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Bhattacharyya P, Christopherson RI, Skarratt KK, Fuller SJ. Method for B Cell Receptor Enrichment in Malignant B Cells. Cancers (Basel) 2024; 16:2341. [PMID: 39001403 PMCID: PMC11240526 DOI: 10.3390/cancers16132341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/17/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
B cells are central to the adaptive immune response and provide long-lasting immunity after infection. B cell activation is mediated by the surface membrane-bound B cell receptor (BCR) following recognition of a specific antigen. The BCR has been challenging to analyse using mass spectrometry (MS) due to the difficulty of isolating and enriching this membrane-bound protein complex. There are approximately 120,000 BCRs on the B cell surface; however, depending on the B cell activation state, there may be hundreds-of-millions to billions of proteins in a B cell. Consequently, advanced proteomic techniques such as MS workflows that use purified proteins to yield structural and protein-interaction information have not been published for the BCR complex. This paper describes a method for enriching the BCR complex that is MS-compatible. The method involves a Protein G pull down on agarose beads using an intermediary antibody to each of the BCR complex subcomponents (CD79a, CD79b, and membrane immunoglobulin). The enrichment process is shown to pull down the entire BCR complex and has the advantage of being readily compatible with further proteomic study including MS analysis. Using intermediary antibodies has the potential to enrich all isotypes of the BCR, unlike previous methods described in the literature that use protein G-coated beads to directly pull down the membrane IgG (mIgG) but cannot be used for other mIg isotypes.
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Affiliation(s)
- Puja Bhattacharyya
- Sydney Medical School Nepean, Faculty of Medicine and Health, The University of Sydney, Penrith, NSW 2750, Australia; (P.B.); (K.K.S.)
- Blacktown Hospital, Blacktown Rd., Blacktown, NSW 2148, Australia
| | | | - Kristen K. Skarratt
- Sydney Medical School Nepean, Faculty of Medicine and Health, The University of Sydney, Penrith, NSW 2750, Australia; (P.B.); (K.K.S.)
- Nepean Hospital, Derby Str., Kingswood, NSW 2747, Australia
| | - Stephen J. Fuller
- Sydney Medical School Nepean, Faculty of Medicine and Health, The University of Sydney, Penrith, NSW 2750, Australia; (P.B.); (K.K.S.)
- Nepean Hospital, Derby Str., Kingswood, NSW 2747, Australia
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2
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Kruglova N, Filatov A. Detecting PTP Protein-Protein Interactions by Fluorescent Immunoprecipitation Analysis (FIPA). Methods Mol Biol 2024; 2743:181-194. [PMID: 38147216 DOI: 10.1007/978-1-0716-3569-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Identifying protein-protein interactions is crucial for revealing protein functions and characterizing cellular processes. Manipulating PPIs has become widespread in treating human diseases such as cancer, autoimmunity, and infections. It has been recently applied to the regulation of protein tyrosine phosphatases (PTPs) previously considered undruggable. A broad panel of methods is available for studying PPIs. To complement the existing toolkit, we developed a simple method called fluorescent immunoprecipitation analysis (FIPA). This method is based on coimmunoprecipitation followed by protein gel electrophoresis and fluorescent imaging to visualize components of a protein complex simultaneously on a gel. The FIPA allows the detection of proteins expressed under native conditions and is compatible with mass spectrometry identification of protein bands.
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Affiliation(s)
- Natalia Kruglova
- Cell and Gene Technology Group, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, Russia
- National Research Center, Institute of Immunology of Federal Medical Biological Agency of Russia, Moscow, Russia
| | - Alexander Filatov
- National Research Center, Institute of Immunology of Federal Medical Biological Agency of Russia, Moscow, Russia
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3
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Hu J, Kim J, Hilty C. Detection of Protein-Ligand Interactions by 19F Nuclear Magnetic Resonance Using Hyperpolarized Water. J Phys Chem Lett 2022; 13:3819-3823. [PMID: 35465675 PMCID: PMC9088881 DOI: 10.1021/acs.jpclett.2c00448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The transfer of nuclear spin hyperpolarization from water to ligand 19F spins results in a transient signal change that is indicative of protein-ligand interaction. The 19F nucleus allows for background-free detection of these signals, which are modulated by polarization transfer via pathways similar to those in a hyperpolarized 1H water LOGSY experiment. Quantification of the apparent heteronuclear cross-relaxation rates is facilitated by a simultaneous dual-channel detection of 1H and 19F signals. Calculated cross-relaxation rates for the 1H-19F transfer step indicate that these rates are sensitive to binding to medium- and large-sized proteins. The heteronuclear observation of hyperpolarization transfer from water may be used to screen protein-ligand interactions in drug discovery and other applications.
