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Basant A, Way M. The relative binding position of Nck and Grb2 adaptors impacts actin-based motility of Vaccinia virus. eLife 2022; 11:74655. [PMID: 35796545 PMCID: PMC9333988 DOI: 10.7554/elife.74655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Phosphotyrosine (pTyr) motifs in unstructured polypeptides orchestrate important cellular processes by engaging SH2-containing adaptors to assemble complex signalling networks. The concept of phase separation has recently changed our appreciation of multivalent networks, however, the role of pTyr motif positioning in their function remains to be explored. We have now investigated this parameter in the operation of the signalling cascade driving actin-based motility and spread of Vaccinia virus. This network involves two pTyr motifs in the viral protein A36 that recruit the adaptors Nck and Grb2 upstream of N-WASP and Arp2/3 complex-mediated actin polymerisation. Manipulating the position of pTyr motifs in A36 and the unrelated p14 from Orthoreovirus, we find that only specific spatial arrangements of Nck and Grb2 binding sites result in robust N-WASP recruitment, Arp2/3 complex driven actin polymerisation and viral spread. This suggests that the relative position of pTyr adaptor binding sites is optimised for signal output. This finding may explain why the relative positions of pTyr motifs are frequently conserved in proteins from widely different species. It also has important implications for regulation of physiological networks, including those undergoing phase transitions.
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Affiliation(s)
- Angika Basant
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Way
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
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2
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Affinity of disordered protein complexes is modulated by entropy-energy reinforcement. Proc Natl Acad Sci U S A 2022; 119:e2120456119. [PMID: 35727975 PMCID: PMC9245678 DOI: 10.1073/pnas.2120456119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Intrinsically disordered proteins (IDPs), which are very common and essential to many biological activities, sometimes function via interaction with another IDP and form a fuzzy complex, which can be highly stable. It is unclear what the biophysical forces are that govern their thermodynamics and specificity, which are essential for de novo fuzzy complex design. Here, we explored the fuzzy complex formed between ProTα and H1, which are oppositely charged IDPs, by swapping the charges between them, generating variants that have either greater polyampholytic or polyelectrolytic nature as well as different charge patterns. Charge swapping and shuffling dramatically change the affinity of the fuzzy complex, which is contributed to by both enthalpy and entropy, where the latter is dominated by counterion release. The association between two intrinsically disordered proteins (IDPs) may produce a fuzzy complex characterized by a high binding affinity, similar to that found in the ultrastable complexes formed between two well-structured proteins. Here, using coarse-grained simulations, we quantified the biophysical forces driving the formation of such fuzzy complexes. We found that the high-affinity complex formed between the highly and oppositely charged H1 and ProTα proteins is sensitive to electrostatic interactions. We investigated 52 variants of the complex by swapping charges between the two oppositely charged proteins to produce sequences whose negatively or positively charged residue content was more homogeneous or heterogenous (i.e., polyelectrolytic or polyampholytic, having higher or lower absolute net charges, respectively) than the wild type. We also changed the distributions of oppositely charged residues within each participating sequence to produce variants in which the charges were segregated or well mixed. Both types of changes significantly affect binding affinity in fuzzy complexes, which is governed by both enthalpy and entropy. The formation of H1–ProTa is supported by an increase in configurational entropy and by entropy due to counterion release. The latter can be twice as large as the former, illustrating the dominance of counterion entropy in modulating the binding thermodynamics. Complexes formed between proteins with greater absolute net charges are more stable, both enthalpically and entropically, indicating that enthalpy and entropy have a mutually reinforcing effect. The sensitivity of the thermodynamics of the complex to net charge and the charge pattern within each of the binding constituents may provide a means to achieve binding specificity between IDPs.
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3
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Loureiro CA, Pinto FR, Barros P, Matos P, Jordan P. A SYK/SHC1 pathway regulates the amount of CFTR in the plasma membrane. Cell Mol Life Sci 2020; 77:4997-5015. [PMID: 31974654 PMCID: PMC11105000 DOI: 10.1007/s00018-020-03448-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/06/2019] [Accepted: 01/02/2020] [Indexed: 11/24/2022]
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause the recessive genetic disease cystic fibrosis, where the chloride transport across the apical membrane of epithelial cells mediated by the CFTR protein is impaired. CFTR protein trafficking to the plasma membrane (PM) is the result of a complex interplay between the secretory and membrane recycling pathways that control the number of channels present at the membrane. In addition, the ion transport activity of CFTR at the PM is modulated through post-translational protein modifications. Previously we described that spleen tyrosine kinase (SYK) phosphorylates a specific tyrosine residue in the nucleotide-binding domain 1 domain and this modification can regulate the PM abundance of CFTR. Here we identified the underlying biochemical mechanism using peptide pull-down assays followed by mass spectrometry. We identified in bronchial epithelial cells that the adaptor protein SHC1 recognizes tyrosine-phosphorylated CFTR through its phosphotyrosine-binding domain and that the formation of a complex between SHC1 and CFTR is induced at the PM in the presence of activated SYK. The depletion of endogenous SHC1 expression was sufficient to promote an increase in CFTR at the PM of these cells. The results identify a SYK/SHC1 pathway that regulates the PM levels of CFTR channels, contributing to a better understanding of how CFTR-mediated chloride secretion is regulated.
