1
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Defining How Oncogenic and Developmental Mutations of PIK3R1 Alter the Regulation of Class IA Phosphoinositide 3-Kinases. Structure 2019; 28:145-156.e5. [PMID: 31831213 DOI: 10.1016/j.str.2019.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/27/2019] [Accepted: 11/15/2019] [Indexed: 11/21/2022]
Abstract
The class I phosphoinositide 3-kinases (PI3Ks) are key signaling enzymes composed of a heterodimer of a p110 catalytic subunit and a p85 regulatory subunit, with PI3K mutations being causative of multiple human diseases including cancer, primary immunodeficiencies, and developmental disorders. Mutations in the p85α regulatory subunit encoded by PIK3R1 can both activate PI3K through oncogenic truncations in the iSH2 domain, or inhibit PI3K through developmental disorder mutations in the cSH2 domain. Using a combined biochemical and hydrogen deuterium exchange mass spectrometry approach we have defined the molecular basis for how these mutations alter the activity of p110α/p110δ catalytic subunits. We find that the oncogenic Q572∗ truncation of PIK3R1 disrupts all p85-inhibitory inputs, with p110α being hyper-activated compared with p110δ. In addition, we find that the R649W mutation in the cSH2 of PIK3R1 decreases sensitivity to activation by receptor tyrosine kinases. This work reveals unique insight into isoform-specific regulation of p110s by p85α.
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2
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Wei X, Li ZC, Li SJ, Peng XB, Zhao Q. Protein structure determination using a Riemannian approach. FEBS Lett 2019; 594:1036-1051. [PMID: 31769509 DOI: 10.1002/1873-3468.13688] [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: 05/23/2019] [Revised: 10/31/2019] [Accepted: 11/14/2019] [Indexed: 11/05/2022]
Abstract
Protein NMR structure determination is one of the most extensively studied problems. Here, we adopt a novel method based on a matrix completion technique - the Riemannian approach - to rebuild the protein structure from the nuclear Overhauser effect distance restraints and the dihedral angle restraints. In comparison with the cyana method, the results generated via the Riemannian approach are more similar to the standard X-ray crystallographic structures as a result of the simple but powerful internal calculation processing function. In addition, our results demonstrate that the Riemannian approach has a comparable or even better performance than the cyana method on other structural assessment metrics, including the stereochemical quality and restraint violations. The Riemannian approach software is available at: https://github.com/xubiaopeng/Protein_Recon_MCRiemman.
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Affiliation(s)
- Xian Wei
- Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, China.,Department of Science, Taiyuan Institute of Technology, China
| | - Zhi-Cheng Li
- Department of Physics, Taiyuan Normal University, China
| | - Shi-Jian Li
- Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, China
| | - Xu-Biao Peng
- Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, China
| | - Qing Zhao
- Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, China
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3
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A Comprehensive Survey of the Roles of Highly Disordered Proteins in Type 2 Diabetes. Int J Mol Sci 2017; 18:ijms18102010. [PMID: 28934129 PMCID: PMC5666700 DOI: 10.3390/ijms18102010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/04/2017] [Accepted: 09/12/2017] [Indexed: 01/03/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a chronic and progressive disease that is strongly associated with hyperglycemia (high blood sugar) related to either insulin resistance or insufficient insulin production. Among the various molecular events and players implicated in the manifestation and development of diabetes mellitus, proteins play several important roles. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database has information on 34 human proteins experimentally shown to be related to the T2DM pathogenesis. It is known that many proteins associated with different human maladies are intrinsically disordered as a whole, or contain intrinsically disordered regions. The presented study shows that T2DM is not an exception to this rule, and many proteins known to be associated with pathogenesis of this malady are intrinsically disordered. The multiparametric bioinformatics analysis utilizing several computational tools for the intrinsic disorder characterization revealed that IRS1, IRS2, IRS4, MAFA, PDX1, ADIPO, PIK3R2, PIK3R5, SoCS1, and SoCS3 are expected to be highly disordered, whereas VDCC, SoCS2, SoCS4, JNK9, PRKCZ, PRKCE, insulin, GCK, JNK8, JNK10, PYK, INSR, TNF-α, MAPK3, and Kir6.2 are classified as moderately disordered proteins, and GLUT2, GLUT4, mTOR, SUR1, MAPK1, IKKA, PRKCD, PIK3CB, and PIK3CA are predicted as mostly ordered. More focused computational analyses and intensive literature mining were conducted for a set of highly disordered proteins related to T2DM. The resulting work represents a comprehensive survey describing the major biological functions of these proteins and functional roles of their intrinsically disordered regions, which are frequently engaged in protein–protein interactions, and contain sites of various posttranslational modifications (PTMs). It is also shown that intrinsic disorder-associated PTMs may play important roles in controlling the functions of these proteins. Consideration of the T2DM proteins from the perspective of intrinsic disorder provides useful information that can potentially lead to future experimental studies that may uncover latent and novel pathways associated with the disease.
