de Génétique, Hôpital Robert Debré, Paris, France.,INSERM UMR_S1131, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris-Sorbonne-Cité, Paris, France
| | - Martin Zenker
- Institute of Human Genetics, University Hospital of Magdeburg, Otto-von-Guericke-University, Magdeburg, Germany
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Rome, Italy
| | - Giovanni B Ferrero
- Department of Pediatric and Public Health Sciences, University of Torino, Torino, Italy
| | - Simone Martinelli
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
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37
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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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38
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Kano Y, Cook JD, Lee JE, Ohh M. New structural and functional insight into the regulation of Ras. Semin Cell Dev Biol 2016; 58:70-8. [DOI: 10.1016/j.semcdb.2016.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 10/21/2022]
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39
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Rosu C, Cueto R, Russo PS. Poly(colloid)s: "Polymerization" of Poly(l-tyrosine)-silica Composite Particles through the Photoinduced Cross-Linking of Unmodified Proteins Method. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8392-8402. [PMID: 27504929 DOI: 10.1021/acs.langmuir.6b01815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photoinduced cross-linking of unmodified proteins, PICUP, was extended to core-shell silica-polypeptide composite particles to produce poly(colloid)s. Silica particles coated with poly(l-tyrosine), PTYR-SiO2, served as the monomer units. The PICUP reaction accomplished the formation of dityrosil linkages between the tyrosine units by illumination of photo-oxidizing ruthenium(II) bipyridyl catalyst under physiological conditions. The PICUP method was compared with an enzymatic route intermediated by horseradish peroxidase as catalyst. The PTYR-SiO2 particles feature high PTYR content in the shell, which facilitated the formation of heavily cross-linked but unstructured aggregates. After magnetic alignment of superparamagnetic PTYR-SiO2-cobalt composite particles, only the PICUP approach enabled the preparation of isolated chain-like poly(colloid)s. The cross-linking products were confirmed by FTIR. The native secondary structure of poly(l-tyrosine) is preserved in these poly(colloid)s. Because the PICUP reaction does not require the modification of the polypeptide structure, the cross-linked PTYR will retain its characteristic functions as a poly(amino acid). The PICUP method opens the door to a variety of PTYR-based poly(colloid) architectures.
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Affiliation(s)
- Cornelia Rosu
- School of Materials Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
- Department of Chemistry and Macromolecular Studies Group, Louisiana State University , Baton Rouge, Louisiana 70803, United States
- Georgia Tech Polymer Network, GTPN, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Rafael Cueto
- Department of Chemistry and Macromolecular Studies Group, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Paul S Russo
- School of Materials Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
- Department of Chemistry and Macromolecular Studies Group, Louisiana State University , Baton Rouge, Louisiana 70803, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
- Georgia Tech Polymer Network, GTPN, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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40
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Coulombe G, Langlois A, De Palma G, Langlois MJ, McCarville JL, Gagné-Sanfaçon J, Perreault N, Feng GS, Bercik P, Boudreau F, Verdu EF, Rivard N. SHP-2 Phosphatase Prevents Colonic Inflammation by Controlling Secretory Cell Differentiation and Maintaining Host-Microbiota Homeostasis. J Cell Physiol 2016; 231:2529-40. [PMID: 27100271 PMCID: PMC5330278 DOI: 10.1002/jcp.25407] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 04/19/2016] [Indexed: 12/18/2022]
Abstract
Polymorphisms in the PTPN11 gene encoding for the tyrosine phosphatase SHP‐2 were described in patients with ulcerative colitis. We have recently demonstrated that mice with an intestinal epithelial cell‐specific deletion of SHP‐2 (SHP‐2IEC‐KO) develop severe colitis 1 month after birth. However, the mechanisms by which SHP‐2 deletion induces colonic inflammation remain to be elucidated. We generated SHP‐2IEC‐KO mice lacking Myd88 exclusively in the intestinal epithelium. The colonic phenotype was histologically analyzed and cell differentiation was determined by electron microscopy and lysozyme or Alcian blue staining. Microbiota composition was analyzed by 16S sequencing. Results show that innate defense genes including those specific to Paneth cells were strongly up‐regulated in SHP‐2‐deficient colons. Expansion of intermediate cells (common progenitors of the Goblet and Paneth cell lineages) was found in the colon of SHP‐2IEC‐KO mice whereas Goblet cell number was clearly diminished. These alterations in Goblet/intermediate cell ratio were noticed 2 weeks after birth, before the onset of inflammation and were associated with significant alterations in microbiota composition. Indeed, an increase in Enterobacteriaceae and a decrease in Firmicutes were observed in the colon of these mice, indicating that dysbiosis also occurred prior to inflammation. Importantly, loss of epithelial Myd88 expression inhibited colitis development in SHP‐2IEC‐KO mice, rescued Goblet/intermediate cell ratio, and prevented NFκB hyperactivation and inflammation. These data indicate that SHP‐2 is functionally important for the maintenance of appropriate barrier function and host‐microbiota homeostasis in the large intestine. J. Cell. Physiol. 231: 2529–2540, 2016. © 2016 The Authors. Journal of Cellular Physiology published by Wiley Periodicals, Inc.
