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Abstract
The Src Homology 2 (SH2) domain is the prototypical protein interaction module that lies at the heart of phosphotyrosine signaling. Since its serendipitous discovery, there has been a tremendous advancement in technologies and an array of techniques available for studying SH2 domains and phosphotyrosine signaling. In this chapter, we provide a glimpse of the history of SH2 domains and describe many of the tools and techniques that have been developed along the way and discuss future directions for SH2 domain studies. We highlight the gist of each chapter in this volume in the context of: the structural biology and phosphotyrosine binding; characterizing SH2 specificity and generating prediction models; systems biology and proteomics; SH2 domains in signal transduction; and SH2 domains in disease, diagnostics, and therapeutics. Many of the individual chapters provide an in-depth approach that will allow scientists to interrogate the function and role of SH2 domains.
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Affiliation(s)
- Bernard A Liu
- Broad Institute of Harvard and MIT, 415 Main St., 5175 JJ, Cambridge, MA, 02142, USA.
| | - Kazuya Machida
- Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Ave., Farmington, CT, 06030, USA.
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52
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Shu K, Noguchi T, Honda K, Kondoh Y, Osada H, Ohno H, Fujii N, Oishi S. Synthesis of the Src SH2 domain and its application in bioassays for mirror-image screening. RSC Adv 2017. [DOI: 10.1039/c7ra07445j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Mirror-image screening systems for Src SH2 domain inhibitors were established using a synthetic Src SH2 domain.
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Affiliation(s)
- Keitou Shu
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501
- Japan
- Graduate School of Advanced Integrated Studies in Human Survivability
| | - Taro Noguchi
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Kaori Honda
- Chemical Biology Research Group
- RIKEN Center for Sustainable Resource Science
- Saitama 351-0198
- Japan
| | - Yasumitsu Kondoh
- Chemical Biology Research Group
- RIKEN Center for Sustainable Resource Science
- Saitama 351-0198
- Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group
- RIKEN Center for Sustainable Resource Science
- Saitama 351-0198
- Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Nobutaka Fujii
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501
- Japan
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53
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Dragan AI, Read CM, Crane-Robinson C. Enthalpy-entropy compensation: the role of solvation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:301-308. [PMID: 27796417 PMCID: PMC5384952 DOI: 10.1007/s00249-016-1182-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/06/2016] [Accepted: 10/17/2016] [Indexed: 11/24/2022]
Abstract
Structural modifications to interacting systems frequently lead to changes in both the enthalpy (heat) and entropy of the process that compensate each other, so that the Gibbs free energy is little changed: a major barrier to the development of lead compounds in drug discovery. The conventional explanation for such enthalpy–entropy compensation (EEC) is that tighter contacts lead to a more negative enthalpy but increased molecular constraints, i.e., a compensating conformational entropy reduction. Changes in solvation can also contribute to EEC but this contribution is infrequently discussed. We review long-established and recent cases of EEC and conclude that the large fluctuations in enthalpy and entropy observed are too great to be a result of only conformational changes and must result, to a considerable degree, from variations in the amounts of water immobilized or released on forming complexes. Two systems exhibiting EEC show a correlation between calorimetric entropies and local mobilities, interpreted to mean conformational control of the binding entropy/free energy. However, a substantial contribution from solvation gives the same effect, as a consequence of a structural link between the amount of bound water and the protein flexibility. Only by assuming substantial changes in solvation—an intrinsically compensatory process—can a more complete understanding of EEC be obtained. Faced with such large, and compensating, changes in the enthalpies and entropies of binding, the best approach to engineering elevated affinities must be through the addition of ionic links, as they generate increased entropy without affecting the enthalpy.
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Affiliation(s)
- Anatoliy I Dragan
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, 64, Volodymyrs'ka St., Kiev, 01601, Ukraine.,Institute of Molecular Biology and Genetics, NASU, 150, Zabolotnogo St., Kiev, 03680, Ukraine
| | - Christopher M Read
- Biophysics Laboratories, School of Biology, University of Portsmouth, Portsmouth, PO1 2DT, UK
| | - Colyn Crane-Robinson
- Biophysics Laboratories, School of Biology, University of Portsmouth, Portsmouth, PO1 2DT, UK.
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54
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Tchaicheeyan O, Meirovitch E. An SRLS Study of 2H Methyl-Moiety Relaxation and Related Conformational Entropy in Free and Peptide-Bound PLCγ1C SH2. J Phys Chem B 2016; 120:10695-10705. [DOI: 10.1021/acs.jpcb.6b08264] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oren Tchaicheeyan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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55
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Arginine phosphorylation marks proteins for degradation by a Clp protease. Nature 2016; 539:48-53. [PMID: 27749819 DOI: 10.1038/nature20122] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 09/29/2016] [Indexed: 11/08/2022]
Abstract
Protein turnover is a tightly controlled process that is crucial for the removal of aberrant polypeptides and for cellular signalling. Whereas ubiquitin marks eukaryotic proteins for proteasomal degradation, a general tagging system for the equivalent bacterial Clp proteases is not known. Here we describe the targeting mechanism of the ClpC-ClpP proteolytic complex from Bacillus subtilis. Quantitative affinity proteomics using a ClpP-trapping mutant show that proteins phosphorylated on arginine residues are selectively targeted to ClpC-ClpP. In vitro reconstitution experiments demonstrate that arginine phosphorylation by the McsB kinase is required and sufficient for the degradation of substrate proteins. The docking site for phosphoarginine is located in the amino-terminal domain of the ClpC ATPase, as resolved at high resolution in a co-crystal structure. Together, our data demonstrate that phosphoarginine functions as a bona fide degradation tag for the ClpC-ClpP protease. This system, which is widely distributed across Gram-positive bacteria, is functionally analogous to the eukaryotic ubiquitin-proteasome system.
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56
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Ju T, Niu W, Guo J. Evolution of Src Homology 2 (SH2) Domain to Recognize Sulfotyrosine. ACS Chem Biol 2016; 11:2551-7. [PMID: 27428792 DOI: 10.1021/acschembio.6b00555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein tyrosine O-sulfation is considered as the most common type of post-translational tyrosine modification in nature and plays important roles in extracellular biomolecular interactions. To facilitate the mapping, biological study, and medicinal application of this type of post-translational modification, we seek to evolve a small protein scaffold that recognizes sulfotyrosine with high affinity. We focused our efforts on the engineering of the Src Homology 2 (SH2) domain, which represents the largest class of known phosphotyrosine-recognition domain in nature and has a highly evolvable binding pocket. By using phage display, we successfully engineered the SH2 domain to recognize sulfotyrosine with high affinity. The best mutant, SH2-60.1, displayed more than 1700 fold higher sulfotyrosine-binding affinity than that of the wild-type SH2 domain. We also demonstrated that the evolved SH2 domain mutants could be used to detect sulfoprotein levels on the cell surface. These evolved SH2 domain mutants can be potentially applied to the study of protein tyrosine O-sulfation with proper experimental designs.
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Affiliation(s)
- Tong Ju
- Department
of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
| | - Jiantao Guo
- Department
of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588, United States
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57
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Sheng R, Jung DJ, Silkov A, Kim H, Singaram I, Wang ZG, Xin Y, Kim E, Park MJ, Thiagarajan-Rosenkranz P, Smrt S, Honig B, Baek K, Ryu S, Lorieau J, Kim YM, Cho W. Lipids Regulate Lck Protein Activity through Their Interactions with the Lck Src Homology 2 Domain. J Biol Chem 2016; 291:17639-50. [PMID: 27334919 DOI: 10.1074/jbc.m116.720284] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Indexed: 11/06/2022] Open
Abstract
Lymphocyte-specific protein-tyrosine kinase (Lck) plays an essential role in T cell receptor (TCR) signaling and T cell development, but its activation mechanism is not fully understood. To explore the possibility that plasma membrane (PM) lipids control TCR signaling activities of Lck, we measured the membrane binding properties of its regulatory Src homology 2 (SH2) and Src homology 3 domains. The Lck SH2 domain binds anionic PM lipids with high affinity but with low specificity. Electrostatic potential calculation, NMR analysis, and mutational studies identified the lipid-binding site of the Lck SH2 domain that includes surface-exposed basic, aromatic, and hydrophobic residues but not the phospho-Tyr binding pocket. Mutation of lipid binding residues greatly reduced the interaction of Lck with the ζ chain in the activated TCR signaling complex and its overall TCR signaling activities. These results suggest that PM lipids, including phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate, modulate interaction of Lck with its binding partners in the TCR signaling complex and its TCR signaling activities in a spatiotemporally specific manner via its SH2 domain.