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4
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LoPiccolo J, Kim SJ, Shi Y, Wu B, Wu H, Chait BT, Singer RH, Sali A, Brenowitz M, Bresnick AR, Backer JM. Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer. J Biol Chem 2015; 290:30390-405. [PMID: 26475863 DOI: 10.1074/jbc.m115.689604] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Indexed: 11/06/2022] Open
Abstract
Phosphoinositide 3-kinases (PI3Ks) are a family of lipid kinases that are activated by growth factor and G-protein-coupled receptors and propagate intracellular signals for growth, survival, proliferation, and metabolism. p85α, a modular protein consisting of five domains, binds and inhibits the enzymatic activity of class IA PI3K catalytic subunits. Here, we describe the structural states of the p85α dimer, based on data from in vivo and in vitro solution characterization. Our in vitro assembly and structural analyses have been enabled by the creation of cysteine-free p85α that is functionally equivalent to native p85α. Analytical ultracentrifugation studies showed that p85α undergoes rapidly reversible monomer-dimer assembly that is highly exothermic in nature. In addition to the documented SH3-PR1 dimerization interaction, we identified a second intermolecular interaction mediated by cSH2 domains at the C-terminal end of the polypeptide. We have demonstrated in vivo concentration-dependent dimerization of p85α using fluorescence fluctuation spectroscopy. Finally, we have defined solution conditions under which the protein is predominantly monomeric or dimeric, providing the basis for small angle x-ray scattering and chemical cross-linking structural analysis of the discrete dimer. These experimental data have been used for the integrative structure determination of the p85α dimer. Our study provides new insight into the structure and assembly of the p85α homodimer and suggests that this protein is a highly dynamic molecule whose conformational flexibility allows it to transiently associate with multiple binding proteins.
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Affiliation(s)
| | - Seung Joong Kim
- the Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, and
| | - Yi Shi
- the Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065
| | - Bin Wu
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Haiyan Wu
- From the Department of Molecular Pharmacology
| | - Brian T Chait
- the Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Andrej Sali
- the Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, and
| | | | | | - Jonathan M Backer
- From the Department of Molecular Pharmacology, Department of Biochemistry,
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5
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Bulloch EM, Kingston RL. Identifying protein domains by global analysis of soluble fragment data. Anal Biochem 2014; 465:53-62. [DOI: 10.1016/j.ab.2014.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 06/17/2014] [Accepted: 06/25/2014] [Indexed: 01/11/2023]
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6
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Burke JE, Williams RL. Dynamic steps in receptor tyrosine kinase mediated activation of class IA phosphoinositide 3-kinases (PI3K) captured by H/D exchange (HDX-MS). Adv Biol Regul 2012. [PMID: 23194976 PMCID: PMC3613897 DOI: 10.1016/j.jbior.2012.09.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The catalytic subunits of all class IA phosphoinositide 3-kinases (PI3Ks) associate with identical p85-related subunits and phosphorylate PIP2 yielding PIP3, but they can vary greatly in the signaling pathways in which they participate. The binding of the p85 subunit to the p110 catalytic subunits is constitutive, and this inhibits activity, but some of the inhibitory contacts are reversible and subject to regulation. Interaction with phosphotyrosine-containing peptides (RTK-pY) releases a subset of these inhibitory contacts. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) provides a map of the dynamic interactions unique to each of the isotypes. RTK-pY binding exposes the p110 helical domains for all class IA enzymes (due to release of the nSH2 contact) and exposes the C-lobe of the kinase domains of p110β and p110δ (resulting from release of the cSH2 contact). Consistent with this, our in vitro assays show that all class IA isoforms are inhibited by the nSH2, but only p110β and p110δ are inhibited by the cSH2. While a C2/iSH2 inhibitory contact exists in all isoforms, HDX indicates that p110β releases this contact most readily. The unique dynamic relationships of the different p110 isozymes to the p85 subunit may facilitate new strategies for specific inhibitors of the PI3Ks.