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Affiliation(s)
- Jiandu Hu
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, TX 77843, USA
| | | | - Christian Hilty
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, TX 77843, USA
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4
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Jeong D, Kim HS, Kim HY, Kang MJ, Jung H, Oh Y, Kim D, Koh J, Cho SY, Jeon YK, Lee EB, Lee SH, Shin EC, Kim HM, Yi EC, Chung DH. Soluble Fas ligand drives autoantibody-induced arthritis by binding to DR5/TRAIL-R2. eLife 2021; 10:48840. [PMID: 34223817 PMCID: PMC8257255 DOI: 10.7554/elife.48840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
To date, no study has demonstrated that soluble Fas ligand (sFasL)-mediated inflammation is regulated via interaction with Fas in vivo. We found that FasL interacts specifically with tumor necrosis factor receptor superfamily (TNFRSF)10B, also known as death receptor (DR)5. Autoantibody-induced arthritis (AIA) was attenuated in FasL (Faslgld/gld)- and soluble FasL (FaslΔs/Δs)-deficient mice, but not in Fas (Faslpr/lpr and Fas–/–)- or membrane FasL (FaslΔm/Δm)-deficient mice, suggesting sFasL promotes inflammation by binding to a Fas-independent receptor. Affinity purification mass spectrometry analysis using human (h) fibroblast-like synovial cells (FLSCs) identified DR5 as one of several proteins that could be the elusive Fas-independent FasL receptor. Subsequent cellular and biochemical analyses revealed that DR5 interacted specifically with recombinant FasL–Fc protein, although the strength of this interaction was approximately 60-fold lower than the affinity between TRAIL and DR5. A microarray assay using joint tissues from mice with arthritis implied that the chemokine CX3CL1 may play an important downstream role of the interaction. The interaction enhanced Cx3cl1 transcription and increased sCX3CL1 production in FLSCs, possibly in an NF-κB-dependent manner. Moreover, the sFasL–DR5 interaction-mediated CX3CL1–CX3CR1 axis initiated and amplified inflammation by enhancing inflammatory cell influx and aggravating inflammation via secondary chemokine production. Blockade of FasL or CX3CR1 attenuated AIA. Therefore, the sFasL–DR5 interaction promotes inflammation and is a potential therapeutic target.
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Affiliation(s)
- Dongjin Jeong
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Laboratory of Immune Regulation in Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hye Sung Kim
- Laboratory of Immune Regulation in Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hye Young Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Min Jueng Kang
- Department of Molecular Medicine and Biopharmaceutical Sciences, School of Convergence Science, Seoul, Republic of Korea.,Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Hyeryeon Jung
- Department of Molecular Medicine and Biopharmaceutical Sciences, School of Convergence Science, Seoul, Republic of Korea.,Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Yumi Oh
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Donghyun Kim
- Laboratory of Immune Regulation in Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jaemoon Koh
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Yup Cho
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eun Bong Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung Hyo Lee
- Graduate School of Medical Science and Engineering, Korean Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Eui-Cheol Shin
- Graduate School of Medical Science and Engineering, Korean Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Ho Min Kim
- Graduate School of Medical Science and Engineering, Korean Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences, School of Convergence Science, Seoul, Republic of Korea.,Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Doo Hyun Chung
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Laboratory of Immune Regulation in Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
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5
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Biological Applications for LC-MS-Based Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1336:17-29. [PMID: 34628625 DOI: 10.1007/978-3-030-77252-9_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Since its inception, liquid chromatography-mass spectrometry (LC-MS) has been continuously improved upon in many aspects, including instrument capabilities, sensitivity, and resolution. Moreover, the costs to purchase and operate mass spectrometers and liquid chromatography systems have decreased, thus increasing affordability and availability in sectors outside of academic and industrial research. Processing power has also grown immensely, cutting the time required to analyze samples, allowing more data to be feasibly processed, and allowing for standardized processing pipelines. As a result, proteomics via LC-MS has become popular in many areas of biological sciences, forging an important seat for itself in targeted and untargeted assays, pure and applied science, the laboratory, and the clinic. In this chapter, many of these applications of LC-MS-based proteomics and an outline of how they can be executed will be covered. Since the field of personalized medicine has matured alongside proteomics, it has also come to rely on various mass spectrometry methods and will be elaborated upon as well. As time goes on and mass spectrometry evolves, there is no doubt that its presence in these areas, and others, will only continue to grow.