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Affiliation(s)
- Ren Sheng
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Da-Jung Jung
- the Division of Integrative Biosciences and Biotechnology and
| | - Antonina Silkov
- the Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York 11032, and
| | - Hyunjin Kim
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Indira Singaram
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Zhi-Gang Wang
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Yao Xin
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Eui Kim
- the Division of Integrative Biosciences and Biotechnology and
| | - Mi-Jeong Park
- the Division of Integrative Biosciences and Biotechnology and
| | | | - Sean Smrt
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Barry Honig
- the Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York 11032, and
| | - Kwanghee Baek
- the Department of Genetic Engineering, Kyung Hee University, Yongin 446-701, Korea
| | - Sungho Ryu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Justin Lorieau
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - You-Me Kim
- the Division of Integrative Biosciences and Biotechnology and Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea,
| | - Wonhwa Cho
- From the Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, the Department of Genetic Engineering, Kyung Hee University, Yongin 446-701, Korea
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58
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SH2 Domains Serve as Lipid-Binding Modules for pTyr-Signaling Proteins. Mol Cell 2016; 62:7-20. [PMID: 27052731 DOI: 10.1016/j.molcel.2016.01.027] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/21/2015] [Accepted: 01/26/2016] [Indexed: 01/26/2023]
Abstract
The Src-homology 2 (SH2) domain is a protein interaction domain that directs myriad phosphotyrosine (pY)-signaling pathways. Genome-wide screening of human SH2 domains reveals that ∼90% of SH2 domains bind plasma membrane lipids and many have high phosphoinositide specificity. They bind lipids using surface cationic patches separate from pY-binding pockets, thus binding lipids and the pY motif independently. The patches form grooves for specific lipid headgroup recognition or flat surfaces for non-specific membrane binding and both types of interaction are important for cellular function and regulation of SH2 domain-containing proteins. Cellular studies with ZAP70 showed that multiple lipids bind its C-terminal SH2 domain in a spatiotemporally specific manner and thereby exert exquisite spatiotemporal control over its protein binding and signaling activities in T cells. Collectively, this study reveals how lipids control SH2 domain-mediated cellular protein-protein interaction networks and suggest a new strategy for therapeutic modulation of pY-signaling pathways.
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59
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Liu S, Wu X, Zong M, Tempel W, Loppnau P, Liu Y. Structural basis for a novel interaction between TXNIP and Vav2. FEBS Lett 2016; 590:857-65. [DOI: 10.1002/1873-3468.12110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/08/2016] [Accepted: 02/17/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Shasha Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; College of Life Science; Central China Normal University; Wuhan China
| | - Xue Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; College of Life Science; Central China Normal University; Wuhan China
| | - Minru Zong
- China-Japan Union Hospital of Jilin University; Changchun China
| | - Wolfram Tempel
- Structural Genomics Consortium; University of Toronto; Ontario Canada
| | - Peter Loppnau
- Structural Genomics Consortium; University of Toronto; Ontario Canada
| | - Yanli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; College of Life Science; Central China Normal University; Wuhan China
- Structural Genomics Consortium; University of Toronto; Ontario Canada
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60
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Hua DP, Huang H, Roy A, Post CB. Evaluating the dynamics and electrostatic interactions of folded proteins in implicit solvents. Protein Sci 2016; 25:204-18. [PMID: 26189497 PMCID: PMC4815311 DOI: 10.1002/pro.2753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/15/2015] [Indexed: 11/11/2022]
Abstract
Three implicit solvent models, namely GBMVII, FACTS, and SCPISM, were evaluated for their abilities to emulate an explicit solvent environment by comparing the simulated conformational ensembles, dynamics, and electrostatic interactions of the Src SH2 domain and the Lyn kinase domain. This assessment in terms of structural features in folded proteins expands upon the use of hydration energy as a metric for comparison. All-against-all rms coordinate deviation, average positional fluctuations, and ion-pair distance distribution were used to compare the implicit solvent models with the TIP3P explicit solvent model. Our study shows that the Src SH2 domains solvated with TIP3P, GBMVII, and FACTS sample similar global conformations. Additionally, the Src SH2 ion-pair distance distributions of solvent-exposed side chains corresponding to TIP3P, GBMVII, and FACTS do not differ substantially, indicating that GBMVII and FACTS are capable of modeling these electrostatic interactions. The ion-pair distance distributions of SCPISM are distinct from others, demonstrating that these electrostatic interactions are not adequately reproduced with the SCPISM model. On the other hand, for the Lyn kinase domain, a non-globular protein with bilobal structure and a large concavity on the surface, implicit solvent does not accurately model solvation to faithfully reproduce partially buried electrostatic interactions and lobe-lobe conformations. Our work reveals that local structure and dynamics of small, globular proteins are modeled well using FACTS and GBMVII. Nonetheless, global conformations and electrostatic interactions in concavities of multi-lobal proteins resulting from simulations with implicit solvent models do not match those obtained from explicit water simulations.
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Affiliation(s)
- Duy P Hua
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907
| | - He Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907
| | - Amitava Roy
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, 47907
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61
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Song X, Shang X, Ju T, Cerny R, Niu W, Guo J. A photoactivatable Src homology 2 (SH2) domain. RSC Adv 2016. [DOI: 10.1039/c6ra06211c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A photoactivatable SH2 domain that can be potentially applied as an optogenetic tool to the photocontrol of phosphotyrosine-associated biological processes.
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Affiliation(s)
- X. Song
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - X. Shang
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - T. Ju
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - R. Cerny
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
| | - W. Niu
- Department of Chemical & Biomolecular Engineering
- University of Nebraska-Lincoln
- Lincoln
- USA
| | - J. Guo
- Department of Chemistry
- University of Nebraska – Lincoln
- Lincoln
- USA
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62
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Papaioannou D, Geibel S, Kunze MBA, Kay CWM, Waksman G. Structural and biophysical investigation of the interaction of a mutant Grb2 SH2 domain (W121G) with its cognate phosphopeptide. Protein Sci 2015; 25:627-37. [PMID: 26645482 DOI: 10.1002/pro.2856] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/27/2015] [Indexed: 11/11/2022]
Abstract
The adaptor protein Grb2 is a key element of mitogenetically important signaling pathways. With its SH2 domain it binds to upstream targets while its SH3 domains bind to downstream proteins thereby relaying signals from the cell membranes to the nucleus. The Grb2 SH2 domain binds to its targets by recognizing a phosphotyrosine (pY) in a pYxNx peptide motif, requiring an Asn at the +2 position C-terminal to the pY with the residue either side of this Asn being hydrophobic. Structural analysis of the Grb2 SH2 domain in complex with its cognate peptide has shown that the peptide adopts a unique β-turn conformation, unlike the extended conformation that phosphopeptides adopt when bound to other SH2 domains. TrpEF1 (W121) is believed to force the peptide into this unusual conformation conferring this unique specificity to the Grb2 SH2 domain. Using X-ray crystallography, electron paramagnetic resonance (EPR) spectroscopy, and isothermal titration calorimetry (ITC), we describe here a series of experiments that explore the role of TrpEF1 in determining the specificity of the Grb2 SH2 domain. Our results demonstrate that the ligand does not adopt a pre-organized structure before binding to the SH2 domain, rather it is the interaction between the two that imposes the hairpin loop to the peptide. Furthermore, we find that the peptide adopts a similar structure when bound to both the wild-type Grb2 SH2 domain and a TrpEF1Gly mutant. This suggests that TrpEF1 is not the determining factor for the conformation of the phosphopeptide.