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Affiliation(s)
- John E Burke
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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7
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Comb WC, Hutti JE, Cogswell P, Cantley LC, Baldwin AS. p85α SH2 domain phosphorylation by IKK promotes feedback inhibition of PI3K and Akt in response to cellular starvation. Mol Cell 2012; 45:719-30. [PMID: 22342344 DOI: 10.1016/j.molcel.2012.01.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Revised: 11/03/2011] [Accepted: 01/05/2012] [Indexed: 12/31/2022]
Abstract
The IκB kinase (IKK) pathway is an essential mediator of inflammatory, oncogenic, and cell stress pathways. Recently IKK was shown to be essential for autophagy induction in mammalian cells independent of its ability to regulate NF-κB, but the mechanism by which this occurs is unclear. Here we demonstrate that the p85 regulatory subunit of PI3K is an IKK substrate, phosphorylated at S690 in vitro and in vivo in response to cellular starvation. Cells expressing p85 S690A or inhibited for IKK activity exhibit increased Akt activity following cell starvation, demonstrating that p85 phosphorylation is required for starvation-induced PI3K feedback inhibition. S690 is in a conserved region of the p85 cSH2 domain, and IKK-mediated phosphorylation of this site results in decreased affinity for tyrosine-phosphorylated proteins and decreased PI3K membrane localization. Finally, leucine deprivation is shown to be necessary and sufficient for starvation-induced, IKK-mediated p85 phosphorylation and PI3K feedback inhibition.
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Affiliation(s)
- William C Comb
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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8
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Abstract
Phosphoinositide 3-kinases (PI3Ks) control cell growth, proliferation, cell survival, metabolic activity, vesicular trafficking, degranulation, and migration. Through these processes, PI3Ks modulate vital physiology. When over-activated in disease, PI3K promotes tumor growth, angiogenesis, metastasis or excessive immune cell activation in inflammation, allergy and autoimmunity. This chapter will introduce molecular activation and signaling of PI3Ks, and connections to target of rapamycin (TOR) and PI3K-related protein kinases (PIKKs). The focus will be on class I PI3Ks, and extend into current developments to exploit mechanistic knowledge for therapy.
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Affiliation(s)
- Matthias Wymann
- Institute Biochemistry & Genetics, Department Biomedicine, University of Basel, Mattenstrasse 28, 4058, Basel, Switzerland,
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9
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Burke JE, Vadas O, Berndt A, Finegan T, Perisic O, Williams RL. Dynamics of the phosphoinositide 3-kinase p110δ interaction with p85α and membranes reveals aspects of regulation distinct from p110α. Structure 2011; 19:1127-37. [PMID: 21827948 PMCID: PMC3155019 DOI: 10.1016/j.str.2011.06.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 05/06/2011] [Accepted: 06/07/2011] [Indexed: 12/12/2022]
Abstract
Phosphoinositide 3-kinase δ is upregulated in lymphocytic leukemias. Because the p85-regulatory subunit binds to any class IA subunit, it was assumed there is a single universal p85-mediated regulatory mechanism; however, we find isozyme-specific inhibition by p85α. Using deuterium exchange mass spectrometry (DXMS), we mapped regulatory interactions of p110δ with p85α. Both nSH2 and cSH2 domains of p85α contribute to full inhibition of p110δ, the nSH2 by contacting the helical domain and the cSH2 via the C terminus of p110δ. The cSH2 inhibits p110β and p110δ, but not p110α, implying that p110α is uniquely poised for oncogenic mutations. Binding RTK phosphopeptides disengages the SH2 domains, resulting in exposure of the catalytic subunit. We find that phosphopeptides greatly increase the affinity of the heterodimer for PIP2-containing membranes measured by FRET. DXMS identified regions decreasing exposure at membranes and also regions gaining exposure, indicating loosening of interactions within the heterodimer at membranes.