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Affiliation(s)
- Geneviève Coulombe
- Faculty of Medicine and Health Sciences, Department of Anatomy and Cell Biology, Cancer Research Pavilion, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Ariane Langlois
- Faculty of Medicine and Health Sciences, Department of Anatomy and Cell Biology, Cancer Research Pavilion, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Giada De Palma
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Marie-Josée Langlois
- Faculty of Medicine and Health Sciences, Department of Anatomy and Cell Biology, Cancer Research Pavilion, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Justin L McCarville
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Jessica Gagné-Sanfaçon
- Faculty of Medicine and Health Sciences, Department of Anatomy and Cell Biology, Cancer Research Pavilion, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Nathalie Perreault
- Faculty of Medicine and Health Sciences, Department of Anatomy and Cell Biology, Cancer Research Pavilion, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Gen-Sheng Feng
- Department of Pathology and Division of Biological Sciences, University of California San Diego, La Jolla, California
| | - Premysl Bercik
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - François Boudreau
- Faculty of Medicine and Health Sciences, Department of Anatomy and Cell Biology, Cancer Research Pavilion, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Elena F Verdu
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Nathalie Rivard
- Faculty of Medicine and Health Sciences, Department of Anatomy and Cell Biology, Cancer Research Pavilion, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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41
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Li X, Köhn M. Prediction and verification of novel peptide targets of protein tyrosine phosphatase 1B. Bioorg Med Chem 2016; 24:3255-8. [PMID: 27025565 PMCID: PMC4957924 DOI: 10.1016/j.bmc.2016.03.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/14/2016] [Accepted: 03/16/2016] [Indexed: 11/26/2022]
Abstract
Phosphotyrosine peptides are useful starting points for inhibitor design and for the search for protein tyrosine phosphatase (PTP) phosphoprotein substrates. To identify novel phosphopeptide substrates of PTP1B, we developed a computational prediction protocol based on a virtual library of protein sequences with known phosphotyrosine sites. To these we applied sequence-based methods, biologically meaningful filters and molecular docking. Five peptides were selected for biochemical testing of their potential as PTP1B substrates. All five peptides were equally good substrates for PTP1B compared to a known peptide substrate whereas appropriate control peptides were not recognized, showing that our protocol can be used to identify novel peptide substrates of PTP1B.
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Affiliation(s)
- Xun Li
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany; European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Maja Köhn
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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42
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Beck JR, Lawrence A, Tung AS, Harris EN, Stains CI. Interrogating Endogenous Protein Phosphatase Activity with Rationally Designed Chemosensors. ACS Chem Biol 2016; 11:284-90. [PMID: 26580981 DOI: 10.1021/acschembio.5b00506] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We introduce a versatile approach for repurposing protein kinase chemosensors, containing the phosphorylation-sensitive sulfonamido-oxine fluorophore termed Sox, for the specific determination of endogenous protein phosphatase activity from whole cell lysates and tissue homogenates. As a demonstration of this approach, we design and evaluate a direct chemosensor for protein tyrosine phosphatase-1B (PTP1B), an established signaling node in human disease. The optimal sensor design is capable of detecting as little as 6 pM (12 pg) full-length recombinant PTP1B and is remarkably selective for PTP1B among a panel of highly homologous tyrosine phosphatases. Coupling this robust activity probe with the specificity of antibodies allowed for the temporal analysis of endogenous PTP1B activity dynamics in lysates generated from HepG2 cells after stimulation with insulin. Lastly, we leveraged this assay format to profile PTP1B activity perturbations in a rat model of nonalcoholic fatty liver disease (NAFLD), providing direct evidence for elevated PTP1B catalytic activity in this disease state. Given the modular nature of this assay, we anticipate that this approach will have broad utility in monitoring phosphatase activity dynamics in human disease states.