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Affiliation(s)
- Cláudia Almeida Loureiro
- Department of Human Genetics, National Health Institute 'Dr. Ricardo Jorge', Avenida Padre Cruz, 1649-016, Lisbon, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Francisco R Pinto
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
- Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Patrícia Barros
- Department of Human Genetics, National Health Institute 'Dr. Ricardo Jorge', Avenida Padre Cruz, 1649-016, Lisbon, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Paulo Matos
- Department of Human Genetics, National Health Institute 'Dr. Ricardo Jorge', Avenida Padre Cruz, 1649-016, Lisbon, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
- Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Peter Jordan
- Department of Human Genetics, National Health Institute 'Dr. Ricardo Jorge', Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal.
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4
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Jin J, Pawson T. Modular evolution of phosphorylation-based signalling systems. Philos Trans R Soc Lond B Biol Sci 2012; 367:2540-55. [PMID: 22889906 DOI: 10.1098/rstb.2012.0106] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Phosphorylation sites are formed by protein kinases ('writers'), frequently exert their effects following recognition by phospho-binding proteins ('readers') and are removed by protein phosphatases ('erasers'). This writer-reader-eraser toolkit allows phosphorylation events to control a broad range of regulatory processes, and has been pivotal in the evolution of new functions required for the development of multi-cellular animals. The proteins that comprise this system of protein kinases, phospho-binding targets and phosphatases are typically modular in organization, in the sense that they are composed of multiple globular domains and smaller peptide motifs with binding or catalytic properties. The linkage of these binding and catalytic modules in new ways through genetic recombination, and the selection of particular domain combinations, has promoted the evolution of novel, biologically useful processes. Conversely, the joining of domains in aberrant combinations can subvert cell signalling and be causative in diseases such as cancer. Major inventions such as phosphotyrosine (pTyr)-mediated signalling that flourished in the first multi-cellular animals and their immediate predecessors resulted from stepwise evolutionary progression. This involved changes in the binding properties of interaction domains such as SH2 and their linkage to new domain types, and alterations in the catalytic specificities of kinases and phosphatases. This review will focus on the modular aspects of signalling networks and the mechanism by which they may have evolved.
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Affiliation(s)
- Jing Jin
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada.
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5
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Hsieh MY, Yang S, Raymond-Stinz MA, Edwards JS, Wilson BS. Spatio-temporal modeling of signaling protein recruitment to EGFR. BMC SYSTEMS BIOLOGY 2010; 4:57. [PMID: 20459599 PMCID: PMC2877007 DOI: 10.1186/1752-0509-4-57] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 05/06/2010] [Indexed: 12/31/2022]
Abstract
Background A stochastic simulator was implemented to study EGFR signal initiation in 3D with single molecule detail. The model considers previously unexplored contributions to receptor-adaptor coupling, such as receptor clustering and diffusive properties of both receptors and binding partners. The agent-based and rule-based approach permits consideration of combinatorial complexity, a problem associated with multiple phosphorylation sites and the potential for simultaneous binding of adaptors. Results The model was used to simulate recruitment of four different signaling molecules (Grb2, PLCγ1, Stat5, Shc) to the phosphorylated EGFR tail, with rules based on coarse-grained prediction of spatial constraints. Parameters were derived in part from quantitative immunoblotting, immunoprecipitation and electron microscopy data. Results demonstrate that receptor clustering increases the efficiency of individual adaptor retainment on activated EGFR, an effect that is overridden if crowding is imposed by receptor overexpression. Simultaneous docking of multiple proteins is highly dependent on receptor-adaptor stability and independent of clustering. Conclusions Overall, we propose that receptor density, reaction kinetics and membrane spatial organization all contribute to signaling efficiency and influence the carcinogenesis process.
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Affiliation(s)
- Ming-yu Hsieh
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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6
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George R, Schuller AC, Harris R, Ladbury JE. A phosphorylation-dependent gating mechanism controls the SH2 domain interactions of the Shc adaptor protein. J Mol Biol 2007; 377:740-7. [PMID: 18279888 DOI: 10.1016/j.jmb.2007.12.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 12/18/2007] [Accepted: 12/19/2007] [Indexed: 11/26/2022]
Abstract
The Shc (Src homology collagen-like) adaptor protein plays a crucial role in linking stimulated receptors to mitogen-activated protein kinase activation through the formation of dynamic signalling complexes. Shc comprises an N-terminal phosphotyrosine binding (PTB) domain, a C-terminal Src homology 2 (SH2) domain and a central proline-rich collagen homology 1 domain. The latter domain contains three tyrosine residues that are known to become phosphorylated. We have expressed and purified the human p52Shc isoform and characterised its binding to different ligands. CD spectra revealed that some parts of the Shc protein are not fully folded, remaining largely unaffected by the binding of ligands. The PTB domain binds peptide and Ins-1,4,5-P(3) (but not Ins-1,3,5-P(3)) independently, suggesting two distinct sites of interaction. In the unphosphorylated Shc, the SH2 domain is non-functional. Ligand binding to the PTB domain does not affect this. However, phosphorylation of the three tyrosine residues promotes binding to the SH2 domain. Thus, Shc has an intrinsic phosphorylation-dependent gating mechanism where the SH2 domain adopts an open conformation only when tyrosine phosphorylation has occurred.