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Affiliation(s)
- John E Burke
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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10
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ORF-selector ESPRIT: A second generation library screen for soluble protein expression employing precise open reading frame selection. J Struct Biol 2011; 175:189-97. [DOI: 10.1016/j.jsb.2011.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 04/09/2011] [Accepted: 04/10/2011] [Indexed: 12/24/2022]
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11
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Zhang X, Vadas O, Perisic O, Anderson KE, Clark J, Hawkins PT, Stephens LR, Williams RL. Structure of lipid kinase p110β/p85β elucidates an unusual SH2-domain-mediated inhibitory mechanism. Mol Cell 2011; 41:567-78. [PMID: 21362552 PMCID: PMC3670040 DOI: 10.1016/j.molcel.2011.01.026] [Citation(s) in RCA: 146] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 12/07/2010] [Accepted: 12/22/2010] [Indexed: 12/21/2022]
Abstract
Phosphoinositide 3-kinases (PI3Ks) are essential for cell growth, migration, and survival. The structure of a p110β/p85β complex identifies an inhibitory function for the C-terminal SH2 domain (cSH2) of the p85 regulatory subunit. Mutagenesis of a cSH2 contact residue activates downstream signaling in cells. This inhibitory contact ties up the C-terminal region of the p110β catalytic subunit, which is essential for lipid kinase activity. In vitro, p110β basal activity is tightly restrained by contacts with three p85 domains: the cSH2, nSH2, and iSH2. RTK phosphopeptides relieve inhibition by nSH2 and cSH2 using completely different mechanisms. The binding site for the RTK's pYXXM motif is exposed on the cSH2, requiring an extended RTK motif to reach and disrupt the inhibitory contact with p110β. This contrasts with the nSH2 where the pY-binding site itself forms the inhibitory contact. This establishes an unusual mechanism by which p85 SH2 domains contribute to RTK signaling specificities.
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Affiliation(s)
- Xuxiao Zhang
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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12
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Backer JM. The regulation of class IA PI 3-kinases by inter-subunit interactions. Curr Top Microbiol Immunol 2011; 346:87-114. [PMID: 20544340 DOI: 10.1007/82_2010_52] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Phosphoinositide 3-kinases (PI 3-kinases) are activated by growth factor and hormone receptors, and regulate cell growth, survival, motility, and responses to changes in nutritional conditions (Engelman et al. 2006). PI 3-kinases have been classified according to their subunit composition and their substrate specificity for phosphoinositides (Vanhaesebroeck et al. 2001). The class IA PI 3-kinase is a heterodimer consisting of one regulatory subunit (p85α, p85β, p55α, p50α, or p55γ) and one 110-kDa catalytic subunit (p110α, β or δ). The Class IB PI 3-kinase is also a dimer, composed of one regulatory subunit (p101 or p87) and one catalytic subunit (p110γ) (Wymann et al. 2003). Class I enzymes will utilize PI, PI[4]P, or PI[4,5]P2 as substrates in vitro, but are thought to primarily produce PI[3,4,5]P3 in cells.The crystal structure of the Class IB PI 3-kinase catalytic subunit p110γ was solved in 1999 (Walker et al. 1999), and crystal or NMR structures of the Class IA p110α catalytic subunit and all of the individual domains of the Class IA p85α regulatory subunit have been solved (Booker et al. 1992; Günther et al. 1996; Hoedemaeker et al. 1999; Huang et al. 2007; Koyama et al. 1993; Miled et al. 2007; Musacchio et al. 1996; Nolte et al. 1996; Siegal et al. 1998). However, a structure of an intact PI 3-kinase enzyme has remained elusive. In spite of this, studies over the past 10 years have lead to important insights into how the enzyme is regulated under physiological conditions. This chapter will specifically discuss the regulation of Class IA PI 3-kinase enzymatic activity, focusing on regulatory interactions between the p85 and p110 subunits and the modulation of these interactions by physiological activators and oncogenic mutations. The complex web of signaling downstream from Class IA PI 3-kinases will be discussed in other chapters in this volume.