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Affiliation(s)
- Jon R. Beck
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Antoneal Lawrence
- Department
of Chemistry, Lincoln University, Lincoln University, Pennsylvania 19352, United States
| | - Amar S. Tung
- Department
of Chemistry, Lincoln University, Lincoln University, Pennsylvania 19352, United States
| | - Edward N. Harris
- Department
of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Cliff I. Stains
- Department
of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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43
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Bunda S, Burrell K, Heir P, Zeng L, Alamsahebpour A, Kano Y, Raught B, Zhang ZY, Zadeh G, Ohh M. Inhibition of SHP2-mediated dephosphorylation of Ras suppresses oncogenesis. Nat Commun 2015; 6:8859. [PMID: 26617336 PMCID: PMC4674766 DOI: 10.1038/ncomms9859] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/12/2015] [Indexed: 11/22/2022] Open
Abstract
Ras is phosphorylated on a conserved tyrosine at position 32 within the switch I region via Src kinase. This phosphorylation inhibits the binding of effector Raf while promoting the engagement of GTPase-activating protein (GAP) and GTP hydrolysis. Here we identify SHP2 as the ubiquitously expressed tyrosine phosphatase that preferentially binds to and dephosphorylates Ras to increase its association with Raf and activate downstream proliferative Ras/ERK/MAPK signalling. In comparison to normal astrocytes, SHP2 activity is elevated in astrocytes isolated from glioblastoma multiforme (GBM)-prone H-Ras(12V) knock-in mice as well as in glioma cell lines and patient-derived GBM specimens exhibiting hyperactive Ras. Pharmacologic inhibition of SHP2 activity attenuates cell proliferation, soft-agar colony formation and orthotopic GBM growth in NOD/SCID mice and decelerates the progression of low-grade astrocytoma to GBM in a spontaneous transgenic glioma mouse model. These results identify SHP2 as a direct activator of Ras and a potential therapeutic target for cancers driven by a previously ‘undruggable' oncogenic or hyperactive Ras. Aberrant Ras signalling resulting in downstream Mek/Erk pathway activation is found in many cancers. Here, the authors show that the phosphatase SHP2 dephosphorylates Ras resulting in increased Ras activity, and that increased SHP2 activity is found in glioblastomas.
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Affiliation(s)
- Severa Bunda
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, M5S1A8 Ontario, Canada
| | - Kelly Burrell
- Brain Tumour Research Centre, Hospital for Sick Children, University Health Network, Toronto Medical Discovery Tower, 101 College Street, East Tower, Toronto, M5G1L7 Ontario, Canada
| | - Pardeep Heir
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, M5S1A8 Ontario, Canada
| | - Lifan Zeng
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
| | - Amir Alamsahebpour
- Brain Tumour Research Centre, Hospital for Sick Children, University Health Network, Toronto Medical Discovery Tower, 101 College Street, East Tower, Toronto, M5G1L7 Ontario, Canada
| | - Yoshihito Kano
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, M5S1A8 Ontario, Canada.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, M5S1A8 Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, Toronto Medical Discovery Tower, 9-701A, 101 College Street, Toronto, M5G1L7 Ontario, Canada
| | - Zhong-Yin Zhang
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, 635 Barnhill Drive, Indianapolis, Indiana 46202, USA
| | - Gelareh Zadeh
- Brain Tumour Research Centre, Hospital for Sick Children, University Health Network, Toronto Medical Discovery Tower, 101 College Street, East Tower, Toronto, M5G1L7 Ontario, Canada
| | - Michael Ohh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, M5S1A8 Ontario, Canada.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, M5S1A8 Ontario, Canada
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44
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Rowland MA, Harrison B, Deeds EJ. Phosphatase specificity and pathway insulation in signaling networks. Biophys J 2015; 108:986-996. [PMID: 25692603 DOI: 10.1016/j.bpj.2014.12.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/13/2014] [Accepted: 12/05/2014] [Indexed: 12/31/2022] Open
