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Ertl FJ, Kopanchuk S, Dijon NC, Veikšina S, Tahk MJ, Laasfeld T, Schettler F, Gattor AO, Hübner H, Archipowa N, Köckenberger J, Heinrich MR, Gmeiner P, Kutta RJ, Holliday ND, Rinken A, Keller M. Dually Labeled Neurotensin NTS 1R Ligands for Probing Radiochemical and Fluorescence-Based Binding Assays. J Med Chem 2024; 67:16664-16691. [PMID: 39261089 DOI: 10.1021/acs.jmedchem.4c01470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
The determination of ligand-receptor binding affinities plays a key role in the development process of pharmaceuticals. While the classical radiochemical binding assay uses radioligands, fluorescence-based binding assays require fluorescent probes. Usually, radio- and fluorescence-labeled ligands are dissimilar in terms of structure and bioactivity, and can be used in either radiochemical or fluorescence-based assays. Aiming for a close comparison of both assay types, we synthesized tritiated fluorescent neurotensin receptor ligands ([3H]13, [3H]18) and their nontritiated analogues (13, 18). The labeled probes were studied in radiochemical and fluorescence-based (high-content imaging, flow cytometry, fluorescence anisotropy) binding assays. Equilibrium saturation binding yielded well-comparable ligand-receptor affinities, indicating that all these setups can be used for the screening of new drugs. In contrast, discrepancies were found in the kinetic behavior of the probes, which can be attributed to technical differences of the methods and require further studies with respect to the elucidation of the underlying mechanisms.
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Affiliation(s)
- Fabian J Ertl
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Sergei Kopanchuk
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Nicola C Dijon
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, U.K
| | - Santa Veikšina
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Maris-Johanna Tahk
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Tõnis Laasfeld
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Franziska Schettler
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Albert O Gattor
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straβe 10, D-91058 Erlangen, Germany
| | - Nataliya Archipowa
- Institute of Biophysics and Physical Biochemistry, Faculty of Biology and Preclinical Medicine, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Johannes Köckenberger
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straβe 10, D-91058 Erlangen, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straβe 10, D-91058 Erlangen, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straβe 10, D-91058 Erlangen, Germany
| | - Roger J Kutta
- Institute of Physical and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Nicholas D Holliday
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, U.K
| | - Ago Rinken
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
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Kot EF, Franco ML, Vasilieva EV, Shabalkina AV, Arseniev AS, Goncharuk SA, Mineev KS, Vilar M. Intrinsically disordered regions couple the ligand binding and kinase activation of Trk neurotrophin receptors. iScience 2022; 25:104348. [PMID: 35601915 PMCID: PMC9117555 DOI: 10.1016/j.isci.2022.104348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/22/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022] Open
Abstract