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Affiliation(s)
- Jonathan M Backer
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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13
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Jaiswal BS, Janakiraman V, Kljavin NM, Chaudhuri S, Stern HM, Wang W, Kan Z, Dbouk HA, Peters BA, Waring P, Vega TD, Kenski DM, Bowman K, Lorenzo M, Li H, Wu J, Modrusan Z, Stinson J, Eby M, Yue P, Kaminker J, de Sauvage FJ, Backer JM, Seshagiri S. Somatic mutations in p85alpha promote tumorigenesis through class IA PI3K activation. Cancer Cell 2009; 16:463-74. [PMID: 19962665 PMCID: PMC2804903 DOI: 10.1016/j.ccr.2009.10.016] [Citation(s) in RCA: 245] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 08/18/2009] [Accepted: 10/19/2009] [Indexed: 12/19/2022]
Abstract
Members of the mammalian phosphoinositide-3-OH kinase (PI3K) family of proteins are critical regulators of various cellular process including cell survival, growth, proliferation, and motility. Oncogenic activating mutations in the p110alpha catalytic subunit of the heterodimeric p110/p85 PI3K enzyme are frequent in human cancers. Here we show the presence of frequent mutations in p85alpha in colon cancer, a majority of which occurs in the inter-Src homology-2 (iSH2) domain. These mutations uncouple and retain p85alpha's p110-stabilizing activity, while abrogating its p110-inhibitory activity. The p85alpha mutants promote cell survival, AKT activation, anchorage-independent cell growth, and oncogenesis in a p110-dependent manner.
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Affiliation(s)
- Bijay S. Jaiswal
- Department of Molecular Biology, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | | | - Noelyn M. Kljavin
- Department of Molecular Biology, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Subhra Chaudhuri
- Department of Molecular Biology, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Howard M. Stern
- Department of Pathology, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Weiru Wang
- Department of Protein Engineering, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Zhengyan Kan
- Department of Molecular Biology, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Hashem A. Dbouk
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Brock A. Peters
- Department of Molecular Biology, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Paul Waring
- Department of Pathology, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Trisha Dela Vega
- Department of Protein Engineering, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Denise M. Kenski
- Department of Molecular Biology, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Krista Bowman
- Department of Protein Engineering, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Maria Lorenzo
- Department of Protein Chemistry, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Hong Li
- Department of Protein Chemistry, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Jiansheng Wu
- Department of Protein Chemistry, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Zora Modrusan
- Department of Molecular Biology, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Jeremy Stinson
- Department of Molecular Biology, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Michael Eby
- Department of Translational Oncology, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Peng Yue
- Department of Bioinformatics, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Josh Kaminker
- Department of Bioinformatics, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Frederic J. de Sauvage
- Department of Molecular Biology, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
| | - Jonathan M. Backer
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Somasekar Seshagiri
- Department of Molecular Biology, Genentech Inc., 1 DNA WAY, South San Francisco, CA 94080
- Correspondence: ; phone: 650-225-1000; fax: 650-225-1762
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14
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Gabelli SB, Mandelker D, Schmidt-Kittler O, Vogelstein B, Amzel LM. Somatic mutations in PI3Kalpha: structural basis for enzyme activation and drug design. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:533-40. [PMID: 19962457 DOI: 10.1016/j.bbapap.2009.11.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 11/23/2009] [Accepted: 11/25/2009] [Indexed: 12/27/2022]
Abstract
The PI3K pathway is a communication hub coordinating critical cell functions including cell survival, cell growth, proliferation, motility and metabolism. Because PI3Kalpha harbors recurrent somatic mutations resulting in gains of function in human cancers, it has emerged as an important drug target for many types of solid tumors. Various PI3K isoforms are also being evaluated as potential therapeutic targets for inflammation, heart disease, and hematological malignancies. Structural biology is providing insights into the flexibility of the PI3Ks, and providing basis for understanding the effects of mutations, drug resistance and specificity.