Abstract
Phosphatases play an important role in cellular signaling networks by regulating the phosphorylation state of proteins. Phosphatases are classically considered to be promiscuous, acting on tens to hundreds of different substrates. We recently demonstrated that a shared phosphatase can couple the responses of two proteins to incoming signals, even if those two substrates are from otherwise isolated areas of the network. This finding raises a potential paradox: if phosphatases are indeed highly promiscuous, how do cells insulate themselves against unwanted crosstalk? Here, we use mathematical models to explore three possible insulation mechanisms. One approach involves evolving phosphatase KM values that are large enough to prevent saturation by the phosphatase's substrates. Although this is an effective method for generating isolation, the phosphatase becomes a highly inefficient enzyme, which prevents the system from achieving switch-like responses and can result in slow response kinetics. We also explore the idea that substrate degradation can serve as an effective phosphatase. Assuming that degradation is unsaturatable, this mechanism could insulate substrates from crosstalk, but it would also preclude ultrasensitive responses and would require very high substrate turnover to achieve rapid dephosphorylation kinetics. Finally, we show that adaptor subunits, such as those found on phosphatases like PP2A, can provide effective insulation against phosphatase crosstalk, but only if their binding to substrates is uncoupled from their binding to the catalytic core. Analysis of the interaction network of PP2A's adaptor domains reveals that although its adaptors may isolate subsets of targets from one another, there is still a strong potential for phosphatase crosstalk within those subsets. Understanding how phosphatase crosstalk and the insulation mechanisms described here impact the function and evolution of signaling networks represents a major challenge for experimental and computational systems biology.
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Affiliation(s)
- Michael A Rowland
- Center for Computational Biology, University of Kansas, Lawrence, Kansas
| | - Brian Harrison
- Center for Computational Biology, University of Kansas, Lawrence, Kansas
| | - Eric J Deeds
- Center for Computational Biology, University of Kansas, Lawrence, Kansas; Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas; Santa Fe Institute, Santa Fe, New Mexico.
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45
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Dascenco D, Erfurth ML, Izadifar A, Song M, Sachse S, Bortnick R, Urwyler O, Petrovic M, Ayaz D, He H, Kise Y, Thomas F, Kidd T, Schmucker D. Slit and Receptor Tyrosine Phosphatase 69D Confer Spatial Specificity to Axon Branching via Dscam1. Cell 2015; 162:1140-54. [PMID: 26317474 PMCID: PMC4699798 DOI: 10.1016/j.cell.2015.08.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 06/30/2015] [Accepted: 07/10/2015] [Indexed: 11/26/2022]
Abstract
Axonal branching contributes substantially to neuronal circuit complexity. Studies in Drosophila have shown that loss of Dscam1 receptor diversity can fully block axon branching in mechanosensory neurons. Here we report that cell-autonomous loss of the receptor tyrosine phosphatase 69D (RPTP69D) and loss of midline-localized Slit inhibit formation of specific axon collaterals through modulation of Dscam1 activity. Genetic and biochemical data support a model in which direct binding of Slit to Dscam1 enhances the interaction of Dscam1 with RPTP69D, stimulating Dscam1 dephosphorylation. Single-growth-cone imaging reveals that Slit/RPTP69D are not required for general branch initiation but instead promote the extension of specific axon collaterals. Hence, although regulation of intrinsic Dscam1-Dscam1 isoform interactions is essential for formation of all mechanosensory-axon branches, the local ligand-induced alterations of Dscam1 phosphorylation in distinct growth-cone compartments enable the spatial specificity of axon collateral formation.