Receptor tyrosine kinases (RTKs) are key players in development and several diseases. Understanding the molecular mechanism of RTK activation by its ligand could lead to the design of new RTK inhibitors. How the extracellular domain is coupled to the intracellular kinase domain is a matter of debate. Ligand-induced dimerization and ligand-induced conformational change of pre-formed dimers are two of the most proposed models. Recently we proposed that TrkA, the RTK for nerve growth factor (NGF), is activated by rotation of the transmembrane domain (TMD) pre-formed dimers upon NGF binding. However, one of the unsolved issues is how the ligand binding is conformationally coupled to the TMD rotation if unstructured extracellular juxtamembrane (eJTM) regions separate them. Here we use nuclear magnetic resonance in bicelles and functional studies to demonstrate that eJTM regions from the Trk family are intrinsically disordered and couple the ligand-binding domains and TMDs possibly via the interaction with NGF. Extracellular juxtamembrane region is required for NGF binding and TrkA activation TrkA extracellular juxtamembrane region is unstructured and flexible This region couples neurotrophin-binding and transmembrane domain rotation The extracellular juxtamembrane region might play a role in neurotrophin recognition
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Affiliation(s)
- Erik F. Kot
- Moscow Institute of Physics and Technology, 141707 Dolgoprudnyi, Russian Federation
| | - María L. Franco
- Molecular Basis of Neurodegeneration Unit, Institute of Biomedicine of València (IBV-CSIC), C/ Jaume Roig 11, 46010 València, Spain
| | - Ekaterina V. Vasilieva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russian Federation
| | - Alexandra V. Shabalkina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russian Federation
- Moscow Institute of Physics and Technology, 141707 Dolgoprudnyi, Russian Federation
| | - Alexander S. Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russian Federation
- Moscow Institute of Physics and Technology, 141707 Dolgoprudnyi, Russian Federation
- Corresponding author
| | - Sergey A. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russian Federation
- Moscow Institute of Physics and Technology, 141707 Dolgoprudnyi, Russian Federation
- Corresponding author
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russian Federation
- Moscow Institute of Physics and Technology, 141707 Dolgoprudnyi, Russian Federation
- Corresponding author
| | - Marçal Vilar
- Molecular Basis of Neurodegeneration Unit, Institute of Biomedicine of València (IBV-CSIC), C/ Jaume Roig 11, 46010 València, Spain
- Corresponding author
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Kumra Ahnlide V, de Neergaard T, Sundwall M, Ambjörnsson T, Nordenfelt P. A Predictive Model of Antibody Binding in the Presence of IgG-Interacting Bacterial Surface Proteins. Front Immunol 2021; 12:629103. [PMID: 33828549 PMCID: PMC8019711 DOI: 10.3389/fimmu.2021.629103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/19/2021] [Indexed: 11/24/2022] Open
Abstract
Many bacteria can interfere with how antibodies bind to their surfaces. This bacterial antibody targeting makes it challenging to predict the immunological function of bacteria-associated antibodies. The M and M-like proteins of group A streptococci (GAS) exhibit IgGFc-binding regions, which they use to reverse IgG binding orientation depending on the host environment. Unraveling the mechanism behind these binding characteristics may identify conditions under which bound IgG can drive an efficient immune response. Here, we have developed a biophysical model for describing these complex protein-antibody interactions. We show how the model can be used as a tool for studying the binding behavior of various IgG samples to M protein by performing in silico simulations and correlating this data with experimental measurements. Besides its use for mechanistic understanding, this model could potentially be used as a tool to aid in the development of antibody treatments. We illustrate this by simulating how IgG binding to GAS in serum is altered as specified amounts of monoclonal or pooled IgG is added. Phagocytosis experiments link this altered antibody binding to a physiological function and demonstrate that it is possible to predict the effect of an IgG treatment with our model. Our study gives a mechanistic understanding of bacterial antibody targeting and provides a tool for predicting the effect of antibody treatments in the presence of bacteria with IgG-modulating surface proteins.
