301
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Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes. Biochem J 2013; 454:361-9. [PMID: 23988124 DOI: 10.1042/bj20130545] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Because of their pervasiveness in eukaryotic genomes and their unique properties, understanding the role that ID (intrinsically disordered) regions in proteins play in the interactome is essential for gaining a better understanding of the network. Especially critical in determining this role is their ability to bind more than one partner using the same region. Studies have revealed that proteins containing ID regions tend to take a central role in protein interaction networks; specifically, they act as hubs, interacting with multiple different partners across time and space, allowing for the co-ordination of many cellular activities. There appear to be three different modules within ID regions responsible for their functionally promiscuous behaviour: MoRFs (molecular recognition features), SLiMs (small linear motifs) and LCRs (low complexity regions). These regions allow for functionality such as engaging in the formation of dynamic heteromeric structures which can serve to increase local activity of an enzyme or store a collection of functionally related molecules for later use. However, the use of promiscuity does not come without a cost: a number of diseases that have been associated with ID-containing proteins seem to be caused by undesirable interactions occurring upon altered expression of the ID-containing protein.
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302
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Mosca R, Céol A, Stein A, Olivella R, Aloy P. 3did: a catalog of domain-based interactions of known three-dimensional structure. Nucleic Acids Res 2013; 42:D374-9. [PMID: 24081580 PMCID: PMC3965002 DOI: 10.1093/nar/gkt887] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The database of 3D interacting domains (3did, available online for browsing and bulk download at http://3did.irbbarcelona.org) is a catalog of protein–protein interactions for which a high-resolution 3D structure is known. 3did collects and classifies all structural templates of domain–domain interactions in the Protein Data Bank, providing molecular details for such interactions. The current version also includes a pipeline for the discovery and annotation of novel domain–motif interactions. For every interaction, 3did identifies and groups different binding modes by clustering similar interfaces into ‘interaction topologies’. By maintaining a constantly updated collection of domain-based structural interaction templates, 3did is a reference source of information for the structural characterization of protein interaction networks. 3did is updated every 6 months.
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Affiliation(s)
- Roberto Mosca
- Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain, Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy, California Institute for Quantitative Biomedical Research (qb3) and Department of Bioengineering and Therapeutic Sciences, MC 2530, University of California San Francisco (UCSF) CA 94158-2330, USA and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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303
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Idan O, Hess H. Engineering enzymatic cascades on nanoscale scaffolds. Curr Opin Biotechnol 2013; 24:606-11. [DOI: 10.1016/j.copbio.2013.01.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 12/17/2012] [Accepted: 01/02/2013] [Indexed: 12/28/2022]
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304
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On eukaryotic intelligence: signaling system's guidance in the evolution of multicellular organization. Biosystems 2013; 114:8-24. [PMID: 23850535 DOI: 10.1016/j.biosystems.2013.06.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 06/28/2013] [Accepted: 06/30/2013] [Indexed: 12/11/2022]
Abstract
Communication with the environment is an essential characteristic of the living cell, even more when considering the origins and evolution of multicellularity. A number of changes and tinkering inventions were necessary in the evolutionary transition between prokaryotic and eukaryotic cells, which finally made possible the appearance of genuine multicellular organisms. In the study of this process, however, the transformations experimented by signaling systems themselves have been rarely object of analysis, obscured by other more conspicuous biological traits: incorporation of mitochondria, segregated nucleus, introns/exons, flagellum, membrane systems, etc. Herein a discussion of the main avenues of change from prokaryotic to eukaryotic signaling systems and a review of the signaling resources and strategies underlying multicellularity will be attempted. In the expansion of prokaryotic signaling systems, four main systemic resources were incorporated: molecular tools for detection of solutes, molecular tools for detection of solvent (Donnan effect), the apparatuses of cell-cycle control, and the combined system endocytosis/cytoskeleton. The multiple kinds of enlarged, mixed pathways that emerged made possible the eukaryotic revolution in morphological and physiological complexity. The massive incorporation of processing resources of electro-molecular nature, derived from the osmotic tools counteracting the Donnan effect, made also possible the organization of a computational tissue with huge information processing capabilities: the nervous system. In the central nervous systems of vertebrates, and particularly in humans, neurons have achieved both the highest level of molecular-signaling complexity and the highest degree of information-processing adaptability. Theoretically, it can be argued that there has been an accelerated pace of evolutionary change in eukaryotic signaling systems, beyond the other general novelties introduced by eukaryotic cells in their handling of DNA processes. Under signaling system's guidance, the whole processes of transcription, alternative splicing, mobile elements, and other elements of domain recombination have become closely intertwined and have propelled the differentiation capabilities of multicellular tissues and morphologies. An amazing variety of signaling and self-construction strategies have emerged out from the basic eukaryotic design of multicellular complexity, in millions and millions of new species evolved. This design can also be seen abstractly as a new kind of quasi-universal problem-solving 'engine' implemented at the biomolecular scale-providing the fundamentals of eukaryotic 'intelligence'. Analyzing in depth the problem-solving intelligence of eukaryotic cells would help to establish an integrative panorama of their information processing organization, and of their capability to handle the morphological and physiological complexity associated. Whether an informational updating of the venerable "cell theory" is feasible or not, becomes, at the time being - right in the middle of the massive data deluge/revolution from omic disciplines - a matter to careful consider.
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305
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Reddy Guduru SK, Chamakuri S, Chandrasekar G, Kitambi SS, Arya P. Tetrahydroquinoline-derived macrocyclic toolbox: the discovery of antiangiogenesis agents in zebrafish assay. ACS Med Chem Lett 2013; 4:666-70. [PMID: 24900727 DOI: 10.1021/ml400026n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 05/24/2013] [Indexed: 02/06/2023] Open
Abstract
A novel approach to incorporate the macrocyclic rings onto the privileged substructure, i.e., tetrahydroquinoline scaffold, is developed. The presence of an amino acid-derived moiety in the macrocyclic skeleton provides an opportunity to modulate the nature of the chiral side chain. Further, evaluation in a zebrafish screen identified three active small molecules (2.5b, 3.2d, and 4.2) as antiangiogenesis agents at 2.5 μM.
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Affiliation(s)
- Shiva Krishna Reddy Guduru
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | - Srinivas Chamakuri
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
| | | | - Satish Srinivas Kitambi
- School of Life Sciences, Södertörns Högskola, Sweden
- Division of Molecular Neurobiology and Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Prabhat Arya
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India
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306
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Adhikary R, Zimmermann J, Liu J, Dawson PE, Romesberg FE. Experimental characterization of electrostatic and conformational heterogeneity in an SH3 domain. J Phys Chem B 2013; 117:13082-9. [PMID: 23834285 DOI: 10.1021/jp402772x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electrostatic and conformational heterogeneity make central contributions to protein function, but their experimental characterization requires a combination of spatial and temporal resolution that is challenging to achieve. Src homology 3 (SH3) domains mediate protein-protein interactions, and NMR studies have demonstrated that most possess conformational heterogeneity, which could be critical for their function. Here, we use the IR absorptions of carbon-deuterium (C-D) bonds site-selectively incorporated throughout the N-terminal SH3 domain from the murine adapter protein Crk-II to characterize its different microenvironments with high spatial and temporal resolution. The C-D absorptions are only differentiated in the folded state of the protein where they show evidence of significant environmental heterogeneity. However, the spectra of the folded state are independent of temperature, and upon thermal denaturation the protein undergoes a single, global unfolding transition. While some evidence of conformational heterogeneity is found within the peptide backbone, the majority of the environmental heterogeneity appears to result from electrostatics.
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Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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307
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Jogula S, Dasari B, Khatravath M, Chandrasekar G, Kitambi SS, Arya P. Building a Macrocyclic Toolbox fromC-Linked Carbohydrates Identifies Antiangiogenesis Agents from Zebrafish Assay. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300548] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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308
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Balanced nucleocytosolic partitioning defines a spatial network to coordinate circadian physiology in plants. Dev Cell 2013; 26:73-85. [PMID: 23830866 DOI: 10.1016/j.devcel.2013.06.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 03/14/2013] [Accepted: 06/06/2013] [Indexed: 01/13/2023]
Abstract
Biological networks consist of a defined set of regulatory motifs. Subcellular compartmentalization of regulatory molecules can provide a further dimension in implementing regulatory motifs. However, spatial regulatory motifs and their roles in biological networks have rarely been explored. Here we show, using experimentation and mathematical modeling, that spatial segregation of GIGANTEA (GI), a critical component of plant circadian systems, into nuclear and cytosolic compartments leads to differential functions as positive and negative regulators of the circadian core gene, LHY, forming an incoherent feedforward loop to regulate LHY. This regulatory motif formed by nucleocytoplasmic partitioning of GI confers, through the balanced operation of the nuclear and cytosolic GI, strong rhythmicity and robustness to external and internal noises to the circadian system. Our results show that spatial and functional segregation of a single molecule species into different cellular compartments provides a means for extending the regulatory capabilities of biological networks.