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6
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Doan ND, DiChiara AS, Del Rosario AM, Schiavoni RP, Shoulders MD. Mass Spectrometry-Based Proteomics to Define Intracellular Collagen Interactomes. Methods Mol Biol 2019; 1944:95-114. [PMID: 30840237 DOI: 10.1007/978-1-4939-9095-5_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present the development, optimization, and application of constructs, cell lines, covalent cross-linking methods, and immunoprecipitation strategies that enable robust and accurate determination of collagen interactomes via mass spectrometry-based proteomics. Using collagen type-I as an example, protocols for working with large, repetitive, and GC-rich collagen genes are described, followed by strategies for engineering cells that stably and inducibly express antibody epitope-tagged collagen-I. Detailed steps to optimize collagen interactome cross-linking and perform immunoprecipitations are then presented. We conclude with a discussion of methods to elute collagen interactomes and prepare samples for mass spectrometry-mediated identification of interactors. Throughout, caveats and potential problems researchers may encounter when working with collagen are discussed. We note that the protocols presented herein may be readily adapted to define interactomes of other collagen types, as well as to determine comparative interactomes of normal and disease-causing collagen variants using quantitative isotopic labeling (SILAC)- or isobaric mass tags (iTRAQ or TMT)-based mass spectrometry analysis.
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Affiliation(s)
- Ngoc-Duc Doan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew S DiChiara
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
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7
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Cummins TD, Sapkota GP. Characterization of Protein Complexes Using Chemical Cross-Linking Coupled Electrospray Mass Spectrometry. Methods Mol Biol 2018; 1788:43-61. [PMID: 29064006 DOI: 10.1007/7651_2017_85] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Identification and characterization of large protein complexes is a mainstay of biochemical toolboxes. Utilization of cross-linking chemicals can facilitate the capture and identification of transient or weak interactions of a transient nature (Huang and Kim, PloS One 8:e61430, 2013; Gao et al., J Vis Exp doi: 10.3791/51387, 2014). Here we describe a detailed methodology for a cell culture-based proteomic approach. We describe the generation of cells stably expressing green fluorescent protein (GFP)-tagged proteins under the tetracycline-inducible promoter and subsequent proteomic analysis of GFP-interacting proteins. We include a list of proteins that were identified as interactors of GFP.
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Affiliation(s)
- Timothy D Cummins
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Division of Nephrology and Hypertension, Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, KY, USA
| | - Gopal P Sapkota
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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8
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Vannecke W, Ampe C, Van Troys M, Beltramo M, Madder A. Cross-Linking Furan-Modified Kisspeptin-10 to the KISS Receptor. ACS Chem Biol 2017; 12:2191-2200. [PMID: 28714670 DOI: 10.1021/acschembio.7b00396] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemical cross-linking is well-established for investigating protein-protein interactions. Traditionally, photo cross-linking is used but is associated with problems of selectivity and UV toxicity in a biological context. We here describe, with live cells and under normal growth conditions, selective cross-linking of a furan-modified peptide ligand to its membrane-presented receptor with zero toxicity, high efficiency, and spatio-specificity. Furan-modified kisspeptin-10 is covalently coupled to its glycosylated membrane receptor, GPR54(KISS1R). This newly expands the applicability of furan-mediated cross-linking not only to protein-protein cross-linking but also to cross-linking in situ. Moreover, in our earlier reports on nucleic acid interstrand cross-linking, furan activation required external triggers of oxidation (via addition of N-bromo succinimide or singlet oxygen). In contrast, we here show, for multiple cell lines, the spontaneous endogenous oxidation of the furan moiety with concurrent selective cross-link formation. We propose that reactive oxygen species produced by NADPH oxidase (NOX) enzymes form the cellular source establishing furan oxidation.