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Affiliation(s)
- Dan Dascenco
- Neuronal Wiring Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium; Department of Oncology, School of Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Maria-Luise Erfurth
- Neuronal Wiring Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium; Department of Oncology, School of Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; Institute of Biochemistry, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098 Kiel, Germany
| | - Azadeh Izadifar
- Neuronal Wiring Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium; Department of Oncology, School of Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Minmin Song
- Biology/MS 314, University of Nevada, Reno, NV 89557, USA
| | - Sonja Sachse
- Neuronal Wiring Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium; Department of Oncology, School of Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; Department of Biology, Chemistry & Pharmacy, Free University Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Rachel Bortnick
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Olivier Urwyler
- Neuronal Wiring Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium; Department of Oncology, School of Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Milan Petrovic
- Neuronal Wiring Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium; Department of Oncology, School of Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Derya Ayaz
- Neuronal Wiring Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium
| | - Haihuai He
- Neuronal Wiring Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium
| | - Yoshiaki Kise
- Neuronal Wiring Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium; Department of Oncology, School of Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Franziska Thomas
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Thomas Kidd
- Biology/MS 314, University of Nevada, Reno, NV 89557, USA
| | - Dietmar Schmucker
- Neuronal Wiring Laboratory, VIB, Herestraat 49, 3000 Leuven, Belgium; Department of Oncology, School of Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium.
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Fan G, Aleem S, Yang M, Miller WT, Tonks NK. Protein-tyrosine Phosphatase and Kinase Specificity in Regulation of SRC and Breast Tumor Kinase. J Biol Chem 2015; 290:15934-47. [PMID: 25897081 DOI: 10.1074/jbc.m115.651703] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 11/06/2022] Open
Abstract
Despite significant evidence to the contrary, the view that phosphatases are "nonspecific" still pervades the field. Systems biology approaches to defining how signal transduction pathways are integrated at the level of whole organisms also often downplay the contribution of phosphatases, defining them as "erasers" that serve merely to restore the system to its basal state. Here, we present a study that counteracts the idea of "nonspecific phosphatases." We have characterized two structurally similar and functionally related kinases, BRK and SRC, which are regulated by combinations of activating autophosphorylation and inhibitory C-terminal sites of tyrosine phosphorylation. We demonstrated specificity at the level of the kinases in that SRMS phosphorylated the C terminus of BRK, but not SRC; in contrast, CSK is the kinase responsible for C-terminal phosphorylation of SRC, but not BRK. For the phosphatases, we observed that RNAi-mediated suppression of PTP1B resulted in opposing effects on the activity of BRK and SRC and have defined the mechanisms underlying this specificity. PTP1B inhibited BRK by directly dephosphorylating the Tyr-342 autophosphorylation site. In contrast, PTP1B potentiated SRC activity, but not by dephosphorylating SRC itself directly; instead, PTP1B regulated the interaction between CBP/PAG and CSK. SRC associated with, and phosphorylated, the transmembrane protein CBP/PAG at Tyr-317, resulting in CSK recruitment. We identified PAG as a substrate of PTP1B, and dephosphorylation abolished recruitment of the inhibitory kinase CSK. Overall, these findings illustrate how the combinatorial effects of PTKs and PTPs may be integrated to regulate signaling, with both classes of enzymes displaying exquisite specificity.
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Affiliation(s)
- Gaofeng Fan
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724-2208 and
| | - Saadat Aleem
- the Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794-8661
| | - Ming Yang
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724-2208 and
| | - W Todd Miller
- the Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794-8661
| | - Nicholas K Tonks
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724-2208 and
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47
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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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48
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St-Germain JR, Taylor P, Zhang W, Li Z, Ketela T, Moffat J, Neel BG, Trudel S, Moran MF. Differential regulation of FGFR3 by PTPN1 and PTPN2. Proteomics 2014; 15:419-33. [PMID: 25311528 DOI: 10.1002/pmic.201400259] [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: 06/06/2014] [Revised: 09/04/2014] [Accepted: 10/08/2014] [Indexed: 11/06/2022]
Abstract
Aberrant expression and activation of FGFR3 is associated with disease states including bone dysplasia and malignancies of bladder, cervix, and bone marrow. MS analysis of protein-phosphotyrosine in multiple myeloma cells revealed a prevalent phosphorylated motif, D/EYYR/K, derived from the kinase domain activation loops of tyrosine kinases including FGFR3 corresponding to a recognition sequence of protein-tyrosine phosphatase PTPN1. Knockdown of PTPN1 or the related enzyme PTPN2 by RNAi resulted in ligand-independent activation of FGFR3. Modulation of FGFR3 activation loop phosphorylation by both PTPN1 and PTPN2 was a function of receptor trafficking and phosphotyrosine phosphatase (PTP) compartmentalization. The FGFR3 activation loop motif DYYKK(650) is altered to DYYKE(650) in the oncogenic variant FGFR3(K650E) , and consequently it is constitutively fully activated and unaffected by activation loop phosphorylation. FGFR3(K650E) was nevertheless remarkably sensitive to negative regulation by PTPN1 and PTPN2. This suggests that in addition to modulating FGFR3 phosphorylation, PTPN1 and PTPN2 constrain the kinase domain by fostering an inactive-state. Loss of this constraint in response to ligand or impaired PTPN1/N2 may initiate FGFR3 activation. These results suggest a model wherein PTP expression levels may define conditions that select for ectopic FGFR3 expression and activation during tumorigenesis.