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Affiliation(s)
- Danai Papaioannou
- UCL And Birkbeck, Institute of Structural and Molecular Biology, Malet Street, London, WC1E 7HX, United Kingdom
| | - Sebastian Geibel
- UCL And Birkbeck, Institute of Structural and Molecular Biology, Malet Street, London, WC1E 7HX, United Kingdom.,Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2, Haus D15, Würzburg, 97080, Germany
| | - Micha B A Kunze
- UCL And Birkbeck, Institute of Structural and Molecular Biology, Malet Street, London, WC1E 7HX, United Kingdom
| | - Christopher W M Kay
- UCL And Birkbeck, Institute of Structural and Molecular Biology, Malet Street, London, WC1E 7HX, United Kingdom.,London Centre for Nanotechnology, 17-19 Gordon Street, London, WC1H 0AH, United Kingdom
| | - Gabriel Waksman
- UCL And Birkbeck, Institute of Structural and Molecular Biology, Malet Street, London, WC1E 7HX, United Kingdom
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63
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Lu X, Hu X, Song L, An L, Duan M, Chen S, Zhao S. The SH2 domain is crucial for function of Fyn in neuronal migration and cortical lamination. BMB Rep 2015; 48:97-102. [PMID: 24912779 PMCID: PMC4352619 DOI: 10.5483/bmbrep.2015.48.2.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Indexed: 11/20/2022] Open
Abstract
Neurons in the developing brain form the cortical plate (CP) in an inside-out manner, in which the late-born neurons are located more superficially than the early-born neurons. Fyn, a member of the Src family kinases, plays an important role in neuronal migration by binding to many substrates. However, the role of the Src-homology 2 (SH2) domain in function of Fyn in neuronal migration remains poorly understood. Here, we demonstrate that the SH2 domain is essential for the action of Fyn in neuronal migration and cortical lamination. A point mutation in the Fyn SH2 domain (FynR176A) impaired neuronal migration and their final location in the cerebral cortex, by inducing neuronal aggregation and branching. Thus, we provide the first evidence of the Fyn SH2 domain contributing to neuronal migration and neuronal morphogenesis. [BMB Reports 2015; 48(2): 97-102]
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Affiliation(s)
- Xi Lu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Xinde Hu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Lingzhen Song
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Lei An
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Minghui Duan
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Shulin Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Shanting Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
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64
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Nieto L, Tharun IM, Balk M, Wienk H, Boelens R, Ottmann C, Milroy LG, Brunsveld L. Estrogen Receptor Folding Modulates cSrc Kinase SH2 Interaction via a Helical Binding Mode. ACS Chem Biol 2015; 10:2624-32. [PMID: 26352092 DOI: 10.1021/acschembio.5b00568] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The estrogen receptors (ERs) feature, next to their transcriptional role, important nongenomic signaling actions, with emerging clinical relevance. The Src Homology 2 (SH2) domain mediated interaction between cSrc kinase and ER plays a key role in this; however the molecular determinants of this interaction have not been elucidated. Here, we used phosphorylated ER peptide and semisynthetic protein constructs in a combined biochemical and structural study to, for the first time, provide a quantitative and structural characterization of the cSrc SH2-ER interaction. Fluorescence polarization experiments delineated the SH2 binding motif in the ER sequence. Chemical shift perturbation analysis by nuclear magnetic resonance (NMR) together with molecular dynamics (MD) simulations allowed us to put forward a 3D model of the ER-SH2 interaction. The structural basis of this protein-protein interaction has been compared with that of the high affinity SH2 binding sequence GpYEEI. The ER features a different binding mode from that of the "two-pronged plug two-hole socket" model in the so-called specificity determining region. This alternative binding mode is modulated via the folding of ER helix 12, a structural element directly C-terminal of the key phosphorylated tyrosine. The present findings provide novel molecular entries for understanding nongenomic ER signaling and targeting the corresponding disease states.
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Affiliation(s)
- Lidia Nieto
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Inga M. Tharun
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Mark Balk
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Hans Wienk
- Bijvoet
Center for Biomolecular Research, NMR Spectroscopy Utrecht University, 3584CH Utrecht, The Netherlands
| | - Rolf Boelens
- Bijvoet
Center for Biomolecular Research, NMR Spectroscopy Utrecht University, 3584CH Utrecht, The Netherlands
| | - Christian Ottmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
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65
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Banerjee M, Duan Q, Xie Z. SH2 Ligand-Like Effects of Second Cytosolic Domain of Na/K-ATPase α1 Subunit on Src Kinase. PLoS One 2015; 10:e0142119. [PMID: 26551526 PMCID: PMC4638348 DOI: 10.1371/journal.pone.0142119] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/16/2015] [Indexed: 01/08/2023] Open
Abstract
Our previous studies have suggested that the α1 Na/K-ATPase interacts with Src to form a receptor complex. In vitro binding assays indicate an interaction between second cytosolic domain (CD2) of Na/K-ATPase α1 subunit and Src SH2 domain. Since SH2 domain targets Src to specific signaling complexes, we expressed CD2 as a cytosolic protein and studied whether it could act as a Src SH2 ligand in LLC-PK1 cells. Co-immunoprecipitation analyses indicated a direct binding of CD2 to Src, consistent with the in vitro binding data. Functionally, CD2 expression increased basal Src activity, suggesting a Src SH2 ligand-like property of CD2. Consistently, we found that CD2 expression attenuated several signaling pathways where Src plays an important role. For instance, although it increased surface expression of Na/K-ATPase, it decreased ouabain-induced activation of Src and ERK by blocking the formation of Na/K-ATPase/Src complex. Moreover, it also attenuated cell attachment-induced activation of Src/FAK. Consequently, CD2 delayed cell spreading, and inhibited cell proliferation. Furthermore, these effects appear to be Src-specific because CD2 expression had no effect on EGF-induced activation of EGF receptor and ERK. Hence, the new findings indicate the importance of Na/K-ATPase/Src interaction in ouabain-induced signal transduction, and support the proposition that the CD2 peptide may be utilized as a Src SH2 ligand capable of blocking Src-dependent signaling pathways via a different mechanism from a general Src kinase inhibitor.
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Affiliation(s)
- Moumita Banerjee
- Marshall Institute for Interdisciplinary Research (MIIR), Marshall University, Huntington, West Virginia, United States of America
| | - Qiming Duan
- Case Cardiovascular Research Institute, Department of Medicine, Case Western Reserve University School of Medicine and Harrington Heart and Vascular Institute, Cleveland, Ohio, United States of America
| | - Zijian Xie
- Marshall Institute for Interdisciplinary Research (MIIR), Marshall University, Huntington, West Virginia, United States of America
- * E-mail:
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66
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Structural basis for the regulatory role of the PPxY motifs in the thioredoxin-interacting protein TXNIP. Biochem J 2015; 473:179-87. [PMID: 26527736 DOI: 10.1042/bj20150830] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/02/2015] [Indexed: 11/17/2022]
Abstract
TXNIP (thioredoxin-interacting protein) negatively regulates the antioxidative activity of thioredoxin and participates in pleiotropic cellular processes. Its deregulation is linked to various human diseases, including diabetes, acute myeloid leukaemia and cardiovascular diseases. The E3 ubiquitin ligase Itch (Itchy homologue) polyubiquitinates TXNIP to promote its degradation via the ubiquitin-proteasome pathway, and this Itch-mediated polyubiquitination of TXNIP is dependent on the interaction of the four WW domains of Itch with the two PPxY motifs of TXNIP. However, the molecular mechanism of this interaction of TXNIP with Itch remains elusive. In the present study, we found that each of the four WW domains of Itch exhibited different binding affinities for TXNIP, whereas multivalent engagement between the four WW domains of Itch and the two PPxY motifs of TXNIP resulted in their strong binding avidity. Our structural analyses demonstrated that the third and fourth WW domains of Itch were able to recognize both PPxY motifs of TXNIP simultaneously, supporting a multivalent binding mode between Itch and TXNIP. Interestingly, the phosphorylation status on the tyrosine residue of the PPxY motifs of TXNIP serves as a molecular switch in its choice of binding partners and thereby downstream biological signalling outcomes. Phosphorylation of this tyrosine residue of TXNIP diminished the binding capability of PPxY motifs of TXNIP to Itch, whereas this phosphorylation is a prerequisite to the binding activity of TXNIP to SHP2 [SH2 (Src homology 2) domain-containing protein tyrosine phosphatase 2] and their roles in stabilizing the phosphorylation and activation of CSK (c-Src tyrosine kinase).