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Affiliation(s)
- Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University, Baltimore, MD 21205, USA.
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15
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Regulation of Class IA PI 3-kinases: C2 domain-iSH2 domain contacts inhibit p85/p110alpha and are disrupted in oncogenic p85 mutants. Proc Natl Acad Sci U S A 2009; 106:20258-63. [PMID: 19915146 DOI: 10.1073/pnas.0902369106] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We previously proposed a model of Class IA PI3K regulation in which p85 inhibition of p110alpha requires (i) an inhibitory contact between the p85 nSH2 domain and the p110alpha helical domain, and (ii) a contact between the p85 nSH2 and iSH2 domains that orients the nSH2 so as to inhibit p110alpha. We proposed that oncogenic truncations of p85 fail to inhibit p110 due to a loss of the iSH2-nSH2 contact. However, we now find that within the context of a minimal regulatory fragment of p85 (the nSH2-iSH2 fragment, termed p85ni), the nSH2 domain rotates much more freely (tau(c) approximately 12.7 ns) than it could if it were interacting rigidly with the iSH2 domain. These data are not compatible with our previous model. We therefore tested an alternative model in which oncogenic p85 truncations destabilize an interface between the p110alpha C2 domain (residue N345) and the p85 iSH2 domain (residues D560 and N564). p85ni-D560K/N564K shows reduced inhibition of p110alpha, similar to the truncated p85ni-572(STOP). Conversely, wild-type p85ni poorly inhibits p110alphaN345K. Strikingly, the p110alphaN345K mutant is inhibited to the same extent by the wild-type or truncated p85ni, suggesting that mutation of p110alpha-N345 is not additive with the p85ni-572(STOP) mutation. Similarly, the D560K/N564K mutation is not additive with the p85ni-572(STOP) mutant for downstream signaling or cellular transformation. Thus, our data suggests that mutations at the C2-iSH2 domain contact and truncations of the iSH2 domain, which are found in human tumors, both act by disrupting the C2-iSH2 domain interface.
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16
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Reich S, Puckey LH, Cheetham CL, Harris R, Ali AAE, Bhattacharyya U, Maclagan K, Powell KA, Prodromou C, Pearl LH, Driscoll PC, Savva R. Combinatorial Domain Hunting: An effective approach for the identification of soluble protein domains adaptable to high-throughput applications. Protein Sci 2007; 15:2356-65. [PMID: 17008718 PMCID: PMC2242398 DOI: 10.1110/ps.062082606] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Exploitation of potential new targets for drug and vaccine development has an absolute requirement for multimilligram quantities of soluble protein. While recombinant expression of full-length proteins is frequently problematic, high-yield soluble expression of functional subconstructs is an effective alternative, so long as appropriate termini can be identified. Bioinformatics localizes domains, but doesn't predict boundaries with sufficient accuracy, so that subconstructs are typically found by trial and error. Combinatorial Domain Hunting (CDH) is a technology for discovering soluble, highly expressed constructs of target proteins. CDH combines unbiased, finely sampled gene-fragment libraries, with a screening protocol that provides "holistic" readout of solubility and yield for thousands of protein fragments. CDH is free of the "passenger solubilization" and out-of-frame translational start artifacts of fusion-protein systems, and hits are ready for scale-up expression. As a proof of principle, we applied CDH to p85alpha, successfully identifying soluble and highly expressed constructs encapsulating all the known globular domains, and immediately suitable for downstream applications.