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309
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Meyer MR, Shah S, Rao AG. Insights into molecular interactions between the juxtamembrane and kinase subdomains of the Arabidopsis Crinkly-4 receptor-like kinase. Arch Biochem Biophys 2013; 535:101-10. [DOI: 10.1016/j.abb.2013.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 01/10/2023]
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310
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Matt U, Sharif O, Martins R, Furtner T, Langeberg L, Gawish R, Elbau I, Zivkovic A, Lakovits K, Oskolkova O, Doninger B, Vychytil A, Perkmann T, Schabbauer G, Binder CJ, Bochkov VN, Scott JD, Knapp S. WAVE1 mediates suppression of phagocytosis by phospholipid-derived DAMPs. J Clin Invest 2013; 123:3014-24. [PMID: 23934128 DOI: 10.1172/jci60681] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 05/02/2013] [Indexed: 01/20/2023] Open
Abstract
Clearance of invading pathogens is essential to preventing overwhelming inflammation and sepsis that are symptomatic of bacterial peritonitis. Macrophages participate in this innate immune response by engulfing and digesting pathogens, a process called phagocytosis. Oxidized phospholipids (OxPL) are danger-associated molecular patterns (DAMPs) generated in response to infection that can prevent the phagocytic clearance of bacteria. We investigated the mechanism underlying OxPL action in macrophages. Exposure to OxPL induced alterations in actin polymerization, resulting in spreading of peritoneal macrophages and diminished uptake of E. coli. Pharmacological and cell-based studies showed that an anchored pool of PKA mediates the effects of OxPL. Gene silencing approaches identified the A-kinase anchoring protein (AKAP) WAVE1 as an effector of OxPL action in vitro. Chimeric Wave1(-/-) mice survived significantly longer after infection with E. coli and OxPL treatment in vivo. Moreover, we found that endogenously generated OxPL in human peritoneal dialysis fluid from end-stage renal failure patients inhibited phagocytosis via WAVE1. Collectively, these data uncover an unanticipated role for WAVE1 as a critical modulator of the innate immune response to severe bacterial infections.
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Affiliation(s)
- Ulrich Matt
- Research Center for Molecular Medicine of Austrian Academy of Sciences, Vienna, Austria
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311
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Belotti E, Polanowska J, Daulat AM, Audebert S, Thomé V, Lissitzky JC, Lembo F, Blibek K, Omi S, Lenfant N, Gangar A, Montcouquiol M, Santoni MJ, Sebbagh M, Aurrand-Lions M, Angers S, Kodjabachian L, Reboul J, Borg JP. The human PDZome: a gateway to PSD95-Disc large-zonula occludens (PDZ)-mediated functions. Mol Cell Proteomics 2013; 12:2587-603. [PMID: 23722234 PMCID: PMC3769332 DOI: 10.1074/mcp.o112.021022] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein–protein interactions organize the localization, clustering, signal transduction, and degradation of cellular proteins and are therefore implicated in numerous biological functions. These interactions are mediated by specialized domains able to bind to modified or unmodified peptides present in binding partners. Among the most broadly distributed protein interaction domains, PSD95-disc large-zonula occludens (PDZ) domains are usually able to bind carboxy-terminal sequences of their partners. In an effort to accelerate the discovery of PDZ domain interactions, we have constructed an array displaying 96% of the human PDZ domains that is amenable to rapid two-hybrid screens in yeast. We have demonstrated that this array can efficiently identify interactions using carboxy-terminal sequences of PDZ domain binders such as the E6 oncoviral protein and protein kinases (PDGFRβ, BRSK2, PCTK1, ACVR2B, and HER4); this has been validated via mass spectrometry analysis. Taking advantage of this array, we show that PDZ domains of Scrib and SNX27 bind to the carboxy-terminal region of the planar cell polarity receptor Vangl2. We also have demonstrated the requirement of Scrib for the promigratory function of Vangl2 and described the morphogenetic function of SNX27 in the early Xenopus embryo. The resource presented here is thus adapted for the screen of PDZ interactors and, furthermore, should facilitate the understanding of PDZ-mediated functions.
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Affiliation(s)
- Edwige Belotti
- CRCM, Equipe labellisée Ligue Contre le Cancer, Inserm, U1068, CRCM, Marseille, F-13009, France
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312
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Chamakuri S, Guduru SKR, Pamu S, Chandrasekar G, Kitambi SS, Arya P. A Modular Approach to Build Macrocyclic Diversity in Aminoindoline Scaffolds Identifies Antiangiogenesis Agents from a Zebrafish Assay. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300409] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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313
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Bachmann VA, Riml A, Huber RG, Baillie GS, Liedl KR, Valovka T, Stefan E. Reciprocal regulation of PKA and Rac signaling. Proc Natl Acad Sci U S A 2013; 110:8531-6. [PMID: 23657011 PMCID: PMC3666698 DOI: 10.1073/pnas.1215902110] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Activated G protein-coupled receptors (GPCRs) and receptor tyrosine kinases relay extracellular signals through spatial and temporal controlled kinase and GTPase entities. These enzymes are coordinated by multifunctional scaffolding proteins for precise intracellular signal processing. The cAMP-dependent protein kinase A (PKA) is the prime example for compartmentalized signal transmission downstream of distinct GPCRs. A-kinase anchoring proteins tether PKA to specific intracellular sites to ensure precision and directionality of PKA phosphorylation events. Here, we show that the Rho-GTPase Rac contains A-kinase anchoring protein properties and forms a dynamic cellular protein complex with PKA. The formation of this transient core complex depends on binary interactions with PKA subunits, cAMP levels and cellular GTP-loading accounting for bidirectional consequences on PKA and Rac downstream signaling. We show that GTP-Rac stabilizes the inactive PKA holoenzyme. However, β-adrenergic receptor-mediated activation of GTP-Rac-bound PKA routes signals to the Raf-Mek-Erk cascade, which is critically implicated in cell proliferation. We describe a further mechanism of how cAMP enhances nuclear Erk1/2 signaling: It emanates from transphosphorylation of p21-activated kinases in their evolutionary conserved kinase-activation loop through GTP-Rac compartmentalized PKA activities. Sole transphosphorylation of p21-activated kinases is not sufficient to activate Erk1/2. It requires complex formation of both kinases with GTP-Rac1 to unleash cAMP-PKA-boosted activation of Raf-Mek-Erk. Consequently GTP-Rac functions as a dual kinase-tuning scaffold that favors the PKA holoenzyme and contributes to potentiate Erk1/2 signaling. Our findings offer additional mechanistic insights how β-adrenergic receptor-controlled PKA activities enhance GTP-Rac-mediated activation of nuclear Erk1/2 signaling.
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Affiliation(s)
- Verena A. Bachmann
- Institutes of Biochemistry and
- Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria; and
| | - Anna Riml
- Institutes of Biochemistry and
- Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria; and
| | - Roland G. Huber
- Theoretical Chemistry and
- Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria; and
| | - George S. Baillie
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Klaus R. Liedl
- Theoretical Chemistry and
- Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria; and
| | - Taras Valovka
- Institutes of Biochemistry and
- Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria; and
| | - Eduard Stefan
- Institutes of Biochemistry and
- Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria; and
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314
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Gold MG, Fowler DM, Means CK, Pawson CT, Stephany JJ, Langeberg LK, Fields S, Scott JD. Engineering A-kinase anchoring protein (AKAP)-selective regulatory subunits of protein kinase A (PKA) through structure-based phage selection. J Biol Chem 2013; 288:17111-21. [PMID: 23625929 PMCID: PMC3682517 DOI: 10.1074/jbc.m112.447326] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
PKA is retained within distinct subcellular environments by the association of its regulatory type II (RII) subunits with A-kinase anchoring proteins (AKAPs). Conventional reagents that universally disrupt PKA anchoring are patterned after a conserved AKAP motif. We introduce a phage selection procedure that exploits high-resolution structural information to engineer RII mutants that are selective for a particular AKAP. Selective RII (RSelect) sequences were obtained for eight AKAPs following competitive selection screening. Biochemical and cell-based experiments validated the efficacy of RSelect proteins for AKAP2 and AKAP18. These engineered proteins represent a new class of reagents that can be used to dissect the contributions of different AKAP-targeted pools of PKA. Molecular modeling and high-throughput sequencing analyses revealed the molecular basis of AKAP-selective interactions and shed new light on native RII-AKAP interactions. We propose that this structure-directed evolution strategy might be generally applicable for the investigation of other protein interaction surfaces.
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Affiliation(s)
- Matthew G Gold
- Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington 98195, USA.