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67
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Huculeci R, Garcia-Pino A, Buts L, Lenaerts T, van Nuland N. Structural insights into the intertwined dimer of fyn SH2. Protein Sci 2015; 24:1964-78. [PMID: 26384592 DOI: 10.1002/pro.2806] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 09/13/2015] [Accepted: 09/16/2015] [Indexed: 01/01/2023]
Abstract
Src homology 2 domains are interaction modules dedicated to the recognition of phosphotyrosine sites incorporated in numerous proteins found in intracellular signaling pathways. Here we provide for the first time structural insight into the dimerization of Fyn SH2 both in solution and in crystalline conditions, providing novel crystal structures of both the dimer and peptide-bound structures of Fyn SH2. Using nuclear magnetic resonance chemical shift analysis, we show how the peptide is able to eradicate the dimerization, leading to monomeric SH2 in its bound state. Furthermore, we show that Fyn SH2's dimer form differs from other SH2 dimers reported earlier. Interestingly, the Fyn dimer can be used to construct a completed dimer model of Fyn without any steric clashes. Together these results extend our understanding of SH2 dimerization, giving structural details, on one hand, and suggesting a possible physiological relevance of such behavior, on the other hand.
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Affiliation(s)
- Radu Huculeci
- Structural Biology Brussels, Jean Jeener NMR Center, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center, VIB, Brussels, Belgium
| | - Abel Garcia-Pino
- Structural Biology Brussels, Jean Jeener NMR Center, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center, VIB, Brussels, Belgium
| | - Lieven Buts
- Structural Biology Brussels, Jean Jeener NMR Center, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center, VIB, Brussels, Belgium
| | - Tom Lenaerts
- MLG, Département d'Informatique, Université Libre de Bruxelles, Brussels, Belgium.,AI-Lab,Vakgroep Computerwetenschappen, Vrije Universiteit Brussel, Brussels, Belgium.,Interuniversity Institute of Bioinformatics Brussels (IB2), ULB-VUB, Brussels, Belgium
| | - Nico van Nuland
- Structural Biology Brussels, Jean Jeener NMR Center, Vrije Universiteit Brussel, Brussels, Belgium.,Structural Biology Research Center, VIB, Brussels, Belgium
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68
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The discovery of modular binding domains: building blocks of cell signalling. Nat Rev Mol Cell Biol 2015; 16:691-8. [PMID: 26420231 DOI: 10.1038/nrm4068] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cell signalling - the ability of a cell to process information from the environment and change its behaviour in response - is a central property of life. Signalling depends on proteins that are assembled from a toolkit of modular domains, each of which confers a specific activity or function. The discovery of modular protein- and lipid-binding domains was a crucial turning point in understanding the logic and evolution of signalling mechanisms.
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69
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Watson GM, Gunzburg MJ, Ambaye ND, Lucas WAH, Traore DA, Kulkarni K, Cergol KM, Payne RJ, Panjikar S, Pero SC, Perlmutter P, Wilce MCJ, Wilce JA. Cyclic Peptides Incorporating Phosphotyrosine Mimetics as Potent and Specific Inhibitors of the Grb7 Breast Cancer Target. J Med Chem 2015; 58:7707-18. [DOI: 10.1021/acs.jmedchem.5b00609] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | | | | | | | | | | | - Katie M. Cergol
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Richard J. Payne
- School
of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Santosh Panjikar
- Australian Synchrotron, 800 Blackburn
Road, Clayton, Victoria 3168, Australia
| | - Stephanie C. Pero
- Department
of Surgery and Vermont Cancer Center, University of Vermont, Burlington, Vermont 05401, United States
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70
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Gerbec ZJ, Thakar MS, Malarkannan S. The Fyn-ADAP Axis: Cytotoxicity Versus Cytokine Production in Killer Cells. Front Immunol 2015; 6:472. [PMID: 26441977 PMCID: PMC4584950 DOI: 10.3389/fimmu.2015.00472] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/31/2015] [Indexed: 11/13/2022] Open
Abstract
Lymphocyte signaling cascades responsible for anti-tumor cytotoxicity and inflammatory cytokine production must be tightly regulated in order to control an immune response. Disruption of these cascades can cause immune suppression as seen in a tumor microenvironment, and loss of signaling integrity can lead to autoimmunity and other forms of host-tissue damage. Therefore, understanding the distinct signaling events that exclusively control specific effector functions of “killer” lymphocytes (T and NK cells) is critical for understanding disease progression and formulating successful immunotherapy. Elucidation of divergent signaling pathways involved in receptor-mediated activation has provided insights into the independent regulation of cytotoxicity and cytokine production in lymphocytes. Specifically, the Fyn signaling axis represents a branch point for killer cell effector functions and provides a model for how cytotoxicity and cytokine production are differentially regulated. While the Fyn–PI(3)K pathway controls multiple functions, including cytotoxicity, cell development, and cytokine production, the Fyn–ADAP pathway preferentially regulates cytokine production in NK and T cells. In this review, we discuss how the structure of Fyn controls its function in lymphocytes and the role this plays in mediating two facets of lymphocyte effector function, cytotoxicity and production of inflammatory cytokines. This offers a model for using mechanistic and structural approaches to understand clinically relevant lymphocyte signaling.
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Affiliation(s)
- Zachary J Gerbec
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Medical College of Wisconsin , Milwaukee, WI , USA ; Department of Microbiology, Immunology and Molecular Genetics, Medical College of Wisconsin , Milwaukee, WI , USA
| | - Monica S Thakar
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Medical College of Wisconsin , Milwaukee, WI , USA ; Department of Pediatrics, Medical College of Wisconsin , Milwaukee, WI , USA ; Department of Medicine, Medical College of Wisconsin , Milwaukee, WI , USA
| | - Subramaniam Malarkannan
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Medical College of Wisconsin , Milwaukee, WI , USA ; Department of Microbiology, Immunology and Molecular Genetics, Medical College of Wisconsin , Milwaukee, WI , USA ; Department of Pediatrics, Medical College of Wisconsin , Milwaukee, WI , USA ; Department of Medicine, Medical College of Wisconsin , Milwaukee, WI , USA
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71
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Crystal structure of an SH2-kinase construct of c-Abl and effect of the SH2 domain on kinase activity. Biochem J 2015; 468:283-91. [PMID: 25779001 PMCID: PMC5936049 DOI: 10.1042/bj20141492] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Constitutive activation of the non-receptor tyrosine kinase c-Abl (cellular Abelson tyrosine protein kinase 1, Abl1) in the Bcr (breakpoint cluster region)-Abl1 fusion oncoprotein is the molecular cause of chronic myeloid leukaemia (CML). Recent studies have indicated that an interaction between the SH2 (Src-homology 2) domain and the N-lobe (N-terminal lobe) of the c-Abl kinase domain (KD) has a critical role in leukaemogenesis [Grebien et al. (2011) Cell 147, 306-319; Sherbenou et al. (2010) Blood 116, 3278-3285]. To dissect the structural basis of this phenomenon, we studied c-Abl constructs comprising the SH2 and KDs in vitro. We present a crystal structure of an SH2-KD construct bound to dasatinib, which contains the relevant interface between the SH2 domain and the N-lobe of the KD. We show that the presence of the SH2 domain enhances kinase activity moderately and that this effect depends on contacts in the SH2/N-lobe interface and is abrogated by specific mutations. Consistently, formation of the interface decreases slightly the association rate of imatinib with the KD. That the effects are small compared with the dramatic in vivo consequences suggests an important function of the SH2-N-lobe interaction might be to help disassemble the auto-inhibited conformation of c-Abl and promote processive phosphorylation, rather than substantially stimulate kinase activity.
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72
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Jin LL, Wybenga-Groot LE, Tong J, Taylor P, Minden MD, Trudel S, McGlade CJ, Moran MF. Tyrosine phosphorylation of the Lyn Src homology 2 (SH2) domain modulates its binding affinity and specificity. Mol Cell Proteomics 2015; 14:695-706. [PMID: 25587033 DOI: 10.1074/mcp.m114.044404] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Src homology 2 (SH2) domains are modular protein structures that bind phosphotyrosine (pY)-containing polypeptides and regulate cellular functions through protein-protein interactions. Proteomics analysis showed that the SH2 domains of Src family kinases are themselves tyrosine phosphorylated in blood system cancers, including acute myeloid leukemia, chronic lymphocytic leukemia, and multiple myeloma. Using the Src family kinase Lyn SH2 domain as a model, we found that phosphorylation at the conserved SH2 domain residue Y(194) impacts the affinity and specificity of SH2 domain binding to pY-containing peptides and proteins. Analysis of the Lyn SH2 domain crystal structure supports a model wherein phosphorylation of Y(194) on the EF loop modulates the binding pocket that engages amino acid side chains at the pY+2/+3 position. These data indicate another level of regulation wherein SH2-mediated protein-protein interactions are modulated by SH2 kinases and phosphatases.