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Affiliation(s)
- Vibha Kumra Ahnlide
- Division of Infection Medicine, Department of Clinical Sciences, Faculty of Medicine, Lund University, Lund, Sweden
| | - Therese de Neergaard
- Division of Infection Medicine, Department of Clinical Sciences, Faculty of Medicine, Lund University, Lund, Sweden
| | - Martin Sundwall
- Division of Infection Medicine, Department of Clinical Sciences, Faculty of Medicine, Lund University, Lund, Sweden
| | - Tobias Ambjörnsson
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Pontus Nordenfelt
- Division of Infection Medicine, Department of Clinical Sciences, Faculty of Medicine, Lund University, Lund, Sweden
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Lifetime encoding in flow cytometry for bead-based sensing of biomolecular interaction. Sci Rep 2020; 10:19477. [PMID: 33173064 PMCID: PMC7655863 DOI: 10.1038/s41598-020-76150-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/07/2020] [Indexed: 12/19/2022] Open
Abstract
To demonstrate the potential of time-resolved flow cytometry (FCM) for bioanalysis, clinical diagnostics, and optically encoded bead-based assays, we performed a proof-of-principle study to detect biomolecular interactions utilizing fluorescence lifetime (LT)-encoded micron-sized polymer beads bearing target-specific bioligands and a recently developed prototype lifetime flow cytometer (LT-FCM setup). This instrument is equipped with a single excitation light source and different fluorescence detectors, one operated in the photon-counting mode for time-resolved measurements of fluorescence decays and three detectors for conventional intensity measurements in different spectral windows. First, discrimination of bead-bound biomolecules was demonstrated in the time domain exemplarily for two targets, Streptavidin (SAv) and the tumor marker human chorionic gonadotropin (HCG). In a second step, the determination of biomolecule concentration levels was addressed representatively for the inflammation-related biomarker tumor necrosis factor (TNF-α) utilizing fluorescence intensity measurements in a second channel of the LT-FCM instrument. Our results underline the applicability of LT-FCM in the time domain for measurements of biomolecular interactions in suspension assays. In the future, the combination of spectral and LT encoding and multiplexing and the expansion of the time scale from the lower nanosecond range to the longer nanosecond and the microsecond region is expected to provide many distinguishable codes. This enables an increasing degree of multiplexing which could be attractive for high throughput screening applications.
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Culhane KJ, Belina ME, Sims JN, Cai Y, Liu Y, Wang PSP, Yan ECY. Parathyroid Hormone Senses Extracellular Calcium To Modulate Endocrine Signaling upon Binding to the Family B GPCR Parathyroid Hormone 1 Receptor. ACS Chem Biol 2018; 13:2347-2358. [PMID: 29952553 PMCID: PMC10640708 DOI: 10.1021/acschembio.8b00568] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Parathyroid hormone (PTH) binds to a family B G protein coupled receptor, parathyroid hormone 1 receptor (PTH1R). One of its functions is to regulate Ca2+ homeostasis in bone remodeling, during which Ca2+ can reach up to 40 mM. A truncated version of PTH, PTH(1-34), can fully activate PTH1R and has been used for osteoporosis treatments. Here, we used fluorescence anisotropy to examine the binding of PTH(1-34) to PTH1R purified in nanodiscs (PTH1R-ND) and found that the affinity increases 5-fold in the presence of 15 mM Ca2+. However, PTHrP(1-36), another truncated endogenous agonist for PTH1R, does not show this Ca2+ effect. Mutations of Glu19 and Glu22 in PTH(1-34) that are not conserved in PTHrP(1-36) largely abolished the Ca2+ effect. The results support that PTH(1-34) not only activates PTH1R but also uniquely senses Ca2+. This dual function of a peptide hormone is a novel observation that couples changes in extracellular environment with endocrine signaling. Understanding this can potentially reveal the complex role of PTH signaling in bone remodeling and improve the PTH(1-34) treatment for osteoporosis.