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315
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Cell signaling experiments driven by optical manipulation. Int J Mol Sci 2013; 14:8963-84. [PMID: 23698758 PMCID: PMC3676767 DOI: 10.3390/ijms14058963] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 04/08/2013] [Accepted: 04/14/2013] [Indexed: 01/09/2023] Open
Abstract
Cell signaling involves complex transduction mechanisms in which information released by nearby cells or extracellular cues are transmitted to the cell, regulating fundamental cellular activities. Understanding such mechanisms requires cell stimulation with precise control of low numbers of active molecules at high spatial and temporal resolution under physiological conditions. Optical manipulation techniques, such as optical tweezing, mechanical stress probing or nano-ablation, allow handling of probes and sub-cellular elements with nanometric and millisecond resolution. PicoNewton forces, such as those involved in cell motility or intracellular activity, can be measured with femtoNewton sensitivity while controlling the biochemical environment. Recent technical achievements in optical manipulation have new potentials, such as exploring the actions of individual molecules within living cells. Here, we review the progress in optical manipulation techniques for single-cell experiments, with a focus on force probing, cell mechanical stimulation and the local delivery of active molecules using optically manipulated micro-vectors and laser dissection.
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316
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Diss G, Filteau M, Freschi L, Leducq JB, Rochette S, Torres-Quiroz F, Landry CR. Integrative avenues for exploring the dynamics and evolution of protein interaction networks. Curr Opin Biotechnol 2013; 24:775-83. [PMID: 23571097 DOI: 10.1016/j.copbio.2013.02.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/14/2013] [Accepted: 02/24/2013] [Indexed: 01/09/2023]
Abstract
Over the past decade, the study of protein interaction networks (PINs) has shed light on the organizing principles of living cells. However, PINs have been mostly mapped in one single condition. We outline three of the most promising avenues of investigation in this field, namely the study of first, how PINs are rewired by mutations and environmental perturbations; secondly, how inter-species interactions affect PIN achitectures; thirdly, what mechanisms and forces drive PIN evolution. These investigations will unravel the dynamics and condition dependence of PINs and will thus lead to a better functional annotation of network architecture. One major challenge to reach these goals is the integration of PINs with other cellular regulatory networks in the context of complex cellular phenotypes.
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Affiliation(s)
- Guillaume Diss
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), PROTEO, Université Laval, Québec, Canada G1V 0A6
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317
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Siglin AE, Sun S, Moore JK, Tan S, Poenie M, Lear JD, Polenova T, Cooper JA, Williams JC. Dynein and dynactin leverage their bivalent character to form a high-affinity interaction. PLoS One 2013; 8:e59453. [PMID: 23577064 PMCID: PMC3618186 DOI: 10.1371/journal.pone.0059453] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/14/2013] [Indexed: 11/19/2022] Open
Abstract
Cytoplasmic dynein and dynactin participate in retrograde transport of organelles, checkpoint signaling and cell division. The principal subunits that mediate this interaction are the dynein intermediate chain (IC) and the dynactin p150(Glued); however, the interface and mechanism that regulates this interaction remains poorly defined. Herein, we use multiple methods to show the N-terminus of mammalian dynein IC, residues 10-44, is sufficient for binding p150(Glued). Consistent with this mapping, monoclonal antibodies that antagonize the dynein-dynactin interaction also bind to this region of the IC. Furthermore, double and triple alanine point mutations spanning residues 6 to 19 in the yeast IC homolog, Pac11, produce significant defects in spindle positioning. Using the same methods we show residues 381 to 530 of p150(Glued) form a minimal fragment that binds to the dynein IC. Sedimentation equilibrium experiments indicate that these individual fragments are predominantly monomeric, but admixtures of the IC and p150(Glued) fragments produce a 2:2 complex. This tetrameric complex is sensitive to salt, temperature and pH, suggesting that the binding is dominated by electrostatic interactions. Finally, circular dichroism (CD) experiments indicate that the N-terminus of the IC is disordered and becomes ordered upon binding p150(Glued). Taken together, the data indicate that the dynein-dynactin interaction proceeds through a disorder-to-order transition, leveraging its bivalent-bivalent character to form a high affinity, but readily reversible interaction.
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Affiliation(s)
- Amanda E. Siglin
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Shangjin Sun
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
| | - Jeffrey K. Moore
- Department of Cell Biology & Physiology, Washington University in Saint Louis, Saint Louis, Missouri, United States of America
| | - Sarah Tan
- Department of Cell and Molecular Biology, University of Texas, Austin, Texas, United States of America
| | - Martin Poenie
- Department of Cell and Molecular Biology, University of Texas, Austin, Texas, United States of America
| | - James D. Lear
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
| | - John A. Cooper
- Department of Cell Biology & Physiology, Washington University in Saint Louis, Saint Louis, Missouri, United States of America
| | - John C. Williams
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- Department of Molecular Medicine, Beckman Research Institute at City of Hope, Duarte, California, United States of America
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318
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Lim GE, Piske M, Johnson JD. 14-3-3 proteins are essential signalling hubs for beta cell survival. Diabetologia 2013; 56:825-37. [PMID: 23354124 DOI: 10.1007/s00125-012-2820-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 12/11/2012] [Indexed: 11/27/2022]
Abstract
AIMS/HYPOTHESIS Diabetes is characterised by pancreatic beta cell death and dysfunction, resulting from unbalanced pro-survival and pro-death signalling. The 14-3-3 proteins are molecular adaptors that integrate numerous signalling pathways, including the v-raf-leukaemia viral oncogene 1 (RAF1)/B cell leukaemia/lymphoma 2 (BCL-2)-associated agonist of cell death (BAD) pathway, which we have previously implicated in insulin-dependent beta cell survival. Nevertheless, the roles of 14-3-3 proteins in beta cell fate and function have not been investigated. METHODS We examined the abundance, localisation, modulation and roles of 14-3-3 proteins using quantitative RT-PCR, immunoblot or imaging. MIN6 cells or mouse islets cells were manipulated with inhibitors, short interfering RNA (siRNA) or plasmids overexpressing 14-3-3. RESULTS We first characterised the abundance and subcellular location of all seven 14-3-3 isoforms in mouse and human beta cells. Most isoforms were cytoplasmic, except 14-3-3σ, which appeared to be nuclear. Analysis of 14-3-3 abundance under stress conditions revealed distinct modulation in mouse islets and MIN6 cells. Generalised 14-3-3 inhibition promoted apoptosis and dysfunction, and siRNA-mediated knockdown revealed isoform-specific roles in caspase-3-dependent beta cell apoptosis, with a clear role for 14-3-3ζ. Overabundance of 14-3-3ζ sequestered BAD-BCL2-associated X protein (BAX) from mitochondria, attenuated Dp5 (also known as Hrk) and Puma (also known as Bbc3) induction, and increased survival in response to pro-inflammatory cytokines or thapsigargin. Anti-apoptotic insulin treatment increased the sequestration of BAD/BAX by 14-3-3ζ. BAD mutants that were unable to bind 14-3-3ζ localised to mitochondria and induced apoptosis. CONCLUSIONS/INTERPRETATION This first study of the 14-3-3 family in beta cells revealed specific regulation, localisation and anti-apoptotic roles among the isoforms. Focus on 14-3-3ζ revealed its importance in preventing BAD-BAX mitochondrial localisation and protecting beta cells from multiple stresses. Thus, some 14-3-3 proteins are pro-survival signalling hubs.
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Affiliation(s)
- G E Lim
- Diabetes Research Group, Department of Cellular and Physiological Sciences, University of British Columbia, 5358 Life Sciences Building, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3
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319
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Loughran PA, Stolz DB, Barrick SR, Wheeler DS, Friedman PA, Rachubinski RA, Watkins SC, Billiar TR. PEX7 and EBP50 target iNOS to the peroxisome in hepatocytes. Nitric Oxide 2013; 31:9-19. [PMID: 23474170 DOI: 10.1016/j.niox.2013.02.084] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 02/08/2013] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
Abstract
iNOS localizes to both the cytosol and peroxisomes in hepatocytes in vitro and in vivo. The structural determinants for iNOS localization are not known. One plausible mechanism for iNOS localization to the peroxisome is through the interaction with peroxisomal import proteins PEX5 or PEX7. siRNA knockdown of PEX7 reduced iNOS colocalization with the peroxisomal protein PMP70. Proteomic studies using MALDI-MS identified iNOS association with the 50-kD ezrin binding PDZ protein (EBP50). Confocal microscopy studies and immunoelectron microscopy confirmed iNOS association with EBP50, with greatest colocalization occurring at 8h of cytokine exposure. EBP50 associated with peroxisomes in a PEX5 and PEX7-dependent manner. iNOS localization to peroxisomes was contingent on EBP50 expression in LPS-treated mice. Thus, iNOS targeting to peroxisomes in hepatocytes involves interaction with PEX7 and EBP50. The targeting of iNOS protein to the peroxisome may shift the balance of metabolic processes that rely on heme proteins susceptible to modification by radical oxygen and nitrogen radicals.