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Affiliation(s)
- Lily L Jin
- From the ‡Molecular Structure and Function, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada; ‡‡Departments of Molecular Genetics, Medical Science Building, Room 4386, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Leanne E Wybenga-Groot
- §Cell Biology, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada; ¶The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada
| | - Jiefei Tong
- From the ‡Molecular Structure and Function, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada
| | - Paul Taylor
- From the ‡Molecular Structure and Function, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada
| | - Mark D Minden
- ‖Medical Biophysics, University of Toronto, Medical Science Building, Room 4386, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; **The Princess Margaret Cancer Center, 610 University Avenue, M5G 2M9, Toronto, Canada
| | - Suzanne Trudel
- ‖Medical Biophysics, University of Toronto, Medical Science Building, Room 4386, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; **The Princess Margaret Cancer Center, 610 University Avenue, M5G 2M9, Toronto, Canada
| | - C Jane McGlade
- §Cell Biology, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada; ¶The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada; ‖Medical Biophysics, University of Toronto, Medical Science Building, Room 4386, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Michael F Moran
- From the ‡Molecular Structure and Function, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada; ‡‡Departments of Molecular Genetics, Medical Science Building, Room 4386, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; **The Princess Margaret Cancer Center, 610 University Avenue, M5G 2M9, Toronto, Canada
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73
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A. Karpov O, W. Fearnley G, A. Smith G, Kankanala J, J. McPherson M, C. Tomlinson D, A. Harrison M, Ponnambalam S. Receptor tyrosine kinase structure and function in health and disease. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.476] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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74
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Singh AK, Singh M, Pandya VK, G L B, Singh V, Ekka MK, Mittal M, Kumaran S. Molecular basis of peptide recognition in metallopeptidase Dug1p from Saccharomyces cerevisiae. Biochemistry 2014; 53:7870-83. [PMID: 25427234 DOI: 10.1021/bi501263u] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dug1p, a M20 family metallopeptidase and human orthologue of carnosinase, hydrolyzes Cys-Gly dipeptide, the last step of glutathione (GSH) degradation in Saccharomyces cerevisiae. Molecular bases of peptide recognition by Dug1p and other M20 family peptidases remain unclear in the absence of structural information about enzyme-peptide complexes. We report the crystal structure of Dug1p at 2.55 Å resolution in complex with a Gly-Cys dipeptide and two Zn(2+) ions. The dipeptide is trapped in the tunnel-like active site; its C-terminus is held by residues at the S1' binding pocket, whereas the S1 pocket coordinates Zn(2+) ions and the N-terminus of the peptide. Superposition with the carnosinase structure shows that peptide mimics the inhibitor bestatin, but active site features are altered upon peptide binding. The space occupied by the N-terminus of bestatin is left unoccupied in the Dug1p structure, suggesting that tripeptides could bind. Modeling of tripeptides into the Dug1p active site showed tripeptides fit well. Guided by the structure and modeling, we examined the ability of Dug1p to hydrolyze tripeptides, and results show that Dug1p hydrolyzes tripeptides selectively. Point mutations of catalytic residues do not abolish the peptide binding but abolish the hydrolytic activity, suggesting a noncooperative mode in peptide recognition. In summary, results reveal that peptides are recognized primarily through their amino and carboxyl termini, but hydrolysis depends on the properties of peptide substrates, dictated by their respective sequences. Structural similarity between the Dug1p-peptide complex and the bestatin-bound complex of CN2 suggests that the Dug1p-peptide structure can be used as a template for designing natural peptide inhibitors.
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Affiliation(s)
- Appu Kumar Singh
- G. N. Ramachandran Protein Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR) , Sector 39A, Chandigarh 160036, India
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75
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N-Terminal Acetylation of Phosphopeptides to Enhance the Interaction with SH2 Domain by Electrosprary Ion Trap Mass Spectrometry. Int J Pept Res Ther 2014. [DOI: 10.1007/s10989-014-9422-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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76
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Höfener M, Heinzlmeir S, Kuster B, Sewald N. Probing SH2-domains using Inhibitor Affinity Purification (IAP). Proteome Sci 2014; 12:41. [PMID: 25067910 PMCID: PMC4110944 DOI: 10.1186/1477-5956-12-41] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/09/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Many human diseases are correlated with the dysregulation of signal transduction processes. One of the most important protein interaction domains in the context of signal transduction is the Src homology 2 (SH2) domain that binds phosphotyrosine residues. Hence, appropriate methods for the investigation of SH2 proteins are indispensable in diagnostics and medicinal chemistry. Therefore, an affinity resin for the enrichment of all SH2 proteins in one experiment would be desirable. However, current methods are unable to address all SH2 proteins simultaneously with a single compound or a small array of compounds. RESULTS In order to overcome these limitations for the investigation of this particular protein family in future experiments, a dipeptide-derived probe has been designed, synthesized and evaluated. This probe successfully enriched 22 SH2 proteins from mixed cell lysates which contained 50 SH2 proteins. Further characterization of the SH2 binding properties of the probe using depletion and competition experiments indicated its ability to enrich complexes consisting of SH2 domain bearing regulatory PI3K subunits and catalytic phosphoinositide 3-kinase (PI3K) subunits that have no SH2 domain. CONCLUSION The results make this probe a promising starting point for the development of a mixed affinity resin with complete SH2 protein coverage. Moreover, the additional findings render it a valuable tool for the evaluation of PI3K complex interrupting inhibitors.
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Affiliation(s)
- Michael Höfener
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Stephanie Heinzlmeir
- Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
- German Cancer Consortium (DKTK), Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bernhard Kuster
- Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
- Center for Integrated Protein Science Munich, Freising, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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77
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Roy A, Hua DP, Ward JM, Post CB. Relative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method. J Chem Theory Comput 2014; 10:2759-2768. [PMID: 25061444 PMCID: PMC4095907 DOI: 10.1021/ct500200n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Indexed: 01/09/2023]
Abstract
![]()
The
potential for reliably predicting relative binding enthalpies,
ΔΔE, from a direct method utilizing molecular
dynamics is examined for a system of three phosphotyrosyl peptides
binding to a protein receptor, the Src SH2 domain. The binding enthalpies
were calculated from the potential energy differences between the
bound and the unbound end-states of each peptide from equilibrium
simulations in explicit water. The statistical uncertainties in the
ensemble-mean energy values from multiple, independent simulations
were obtained using a bootstrap method. Simulations were initiated
with different starting coordinates as well as different velocities.
Statistical uncertainties in ΔΔE are
2 to 3 kcal/mol based on calculations from 40, 10 ns trajectories
for each system (three SH2–peptide complexes or unbound peptides).
Uncertainties in relative component energies, comprising solute–solute,
solute–solvent and solvent–solvent interactions, are
considerably larger. Energy values were estimated from an unweighted
ensemble averaging of multiple trajectories with the a priori assumption
that all trajectories are equally likely. Distributions in energy–rmsd
space indicate that the trajectories sample the same basin and the
difference in mean energy values between trajectories is due to sampling
of alternative local regions of this superbasin. The direct estimate
of relative binding enthalpies is concluded to be a reasonable approach
for well-ordered systems with ΔΔE values
greater than ∼3 kcal/mol, although the approach would benefit
from future work to determine properly distributed starting points
that would enable efficient sampling of conformational space using
multiple trajectories.
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Affiliation(s)
- Amitava Roy
- Department of Medicinal Chemistry, Markey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
| | - Duy P Hua
- Department of Medicinal Chemistry, Markey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
| | - Joshua M Ward
- Department of Medicinal Chemistry, Markey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
| | - Carol Beth Post
- Department of Medicinal Chemistry, Markey Center for Structural Biology, and Purdue Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
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78
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Pang X, Zhou HX. Distinct mechanisms of a phosphotyrosyl peptide binding to two SH2 domains. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014; 13:1440003. [DOI: 10.1142/s0219633614400033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein phosphorylation is a very common post-translational modification, catalyzed by kinases, for signaling and regulation. Phosphotyrosines frequently target SH2 domains. The spleen tyrosine kinase (Syk) is critical for tyrosine phosphorylation of multiple proteins and for regulation of important pathways. Phosphorylation of both Y342 and Y346 in Syk linker B is required for optimal signaling. The SH2 domains of Vav1 and PLC-γ both bind this doubly phosphorylated motif. Here we used a recently developed method to calculate the effects of Y342 and Y346 phosphorylation on the rate constants of a peptide from Syk linker B binding to the SH2 domains of Vav1 and PLC-γ. The predicted effects agree well with experimental observations. Moreover, we found that the same doubly phosphorylated peptide binds the two SH2 domains via distinct mechanism, with apparent rigid docking for Vav1 SH2 and dock-and-coalesce for PLC-γ SH2.