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Affiliation(s)
- Willem Vannecke
- Organic
and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan
281 S4, B-9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Christophe Ampe
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Marleen Van Troys
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Massimiliano Beltramo
- Equipe
Neuroendocrinologie Moleculaire de la Reproduction, Physiologie de
la Reproduction et des Comportements, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Annemieke Madder
- Organic
and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan
281 S4, B-9000 Ghent, Belgium
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9
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Orphan GPR110 (ADGRF1) targeted by N-docosahexaenoylethanolamine in development of neurons and cognitive function. Nat Commun 2016; 7:13123. [PMID: 27759003 PMCID: PMC5075789 DOI: 10.1038/ncomms13123] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/05/2016] [Indexed: 12/27/2022] Open
Abstract
Docosahexaenoic acid (DHA, 22:6n-3) is an omega-3 fatty acid essential for proper brain development. N-docosahexaenoylethanolamine (synaptamide), an endogenous metabolite of DHA, potently promotes neurogenesis, neuritogenesis and synaptogenesis; however, the underlying molecular mechanism is not known. Here, we demonstrate orphan G-protein coupled receptor 110 (GPR110, ADGRF1) as the synaptamide receptor, mediating synaptamide-induced bioactivity in a cAMP-dependent manner. Mass spectrometry-based proteomic characterization and cellular fluorescence tracing with chemical analogues of synaptamide reveal specific binding of GPR110 to synaptamide, which triggers cAMP production with low nM potency. Disruption of this binding or GPR110 gene knockout abolishes while GPR110 overexpression enhances synaptamide-induced bioactivity. GPR110 is highly expressed in fetal brains but rapidly decreases after birth. GPR110 knockout mice show significant deficits in object recognition and spatial memory. GPR110 deorphanized as a functional synaptamide receptor provides a novel target for neurodevelopmental control and new insight into mechanisms by which DHA promotes brain development and function.
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10
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Morgan CP, Krey JF, Grati M, Zhao B, Fallen S, Kannan-Sundhari A, Liu XZ, Choi D, Müller U, Barr-Gillespie PG. PDZD7-MYO7A complex identified in enriched stereocilia membranes. eLife 2016; 5:e18312. [PMID: 27525485 PMCID: PMC5005036 DOI: 10.7554/elife.18312] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/14/2016] [Indexed: 12/15/2022] Open
Abstract
While more than 70 genes have been linked to deafness, most of which are expressed in mechanosensory hair cells of the inner ear, a challenge has been to link these genes into molecular pathways. One example is Myo7a (myosin VIIA), in which deafness mutations affect the development and function of the mechanically sensitive stereocilia of hair cells. We describe here a procedure for the isolation of low-abundance protein complexes from stereocilia membrane fractions. Using this procedure, combined with identification and quantitation of proteins with mass spectrometry, we demonstrate that MYO7A forms a complex with PDZD7, a paralog of USH1C and DFNB31. MYO7A and PDZD7 interact in tissue-culture cells, and co-localize to the ankle-link region of stereocilia in wild-type but not Myo7a mutant mice. Our data thus describe a new paradigm for the interrogation of low-abundance protein complexes in hair cell stereocilia and establish an unanticipated link between MYO7A and PDZD7.
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Affiliation(s)
- Clive P Morgan
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Jocelyn F Krey
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, United States
| | - M'hamed Grati
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, United States
| | - Bo Zhao
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, United States
| | - Shannon Fallen
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, United States
| | | | - Xue Zhong Liu
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, United States
| | - Dongseok Choi
- OHSU-PSU School of Public Health, Oregon Health and Science University, Portland, United States
- Graduate School of Dentistry, Kyung Hee University, Seoul, Korea
| | - Ulrich Müller
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, United States
| | - Peter G Barr-Gillespie
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, United States
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11
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Engidawork E, Aradska J, Lubec G. Neurotransmitter receptor complexes: methods for bioanalysis, their potentials and limitations. Rev Neurosci 2016; 27:111-33. [DOI: 10.1515/revneuro-2015-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 08/11/2015] [Indexed: 12/15/2022]
Abstract
AbstractNeurotransmitter receptors are key elements for brain function, but work so far has been focusing on the individual receptor subunits. It is, however, the receptor complexes that execute work rather than the subunits; of course, the multitude of possible combinations of the many receptors forming homomeric or heteromeric complexes is hampering studies. Moreover, not only receptors are observed in the complexes but also their corresponding protein kinases, phosphatases, and anchoring proteins, to name a few. Studying receptor complexes is still an analytical challenge. Thus far, no methods exist to unequivocally characterize or even quantify these assemblies. Major problems and limitations for the analysis exist, such as solubility, as the use of detergents is critical and may dissociate the receptor complexes as well as their separation in the native state. Gel-based techniques are able to separate and semiquantitatively quantify receptor complexes by subsequent immunochemical methods but do not allow the characterization of complex components. Immunoprecipitation methods are highly dependent on antibody availability and specificity, and the result of coimmunoprecipitation does not verify the direct physical interaction of proteins in the immunoprecipitate. Antibody shift assays are suitable to identify individual known proteins within a complex as are immunogold electron microscopic techniques and energy transfer technologies. Most techniques are simply showing the proximity of proteins rather than their physical interaction. Although fluorescence correlation spectroscopy is a promising technique, the use for quantification or comparing biological samples is limited. A lot of work remains to be done to provide tools for the characterization and quantification of receptor complexes in the brain.