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Affiliation(s)
- Patricia A Loughran
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
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320
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Etoc F, Lisse D, Bellaiche Y, Piehler J, Coppey M, Dahan M. Subcellular control of Rac-GTPase signalling by magnetogenetic manipulation inside living cells. NATURE NANOTECHNOLOGY 2013; 8:193-8. [PMID: 23455985 DOI: 10.1038/nnano.2013.23] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 12/31/2012] [Indexed: 05/20/2023]
Abstract
Many cell functions rely on the coordinated activity of signalling pathways at a subcellular scale. However, there are few tools capable of probing and perturbing signalling networks with a spatial resolution matching the intracellular dimensions of their activity patterns. Here we present a generic magnetogenetic approach based on the self-assembly of signalling complexes on the surface of functionalized magnetic nanoparticles inside living cells. The nanoparticles act as nanoscopic hot spots that can be displaced by magnetic forces and trigger signal transduction pathways that bring about a cell response. We applied this strategy to Rho-GTPases, a set of molecular switches known to regulate cell morphology via complex spatiotemporal patterns of activity. We demonstrate that the nanoparticle-mediated activation of signalling pathways leads to local remodelling of the actin cytoskeleton and to morphological changes.
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Affiliation(s)
- F Etoc
- Laboratoire Kastler Brossel, CNRS UMR 8552, Département de Physique et Institut de Biologie, Ecole normale supérieure, Université Pierre et Marie Curie-Paris 6, Paris, France
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321
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Rosner M, Schipany K, Hengstschläger M. Merging high-quality biochemical fractionation with a refined flow cytometry approach to monitor nucleocytoplasmic protein expression throughout the unperturbed mammalian cell cycle. Nat Protoc 2013; 8:602-26. [DOI: 10.1038/nprot.2013.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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322
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Qi Q, He K, Liu X, Pham C, Meyerkord C, Fu H, Ye K. Disrupting the PIKE-A/Akt interaction inhibits glioblastoma cell survival, migration, invasion and colony formation. Oncogene 2013; 32:1030-40. [PMID: 22450747 PMCID: PMC3808079 DOI: 10.1038/onc.2012.109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 01/24/2012] [Accepted: 02/21/2012] [Indexed: 12/15/2022]
Abstract
The cyclin-dependent kinase 4 (CDK4) amplicon is frequently amplified in numerous human cancers including gliomas. PIKE-A, a proto-oncogene that is one of the important components of the CDK4 amplicon, binds to and enhances the kinase activity of Akt, thereby promoting cancer progression. To define the roles of the PIKE-A/Akt interaction in glioblastoma multiform (GBM) progression, we used biochemical protein/protein interaction (PPI) assays and live cell fluorescence-based protein complementation assays to search for small peptide antagonist from these proteins that were able to block their interaction. Here, we show that disruption of the interaction between PIKE-A and Akt by the small peptides significantly reduces glioblastoma cell proliferation, colony formation, migration and invasion. Disruption of PIKE-A/Akt association potently suppressed GBM cell proliferation and sensitized the cells to two clinical drugs that are currently used to treat GBM. Interestingly, GBM cells containing the CDK4 amplicon were more responsive to the inhibition of the PIKE-A/Akt interaction than GBM cells lacking this amplicon. Taken together, our findings provide proof-of-principle that blocking a PPI that is essential for cancer progression provides a valuable strategy for therapeutic discovery.
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Affiliation(s)
- Q Qi
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - K He
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - X Liu
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - C Pham
- Department of Pharmacology, Emory University, Atlanta, GA, USA
| | - C Meyerkord
- Department of Pharmacology, Emory University, Atlanta, GA, USA
- Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA
| | - H Fu
- Department of Pharmacology, Emory University, Atlanta, GA, USA
- Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA
| | - K Ye
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
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Sivadas P, Dienes JM, St Maurice M, Meek WD, Yang P. A flagellar A-kinase anchoring protein with two amphipathic helices forms a structural scaffold in the radial spoke complex. ACTA ACUST UNITED AC 2013; 199:639-51. [PMID: 23148234 PMCID: PMC3494852 DOI: 10.1083/jcb.201111042] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Amphipathic helices in the A-kinase anchoring protein RSP3 bind to spoke proteins involved in the assembly and modulation of the flagellar radial spoke complex, expanding the repertoire of these versatile helical protein motifs. A-kinase anchoring proteins (AKAPs) contain an amphipathic helix (AH) that binds the dimerization and docking (D/D) domain, RIIa, in cAMP-dependent protein kinase A (PKA). Many AKAPs were discovered solely based on the AH–RIIa interaction in vitro. An RIIa or a similar Dpy-30 domain is also present in numerous diverged molecules that are implicated in critical processes as diverse as flagellar beating, membrane trafficking, histone methylation, and stem cell differentiation, yet these molecules remain poorly characterized. Here we demonstrate that an AKAP, RSP3, forms a dimeric structural scaffold in the flagellar radial spoke complex, anchoring through two distinct AHs, the RIIa and Dpy-30 domains, in four non-PKA spoke proteins involved in the assembly and modulation of the complex. Interestingly, one AH can bind both RIIa and Dpy-30 domains in vitro. Thus, AHs and D/D domains constitute a versatile yet potentially promiscuous system for localizing various effector mechanisms. These results greatly expand the current concept about anchoring mechanisms and AKAPs.
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Affiliation(s)
- Priyanka Sivadas
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
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324
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Yang G. Bioimage informatics for understanding spatiotemporal dynamics of cellular processes. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:367-80. [PMID: 23408597 DOI: 10.1002/wsbm.1214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The inner environment of the cell is highly dynamic and heterogeneous yet exquisitely organized. Successful completion of cellular processes within this environment depends on the right molecules or molecular complexes to function at the right place at the right time. Understanding spatiotemporal behaviors of cellular processes is therefore essential to understanding their molecular mechanisms at the systems level. These behaviors are usually visualized and recorded using imaging techniques. However, to infer from them systems-level molecular mechanisms, computational analysis and understanding of recorded image data is crucial, not only for acquiring quantitative behavior measurements but also for comprehending complex interactions among the molecules or molecular complexes involved. The technology of computational analysis and understanding of biological images is often referred to simply as bioimage informatics. This article introduces fundamentals of bioimage informatics for understanding spatiotemporal dynamics of cellular processes and reviews recent advances on this topic. Basic bioimage informatics concepts and techniques for characterizing spatiotemporal cell dynamics are introduced first. Studies on specific cellular processes such as cell migration and signal transduction are then used as examples to analyze and summarize recent advances, with the focus on transforming quantitative measurements of spatiotemporal cellular behaviors into knowledge of underlying molecular mechanisms. Despite the advances made, substantial technological challenges remain, especially in representation of spatiotemporal cellular behaviors and inference of systems-level molecular mechanisms. These challenges are briefly discussed. Overall, understanding spatiotemporal cell dynamics will provide critical insights into how specific cellular processes as well as the entire inner cellular environment are dynamically organized and regulated.
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Affiliation(s)
- Ge Yang
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
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325
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Zhang M, Pascal JM, Schumann M, Armen RS, Zhang JF. Identification of the functional binding pocket for compounds targeting small-conductance Ca²⁺-activated potassium channels. Nat Commun 2013; 3:1021. [PMID: 22929778 PMCID: PMC3563359 DOI: 10.1038/ncomms2017] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 07/20/2012] [Indexed: 12/14/2022] Open
Abstract
Small- and intermediate-conductance Ca2+-activated potassium channels, activated by Ca2+-bound calmodulin, play an important role in regulating membrane excitability. These channels are also linked to clinical abnormalities. A tremendous amount of effort has been devoted to developing small molecule compounds targeting these channels. However, these compounds often suffer from low potency and lack of selectivity, hindering their potentials for clinical use. A key contributing factor is the lack of knowledge of the binding site(s) for these compounds. Here we demonstrate by X-ray crystallography that the binding pocket for the compounds of the 1-EBIO class is located at the calmodulin-channel interface. We show that, based on structure data and molecular docking, mutations of the channel can effectively change the potency of these compounds. Our results provide insight into the molecular nature of the binding pocket and its contribution to the potency and selectivity of the compounds of the 1-EBIO class.
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Affiliation(s)
- Miao Zhang
- Department of Molecular Physiology and Biophysics, Thomas Jefferson University, 1020 Locust Street, Philadelphia, Pennsylvania 19107, USA
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326
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Li J, Bu P, Chen KY, Shen X. Spatial perturbation with synthetic protein scaffold reveals robustness of asymmetric cell division. ACTA ACUST UNITED AC 2013; 6:134-143. [PMID: 25750689 DOI: 10.4236/jbise.2013.62017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Asymmetric cell division is an important mechanism for creating diversity in a cellular population. Stem cells commonly perform asymmetric division to generate both a daughter stem cell for self-renewal and a more differentiated daughter cell to populate the tissue. During asymmetric cell division, protein cell fate determinants asymmetrically localize to the opposite poles of a dividing cell to cause distinct cell fate. However, it remains unclear whether cell fate determination is robust to fluctuations and noise during this spatial allocation process. To answer this question, we engineered Caulobacter, a bacterial model for asymmetric division, to express synthetic scaffolds with modular protein interaction domains. These scaffolds perturbed the spatial distribution of the PleC-DivJ-DivK phospho-signaling network without changing their endogenous expression levels. Surprisingly, enforcing symmetrical distribution of these cell fate determinants did not result in symmetric daughter fate or any morphological defects. Further computational analysis suggested that PleC and DivJ form a robust phospho-switch that can tolerate high amount of spatial variation. This insight may shed light on the presence of similar phospho-switches in stem cell asymmetric division regulation. Overall, our study demonstrates that synthetic protein scaffolds can provide a useful tool to probe biological systems for better understanding of their operating principles.