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Affiliation(s)
- Roger George
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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7
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Král V, Mader P, Collard R, Fábry M, Hořejší M, Řezáčová P, Kožíšek M, Závada J, Sedláček J, Rulíšek L, Brynda J. Stabilization of antibody structure upon association to a human carbonic anhydrase IX epitope studied by X-ray crystallography, microcalorimetry, and molecular dynamics simulations. Proteins 2007; 71:1275-87. [DOI: 10.1002/prot.21821] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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Sharma SC, Rupasinghe CN, Parisien RB, Spaller MR. Design, Synthesis, and Evaluation of Linear and Cyclic Peptide Ligands for PDZ10 of the Multi-PDZ Domain Protein MUPP1. Biochemistry 2007; 46:12709-20. [DOI: 10.1021/bi7008135] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sudhir C. Sharma
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Molecular Pharmacology, Brown University, Providence, Rhode Island 02912
| | - Chamila N. Rupasinghe
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Molecular Pharmacology, Brown University, Providence, Rhode Island 02912
| | - Rachel B. Parisien
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Molecular Pharmacology, Brown University, Providence, Rhode Island 02912
| | - Mark R. Spaller
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Molecular Pharmacology, Brown University, Providence, Rhode Island 02912
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9
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Arouri A, Garidel P, Kliche W, Blume A. Hydrophobic interactions are the driving force for the binding of peptide mimotopes and Staphylococcal protein A to recombinant human IgG1. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:647-60. [PMID: 17318528 DOI: 10.1007/s00249-007-0140-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Revised: 01/24/2007] [Accepted: 01/29/2007] [Indexed: 11/29/2022]
Abstract
We studied the interaction of several nona-peptide mimotopes of different sequence and Staphylococcal protein A (SpA) with a recombinant human IgG1 antibody using isothermal titration calorimetry (ITC). The amino acid primary structure of the peptides was varied in order to identify the specific antibody-peptide binding sites. Additionally, the influence of temperature and salt concentration was investigated. An attempt was made to elucidate the structural changes upon complex formation using the determined thermodynamic parameters. The amino acid composition of the mimotopes determined their binding affinity. The binding constant K (a) of the mimotopes was in the range 1 x 10(4) to 1 x 10(6) M(-1). The binding constant of SpA was on the average about three orders of magnitude higher than that of the peptides. The binding constant of the peptides and of SpA decreased with temperature and the binding process was connected with negative changes in enthalpy, entropy, and heat capacity. The binding of the mimotopes to the Fab part of the IgG1 antibody and binding of SpA to the Fc part of the IgG1 antibody were mainly driven by hydrophobic effects and associated with a relatively large change in water-accessible surface area. Determinants for a strong/reduced antibody-peptide binding were identified.
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Affiliation(s)
- Ahmad Arouri
- Institute of Chemistry, Martin-Luther-University Halle-Wittenberg, Muehlpforte 1, 06108, Halle/Saale, Germany
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10
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Gelkop S, Gish GD, Babichev Y, Pawson T, Isakov N. T cell activation-induced CrkII binding to the Zap70 protein tyrosine kinase is mediated by Lck-dependent phosphorylation of Zap70 tyrosine 315. THE JOURNAL OF IMMUNOLOGY 2006; 175:8123-32. [PMID: 16339550 DOI: 10.4049/jimmunol.175.12.8123] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Zap70 protein tyrosine kinase controls TCR-linked signal transduction pathways and is critical for T cell development and responsiveness. Following engagement of TCR, the Zap70 undergoes phosphorylation on multiple tyrosine residues that are implicated in the regulation of its catalytic activity and interaction with signaling effector molecules downstream of the TCR. We have shown previously that the CT10 regulator of kinase II (CrkII) adapter protein interacts with tyrosine-phosphorylated Zap70 in TCR-engaged T cells, and now extend these studies to show that Tyr315 in the Zap70 interdomain B region is the site of interaction with CrkII. A point mutation of Tyr315 (Y315F) eliminated the CrkII-Zap70 interaction capacity. Phosphorylation of Tyr315 and Zap70 association with CrkII were both dependent upon the Lck protein tyrosine kinase. Previous studies demonstrated the Tyr315 is the Vav-Src homology 2 (SH2) binding site, and that replacement of Tyr315 by Phe impaired the function of Zap70 in TCR signaling. However, fluorescence polarization-based binding studies revealed that the CrkII-SH2 and the Vav-SH2 bind a phosphorylated Tyr315-Zap70-derived peptide with affinities of a similar order of magnitude (Kd of 2.5 and 1.02 microM, respectively). The results suggest therefore that the biological functions attributed to the association of Zap70 with Vav following T cell activation may equally reflect the association of Zap70 with CrkII, and further support a regulatory role for CrkII in the TCR-linked signal transduction pathway.