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Affiliation(s)
- Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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79
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Modular peptide binding: From a comparison of natural binders to designed armadillo repeat proteins. J Struct Biol 2014; 185:147-62. [DOI: 10.1016/j.jsb.2013.07.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 07/26/2013] [Accepted: 07/27/2013] [Indexed: 11/23/2022]
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80
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Majkut P, Claußnitzer I, Merk H, Freund C, Hackenberger CPR, Gerrits M. Completion of proteomic data sets by Kd measurement using cell-free synthesis of site-specifically labeled proteins. PLoS One 2013; 8:e82352. [PMID: 24340019 PMCID: PMC3858276 DOI: 10.1371/journal.pone.0082352] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 10/16/2013] [Indexed: 11/20/2022] Open
Abstract
The characterization of phosphotyrosine mediated protein-protein interactions is vital for the interpretation of downstream pathways of transmembrane signaling processes. Currently however, there is a gap between the initial identification and characterization of cellular binding events by proteomic methods and the in vitro generation of quantitative binding information in the form of equilibrium rate constants (Kd values). In this work we present a systematic, accelerated and simplified approach to fill this gap: using cell-free protein synthesis with site-specific labeling for pull-down and microscale thermophoresis (MST) we were able to validate interactions and to establish a binding hierarchy based on Kd values as a completion of existing proteomic data sets. As a model system we analyzed SH2-mediated interactions of the human T-cell phosphoprotein ADAP. Putative SH2 domain-containing binding partners were synthesized from a cDNA library using Expression-PCR with site-specific biotinylation in order to analyze their interaction with fluorescently labeled and in vitro phosphorylated ADAP by pull-down. On the basis of the pull-down results, selected SH2’s were subjected to MST to determine Kd values. In particular, we could identify an unexpectedly strong binding of ADAP to the previously found binding partner Rasa1 of about 100 nM, while no evidence of interaction was found for the also predicted SH2D1A. Moreover, Kd values between ADAP and its known binding partners SLP-76 and Fyn were determined. Next to expanding data on ADAP suggesting promising candidates for further analysis in vivo, this work marks the first Kd values for phosphotyrosine/SH2 interactions on a phosphoprotein level.
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Affiliation(s)
- Paul Majkut
- Department Chemical Biology II, Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | | | | | - Christian Freund
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Christian P. R. Hackenberger
- Department Chemical Biology II, Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Institut für Chemie, Humboldt-Universität zu Berlin, Berlin, Germany
- * E-mail: (MG); (CH)
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81
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Molecular mechanisms of SH2- and PTB-domain-containing proteins in receptor tyrosine kinase signaling. Cold Spring Harb Perspect Biol 2013; 5:a008987. [PMID: 24296166 DOI: 10.1101/cshperspect.a008987] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Intracellular signaling is mediated by reversible posttranslational modifications (PTMs) that include phosphorylation, ubiquitination, and acetylation, among others. In response to extracellular stimuli such as growth factors, receptor tyrosine kinases (RTKs) typically dimerize and initiate signaling through phosphorylation of their cytoplasmic tails and downstream scaffolds. Signaling effectors are recruited to these phosphotyrosine (pTyr) sites primarily through Src homology 2 (SH2) domains and pTyr-binding (PTB) domains. This review describes how these conserved domains specifically recognize pTyr residues and play a major role in mediating precise downstream signaling events.
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82
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Reinhardt HC, Yaffe MB. Phospho-Ser/Thr-binding domains: navigating the cell cycle and DNA damage response. Nat Rev Mol Cell Biol 2013; 14:563-80. [PMID: 23969844 DOI: 10.1038/nrm3640] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Coordinated progression through the cell cycle is a complex challenge for eukaryotic cells. Following genotoxic stress, diverse molecular signals must be integrated to establish checkpoints specific for each cell cycle stage, allowing time for various types of DNA repair. Phospho-Ser/Thr-binding domains have emerged as crucial regulators of cell cycle progression and DNA damage signalling. Such domains include 14-3-3 proteins, WW domains, Polo-box domains (in PLK1), WD40 repeats (including those in the E3 ligase SCF(βTrCP)), BRCT domains (including those in BRCA1) and FHA domains (such as in CHK2 and MDC1). Progress has been made in our understanding of the motif (or motifs) that these phospho-Ser/Thr-binding domains connect with on their targets and how these interactions influence the cell cycle and DNA damage response.
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Affiliation(s)
- H Christian Reinhardt
- David H. Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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83
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Jones RB. Do low-affinity ErbB receptor protein interactions represent the base of a cell signaling iceberg? Expert Rev Proteomics 2013; 10:115-8. [PMID: 23573776 DOI: 10.1586/epr.12.78] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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84
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Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains. Proc Natl Acad Sci U S A 2013; 110:14924-9. [PMID: 23980151 DOI: 10.1073/pnas.1303640110] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dysregulated tyrosine kinase BCR-ABL causes chronic myelogenous leukemia in humans and forms a large multiprotein complex that includes the Src-homology 2 (SH2) domain-containing phosphatase 2 (SHP2). The expression of SHP2 is necessary for BCR-ABL-dependent oncogenic transformation, but the precise signaling mechanisms of SHP2 are not well understood. We have developed binding proteins, termed monobodies, for the N- and C-terminal SH2 domains of SHP2. Intracellular expression followed by interactome analysis showed that the monobodies are essentially monospecific to SHP2. Two crystal structures revealed that the monobodies occupy the phosphopeptide-binding sites of the SH2 domains and thus can serve as competitors of SH2-phosphotyrosine interactions. Surprisingly, the segments of both monobodies that bind to the peptide-binding grooves run in the opposite direction to that of canonical phosphotyrosine peptides, which may contribute to their exquisite specificity. When expressed in cells, monobodies targeting the N-SH2 domain disrupted the interaction of SHP2 with its upstream activator, the Grb2-associated binder 2 adaptor protein, suggesting decoupling of SHP2 from the BCR-ABL protein complex. Inhibition of either N-SH2 or C-SH2 was sufficient to inhibit two tyrosine phosphorylation events that are critical for SHP2 catalytic activity and to block ERK activation. In contrast, targeting the N-SH2 or C-SH2 revealed distinct roles of the two SH2 domains in downstream signaling, such as the phosphorylation of paxillin and signal transducer and activator of transcription 5. Our results delineate a hierarchy of function for the SH2 domains of SHP2 and validate monobodies as potent and specific antagonists of protein-protein interactions in cancer cells.
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85
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Chudasama KK, Winnay J, Johansson S, Claudi T, König R, Haldorsen I, Johansson B, Woo JR, Aarskog D, Sagen JV, Kahn CR, Molven A, Njølstad PR. SHORT syndrome with partial lipodystrophy due to impaired phosphatidylinositol 3 kinase signaling. Am J Hum Genet 2013; 93:150-7. [PMID: 23810379 DOI: 10.1016/j.ajhg.2013.05.023] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 05/18/2013] [Accepted: 05/24/2013] [Indexed: 01/19/2023] Open
Abstract
The phosphatidylinositol 3 kinase (PI3K) pathway regulates fundamental cellular processes such as metabolism, proliferation, and survival. A central component in this pathway is the p85α regulatory subunit, encoded by PIK3R1. Using whole-exome sequencing, we identified a heterozygous PIK3R1 mutation (c.1945C>T [p.Arg649Trp]) in two unrelated families affected by partial lipodystrophy, low body mass index, short stature, progeroid face, and Rieger anomaly (SHORT syndrome). This mutation led to impaired interaction between p85α and IRS-1 and reduced AKT-mediated insulin signaling in fibroblasts from affected subjects and in reconstituted Pik3r1-knockout preadipocytes. Normal PI3K activity is critical for adipose differentiation and insulin signaling; the mutated PIK3R1 therefore provides a unique link among lipodystrophy, growth, and insulin signaling.