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Affiliation(s)
- Jiahe Li
- Department of Biomedical Engineering, Cornell University, Ithaca, USA
| | - Pengcheng Bu
- School of Electrical and Computer Engineering, Cornell University, Ithaca, USA
| | - Kai-Yuan Chen
- School of Electrical and Computer Engineering, Cornell University, Ithaca, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Cornell University, Ithaca, USA ; School of Electrical and Computer Engineering, Cornell University, Ithaca, USA
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327
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Dasari B, Jogula S, Borhade R, Balasubramanian S, Chandrasekar G, Kitambi SS, Arya P. Macrocyclic Glycohybrid Toolbox Identifies Novel Antiangiogenesis Agents from Zebrafish Assay. Org Lett 2013; 15:432-5. [DOI: 10.1021/ol3032297] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Bhanudas Dasari
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition, Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Srinivas Jogula
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition, Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Ramdas Borhade
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition, Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Sridhar Balasubramanian
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition, Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Gayathri Chandrasekar
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition, Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Satish Srinivas Kitambi
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition, Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Prabhat Arya
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500 046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition, Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
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328
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Aeluri M, Pramanik C, Chetia L, Mallurwar NK, Balasubramanian S, Chandrasekar G, Kitambi SS, Arya P. 14-Membered Macrocyclic Ring-Derived Toolbox: The Identification of Small Molecule Inhibitors of Angiogenesis and Early Embryo Development in Zebrafish Assay. Org Lett 2013; 15:436-9. [DOI: 10.1021/ol3032126] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Madhu Aeluri
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Chinmoy Pramanik
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Lakshindra Chetia
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Naveen Kumar Mallurwar
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Sridhar Balasubramanian
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Gayathri Chandrasekar
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Satish Srinivas Kitambi
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Prabhat Arya
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
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TNiK is required for postsynaptic and nuclear signaling pathways and cognitive function. J Neurosci 2013; 32:13987-99. [PMID: 23035106 DOI: 10.1523/jneurosci.2433-12.2012] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Traf2 and NcK interacting kinase (TNiK) contains serine-threonine kinase and scaffold domains and has been implicated in cell proliferation and glutamate receptor regulation in vitro. Here we report its role in vivo using mice carrying a knock-out mutation. TNiK binds protein complexes in the synapse linking it to the NMDA receptor (NMDAR) via AKAP9. NMDAR and metabotropic receptors bidirectionally regulate TNiK phosphorylation and TNiK is required for AMPA expression and synaptic function. TNiK also organizes nuclear complexes and in the absence of TNiK, there was a marked elevation in GSK3β and phosphorylation levels of its cognate phosphorylation sites on NeuroD1 with alterations in Wnt pathway signaling. We observed impairments in dentate gyrus neurogenesis in TNiK knock-out mice and cognitive testing using the touchscreen apparatus revealed impairments in pattern separation on a test of spatial discrimination. Object-location paired associate learning, which is dependent on glutamatergic signaling, was also impaired. Additionally, TNiK knock-out mice displayed hyperlocomotor behavior that could be rapidly reversed by GSK3β inhibitors, indicating the potential for pharmacological rescue of a behavioral phenotype. These data establish TNiK as a critical regulator of cognitive functions and suggest it may play a regulatory role in diseases impacting on its interacting proteins and complexes.
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Zhao P, Cladman W, Van Tol HHM, Chidiac P. Fine-tuning of GPCR signals by intracellular G protein modulators. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 115:421-53. [PMID: 23415100 DOI: 10.1016/b978-0-12-394587-7.00010-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Heterotrimeric G proteins convey receptor signals to intracellular effectors. Superimposed over the basic GPCR-G protein-effector scheme are three types of auxiliary proteins that also modulate Gα. Regulator of G protein signaling proteins and G protein signaling modifier proteins respectively promote GTPase activity and hinder GTP/GDP exchange to limit Gα activation. There are also diverse proteins that, like GPCRs, can promote nucleotide exchange and thus activation. Here we review the impact of these auxiliary proteins on GPCR signaling. Although their precise physiological functions are not yet clear, all of them can produce significant effects in experimental systems. These signaling changes are generally consistent with established effects on isolated Gα; however, the activation state of Gα is seldom verified and many such changes appear also to reflect the physical disruption of or indirect effects on interactions between Gα and its associated GPCR, Gβγ, and/or effector.
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Affiliation(s)
- Peishen Zhao
- Department of Physiology and Pharmacology, Western University, London, Ontario, Canada
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331
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Wawrzyniak AM, Kashyap R, Zimmermann P. Phosphoinositides and PDZ domain scaffolds. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 991:41-57. [PMID: 23775690 DOI: 10.1007/978-94-007-6331-9_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The discovery that PSD-95/Discs large/ZO-1 (PDZ) domains can function as lipid-binding modules, in particular interacting with phosphoinositides (PIs), was made more than 10 years ago (Mol Cell 9(6): 1215-1225, 2002). Confirmatory studies and a series of functional follow-ups established PDZ domains as dual specificity modules displaying both peptide and lipid binding, and prompted a rethinking of the mode of action of PDZ domains in the control of cell signaling. In this chapter, after introducing PDZ domains, PIs and methods for studying protein-lipid interactions, we focus on (i) the prevalence and the specificity of PDZ-PIs interactions, (ii) the molecular determinants of PDZ-PIs interactions, (iii) the integration of lipid and peptide binding by PDZ domains, (iv) the common features of PIs interacting PDZ domains and (v) the regulation and functional significance of PDZ-PIs interactions.
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Systems Analysis of Arrestin Pathway Functions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 118:431-67. [DOI: 10.1016/b978-0-12-394440-5.00017-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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333
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Koveal D, Schuh-Nuhfer N, Ritt D, Page R, Morrison DK, Peti W. A CC-SAM, for coiled coil-sterile α motif, domain targets the scaffold KSR-1 to specific sites in the plasma membrane. Sci Signal 2012; 5:ra94. [PMID: 23250398 DOI: 10.1126/scisignal.2003289] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Kinase suppressor of Ras-1 (KSR-1) is an essential scaffolding protein that coordinates the assembly of the mitogen-activated protein kinase (MAPK) module, consisting of the MAPK kinase kinase Raf, the MAPK kinase MEK (mitogen-activated or extracellular signal-regulated protein kinase kinase), and the MAPK ERK (extracellular signal-regulated kinase) to facilitate activation of MEK and thus ERK. Although KSR-1 is targeted to the cell membrane in part by its atypical C1 domain, which binds to phospholipids, other domains may be involved. We identified another domain in KSR-1 that we termed CC-SAM, which is composed of a coiled coil (CC) and a sterile α motif (SAM). The CC-SAM domain targeted KSR-1 to specific signaling sites at the plasma membrane in growth factor-treated cells, and it bound directly to various micelles and bicelles in vitro, indicating that the CC-SAM functioned as a membrane-binding module. By combining nuclear magnetic resonance spectroscopy and experiments in cultured cells, we found that membrane binding was mediated by helix α3 of the CC motif and that mutating residues in α3 abolished targeting of KSR-1 to the plasma membrane. Thus, in addition to the atypical C1 domain, the CC-SAM domain is required to target KSR-1 to the plasma membrane.
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Affiliation(s)
- Dorothy Koveal
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA
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334
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Liu BA, Nash PD. Evolution of SH2 domains and phosphotyrosine signalling networks. Philos Trans R Soc Lond B Biol Sci 2012; 367:2556-73. [PMID: 22889907 DOI: 10.1098/rstb.2012.0107] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Src homology 2 (SH2) domains mediate selective protein-protein interactions with tyrosine phosphorylated proteins, and in doing so define specificity of phosphotyrosine (pTyr) signalling networks. SH2 domains and protein-tyrosine phosphatases expand alongside protein-tyrosine kinases (PTKs) to coordinate cellular and organismal complexity in the evolution of the unikont branch of the eukaryotes. Examination of conserved families of PTKs and SH2 domain proteins provides fiduciary marks that trace the evolutionary landscape for the development of complex cellular systems in the proto-metazoan and metazoan lineages. The evolutionary provenance of conserved SH2 and PTK families reveals the mechanisms by which diversity is achieved through adaptations in tissue-specific gene transcription, altered ligand binding, insertions of linear motifs and the gain or loss of domains following gene duplication. We discuss mechanisms by which pTyr-mediated signalling networks evolve through the development of novel and expanded families of SH2 domain proteins and the elaboration of connections between pTyr-signalling proteins. These changes underlie the variety of general and specific signalling networks that give rise to tissue-specific functions and increasingly complex developmental programmes. Examination of SH2 domains from an evolutionary perspective provides insight into the process by which evolutionary expansion and modification of molecular protein interaction domain proteins permits the development of novel protein-interaction networks and accommodates adaptation of signalling networks.