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Affiliation(s)
- Sigal Gelkop
- Department of Microbiology and Immunology, Faculty of Health Sciences, and the Cancer Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
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11
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Ivancic M, Spuches AM, Guth EC, Daugherty MA, Wilcox DE, Lyons BA. Backbone nuclear relaxation characteristics and calorimetric investigation of the human Grb7-SH2/erbB2 peptide complex. Protein Sci 2005; 14:1556-69. [PMID: 15930003 PMCID: PMC2253377 DOI: 10.1110/ps.041102305] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Grb7 is a member of the Grb7 family of proteins, which also includes Grb10 and Grb14. All three proteins have been found to be overexpressed in certain cancers and cancer cell lines. In particular, Grb7 (along with the receptor tyrosine kinase erbB2) is overexpressed in 20%-30% of breast cancers. Grb7 binds to erbB2 and may be involved in cell signaling pathways that promote the formation of metastases and inflammatory responses. In a prior study, we reported the solution structure of the Grb7-SH2/erbB2 peptide complex. In this study, T(1), T(2), and steady-state NOE measurements were performed on the Grb7-SH2 domain, and the backbone relaxation behavior of the domain is discussed with respect to the potential function of an insert region present in all three members of this protein family. Isothermal titration calorimetry (ITC) studies were completed measuring the thermodynamic parameters of the binding of a 10-residue phosphorylated peptide representative of erbB2 to the SH2 domain. These measurements are compared to calorimetric studies performed on other SH2 domain/phosphorylated peptide complexes available in the literature.
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Affiliation(s)
- Monika Ivancic
- Department of Biochemistry, College of Medicine, University of Vermont, Burlington 05405, USA
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12
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Haugh JM, Schneider IC, Lewis JM. On the cross-regulation of protein tyrosine phosphatases and receptor tyrosine kinases in intracellular signaling. J Theor Biol 2004; 230:119-32. [PMID: 15276005 DOI: 10.1016/j.jtbi.2004.04.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2003] [Revised: 03/02/2004] [Accepted: 04/26/2004] [Indexed: 10/26/2022]
Abstract
Intracellular signaling proteins are very often regulated by site-specific phosphorylation. For example, growth factor receptors in eukaryotic cells contain intrinsic tyrosine kinase activity and use inter- and intra-molecular interactions to recruit and orient potential protein substrates for phosphorylation. Equally important in determining the magnitude and kinetics of such a response is protein dephosphorylation, catalysed by phosphatase enzymes. A growing body of evidence indicates that certain protein tyrosine phosphatases (PTPs), like tyrosine kinases, are affected by intermolecular interactions that alter the specific activity or localization of their catalytic domains. Using a detailed kinetic modeling framework, we theoretically explore the regulation of PTPs through their association with receptor tyrosine kinases, as noted for the Src homology 2-domain-containing PTPs, SHP-1 and -2. Receptor-PTP binding, in turn, is expected to influence the phosphorylation pattern of those receptors and proteins they associate with, and we show how PTPs might serve to co- or counter-regulate parallel pathways in a signaling network.
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Affiliation(s)
- Jason M Haugh
- Department of Chemical Engineering, 113 Riddick Lab., Box 7905, North Carolina State University, Raleigh, NC 27695-7905, USA.
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13
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Abstract
The family of proteins accountable for the intracellular movement of lipids is characterized by a 10-stranded beta-barrel that forms an internalized cavity varying in size and binding preferences. The loop connecting beta-strands E and F (the fifth and sixth strands) is the most striking conformational difference between adipocyte lipid binding protein (ALBP; fatty acids) and cellular retinoic acid binding protein type I (CRABP I). A three-residue mutation was made in wild-type (WT)-ALBP [ALBP with a three-residue mutation (EF-ALBP)] to mimic CRABP I. Crystal structures of ligand-free and EF-ALBP with bound oleic acid were solved to resolutions of 1.5 A and 1.7 A, respectively, and compared with previous studies of WT-ALBP. The changes in three residues of one loop of the protein appear to have altered the positioning of the C18 fatty acid, as observed in the electron density of EF-ALBP. The crystallographic studies made it possible to compare the protein conformation and ligand positioning with those found in the WT protein. Although the cavity binding sites in both the retinoid and fatty acid binding proteins are irregular, the ligand atoms appear to favor a relatively planar region of the cavities. Preliminary chemical characterization of the mutant protein indicated changes in some binding properties and overall protein stability.
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Affiliation(s)
- Amy J Reese
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
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14
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Abstract
The family of docker proteins containing phosphotyrosine-binding (PTB) domains appears to represent a family of critically positioned and exquisitely controlled signalling proteins that relay signals from the activated receptors to downstream pathways. These proteins all have a membrane attachment domain, a PTB domain that targets the protein to a subset of receptors and a number of phosphorylatable tyrosines that dock other signalling proteins. Evidence is accruing that suggests that the PTB domain has evolved from a pleckstrin homology (PH) domain to bind to a range of sequences that, while bestowing specificity, allows switching of the docker protein between receptors or signalling systems. The history of the PTB domain and how it influences the participation of docker protein in various signalling pathways are discussed.