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Affiliation(s)
- Kelly J. Culhane
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave, New Haven, Connecticut 06520, USA
| | - Morgan E. Belina
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Jeremiah N. Sims
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Yingying Cai
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Yuting Liu
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Pam S. P. Wang
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
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Barton M, Filardo EJ, Lolait SJ, Thomas P, Maggiolini M, Prossnitz ER. Twenty years of the G protein-coupled estrogen receptor GPER: Historical and personal perspectives. J Steroid Biochem Mol Biol 2018; 176:4-15. [PMID: 28347854 PMCID: PMC5716468 DOI: 10.1016/j.jsbmb.2017.03.021] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 12/24/2022]
Abstract
Estrogens play a critical role in many aspects of physiology, particularly female reproductive function, but also in pathophysiology, and are associated with protection from numerous diseases in premenopausal women. Steroids and the effects of estrogen have been known for ∼90 years, with the first evidence for a receptor for estrogen presented ∼50 years ago. The original ancestral steroid receptor, extending back into evolution more than 500 million years, was likely an estrogen receptor, whereas G protein-coupled receptors (GPCRs) trace their origins back into history more than one billion years. The classical estrogen receptors (ERα and ERβ) are ligand-activated transcription factors that confer estrogen sensitivity upon many genes. It was soon apparent that these, or novel receptors may also be responsible for the "rapid"/"non-genomic" membrane-associated effects of estrogen. The identification of an orphan GPCR (GPR30, published in 1996) opened a new field of research with the description in 2000 that GPR30 expression is required for rapid estrogen signaling. In 2005-2006, the field was greatly stimulated by two studies that described the binding of estrogen to GPR30-expressing cell membranes, followed by the identification of a GPR30-selective agonist (that lacked binding and activity towards ERα and ERβ). Renamed GPER (G protein-coupled estrogen receptor) by IUPHAR in 2007, the total number of articles in PubMed related to this receptor recently surpassed 1000. In this article, the authors present personal perspectives on how they became involved in the discovery and/or advancement of GPER research. These areas include non-genomic effects on vascular tone, receptor cloning, molecular and cellular biology, signal transduction mechanisms and pharmacology of GPER, highlighting the roles of GPER and GPER-selective compounds in diseases such as obesity, diabetes, and cancer and the obligatory role of GPER in propagating cardiovascular aging, arterial hypertension and heart failure through the stimulation of Nox expression.
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Affiliation(s)
- Matthias Barton
- Molecular Internal Medicine, University of Zürich, 8057 Zürich, Switzerland.
| | - Edward J Filardo
- Rhode Island Hospital, Brown University, Providence, RI 02903, USA
| | - Stephen J Lolait
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, School of Clinical Sciences, University of Bristol, Bristol, UK
| | - Peter Thomas
- Marine Science Institute, University of Texas at Austin, Port Aransas, TX 78373, USA
| | - Marcello Maggiolini
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Eric R Prossnitz
- Department of Internal Medicine, University of New Mexico Health Sciences Center and University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA.
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Lv D, Ma QH, Duan JJ, Wu HB, Zhao XL, Yu SC, Bian XW. Optimized dissociation protocol for isolating human glioma stem cells from tumorspheres via fluorescence-activated cell sorting. Cancer Lett 2016; 377:105-15. [PMID: 27091400 DOI: 10.1016/j.canlet.2016.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/12/2016] [Accepted: 04/12/2016] [Indexed: 12/28/2022]
Abstract
Fluorescence-activated cell sorting (FACS) based on the surface marker CD133 is the most common method for isolating glioma stem cells (GSCs) from heterogeneous glioma cell populations. Optimization of this method will have profound implications for the future of GSC research. Five commonly used digestion reagents, Liberase-TL, trypsin, TrypLE, Accutase, and non-enzymatic cell dissociation solution (NECDS), were used to dissociate glioma tumorspheres derived from two primary glioma specimens (091214 and 090116) and the cell lines U87 and T98G. The dissociation time, cell viability, retention of CD133, and stemness capacity were assessed. The results showed that single cells derived from the Liberase-TL (200 µg/ml) group exhibited high viability and less damage to the antigen CD133. However, the efficiency of NECDS for dissociating the tumorspheres into single cells was fairly low. Meanwhile, the use of this digestion reagent resulted in obvious cellular and antigenic impairments. Taken together, Liberase-TL (200 µg/ml) is an ideal reagent for isolating GSCs from tumorspheres. In contrast, the use of NECDS for such a protocol should be carefully considered.