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Affiliation(s)
- Bernard A Liu
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
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335
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Levy ED, Michnick SW, Landry CR. Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information. Philos Trans R Soc Lond B Biol Sci 2012; 367:2594-606. [PMID: 22889910 DOI: 10.1098/rstb.2012.0078] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In eukaryotic cells, protein phosphorylation is an important and widespread mechanism used to regulate protein function. Yet, of the thousands of phosphosites identified to date, only a few hundred at best have a characterized function. It was recently shown that these functional sites are significantly more conserved than phosphosites of unknown function, stressing the importance of considering evolutionary conservation in assessing the global functional landscape of phosphosites. This leads us to review studies that examined the impact of phosphorylation on evolutionary conservation. While all these studies have shown that conservation is greater among phosphorylated sites compared with non-phosphorylated ones, the magnitude of this difference varies greatly. Further, not all studies have considered key factors that may influence the rate of phosphosite evolution. Such key factors are their localization in ordered or disordered regions, their stoichiometry or the abundance of their corresponding protein. Here we take into account all of these factors simultaneously, which reveals remarkable evolutionary patterns. First, while it is well established that protein conservation increases with abundance, we show that phosphosites partly follow an opposite trend. More precisely, Saccharomyces cerevisiae phosphosites present among abundant proteins are 1.5 times more likely to diverge in the closely related species Saccharomyces bayanus when compared with phosphosites present in the 5 per cent least abundant proteins. Second, we show that conservation is coupled to stoichiometry, whereby sites frequently phosphorylated are more conserved than those rarely phosphorylated. Finally, we provide a model of functional and noisy or 'accidental' phosphorylation that explains these observations.
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Affiliation(s)
- Emmanuel D Levy
- Département de Biochimie, Université de Montréal, Montréal, Québec, Canada.
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336
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Jin J, Pawson T. Modular evolution of phosphorylation-based signalling systems. Philos Trans R Soc Lond B Biol Sci 2012; 367:2540-55. [PMID: 22889906 DOI: 10.1098/rstb.2012.0106] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Phosphorylation sites are formed by protein kinases ('writers'), frequently exert their effects following recognition by phospho-binding proteins ('readers') and are removed by protein phosphatases ('erasers'). This writer-reader-eraser toolkit allows phosphorylation events to control a broad range of regulatory processes, and has been pivotal in the evolution of new functions required for the development of multi-cellular animals. The proteins that comprise this system of protein kinases, phospho-binding targets and phosphatases are typically modular in organization, in the sense that they are composed of multiple globular domains and smaller peptide motifs with binding or catalytic properties. The linkage of these binding and catalytic modules in new ways through genetic recombination, and the selection of particular domain combinations, has promoted the evolution of novel, biologically useful processes. Conversely, the joining of domains in aberrant combinations can subvert cell signalling and be causative in diseases such as cancer. Major inventions such as phosphotyrosine (pTyr)-mediated signalling that flourished in the first multi-cellular animals and their immediate predecessors resulted from stepwise evolutionary progression. This involved changes in the binding properties of interaction domains such as SH2 and their linkage to new domain types, and alterations in the catalytic specificities of kinases and phosphatases. This review will focus on the modular aspects of signalling networks and the mechanism by which they may have evolved.
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Affiliation(s)
- Jing Jin
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada.
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337
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Hossain S, Dubielecka PM, Sikorski AF, Birge RB, Kotula L. Crk and ABI1: binary molecular switches that regulate abl tyrosine kinase and signaling to the cytoskeleton. Genes Cancer 2012; 3:402-13. [PMID: 23226578 DOI: 10.1177/1947601912460051] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The nonreceptor tyrosine kinases Abl and Arg are among the most well-characterized tyrosine kinases in the human genome. The activation of Abl by N-terminal fusions with Bcr (Bcr-Abl) or Gag (v-Abl) is responsible for chronic myeloid leukemia or Ph+ acute lymphoblastic leukemia and mouse leukemia virus, respectively. In addition, aberrant Abl and Arg activation downstream of several oncogenic growth factor receptors contributes to the development and progression of a variety of human cancers, often associated with poor clinical outcome, drug resistance, and tumor invasion and metastasis. Abl activation can occur by a variety of mechanisms that include domain interactions involving structural remodeling of autoinhibited conformations as well as direct phosphorylation by upstream kinases and phosphatases. Constitutive activation of Abl plays a significant role in regulating the actin cytoskeleton by modulating cell adhesion, motility, and invadopodia. This review addresses the role of Abl and Arg in tumor progression with particular emphasis on the roles of Crk and Abi1 adapter proteins as distinct molecular switches for Abl transactivation. These insights, combined with new insights into the structure of these kinases, provide the rationale to envision that Crk and Abi1 fine-tune Abl regulation to control signaling to the cytoskeleton.
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Affiliation(s)
- Sajjad Hossain
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA ; Current address: Stony Brook University, Stony Brook, NY, USA
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338
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Wallez Y, Mace PD, Pasquale EB, Riedl SJ. NSP-CAS Protein Complexes: Emerging Signaling Modules in Cancer. Genes Cancer 2012; 3:382-93. [PMID: 23226576 DOI: 10.1177/1947601912460050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The CAS (CRK-associated substrate) family of adaptor proteins comprises 4 members, which share a conserved modular domain structure that enables multiple protein-protein interactions, leading to the assembly of intracellular signaling platforms. Besides their physiological role in signal transduction downstream of a variety of cell surface receptors, CAS proteins are also critical for oncogenic transformation and cancer cell malignancy through associations with a variety of regulatory proteins and downstream effectors. Among the regulatory partners, the 3 recently identified adaptor proteins constituting the NSP (novel SH2-containing protein) family avidly bind to the conserved carboxy-terminal focal adhesion-targeting (FAT) domain of CAS proteins. NSP proteins use an anomalous nucleotide exchange factor domain that lacks catalytic activity to form NSP-CAS signaling modules. Additionally, the NSP SH2 domain can link NSP-CAS signaling assemblies to tyrosine-phosphorylated cell surface receptors. NSP proteins can potentiate CAS function by affecting key CAS attributes such as expression levels, phosphorylation state, and subcellular localization, leading to effects on cell adhesion, migration, and invasion as well as cell growth. The consequences of these activities are well exemplified by the role that members of both families play in promoting breast cancer cell invasiveness and resistance to antiestrogens. In this review, we discuss the intriguing interplay between the NSP and CAS families, with a particular focus on cancer signaling networks.