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Affiliation(s)
- Graeme R Guy
- Signal Transduction Laboratory, Institute of Molecular and Cell Biology, 30 Medical Drive 117609, Singapore.
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15
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Ong SH, Guy GR, Hadari YR, Laks S, Gotoh N, Schlessinger J, Lax I. FRS2 proteins recruit intracellular signaling pathways by binding to diverse targets on fibroblast growth factor and nerve growth factor receptors. Mol Cell Biol 2000; 20:979-89. [PMID: 10629055 PMCID: PMC85215 DOI: 10.1128/mcb.20.3.979-989.2000] [Citation(s) in RCA: 264] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The docking protein FRS2 was implicated in the transmission of extracellular signals from the fibroblast growth factor (FGF) or nerve growth factor (NGF) receptors to the Ras/mitogen-activated protein kinase signaling cascade. The two members of the FRS2 family, FRS2alpha and FRS2beta, are structurally very similar. Each is composed of an N-terminal myristylation signal, a phosphotyrosine-binding (PTB) domain, and a C-terminal tail containing multiple binding sites for the SH2 domains of the adapter protein Grb2 and the protein tyrosine phosphatase Shp2. Here we show that the PTB domains of both the alpha and beta isoforms of FRS2 bind directly to the FGF or NGF receptors. The PTB domains of the FRS2 proteins bind to a highly conserved sequence in the juxtamembrane region of FGFR1. While FGFR1 interacts with FRS2 constitutively, independent of ligand stimulation and tyrosine phosphorylation, NGF receptor (TrkA) binding to FRS2 is strongly dependent on receptor activation. Complex formation with TrkA is dependent on phosphorylation of Y490, a canonical PTB domain binding site that also functions as a binding site for Shc (NPXpY). Using deletion and alanine scanning mutagenesis as well as peptide competition assays, we demonstrate that the PTB domains of the FRS2 proteins specifically recognize two different primary structures in two different receptors in a phosphorylation-dependent or -independent manner. In addition, NGF-induced tyrosine phosphorylation of FRS2alpha is diminished in cells that overexpress a kinase-inactive mutant of FGFR1. This experiment suggests that FGFR1 may regulate signaling via NGF receptors by sequestering a common key element which both receptors utilize for transmitting their signals. The multiple interactions mediated by FRS2 appear to play an important role in target selection and in defining the specificity of several families of receptor tyrosine kinases.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Amino Acid Sequence
- Animals
- Binding Sites
- Cell Line
- GRB2 Adaptor Protein
- Humans
- Intracellular Signaling Peptides and Proteins
- Membrane Proteins/metabolism
- Molecular Sequence Data
- Mutagenesis
- Phosphoproteins/metabolism
- Protein Tyrosine Phosphatase, Non-Receptor Type 1
- Protein Tyrosine Phosphatase, Non-Receptor Type 11
- Protein Tyrosine Phosphatase, Non-Receptor Type 6
- Protein Tyrosine Phosphatases/chemistry
- Protein Tyrosine Phosphatases/metabolism
- Proteins/chemistry
- Proteins/metabolism
- Receptor Protein-Tyrosine Kinases/chemistry
- Receptor Protein-Tyrosine Kinases/genetics
- Receptor Protein-Tyrosine Kinases/metabolism
- Receptor, Fibroblast Growth Factor, Type 1
- Receptors, Fibroblast Growth Factor/chemistry
- Receptors, Fibroblast Growth Factor/genetics
- Receptors, Fibroblast Growth Factor/metabolism
- Receptors, Nerve Growth Factor/chemistry
- Receptors, Nerve Growth Factor/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
- SH2 Domain-Containing Protein Tyrosine Phosphatases
- Sequence Alignment
- Sequence Deletion
- Sequence Homology, Amino Acid
- Signal Transduction/physiology
- Transfection
- src Homology Domains
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Affiliation(s)
- S H Ong
- Signal Transduction Laboratory, Institute of Molecular and Cell Biology, Singapore 117609, Singapore
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16
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Zozulya S, Lioubin M, Hill RJ, Abram C, Gishizky ML. Mapping signal transduction pathways by phage display. Nat Biotechnol 1999; 17:1193-8. [PMID: 10585717 DOI: 10.1038/70736] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Rapid identification of proteins that interact with a novel gene product is an important element of functional genomics. Here we describe a phage display-based technique for interaction screening of complex cDNA libraries using proteins or synthetic peptides as baits. Starting with the epidermal growth factor receptor (EGFR) cytoplasmic tail, we identified known protein interactions that link EGFR to the Ras/MAP kinase signal transduction cascade and several novel interactions. This approach can be used as a rapid and efficient tool for elucidating protein networks and mapping intracellular signal transduction pathways.