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Affiliation(s)
- Donglai Lv
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing 400037, China; Key Laboratory of Tumor Immunology and Pathology of Ministry of Education, Chongqing 400037, China
| | - Qing-Hua Ma
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing 400037, China; Key Laboratory of Tumor Immunology and Pathology of Ministry of Education, Chongqing 400037, China
| | - Jiang-Jie Duan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing 400037, China; Key Laboratory of Tumor Immunology and Pathology of Ministry of Education, Chongqing 400037, China
| | - Hai-Bo Wu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing 400037, China; Key Laboratory of Tumor Immunology and Pathology of Ministry of Education, Chongqing 400037, China
| | - Xi-Long Zhao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing 400037, China; Key Laboratory of Tumor Immunology and Pathology of Ministry of Education, Chongqing 400037, China
| | - Shi-Cang Yu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing 400037, China; Key Laboratory of Tumor Immunology and Pathology of Ministry of Education, Chongqing 400037, China.
| | - Xiu-Wu Bian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing 400037, China; Key Laboratory of Tumor Immunology and Pathology of Ministry of Education, Chongqing 400037, China.
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Gilchrist ML, Ahn K, Li YM. Imaging and Functional Analysis of γ-Secretase and Substrate in a Proteolipobead System with an Activity-Based Probe. Anal Chem 2016; 88:1303-11. [PMID: 26699370 PMCID: PMC4911041 DOI: 10.1021/acs.analchem.5b03762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Investigation of intramembranal protease catalysis demands the generation of intact biomembrane assemblies with structural integrity and lateral mobility. Here, we report the development of a microsphere supported-biomembrane platform enabling characterization of γ-secretase and substrate within proteolipobead assemblies via microscopy and flow cytometry. The active enzyme loading levels were tracked using an activity-based probe, with the biomembranes delineated by carbocyanine lipid reporters. Proteolipobeads formed from HeLa proteoliposomes gave rise to homogeneous distributions of active γ-secretase within supported biomembranes with native-like fluidity. The substrate loading into supported biomembranes was detergent-dependent, as evidenced by even colocalization of substrate and lipid tracers in confocal 3D imaging of individual proteolipobeads. Moreover, the loading level was tunable with bulk substrate concentration. γ-Secretase substrate cleavage and its inhibition within γ-secretase proteolipobeads were observed. This platform offers a means to visualize enzyme and substrate loading, activity, and inhibition in a controllable biomembrane microenvironment.
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Affiliation(s)
- M. Lane Gilchrist
- Department of Chemical Engineering and the Department of Biomedical Engineering, The City College of the City University of New York, 140th Street and Convent Avenue, New York, New York 10031, United States
| | - Kwangwook Ahn
- Chemistry Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
| | - Yue-Ming Li
- Chemistry Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
- Program of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, New York 10021, United States
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Lee CW, Guo L, Matei D, Stantz K. Development of Follicle-Stimulating Hormone Receptor Binding Probes to Image Ovarian Xenografts. ACTA ACUST UNITED AC 2015; 5. [PMID: 26779384 PMCID: PMC4712933 DOI: 10.4172/2155-952x.1000198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The Follicle-Stimulating Hormone Receptor (FSHR) is used as an imaging biomarker for the detection of ovarian cancer (OC). FSHR is highly expressed on ovarian tumors and involved with cancer development and metastatic signaling pathways. A decapeptide specific to the FSHR extracellular domain is synthesized and conjugated to fluorescent dyes to image OC cells in vitro and tumors xenograft model in vivo. The in vitro binding curve and the average number of FSHR per cell are obtained for OVCAR-3 cells by a high resolution flow cytometer. For the decapeptide, the measured EC50 was 160 μM and the average number of receptors per cell was 1.7 × 107. The decapeptide molecular imaging probe reached a maximum tumor to muscle ratio five hours after intravenous injection and a dose-dependent plateau after 24-48 hours. These results indicate the potential application of a small molecular weight imaging probe specific to ovarian cancer through binding to FSHR. Based on these results, multimeric constructs are being developed to optimize binding to ovarian cells and tumors.