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Affiliation(s)
| | - Jana Aradska
- 1Department of Pediatrics, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Gert Lubec
- 3Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
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12
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Investigating Bacterial Protein Synthesis Using Systems Biology Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:21-40. [PMID: 26621460 DOI: 10.1007/978-3-319-23603-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein synthesis is essential for bacterial growth and survival. Its study in Escherichia coli helped uncover features conserved among bacteria as well as universally. The pattern of discovery and the identification of some of the longest-known components of the protein synthesis machinery, including the ribosome itself, tRNAs, and translation factors proceeded through many stages of successively more refined biochemical purifications, finally culminating in the isolation to homogeneity, identification, and mapping of the smallest unit required for performing the given function. These early studies produced a wealth of information. However, many unknowns remained. Systems biology approaches provide an opportunity to investigate protein synthesis from a global perspective, overcoming the limitations of earlier ad hoc methods to gain unprecedented insights. This chapter reviews innovative systems biology approaches, with an emphasis on those designed specifically for investigating the protein synthesis machinery in E. coli.
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13
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Corgiat BA, Nordman JC, Kabbani N. Chemical crosslinkers enhance detection of receptor interactomes. Front Pharmacol 2014; 4:171. [PMID: 24432003 PMCID: PMC3882661 DOI: 10.3389/fphar.2013.00171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 12/17/2013] [Indexed: 01/04/2023] Open
Abstract
Receptor function is dependent on interaction with various intracellular proteins that ensure the localization and signaling of the receptor. While a number of approaches have been optimized for the isolation, purification, and proteomic characterization of receptor-protein interaction networks (interactomes) in cells, the capture of receptor interactomes and their dynamic properties remains a challenge. In particular, the study of interactome components that bind to the receptor with low affinity or can rapidly dissociate from the macromolecular complex is difficult. Here we describe how chemical crosslinking (CC) can aid in the isolation and proteomic analysis of receptor-protein interactions. The addition of CC to standard affinity purification and mass spectrometry protocols boosts the power of protein capture within the proteomic assay and enables the identification of specific binding partners under various cellular and receptor states. The utility of CC in receptor interactome studies is highlighted for the nicotinic acetylcholine receptor as well as several other receptor types. A better understanding of receptors and their interactions with proteins spearheads molecular biology, informs an integral part of bench medicine which helps in drug development, drug action, and understanding the pathophysiology of disease.
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Affiliation(s)
- Brian A Corgiat
- Department of Molecular Neuroscience, Krasnow Institute for Advanced Study, George Mason University Fairfax, VA, USA
| | - Jacob C Nordman
- Department of Molecular Neuroscience, Krasnow Institute for Advanced Study, George Mason University Fairfax, VA, USA
| | - Nadine Kabbani
- Department of Molecular Neuroscience, Krasnow Institute for Advanced Study, George Mason University Fairfax, VA, USA
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14
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Horiuchi K, Kawamura T, Iwanari H, Ohashi R, Naito M, Kodama T, Hamakubo T. Identification of Wilms' tumor 1-associating protein complex and its role in alternative splicing and the cell cycle. J Biol Chem 2013; 288:33292-302. [PMID: 24100041 DOI: 10.1074/jbc.m113.500397] [Citation(s) in RCA: 250] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Wilms' tumor 1-associating protein (WTAP) is a putative splicing regulator that is thought to be required for cell cycle progression through the stabilization of cyclin A2 mRNA and mammalian early embryo development. To further understand how WTAP acts in the context of the cellular machinery, we identified its interacting proteins in human umbilical vein endothelial cells and HeLa cells using shotgun proteomics. Here we show that WTAP forms a novel protein complex including Hakai, Virilizer homolog, KIAA0853, RBM15, the arginine/serine-rich domain-containing proteins BCLAF1 and THRAP3, and certain general splicing regulators, most of which have reported roles in post-transcriptional regulation. The depletion of these respective components of the complex resulted in reduced cell proliferation along with G2/M accumulation. Double knockdown of the serine/arginine-rich (SR)-like proteins BCLAF1 and THRAP3 by siRNA resulted in a decrease in the nuclear speckle localization of WTAP, whereas the nuclear speckles were intact. Furthermore, we found that the WTAP complex regulates alternative splicing of the WTAP pre-mRNA by promoting the production of a truncated isoform, leading to a change in WTAP protein expression. Collectively, these findings show that the WTAP complex is a novel component of the RNA processing machinery, implying an important role in both posttranscriptional control and cell cycle regulation.
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Affiliation(s)
- Keiko Horiuchi
- From the Department of Quantitative Biology and Medicine and
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