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Affiliation(s)
- S Zozulya
- Sugen, Inc., 230 East Grand Ave., South San Francisco, CA 04080, USA
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17
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Abstract
The phosphotyrosine-binding domain is a recently described protein-protein interaction domain which, despite its name, is involved in both phosphotyrosine-dependent and -independent interactions. Proteins with this domain are involved in diverse cellular functions, ranging from receptor signaling to protein targeting.
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18
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Farooq A, Plotnikova O, Zeng L, Zhou MM. Phosphotyrosine binding domains of Shc and insulin receptor substrate 1 recognize the NPXpY motif in a thermodynamically distinct manner. J Biol Chem 1999; 274:6114-21. [PMID: 10037694 DOI: 10.1074/jbc.274.10.6114] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphotyrosine binding (PTB) domains of the adaptor protein Shc and insulin receptor substrate (IRS-1) interact with a distinct set of activated and tyrosine-phosphorylated cytokine and growth factor receptors and play important roles in mediating mitogenic signal transduction. By using the technique of isothermal titration calorimetry, we have studied the thermodynamics of binding of the Shc and IRS-1 PTB domains to tyrosine-phosphorylated NPXY-containing peptides derived from known receptor binding sites. The results showed that relative contributions of enthalpy and entropy to the free energy of binding are dependent on specific phosphopeptides. Binding of the Shc PTB domain to tyrosine-phosphorylated peptides from TrkA, epidermal growth factor, ErbB3, and insulin receptors is achieved via an overall entropy-driven reaction. On the other hand, recognition of the phosphopeptides of insulin and interleukin-4 receptors by the IRS-1 PTB domain is predominantly an enthalpy-driven process. Mutagenesis and amino acid substitution experiments showed that in addition to the tyrosine-phosphorylated NPXY motif, the PTB domains of Shc and IRS-1 prefer a large hydrophobic residue at pY-5 and a small hydrophobic residue at pY-1, respectively (where pY is phosphotyrosine). These results agree with the calculated solvent accessibility of these two key peptide residues in the PTB domain/peptide structures and support the notion that the PTB domains of Shc and IRS-1 employ functionally distinct mechanisms to recognize tyrosine-phosphorylated receptors.
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Affiliation(s)
- A Farooq
- Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, New York 10029-6574, USA
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19
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Novel peptide mimetic building blocks and strategies for efficient lead finding. ADVANCES IN MEDICINAL CHEMISTRY 1999. [DOI: 10.1016/s1067-5698(99)80003-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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20
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Abstract
Nerve growth factor (NGF) initiates its biological effects by promoting the dimerization and activation of the tyrosine kinase receptor TrkA. The requirements for NGF signaling through the TrkA receptor have been defined extensively from studies in immortalized cells, involving transfection of NIH 3T3, COS, and PC12 cells. In the present study, we tested the effects of extracellular and intracellular mutations of TrkA after DNA-mediated transfection in primary cultures of embryonic day 17 hippocampal neurons. We found that the action of the TrkA receptor on neuronal differentiation depends on specific motifs in the extracellular domain and on tyrosine 490 (Y490), the site for SHC protein binding. In contrast with previous observations in a PC12 background, a mutation in the SHC Y490 binding site in TrkA resulted in a loss of NGF-dependent process formation. These results indicate that tyrosine 490 is necessary for neurite outgrowth in hippocampal neurons. Moreover, a constitutively active form of TrkA did not give enhanced responsiveness in hippocampal neurons, indicating that the behavior of TrkA receptors in primary neuronal cells is distinct from that of other cell types.
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Affiliation(s)
- L Aibel
- Skirball Institute, New York University Medical Center, New York 10016, USA
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21
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Abstract
The binding of one protein to another provokes a variety of biophysical changes that can then be used as a measure of the binding reaction. Optical spectroscopy, particularly fluorescence, is the most flexible technique, but surface plasmon resonance biosensors, microcalorimetry and mass spectroscopy have recently shown significant development.
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Affiliation(s)
- J H Lakey
- Department of Biochemistry and Genetics, Medical School, University of Newcastle upon Tyne, UK.
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22
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Xie D, Gulnik S, Collins L, Gustchina E, Suvorov L, Erickson JW. Dissection of the pH dependence of inhibitor binding energetics for an aspartic protease: direct measurement of the protonation states of the catalytic aspartic acid residues. Biochemistry 1997; 36:16166-72. [PMID: 9405050 DOI: 10.1021/bi971550l] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The catalytic activity and inhibitor binding energetics of enzymes are often pH-dependent properties. Aspartic proteases comprise an important class of enzyme targets for structure-based drug design. We have performed a complete thermodynamic study of pepstatin binding to plasmepsin II, an aspartic proteinase found in Plasmodium falciparum, using isothermal titration calorimetry and circular dichroism. Thermodynamic parameters (DeltaG, DeltaH, DeltaCp, and DeltaS) were measured as functions of both pH and temperature. In the pH range from 4.5 to 7.0, pepstatin binding is accompanied by proton transfer between the solvent and the complex. We used thermodynamic proton linkage theory to derive both the pH-independent binding energetics for pepstatin and the number and pKa values of ionizable residues whose pKa values change during ligand binding. These residues were identified as the two catalytic aspartates, with pKas of 6.5 and 3.0, and His 164, with a pKa of 7.5, based on the three-dimensional structure of the pepstatin-plasmepsin II complex. At pH 5.0, where the protease has optimum activity, the proton transfer process contributes almost 40% of the total binding free energy change and the total charge of the active-site aspartic acid residues is -1. These experimental results provide direct measurement for the protonation states of the catalytic aspartates in the presence of bound ligands. Comparison of the thermodynamic and structural data for pepstatin binding with human cathepsin D, a lysosomal aspartic protease that shares 35% sequence identity with plasmepsin II, suggests that the energetic differences between these two proteins are due to a higher interdomain flexibility in plasmepsin II.