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Affiliation(s)
- Stefanie Reich
- School of Crystallography, Birkbeck College, London WC1E 7HX, United Kingdom
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Scharf PJ, Witney J, Daly R, Lyons BA. Solution structure of the human Grb14-SH2 domain and comparison with the structures of the human Grb7-SH2/erbB2 peptide complex and human Grb10-SH2 domain. Protein Sci 2005; 13:2541-6. [PMID: 15322292 PMCID: PMC2280013 DOI: 10.1110/ps.04884704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Grb14 is an adapter protein that is known to be overexpressed in estrogen receptor positive breast cancers, and in a number of prostate cancer cell lines. Grb14 has been demonstrated to bind to a number of activated receptor tyrosine kinases (RTKs) and to modulate signals transduced through these receptors. The RTKs to which Grb14 binds include the insulin receptor (IR), the fibroblast growth factor receptor (FGFR), the platelet-derived growth factor receptor (PDGFR), and the tunica endothelial kinase (Tek/Tie2) receptor. Grb14 has been shown to bind to these activated RTKs through its Src homology 2 (SH2) domain, with the exception of the insulin receptor, where the primary binding interaction is via a small domain adjacent to the SH2 domain (the BPS or PIR domain). Grb14 is a member of the Grb7 family of proteins, which also includes Grb7 and Grb10. We have solved the solution structure of the human Grb14-SH2 domain and compared it with the recently determined Grb7-SH2 and Grb10-SH2 domain structures.
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Affiliation(s)
- Paul J Scharf
- Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405, USA
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18
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Kim S, Zagozdzon R, Meisler A, Baleja JD, Fu Y, Avraham S, Avraham H. Csk homologous kinase (CHK) and ErbB-2 interactions are directly coupled with CHK negative growth regulatory function in breast cancer. J Biol Chem 2002; 277:36465-70. [PMID: 12122014 DOI: 10.1074/jbc.m206018200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Our previous studies demonstrated that Csk homologous kinase (CHK) acts as a negative growth regulator of human breast cancer through inhibition of ErbB-2/neu-mediated Src family kinase activity (Bougeret, C., Jiang, S., Keydar, I., and Avraham, H. (2001) J. Biol. Chem. 276, 33711-33720. The interaction between the CHK SH2 domain and Tyr(P)(1248) of the ErbB-2 receptor has been shown to be specific and critical for CHK function. In this report, we investigated whether the interaction of the CHK SH2 domain and ErbB-2 is directly related to the inhibition of heregulin-stimulated Src kinase activity. We constructed three CHK SH2 domain binding mutants: G129R (enhanced binding), R147K (inhibited binding), and R147A (disrupted binding). NMR spectra for the domains of each construct were used to evaluate their interaction with a Tyr(P)(1248)-containing ErbB-2 peptide. G129R showed enhanced binding to ErbB-2, whereas binding was completely disrupted by R147A. The enhanced binding mutant showed chemical shift changes at the same residues as wild-type CHK, indicating that this mutant has the same binding characteristics as the wild-type protein. Furthermore, inhibition of heregulin-stimulated Src kinase activity was markedly diminished by R147A, whereas G129R-mediated inhibition was stronger as compared with wild-type CHK. These results indicate that the specific interaction of CHK and ErbB-2 via the SH2 domain of CHK is directly related to the growth inhibitory effects of CHK. These new CHK high affinity binding constructs may serve as good candidates for inhibition of the ErbB-2/Src transduction pathway in gene therapy studies in breast cancer.