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Affiliation(s)
- Yann Wallez
- Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
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339
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Bunney T, Esposito D, Mas-Droux C, Lamber E, Baxendale R, Martins M, Cole A, Svergun D, Driscoll P, Katan M. Structural and functional integration of the PLCγ interaction domains critical for regulatory mechanisms and signaling deregulation. Structure 2012; 20:2062-75. [PMID: 23063561 PMCID: PMC3532599 DOI: 10.1016/j.str.2012.09.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/03/2012] [Accepted: 09/07/2012] [Indexed: 11/30/2022]
Abstract
Multidomain proteins incorporating interaction domains are central to regulation of cellular processes. The elucidation of structural organization and mechanistic insights into many of these proteins, however, remain challenging due to their inherent flexibility. Here, we describe the organization and function of four interaction domains in PLCγ1 using a combination of structural biology and biochemical approaches. Intramolecular interactions within the regulatory region center on the cSH2 domain, the only domain that also interacts with the PLC-core. In the context of fibroblast growth-factor receptor signaling, the coordinated involvement of nSH2 and cSH2 domains mediates efficient phosphorylation of PLCγ1 resulting in the interruption of an autoinhibitory interface by direct competition and, independently, dissociation of PLCγ1 from the receptor. Further structural insights into the autoinhibitory surfaces provide a framework to interpret gain-of-function mutations in PLCγ isoforms linked to immune disorders and illustrate a distinct mechanism for regulation of PLC activity by common interaction domains.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Substitution
- Animals
- Catalytic Domain
- Cell Line
- Crystallography, X-Ray
- Enzyme Activation
- Humans
- Inositol Phosphates/chemistry
- Kinetics
- Models, Molecular
- Mutagenesis, Site-Directed
- Nuclear Magnetic Resonance, Biomolecular
- Phospholipase C gamma/chemistry
- Phospholipase C gamma/genetics
- Phospholipase C gamma/metabolism
- Phosphorylation
- Protein Binding
- Protein Interaction Domains and Motifs
- Protein Processing, Post-Translational
- Protein Structure, Secondary
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Receptor, Fibroblast Growth Factor, Type 1/physiology
- Signal Transduction
- Sus scrofa
- Thermodynamics
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Affiliation(s)
- Tom D. Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Diego Esposito
- Division of Molecular Structure, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Corine Mas-Droux
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Ekatarina Lamber
- Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Rhona W. Baxendale
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Marta Martins
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Paul C. Driscoll
- Division of Molecular Structure, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
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340
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Canton DA, Keene CD, Swinney K, Langeberg LK, Nguyen V, Pelletier L, Pawson T, Wordeman L, Stella N, Scott JD. Gravin is a transitory effector of polo-like kinase 1 during cell division. Mol Cell 2012; 48:547-59. [PMID: 23063527 PMCID: PMC3513578 DOI: 10.1016/j.molcel.2012.09.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 07/05/2012] [Accepted: 09/02/2012] [Indexed: 12/20/2022]
Abstract
The mitogenic and second-messenger signals that promote cell proliferation often proceed through multienzyme complexes. The kinase-anchoring protein Gravin integrates cAMP and calcium/phospholipid signals at the plasma membrane by sequestering protein kinases A and C with G protein-coupled receptors. In this report we define a role for Gravin as a temporal organizer of phosphorylation-dependent protein-protein interactions during mitosis. Mass spectrometry, molecular, and cellular approaches show that CDK1/Cyclin B1 phosphorylates Gravin on threonine 766 to prime the recruitment of the polo-like kinase Plk1 at defined phases of mitosis. Fluorescent live-cell imaging reveals that cells depleted of Gravin exhibit mitotic defects that include protracted prometaphase and misalignment of chromosomes. Moreover, a Gravin T766A phosphosite mutant that is unable to interact with Plk1 negatively impacts cell proliferation. In situ detection of phospho-T766 Gravin in biopsy sections of human glioblastomas suggests that this phosphorylation event might identify malignant neoplasms.
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Affiliation(s)
- David A. Canton
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - C. Dirk Keene
- Department of Pathology, Neuropathology Division, University of Washington, Seattle, WA 98195, USA
| | - Katie Swinney
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Lorene K. Langeberg
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Vivian Nguyen
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, Toronto, ON M5G 1X5, Canada
| | - Laurence Pelletier
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, Toronto, ON M5G 1X5, Canada
| | - Tony Pawson
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, Toronto, ON M5G 1X5, Canada
| | - Linda Wordeman
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Nephi Stella
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
- Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - John D. Scott
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
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341
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The A-kinase-anchoring protein AKAP-Lbc facilitates cardioprotective PKA phosphorylation of Hsp20 on Ser(16). Biochem J 2012; 446:437-43. [PMID: 22731613 DOI: 10.1042/bj20120570] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Hsp20 (heat-shock protein of 20 kDa; HspB6) is a cardioprotective agent which combats a number of pathophysiological processes in the heart, including hypertrophy, apoptosis and ischaemia/reperfusion injury. The cardioprotective actions of Hsp20 require its phosphorylation by PKA (cAMP-dependent protein kinase) on Ser(16). Although the extracellular stimuli that promote cAMP-responsive phosphorylation of Hsp20 are well known, less is understood about the molecular processes that regulate this modification. AKAPs (A-kinase-anchoring proteins) physically compartmentalize PKA to specific locations within a cell to both direct PKA phosphorylation toward selected substrates and to orchestrate downstream signalling events. In the present study we used PKA anchoring disruptor peptides to verify that an AKAP underpins the cardioprotective phosphorylation of Hsp20. Biochemical and immunofluorescence techniques identify the cytosolic protein AKAP-Lbc (AKAP13) as the anchoring protein responsible for directing PKA phosphorylation of Hsp20 on Ser(16). Gene silencing and rescue experiments establish that AKAP-Lbc-mediated PKA phosphorylation of Hsp20 is crucial to the anti-apoptotic effects of the Hsp. Thus AKAP-Lbc may serve an ancillary cardioprotective role by favouring the association of PKA with Hsp20.
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342
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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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343
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Hota PK, Buck M. Plexin structures are coming: opportunities for multilevel investigations of semaphorin guidance receptors, their cell signaling mechanisms, and functions. Cell Mol Life Sci 2012; 69:3765-805. [PMID: 22744749 PMCID: PMC11115013 DOI: 10.1007/s00018-012-1019-0] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 04/09/2012] [Accepted: 04/11/2012] [Indexed: 01/13/2023]
Abstract
Plexin transmembrane receptors and their semaphorin ligands, as well as their co-receptors (Neuropilin, Integrin, VEGFR2, ErbB2, and Met kinase) are emerging as key regulatory proteins in a wide variety of developmental, regenerative, but also pathological processes. The diverse arenas of plexin function are surveyed, including roles in the nervous, cardiovascular, bone and skeletal, and immune systems. Such different settings require considerable specificity among the plexin and semaphorin family members which in turn are accompanied by a variety of cell signaling networks. Underlying the latter are the mechanistic details of the interactions and catalytic events at the molecular level. Very recently, dramatic progress has been made in solving the structures of plexins and of their complexes with associated proteins. This molecular level information is now suggesting detailed mechanisms for the function of both the extracellular as well as the intracellular plexin regions. Specifically, several groups have solved structures for extracellular domains for plexin-A2, -B1, and -C1, many in complex with semaphorin ligands. On the intracellular side, the role of small Rho GTPases has been of particular interest. These directly associate with plexin and stimulate a GTPase activating (GAP) function in the plexin catalytic domain to downregulate Ras GTPases. Structures for the Rho GTPase binding domains have been presented for several plexins, some with Rnd1 bound. The entire intracellular domain structure of plexin-A1, -A3, and -B1 have also been solved alone and in complex with Rac1. However, key aspects of the interplay between GTPases and plexins remain far from clear. The structural information is helping the plexin field to focus on key questions at the protein structural, cellular, as well as organism level that collaboratoria of investigations are likely to answer.
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Affiliation(s)
- Prasanta K. Hota
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106 USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106 USA
- Department of Neuroscience, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106 USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106 USA
- Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106 USA
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, OH 44106 USA
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344
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Fernández IF, Pérez-Rivas LG, Blanco S, Castillo-Dominguez AA, Lozano J, Lazo PA. VRK2 anchors KSR1-MEK1 to endoplasmic reticulum forming a macromolecular complex that compartmentalizes MAPK signaling. Cell Mol Life Sci 2012; 69:3881-93. [PMID: 22752157 PMCID: PMC11114894 DOI: 10.1007/s00018-012-1056-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/16/2012] [Accepted: 06/11/2012] [Indexed: 12/30/2022]
Abstract
The spatial and temporal regulation of intracellular signaling is determined by the spatial and temporal organization of complexes assembled on scaffold proteins, which can be modulated by their interactions with additional proteins as well as subcellular localization. The scaffold KSR1 protein interacts with MAPK forming a complex that conveys a differential signaling in response to growth factors. The aim of this work is to determine the unknown mechanism by which VRK2A downregulates MAPK signaling. We have characterized the multiprotein complex formed by KSR1 and the Ser-Thr kinase VRK2A. VRK2A is a protein bound to the endoplasmic reticulum (ER) and retains a fraction of KSR1 complexes on the surface of this organelle. Both proteins, VRK2A and KSR1, directly interact by their respective C-terminal regions. In addition, MEK1 is also incorporated in the basal complex. MEK1 independently interacts with the CA5 region of KSR1 and with the N-terminus of VRK2A. Thus, VRK2A can form a high molecular size (600-1,000 kDa) stable complex with both MEK1 and KSR1. Knockdown of VRK2A resulted in disassembly of these high molecular size complexes. Overexpression of VRK2A increased the amount of KSR1 in the particulate fraction and prevented the incorporation of ERK1/2 into the complex after stimulation with EGF. Neither VRK2A nor KSR1 interact with the VHR, MKP1, MKP2, or MKP3 phosphatases. The KSR1 complex assembled and retained by VRK2A in the ER can have a modulatory effect on the signal mediated by MAPK, thus locally affecting the magnitude of its responses, and can explain differential responses depending on cell type.