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Affiliation(s)
- Chung-Wein Lee
- Medical Physics Program, School of Health Science, Purdue University, West Lafayette, IN, USA
| | - Lili Guo
- Department of Medicine, Indiana University School of Medicine, Indianapolis IN, USA
| | - Daniela Matei
- Department of Medicine, Indiana University School of Medicine, Indianapolis IN, USA
| | - Keith Stantz
- Medical Physics Program, School of Health Science, Purdue University, West Lafayette, IN, USA; Department of Medicine, Indiana University School of Medicine, Indianapolis IN, USA
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Cesa LC, Mapp AK, Gestwicki JE. Direct and Propagated Effects of Small Molecules on Protein-Protein Interaction Networks. Front Bioeng Biotechnol 2015; 3:119. [PMID: 26380257 PMCID: PMC4547496 DOI: 10.3389/fbioe.2015.00119] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/05/2015] [Indexed: 12/15/2022] Open
Abstract
Networks of protein–protein interactions (PPIs) link all aspects of cellular biology. Dysfunction in the assembly or dynamics of PPI networks is a hallmark of human disease, and as such, there is growing interest in the discovery of small molecules that either promote or inhibit PPIs. PPIs were once considered undruggable because of their relatively large buried surface areas and difficult topologies. Despite these challenges, recent advances in chemical screening methodologies, combined with improvements in structural and computational biology have made some of these targets more tractable. In this review, we highlight developments that have opened the door to potent chemical modulators. We focus on how allostery is being used to produce surprisingly robust changes in PPIs, even for the most challenging targets. We also discuss how interfering with one PPI can propagate changes through the broader web of interactions. Through this analysis, it is becoming clear that a combination of direct and propagated effects on PPI networks is ultimately how small molecules re-shape biology.
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Affiliation(s)
- Laura C Cesa
- Program in Chemical Biology, Life Sciences Institute, University of Michigan , Ann Arbor, MI , USA
| | - Anna K Mapp
- Program in Chemical Biology, Life Sciences Institute, University of Michigan , Ann Arbor, MI , USA ; Department of Chemistry, University of Michigan , Ann Arbor, MI , USA
| | - Jason E Gestwicki
- Program in Chemical Biology, Life Sciences Institute, University of Michigan , Ann Arbor, MI , USA ; Department of Pharmaceutical Chemistry, Institute for Neurodegenerative Diseases, University of California San Francisco , San Francisco, CA , USA
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Edwards BS, Sklar LA. Flow Cytometry: Impact on Early Drug Discovery. JOURNAL OF BIOMOLECULAR SCREENING 2015; 20:689-707. [PMID: 25805180 PMCID: PMC4606936 DOI: 10.1177/1087057115578273] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/27/2015] [Indexed: 12/15/2022]
Abstract
Modern flow cytometers can make optical measurements of 10 or more parameters per cell at tens of thousands of cells per second and more than five orders of magnitude dynamic range. Although flow cytometry is used in most drug discovery stages, "sip-and-spit" sampling technology has restricted it to low-sample-throughput applications. The advent of HyperCyt sampling technology has recently made possible primary screening applications in which tens of thousands of compounds are analyzed per day. Target-multiplexing methodologies in combination with extended multiparameter analyses enable profiling of lead candidates early in the discovery process, when the greatest numbers of candidates are available for evaluation. The ability to sample small volumes with negligible waste reduces reagent costs, compound usage, and consumption of cells. Improved compound library formatting strategies can further extend primary screening opportunities when samples are scarce. Dozens of targets have been screened in 384- and 1536-well assay formats, predominantly in academic screening lab settings. In concert with commercial platform evolution and trending drug discovery strategies, HyperCyt-based systems are now finding their way into mainstream screening labs. Recent advances in flow-based imaging, mass spectrometry, and parallel sample processing promise dramatically expanded single-cell profiling capabilities to bolster systems-level approaches to drug discovery.