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Affiliation(s)
- Jonathan R St-Germain
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Canada
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49
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Chylek LA, Akimov V, Dengjel J, Rigbolt KTG, Hu B, Hlavacek WS, Blagoev B. Phosphorylation site dynamics of early T-cell receptor signaling. PLoS One 2014; 9:e104240. [PMID: 25147952 PMCID: PMC4141737 DOI: 10.1371/journal.pone.0104240] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/07/2014] [Indexed: 11/18/2022] Open
Abstract
In adaptive immune responses, T-cell receptor (TCR) signaling impacts multiple cellular processes and results in T-cell differentiation, proliferation, and cytokine production. Although individual protein-protein interactions and phosphorylation events have been studied extensively, we lack a systems-level understanding of how these components cooperate to control signaling dynamics, especially during the crucial first seconds of stimulation. Here, we used quantitative proteomics to characterize reshaping of the T-cell phosphoproteome in response to TCR/CD28 co-stimulation, and found that diverse dynamic patterns emerge within seconds. We detected phosphorylation dynamics as early as 5 s and observed widespread regulation of key TCR signaling proteins by 30 s. Development of a computational model pointed to the presence of novel regulatory mechanisms controlling phosphorylation of sites with central roles in TCR signaling. The model was used to generate predictions suggesting unexpected roles for the phosphatase PTPN6 (SHP-1) and shortcut recruitment of the actin regulator WAS. Predictions were validated experimentally. This integration of proteomics and modeling illustrates a novel, generalizable framework for solidifying quantitative understanding of a signaling network and for elucidating missing links.
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Affiliation(s)
- Lily A. Chylek
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America
| | - Vyacheslav Akimov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Jörn Dengjel
- Department of Dermatology, Medical Center; Freiburg Institute for Advanced Studies (FRIAS); BIOSS Centre for Biological Signalling Studies; ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany
| | - Kristoffer T. G. Rigbolt
- Department of Dermatology, Medical Center; Freiburg Institute for Advanced Studies (FRIAS); BIOSS Centre for Biological Signalling Studies; ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany
| | - Bin Hu
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - William S. Hlavacek
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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50
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Lian W, Jiang B, Qian Z, Pei D. Cell-permeable bicyclic peptide inhibitors against intracellular proteins. J Am Chem Soc 2014; 136:9830-3. [PMID: 24972263 PMCID: PMC4227718 DOI: 10.1021/ja503710n] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Indexed: 01/21/2023]
Abstract
Cyclic peptides have great potential as therapeutic agents and research tools but are generally impermeable to the cell membrane. Fusion of cyclic peptides with a cyclic cell-penetrating peptide produces bicyclic peptides that are cell-permeable and retain the ability to recognize specific intracellular targets. Application of this strategy to protein tyrosine phosphatase 1B and a peptidyl-prolyl cis-trans isomerase (Pin1) isomerase resulted in potent, selective, proteolytically stable, and biologically active inhibitors against the enzymes.
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Affiliation(s)
- Wenlong Lian
- Department
of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Bisheng Jiang
- Department
of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Ziqing Qian
- Department
of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department
of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
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