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Affiliation(s)
- Kishan Kumar Chudasama
- K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway
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86
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O'Donnell MP, Bashaw GJ. Distinct functional domains of the Abelson tyrosine kinase control axon guidance responses to Netrin and Slit to regulate the assembly of neural circuits. Development 2013; 140:2724-33. [PMID: 23720041 DOI: 10.1242/dev.093831] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To develop a functional nervous system, axons must initially navigate through a complex environment, directed by guidance ligands and receptors. These receptors must link to intracellular signaling cascades to direct axon pathfinding decisions. The Abelson tyrosine kinase (Abl) plays a crucial role in multiple Drosophila axon guidance pathways during development, though the mechanism by which Abl elicits a diverse set of guidance outputs is currently unknown. We identified Abl in a genetic screen for genes that contribute to Netrin-dependent axon guidance in midline-crossing (commissural) neurons. We find that Abl interacts both physically and genetically with the Netrin receptor Frazzled, and that disrupting this interaction prevents Abl from promoting midline axon crossing. Moreover, we find that Abl exerts its diverse activities through at least two different mechanisms: (1) a partly kinase-independent, structural function in midline attraction through its C-terminal F-actin binding domain (FABD) and (2) a kinase-dependent inhibition of repulsive guidance pathways that does not require the Abl C terminus. Abl also regulates motor axon pathfinding through a non-overlapping set of functional domains. These results highlight how a multifunctional kinase can trigger diverse axon guidance outcomes through the use of distinct structural motifs.
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Affiliation(s)
- Michael P O'Donnell
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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87
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Interaction domains of Sos1/Grb2 are finely tuned for cooperative control of embryonic stem cell fate. Cell 2013; 152:1008-20. [PMID: 23452850 DOI: 10.1016/j.cell.2013.01.056] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 10/18/2012] [Accepted: 01/31/2013] [Indexed: 12/28/2022]
Abstract
Metazoan evolution involves increasing protein domain complexity, but how this relates to control of biological decisions remains uncertain. The Ras guanine nucleotide exchange factor (RasGEF) Sos1 and its adaptor Grb2 are multidomain proteins that couple fibroblast growth factor (FGF) signaling to activation of the Ras-Erk pathway during mammalian development and drive embryonic stem cells toward the primitive endoderm (PrE) lineage. We show that the ability of Sos1/Grb2 to appropriately regulate pluripotency and differentiation factors and to initiate PrE development requires collective binding of multiple Sos1/Grb2 domains to their protein and phospholipid ligands. This provides a cooperative system that only allows lineage commitment when all ligand-binding domains are occupied. Furthermore, our results indicate that the interaction domains of Sos1 and Grb2 have evolved so as to bind ligands not with maximal strength but with specificities and affinities that maintain cooperativity. This optimized system ensures that PrE lineage commitment occurs in a timely and selective manner during embryogenesis.
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88
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Tanaka H, Akagi KI, Oneyama C, Tanaka M, Sasaki Y, Kanou T, Lee YH, Yokogawa D, Dobenecker MW, Nakagawa A, Okada M, Ikegami T. Identification of a new interaction mode between the Src homology 2 domain of C-terminal Src kinase (Csk) and Csk-binding protein/phosphoprotein associated with glycosphingolipid microdomains. J Biol Chem 2013; 288:15240-54. [PMID: 23548896 DOI: 10.1074/jbc.m112.439075] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins with Src homology 2 (SH2) domains play major roles in tyrosine kinase signaling. Structures of many SH2 domains have been studied, and the regions involved in their interactions with ligands have been elucidated. However, these analyses have been performed using short peptides consisting of phosphotyrosine followed by a few amino acids, which are described as the canonical recognition sites. Here, we report the solution structure of the SH2 domain of C-terminal Src kinase (Csk) in complex with a longer phosphopeptide from the Csk-binding protein (Cbp). This structure, together with biochemical experiments, revealed the existence of a novel binding region in addition to the canonical phosphotyrosine 314-binding site of Cbp. Mutational analysis of this second region in cells showed that both canonical and novel binding sites are required for tumor suppression through the Cbp-Csk interaction. Furthermore, the data indicate an allosteric connection between Cbp binding and Csk activation that arises from residues in the βB/βC loop of the SH2 domain.
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Affiliation(s)
- Hiroaki Tanaka
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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89
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Ju T, Niu W, Cerny R, Bollman J, Roy A, Guo J. Molecular recognition of sulfotyrosine and phosphotyrosine by the Src homology 2 domain. MOLECULAR BIOSYSTEMS 2013; 9:1829-32. [DOI: 10.1039/c3mb70061e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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90
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Kraskouskaya D, Duodu E, Arpin CC, Gunning PT. Progress towards the development of SH2 domain inhibitors. Chem Soc Rev 2013; 42:3337-70. [DOI: 10.1039/c3cs35449k] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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91
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SUEDA S, SHINBOKU Y, KUSABA T. An SH2 Domain-Based Tyrosine Kinase Assay Using Biotin Ligase Modified with a Terbium(III) Complex. ANAL SCI 2013; 29:491-7. [DOI: 10.2116/analsci.29.491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Shinji SUEDA
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
- Research Center for Bio-microsensing Technology, Kyushu Institute of Technology
| | - Yuki SHINBOKU
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
| | - Takeshi KUSABA
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology
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92
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Kaneko T, Joshi R, Feller SM, Li SS. Phosphotyrosine recognition domains: the typical, the atypical and the versatile. Cell Commun Signal 2012; 10:32. [PMID: 23134684 PMCID: PMC3507883 DOI: 10.1186/1478-811x-10-32] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 10/09/2012] [Indexed: 12/21/2022] Open
Abstract
SH2 domains are long known prominent players in the field of phosphotyrosine recognition within signaling protein networks. However, over the years they have been joined by an increasing number of other protein domain families that can, at least with some of their members, also recognise pTyr residues in a sequence-specific context. This superfamily of pTyr recognition modules, which includes substantial fractions of the PTB domains, as well as much smaller, or even single member fractions like the HYB domain, the PKCδ and PKCθ C2 domains and RKIP, represents a fascinating, medically relevant and hence intensely studied part of the cellular signaling architecture of metazoans. Protein tyrosine phosphorylation clearly serves a plethora of functions and pTyr recognition domains are used in a similarly wide range of interaction modes, which encompass, for example, partner protein switching, tandem recognition functionalities and the interaction with catalytically active protein domains. If looked upon closely enough, virtually no pTyr recognition and regulation event is an exact mirror image of another one in the same cell. Thus, the more we learn about the biology and ultrastructural details of pTyr recognition domains, the more does it become apparent that nature cleverly combines and varies a few basic principles to generate a sheer endless number of sophisticated and highly effective recognition/regulation events that are, under normal conditions, elegantly orchestrated in time and space. This knowledge is also valuable when exploring pTyr reader domains as diagnostic tools, drug targets or therapeutic reagents to combat human diseases.
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Affiliation(s)
- Tomonori Kaneko
- Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
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93
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Subramaniam A, Shanmugam MK, Perumal E, Li F, Nachiyappan A, Dai X, Swamy SN, Ahn KS, Kumar AP, Tan BKH, Hui KM, Sethi G. Potential role of signal transducer and activator of transcription (STAT)3 signaling pathway in inflammation, survival, proliferation and invasion of hepatocellular carcinoma. Biochim Biophys Acta Rev Cancer 2012; 1835:46-60. [PMID: 23103770 DOI: 10.1016/j.bbcan.2012.10.002] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 10/18/2012] [Accepted: 10/21/2012] [Indexed: 12/14/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal malignancies, and is also the fourth most common cancer worldwide with around 700,000 new cases each year. Currently, first line chemotherapeutic drugs used for HCC include fluorouracil, cisplatin, doxorubicin, paclitaxel and mitomycin, but most of these are non-selective cytotoxic molecules with significant side effects. Sorafenib is the only approved targeted therapy by the U.S. Food and Drug Administration for HCC treatment, but patients suffer from various kinds of adverse effects, including hypertension. The signal-transducer-and-activator-of-transcription 3 (STAT3) protein, one of the members of STATs transcription factor family, has been implicated in signal transduction by different cytokines, growth factors and oncogenes. In normal cells, STAT3 activation is tightly controlled to prevent dysregulated gene transcription, whereas constitutively activated STAT3 plays an important role in tumorigenesis through the upregulation of genes involved in anti-apoptosis, proliferation and angiogenesis. Thus, pharmacologically safe and effective agents that can block STAT3 activation have the potential both for the prevention and treatment of HCC. In the present review, we discuss the possible role of STAT3 signaling cascade and its interacting partners in the initiation of HCC and also analyze the role of various STAT3 regulated genes in HCC progression, inflammation, survival, invasion and angiogenesis.