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Affiliation(s)
- Soyoun Kim
- Division of Experimental Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
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19
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Fang Y, Johnson LM, Mahon ES, Anderson DH. Two phosphorylation-independent sites on the p85 SH2 domains bind A-Raf kinase. Biochem Biophys Res Commun 2002; 290:1267-74. [PMID: 11812000 DOI: 10.1006/bbrc.2002.6347] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Src homology 2 (SH2) domains mediate phosphotyrosine (pY)-dependent protein:protein interactions involved in signal transduction pathways. We have found that the SH2 domains of the 85-kDa alpha subunit (p85) of phosphatidylinositol 3-kinase (PI3 kinase) bind directly to the serine/threonine kinase A-Raf. In this report we show that the p85 SH2:A-Raf interaction is phosphorylation-independent. The affinity of the p85 C-SH2 domain for A-Raf and phosphopeptide pY751 was similar, raising the possibility that a p85:A-Raf complex may play a role in the coordinated regulation of the PI3 kinase and Raf-MAP kinase pathways. We further show that the p85 C-SH2 domain contains two distinct binding sites for A-Raf; one overlapping the phosphotyrosine-dependent binding site and the other a separate phosphorylation-independent site. This is the first evidence for a second binding site on an SH2 domain, distinct from the phosphotyrosine-binding pocket.
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Affiliation(s)
- Yun Fang
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Avenue, Saskatoon, Saskatchewan, S7N 5E5, Canada
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20
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Chen YW, Dodson EJ, Kleywegt GJ. Does NMR mean "not for molecular replacement"? Using NMR-based search models to solve protein crystal structures. Structure 2000; 8:R213-20. [PMID: 11080645 DOI: 10.1016/s0969-2126(00)00524-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Y W Chen
- Centre for Protein Engineering and Cambridge University Chemical Laboratory, MRC Centre Hills Road CB2 2QH, Cambridge, United Kingdom.
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21
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22
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Kristensen SM, Siegal G, Sankar A, Driscoll PC. Backbone dynamics of the C-terminal SH2 domain of the p85alpha subunit of phosphoinositide 3-kinase: effect of phosphotyrosine-peptide binding and characterization of slow conformational exchange processes. J Mol Biol 2000; 299:771-88. [PMID: 10835283 DOI: 10.1006/jmbi.2000.3760] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The backbone dynamics of the C-terminal SH2 domain from the regulatory subunit p85alpha (p85alpha C-SH2) of phosphoinositide 3-kinase has been investigated in the absence of, and in complex with, a high-affinity phosphotyrosine-containing peptide ligand derived from the platelet-derived growth-factor receptor. (15)N R(1) and R(2) relaxation rates and steady-state [(1)H]-(15)N NOE values were measured by means of (1)H-(15)N correlated two-dimensional methods and were analyzed within the framework of the model-free formalism. Several residues in the BC loop and in the neighbouring secondary structural elements display fast local dynamics in the absence of phosphotyrosine peptide ligand as evidenced by below-average [(1)H]-(15)N NOE values. Furthermore, residue Gln41 (BC3) displays conformational exchange phenomena as indicated by an above-average R(2) relaxation rate. Upon binding of the phosphotyrosine peptide, the NOE values increase to values observed for regular secondary structure and the exchange contribution to the R(2) relaxation rate for Gln41 (BC3) vanishes. These observations indicate a loss of backbone flexibility upon ligand binding. Substantial exchange contributions for His56 (betaD4) and Cys57 (betaD5), which are known to make important interactions with the ligand, are attenuated upon ligand binding. Several residues in the betaD'-FB region and the BG loop, which contribute to the ligand binding surface of the protein, exhibit exchange terms which are reduced or vanish when the ligand is bound. Together, these observations suggest that ligand binding is accompanied by a loss of conformational flexibility on the ligand binding face of the protein. However, comparison with other SH2 domains reveals an apparent lack of consensus in the changes in dynamics induced by ligand binding. Exchange rates for individual residues were quantified in peptide-complexed p85alpha C-SH2 from the dependence of the exchange contributions on the CPMG delay in an R(2) series and show that peptide-complexed p85alpha C-SH2 is affected by multiple conformational exchange processes with exchange rate constants from 10(2) s(-1) to 7.10(3) s(-1). Mapping of the exchange-rate constants on the protein surface show a clustering of residues with similar exchange-rate constants and suggests that clustered residues are affected by a common predominant exchange process.
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Affiliation(s)
- S M Kristensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Kobenhavn O, DK-2100, Denmark.
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