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Affiliation(s)
- Isabel F. Fernández
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Luis G. Pérez-Rivas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Malaga, Spain
- Laboratorio de Oncología Molecular, Fundación IMABIS, Hospital Clínico Universitario Virgen de la Victoria, Malaga, Spain
| | - Sandra Blanco
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Adrián A. Castillo-Dominguez
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Malaga, Spain
- Laboratorio de Oncología Molecular, Fundación IMABIS, Hospital Clínico Universitario Virgen de la Victoria, Malaga, Spain
| | - José Lozano
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Malaga, Spain
- Laboratorio de Oncología Molecular, Fundación IMABIS, Hospital Clínico Universitario Virgen de la Victoria, Malaga, Spain
| | - Pedro A. Lazo
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
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345
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Matheron L, Clavier S, Diebate O, Karoyan P, Bolbach G, Guianvarc'h D, Sachon E. Improving the selectivity of the phosphoric acid β-elimination on a biotinylated phosphopeptide. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1981-1990. [PMID: 22956181 DOI: 10.1007/s13361-012-0467-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 07/16/2012] [Accepted: 08/01/2012] [Indexed: 06/01/2023]
Abstract
This study aims at improving the MALDI-TOF detection of a phosphorylated peptide containing a cysteine residue by β-elimination of H(3)PO(4) hardly enriched by classical methods. The experimental conditions were optimized on this phosphopeptide (biot-pAdd) and its nonphosphorylated counterpart (biot-Add). The major side-reactions were H(2)S elimination on the cysteine residues and H(2)O elimination on the non phosphorylated serine residue of biot-Add. The former dilutes the MALDI-TOF signal for the desired species. The latter gives a product similar to what is obtained by H(3)PO(4) elimination and should prompt to caution when working with a mixture between phosphorylated and non phosphorylated peptides. Modifications on the solvent, the reaction temperature and time, the nature, and concentration of the base were made. Major improvement of the selectivity of the reaction was observed in 30 % ACN, at room temperature for 4 h. However, these optimizations are specific to these sequences and should be performed anew for different peptides. The selectivity of the reaction towards H(3)PO(4) elimination is improved, but the persistence of side-reactions renders a previous sample fractionation necessary. In these optimized conditions, the ionization enhancement is 3-fold and the detection limits for biot-pAdd are similar to biot-Add (100 fmol).
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Affiliation(s)
- Lucrèce Matheron
- Laboratoire des Biomolécules, Université P et M Curie, UMR 7203 UPMC-CNRS-ENS, Paris, France
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346
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Abstract
The regulation of kinases by scaffolding proteins greatly contributes to the fidelity of signal transduction. In the present study, we explored an interaction between the ubiquitous enzyme PKC (protein kinase C) and the scaffolding protein AKAP7 (A-kinase-anchoring protein 7). Using protein biochemistry and surface plasmon resonance approaches, we demonstrate that both AKAP7γ and AKAP7α are capable of high-affinity interactions with multiple isoenzymes of PKC. Furthermore, this interaction is achieved via multi-site binding on both proteins. FRET (fluorescence resonance energy transfer) analysis using a PKC activity reporter suggests that anchoring of the kinase within AKAP7 complexes enhances the phosphorylation of substrate proteins. Finally, we determined using FRAP (fluorescence recovery after photobleaching) and virtual modelling that AKAP7 restricts the mobility of PKC within cells by tethering it to subcellular compartments. Collectively, the results of the present study suggests that AKAP7 could play an integral role in dictating PKC localization and function in tissues where the two proteins are co-expressed.
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347
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Rouquette-Jazdanian AK, Sommers CL, Kortum RL, Morrison DK, Samelson LE. LAT-independent Erk activation via Bam32-PLC-γ1-Pak1 complexes: GTPase-independent Pak1 activation. Mol Cell 2012; 48:298-312. [PMID: 22981863 PMCID: PMC3483363 DOI: 10.1016/j.molcel.2012.08.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 06/18/2012] [Accepted: 08/07/2012] [Indexed: 01/12/2023]
Abstract
In T cells, the adaptor Bam32 is coupled to Erk activation downstream of the TCR by an unknown mechanism. We characterized in Jurkat cells and primary T lymphocytes a pathway dependent on Bam32-PLC-γ1-Pak1 complexes, in which Pak1 kinase activates Raf-1 and Mek-1, both upstream of Erk. In the Bam32-PLC-γ1-Pak1 complex, catalytically inactive PLC-γ1 is used as a scaffold linking Bam32 to Pak1. PLC-γ1(C-SH2) directly binds S141 of Bam32, preventing LAT-mediated activation of Ras by PLC-γ1. The Bam32-PLC-γ1 interaction enhances the binding of the SH3 domain of the phospholipase with Pak1. The PLC-γ1(SH3)-Pak1 interaction activates Pak1 independently of the small GTPases Rac1/Cdc42, previously described as being the only activators of Pak1 in T cells. Direct binding of the SH3 domain of PLC-γ1 to Pak1 dissociates inactive Pak1 homodimers, a mechanism required for Pak1 activation. We have thus uncovered a LAT/Ras-independent, Bam32-nucleated pathway that activates Erk signaling in T cells.
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348
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A-kinase-anchoring protein-Lbc anchors IκB kinase β to support interleukin-6-mediated cardiomyocyte hypertrophy. Mol Cell Biol 2012; 33:14-27. [PMID: 23090968 DOI: 10.1128/mcb.00887-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In response to stress, the heart undergoes a pathological remodeling process associated with hypertrophy and the reexpression of a fetal gene program that ultimately causes cardiac dysfunction and heart failure. In this study, we show that A-kinase-anchoring protein (AKAP)-Lbc and the inhibitor of NF-κB kinase subunit β (IKKβ) form a transduction complex in cardiomyocytes that controls the production of proinflammatory cytokines mediating cardiomyocyte hypertrophy. In particular, we can show that activation of IKKβ within the AKAP-Lbc complex promotes NF-κB-dependent production of interleukin-6 (IL-6), which in turn enhances fetal gene expression and cardiomyocyte growth. These findings provide a new mechanistic hypothesis explaining how hypertrophic signals are coordinated and conveyed to interleukin-mediated transcriptional reprogramming events in cardiomyocytes.
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349
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Abstract
Modular protein interaction domains (PIDs) that recognize linear peptide motifs are found in hundreds of proteins within the human genome. Some PIDs such as SH2, 14-3-3, Chromo, and Bromo domains serve to recognize posttranslational modification (PTM) of amino acids (such as phosphorylation, acetylation, methylation, etc.) and translate these into discrete cellular responses. Other modules such as SH3 and PSD-95/Discs-large/ZO-1 (PDZ) domains recognize linear peptide epitopes and serve to organize protein complexes based on localization and regions of elevated concentration. In both cases, the ability to nucleate-specific signaling complexes is in large part dependent on the selectivity of a given protein module for its cognate peptide ligand. High-throughput (HTP) analysis of peptide-binding domains by peptide or protein arrays, phage display, mass spectrometry, or other HTP techniques provides new insight into the potential protein-protein interactions prescribed by individual or even whole families of modules. Systems level analyses have also promoted a deeper understanding of the underlying principles that govern selective protein-protein interactions and how selectivity evolves. Lastly, there is a growing appreciation for the limitations and potential pitfalls associated with HTP analysis of protein-peptide interactomes. This review will examine some of the common approaches utilized for large-scale studies of PIDs and suggest a set of standards for the analysis and validation of datasets from large-scale studies of peptide-binding modules. We will also highlight how data from large-scale studies of modular interaction domain families can provide insight into systems level properties such as the linguistics of selective interactions.
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Affiliation(s)
- Bernard A Liu
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
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350
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Gagnon-Arsenault I, Marois Blanchet FC, Rochette S, Diss G, Dubé AK, Landry CR. Transcriptional divergence plays a role in the rewiring of protein interaction networks after gene duplication. J Proteomics 2012; 81:112-25. [PMID: 23063722 DOI: 10.1016/j.jprot.2012.09.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/26/2012] [Accepted: 09/30/2012] [Indexed: 01/27/2023]
Abstract
Gene duplication plays a key role in the evolution of protein-protein interaction (PPI) networks. After a gene duplication event, paralogous proteins may diverge through the gain and loss of PPIs. This divergence can be explained by two non-exclusive mechanisms. First, mutations may accumulate in the coding sequences of the paralogs and affect their protein sequences, which can modify, for instance, their binding interfaces and thus their interaction specificity. Second, mutations may accumulate in the non-coding region of the genes and affect their regulatory sequences. The resulting changes in expression profiles can lead to paralogous proteins being differentially expressed and occurring in the cell with different sets of potential interaction partners. These changes could also alter splicing regulation and lead to the inclusion or exclusion of alternative exons. The evolutionary role of these regulatory mechanisms remains largely unexplored. We use bioinformatics analyses of existing PPI data and proteome-wide PPI screening to show that the divergence of transcriptional regulation between paralogs plays a significant role in determining their PPI specificity. Because many gene duplication events are followed by rapid changes in transcriptional regulation, our results suggest that PPI networks may be rewired by gene duplication, without the need for protein to diverge in their binding specificities. This article is part of a Special Issue entitled: From protein structures to clinical applications.
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Affiliation(s)
- Isabelle Gagnon-Arsenault
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, PROTEO, 1030 Avenue de la Médecine, Université Laval, Québec, Québec, Canada G1V 0A6
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