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Affiliation(s)
- Aruljothi Subramaniam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
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94
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Kaneko T, Huang H, Cao X, Li X, Li C, Voss C, Sidhu SS, Li SSC. Superbinder SH2 Domains Act as Antagonists of Cell Signaling. Sci Signal 2012; 5:ra68. [DOI: 10.1126/scisignal.2003021] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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95
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Abstract
c-Src and Bcr-Abl are two cytoplasmatic tyrosine kinases (TKs) involved in the development of malignancies. In particular, Bcr-Abl is the etiologic agent of chronic myeloid leukemia, where Src is also involved; the latter is hyperactivated in several solid tumors. Because of the structural homology between Src and Abl, several compounds originally synthesized as Src inhibitors have also been shown to be Abl inhibitors, useful in overcoming the onset of some types of chronic myeloid leukemia resistances, which frequently appear in the advanced phases of pathology. In recent years, the development of such compounds has been promoted by both excellent preclinical and clinical results, and by the theory that dual or multi-targeted inhibitors might be more effective than selective inhibitors. This review is an update on the most important dual inhibitors already in clinical trials and includes information regarding compounds that have appeared in the literature in recent years.
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96
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Abstract
Suppressors of cytokine signaling 3 (SOCS3) has been shown to be an important and non-redundant feedback inhibitor of several cytokines including leukemia inhibitory factor, IL-6, IL-11, Ciliary neurotrophic factor (CNTF), leptin, and granulocyte colony-stimulating factor (G-CSF). Loss of SOCS3 in vivo has profound effects on placental development, inflammation, fat-induced weight gain, and insulin sensitivity. SOCS3 expression is induced by Janus kinase (JAK)/signal transducers and activators of transcription (STAT) signaling and it then binds to specific cytokine receptors (including gp130, G-CSF, and leptin receptors). SOCS3 then inhibits JAK/STAT signaling in two distinct ways. First, SOCS3 is able to directly inhibit the catalytic activity of JAK1, JAK2, or TYK2 while remaining bound to the cytokine receptor. Second, SOCS3 recruits elongins B/C and Cullin5 to generate an E3 ligase that ubiquitinates both JAK and cytokine receptor targeting them for proteasomal degradation. Detailed in vivo studies have revealed that SOCS3 action not only limits the duration of cytokine signaling to prevent overactivity but it is also important in maintaining the specificity of cytokine signaling.
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Affiliation(s)
- Jeffrey J Babon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.
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97
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Yamashita M, Chattopadhyay S, Fensterl V, Saikia P, Wetzel JL, Sen GC. Epidermal growth factor receptor is essential for Toll-like receptor 3 signaling. Sci Signal 2012; 5:ra50. [PMID: 22810896 DOI: 10.1126/scisignal.2002581] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Toll-like receptors (TLRs) recognize specific microbial products and elicit innate immune signals to activate specific transcription factors that induce protective proteins, such as interferon. TLR3 is localized to endosomes and recognizes double-stranded RNA (dsRNA), which is generated by virally infected or apoptotic cells. TLR3 has been genetically linked to several human diseases, including some without viral etiology. Unlike other TLRs, TLR3 requires phosphorylation of two specific tyrosine residues in its cytoplasmic domain to recruit the adaptor protein TRIF (Toll-interleukin-1 receptor domain-containing adaptor protein inducing interferon-β) and initiate the antiviral response. We showed that two protein tyrosine kinases, the epidermal growth factor receptor (EGFR) ErbB1 and Src, bound sequentially to dsRNA-activated TLR3 and phosphorylated the two tyrosine residues. In cells lacking EGFR or treated with an inhibitor of EGFR, viral replication was enhanced and induction of antiviral genes was impaired. Thus, these results reveal a connection between antiviral innate immunity and cell growth regulators.
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Affiliation(s)
- Michifumi Yamashita
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, NE20, Cleveland, OH 44195, USA
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98
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Tosca L, Glass R, Bronchain O, Philippe L, Ciapa B. PLCγ, G-protein of the Gαq type and cADPr pathway are associated to trigger the fertilization Ca2+ signal in the sea urchin egg. Cell Calcium 2012; 52:388-96. [PMID: 22784667 DOI: 10.1016/j.ceca.2012.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 06/19/2012] [Accepted: 06/20/2012] [Indexed: 11/18/2022]
Abstract
In all species, fertilization triggers in the egg a rapid and transient increase of intracellular free calcium (Cai), but how this signal is generated following sperm and egg interaction has not been clearly characterised yet. In sea urchin, a signalling pathway involving tyrosine kinase and PLCγ has been proposed to be at the origin of the fertilization Cai signal. We report here that injection of src homology-2 (SH2) domains of the sea urchin PLCγ inhibits in a competitive manner the endogenous PLCγ, alters both the amplitude and duration of the fertilization Cai wave, but does not abrogate it. Our results suggest that PLCγ acts in conjunction with a cADPr pathway and G-proteins of the Gαq type to trigger the fertilization Cai wave, and reinforce a crucial role for PLCγ at mitosis and cytokinesis.
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Affiliation(s)
- Lucie Tosca
- INSERM U935/Université Paris Sud/AP-HP, Histologie-Embryologie-Cytogénétique, Hôpital Antoine Béclère, 92141 Clamart, France
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99
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Liu BA, Engelmann BW, Nash PD. The language of SH2 domain interactions defines phosphotyrosine-mediated signal transduction. FEBS Lett 2012; 586:2597-605. [PMID: 22569091 DOI: 10.1016/j.febslet.2012.04.054] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 04/25/2012] [Accepted: 04/26/2012] [Indexed: 10/28/2022]
Abstract
Natural languages arise in an unpremeditated fashion resulting in words and syntax as individual units of information content that combine in a manner that is both complex and contextual, yet intuitive to a native reader. In an analogous manner, protein interaction domains such as the Src Homology 2 (SH2) domain recognize and "read" the information contained within their cognate peptide ligands to determine highly selective protein-protein interactions that underpin much of cellular signal transduction. Herein, we discuss how contextual sequence information, which combines the use of permissive and non-permissive residues within a parent motif, is a defining feature of selective interactions across SH2 domains. Within a system that reads phosphotyrosine modifications this provides crucial information to distinguish preferred interactions. This review provides a structural and biochemical overview of SH2 domain binding to phosphotyrosine-containing peptide motifs and discusses how the diverse set of SH2 domains is able to differentiate phosphotyrosine ligands.
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Affiliation(s)
- Bernard A Liu
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave., Toronto, Ontario, Canada M5G 1X5
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100
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Nash PD. Why modules matter. FEBS Lett 2012; 586:2572-4. [PMID: 22710154 DOI: 10.1016/j.febslet.2012.04.049] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 04/23/2012] [Accepted: 04/24/2012] [Indexed: 11/29/2022]
Abstract
The serendipitous discovery of the SH2 domain unleashed a sea-change in our conceptual molecular understanding of protein function. The reductionist approaches that followed from the recognition of modular protein interaction domains transformed our understanding of cellular signal transduction systems, how they evolve and how they may be manipulated. We now recognize thousands of conserved protein modules - many of which have been described in structure and function, implicated in disease, or underlie targeted therapeutics. The reductionist study of isolated protein modules has enabled the reconstruction of the protein interaction networks that underlie cellular signalling. Protein modules themselves are becoming tools to probe cellular activation states and identify key interactions hubs in both normal and diseased cells and the concept of protein modularity is central to the field of synthetic biology. This brief word of introduction serves to highlight the historical impact of the very powerful idea of protein modules and sets the stage for the exciting on-going discoveries discussed in this issue.
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Affiliation(s)
- Piers D Nash
- Ben May Department for Cancer Research and the Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA.
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