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Affiliation(s)
- D Xie
- Structural Biochemistry Program, SAIC Frederick, National Cancer Institute-Frederick Cancer Research and Development Center, Frederick, Maryland 21702-1201, USA.
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23
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Faiman GA, Horovitz A. Thermodynamic analysis of the interaction between the 0.5beta Fv fragment and the RP135 peptide antigen derived from the V3 loop of HIV-1 gp120. J Biol Chem 1997; 272:31407-11. [PMID: 9395472 DOI: 10.1074/jbc.272.50.31407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The Fv fragment of the 0.5beta monoclonal antibody has recently been constructed, expressed, and purified. It binds with nanomolar affinity to the immunogenic RP135 peptide that is derived from the principal neutralizing determinant of HIV-1 in the third hypervariable region of gp120. Here, we analyzed the temperature-dependence of binding of the 0.5beta Fv fragment to the RP135 peptide and a series of mutants thereof. Our results show that there is almost complete enthalpy-entropy compensation in the effects of mutations in the peptide on binding to the Fv, indicating that the mutations do not change the binding mechanism. There is good correlation, for residues within the antigenic epitope, between mutational effects on DeltaCp and calculated values of DeltaDeltaCp based on the extent of burial of polar and non-polar surface areas of amino acids. The value of DeltaCp for the binding of the 0.5beta Fv fragment to the wild-type RP135 peptide is found to be -5.0 (+/- 0.9) kcal K-1 mol-1 in the presence of 0.1% Tween-20 but only -0.1 (+/- 0.9) kcal K-1 mol-1 in its absence. This result has important implications for the successful application of the structural parameterization approach to predicting changes in heat capacity that accompany binding reactions carried out in the presence of detergent or protein-stabilizing agents.
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Affiliation(s)
- G A Faiman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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24
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Zhang Z, Lee CH, Mandiyan V, Borg JP, Margolis B, Schlessinger J, Kuriyan J. Sequence-specific recognition of the internalization motif of the Alzheimer's amyloid precursor protein by the X11 PTB domain. EMBO J 1997; 16:6141-50. [PMID: 9321393 PMCID: PMC1326298 DOI: 10.1093/emboj/16.20.6141] [Citation(s) in RCA: 135] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The crystal structure of the phosphotyrosine-binding domain (PTB) of the X11 protein has been determined, in complex with unphosphorylated peptides corresponding to a region of beta-amyloid precursor protein (betaAPP) that is required for receptor internalization. The mode of binding to X11 of the unphosphorylated peptides, which contain an NPxY motif, resembles that of phosphorylated peptides bound to the Shc and IRS-1 PTB domains. Eight peptide residues make specific contacts with the X11 PTB domain, and they collectively achieve high affinity (KD = 0.32 microM) and specificity. These results suggest that, in contrast to the SH2 domains, the PTB domains are primarily peptide-binding domains that have, in some cases, acquired specificity for phosphorylated tyrosines.
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Affiliation(s)
- Z Zhang
- Department of Pharmacology, New York University Medical Center, 550 First Avenue, New York, NY 10016, USA
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25
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Yoon SO, Soltoff SP, Chao MV. A dominant role of the juxtamembrane region of the TrkA nerve growth factor receptor during neuronal cell differentiation. J Biol Chem 1997; 272:23231-8. [PMID: 9287331 DOI: 10.1074/jbc.272.37.23231] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
All receptor tyrosine kinases share a common intracellular signaling machinery, including ras activation, whereas cellular responses vary from mitogenesis to cell differentiation. To investigate the structural basis for receptor tyrosine kinase action for nerve growth factor, the juxtamembrane region of TrkA was transferred to a corresponding region of the epidermal growth factor (EGF) receptor. The resulting chimeric receptor contains an additional Shc site, Tyr490, in the juxtamembrane region. In transfected PC12 cell lines, neuronal differentiation was observed with EGF treatment, as evidenced by increased neurite extension. The action of the chimeric receptor was correlated with prolonged activation of MAP kinases and a 3-4-fold increase in phosphatidylinositol 3-kinase activity. The effect of the juxtamembrane chimera was dependent upon the Shc site at Tyr490, because expression of a chimeric receptor containing a Y490F mutation resulted in a complete loss of neuritogenesis by EGF treatment. These findings indicate that the juxtamembrane region of the TrkA receptor serves as a key functional domain that can confer a dominant effect upon neuronal differentiation.
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Affiliation(s)
- S O Yoon
- Beth Israel Deaconess Medical Center, Division of Signal Transduction, Department of Medicine, Boston, Massachusetts 02115, USA
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26
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Stites WE. Proteinminus signProtein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis. Chem Rev 1997; 97:1233-1250. [PMID: 11851449 DOI: 10.1021/cr960387h] [Citation(s) in RCA: 386] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wesley E. Stites
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701-1201
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27
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Haugh JM, Lauffenburger DA. Physical modulation of intracellular signaling processes by locational regulation. Biophys J 1997; 72:2014-31. [PMID: 9129805 PMCID: PMC1184397 DOI: 10.1016/s0006-3495(97)78846-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Recent observations in the field of signal transduction suggest that where a protein is located within a cell can be as important as its activity measured in solution for activation of its downstream pathway. The physical organization of the cell can provide an additional layer of control upon the chemical reaction networks that govern ultimately perceived signals. Using the cytosol and plasma membrane as relevant compartmental distinctions, we analyze the effect of relocation on the rate of association with a membrane-associated target. We quantify this effect as an enhancement factor E in terms of measurable parameters such as the number of available targets, molecular diffusivities, and intrinsic reaction rate constants. We then employ two simple yet relevant example models to illustrate how relocation can affect the dynamics of signal transduction pathways. The temporal profiles and phase behavior of these models are investigated. We also relate experimentally observable aspects of signal transduction such as peak activation and the relative time scales of stimulus and response to quantitative aspects of the relocation mechanisms in our models. In our example schemes, nearly complete relocation of the cytosolic species in the signaling pair is required to generate meaningful activation of the model pathways when the association rate enhancement factor E is as low as 10; when E is 100 or greater, only a small fraction of the protein must be relocated.
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Affiliation(s)
- J M Haugh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge 02139, USA
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28
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Backer JM, Wjasow C, Zhang Y. In vitro binding and phosphorylation of insulin receptor substrate 1 by the insulin receptor. Role of interactions mediated by the phosphotyrosine-binding domain and the pleckstrin-homology domain. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 245:91-6. [PMID: 9128728 DOI: 10.1111/j.1432-1033.1997.t01-1-00091.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Insulin receptor substrate 1 (IRS-1) is a major substrate of the insulin receptor in most cells. The N terminus of IRS-1 contains a phosphotyrosine binding (PTB) domain and a pleckstrin homology (PH) domain, both of which have been identified as important for insulin-stimulated phosphorylation in intact cells. The PTB domain binds to a phosphorylated motif, NPEY(P)960, that is present in the juxtamembrane region of the insulin receptor. A direct interaction between the PH domain of IRS-1 and the receptor has not been demonstrated. In this study, we examine the role of the IRS-1 PTB and PH domains during IRS-1 receptor binding and IRS-1 phosphorylation in intact cells and in vitro. Abrogation of binding of the PTB domain to NPXY(P) by mutation of Tyr960 of the insulin receptor did not reduce the binding of phosphorylated IRS-1 to insulin receptors in intact cells, and had no effect on binding of insulin receptors to IRS-1 or on IRS-1 phosphorylation in vitro. We examined the phosphorylation and receptor binding of a mutant recombinant IRS-1 that lacks the N-terminal PH domain (delta PH-IRS-1). Although phosphorylation of delta PH-IRS-1 by wild-type or [Ala960]insulin receptors was similar to that of IRS-1, binding of insulin receptor to delta PH-IRS-1 was markedly reduced relative to that to IRS-1. We conclude that stable association of IRS-1 with the insulin receptor is unaffected by disruption of PTB-domain-Tyr960 interactions but requires the IRS-1 PH domain, and that efficient phosphorylation of IRS-1 in intact cells correlates with the formation of stable receptor IRS complexes.
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Affiliation(s)
- J M Backer
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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29
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Doyle ML. Characterization of binding interactions by isothermal titration calorimetry. Curr Opin Biotechnol 1997; 8:31-5. [PMID: 9013658 DOI: 10.1016/s0958-1669(97)80154-1] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Isothermal titration calorimetry is a high-accuracy method for measuring binding affinities. Titration calorimetry is a universal method that has broad impact throughout biotechnology. In recent years, microcalorimeters that are capable of characterizing binding interactions of biological macromolecules have become commercially available. Results from these studies are providing new insight into the molecular nature of macromolecular interactions.
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Affiliation(s)
- ML Doyle
- Macromolecular Sciences Department, UE-0447-B SmithKline Beecham Pharmaceuticals 709 Swedeland Road King of Prussia PA 19406-0939 USA
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30
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Zhou MM, Fesik SW. Structure and function of the phosphotyrosine binding (PTB) domain. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1995; 64:221-35. [PMID: 8987385 DOI: 10.1016/s0079-6107(96)00005-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- M M Zhou
- Pharmaceutical Discovery Division, D-47G, AP10, Abbott Laboratories, IL 60064-3500, USA
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