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Affiliation(s)
- Bruce S Edwards
- Center for Molecular Discovery, Innovation Discovery and Training Center, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
| | - Larry A Sklar
- Center for Molecular Discovery, Innovation Discovery and Training Center, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
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12
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Spindel S, Sapsford KE. Evaluation of optical detection platforms for multiplexed detection of proteins and the need for point-of-care biosensors for clinical use. SENSORS (BASEL, SWITZERLAND) 2014; 14:22313-41. [PMID: 25429414 PMCID: PMC4299016 DOI: 10.3390/s141222313] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/12/2014] [Accepted: 11/13/2014] [Indexed: 11/16/2022]
Abstract
This review investigates optical sensor platforms for protein multiplexing, the ability to analyze multiple analytes simultaneously. Multiplexing is becoming increasingly important for clinical needs because disease and therapeutic response often involve the interplay between a variety of complex biological networks encompassing multiple, rather than single, proteins. Multiplexing is generally achieved through one of two routes, either through spatial separation on a surface (different wells or spots) or with the use of unique identifiers/labels (such as spectral separation-different colored dyes, or unique beads-size or color). The strengths and weaknesses of conventional platforms such as immunoassays and new platforms involving protein arrays and lab-on-a-chip technology, including commercially-available devices, are discussed. Three major public health concerns are identified whereby detecting medically-relevant markers using Point-of-Care (POC) multiplex assays could potentially allow for a more efficient diagnosis and treatment of diseases.
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Affiliation(s)
- Samantha Spindel
- Division of Biology, Chemistry, and Materials Science Office of Science and Engineering Laboratories; U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
| | - Kim E Sapsford
- Division of Biology, Chemistry, and Materials Science Office of Science and Engineering Laboratories; U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
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13
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Chigaev A, Smagley Y, Sklar LA. Carbon monoxide down-regulates α4β1 integrin-specific ligand binding and cell adhesion: a possible mechanism for cell mobilization. BMC Immunol 2014; 15:52. [PMID: 25367365 PMCID: PMC4221689 DOI: 10.1186/s12865-014-0052-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/21/2014] [Indexed: 01/13/2023] Open
Abstract
Background Carbon monoxide (CO), a byproduct of heme degradation, is attracting growing attention from the scientific community. At physiological concentrations, CO plays a role as a signal messenger that regulates a number of physiological processes. CO releasing molecules are under evaluation in preclinical models for the management of inflammation, sepsis, ischemia/reperfusion injury, and organ transplantation. Because of our discovery that nitric oxide signaling actively down-regulates integrin affinity and cell adhesion, and the similarity between nitric oxide and CO-dependent signaling, we studied the effects of CO on integrin signaling and cell adhesion. Results We used a cell permeable CO releasing molecule (CORM-2) to elevate intracellular CO, and a fluorescent Very Late Antigen-4 (VLA-4, α4β1-integrin)-specific ligand to evaluate the integrin state in real-time on live cells. We show that the binding of the ligand can be rapidly down-modulated in resting cells and after inside-out activation through several Gαi-coupled receptors. Moreover, cell treatment with hemin, a natural source of CO, resulted in comparable VLA-4 ligand dissociation. Inhibition of VLA-4 ligand binding by CO had a dramatic effect on cell-cell interaction in a VLA-4/VCAM-1-dependent cell adhesion system. Conclusions We conclude that the CO signaling pathway can rapidly down-modulate binding of the VLA-4 -specific ligand. We propose that CO-regulated integrin deactivation provides a basis for modulation of immune cell adhesion as well as rapid cell mobilization, for example as shown for splenic monocytes in response to surgically induced ischemia of the myocardium.
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Affiliation(s)
- Alexandre Chigaev
- Department of Pathology and University of New Mexico Cancer Center, Albuquerque 87131, NM, USA.
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14
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Piyasena ME, Graves SW. The intersection of flow cytometry with microfluidics and microfabrication. LAB ON A CHIP 2014; 14:1044-59. [PMID: 24488050 PMCID: PMC4077616 DOI: 10.1039/c3lc51152a] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A modern flow cytometer can analyze and sort particles on a one by one basis at rates of 50,000 particles per second. Flow cytometers can also measure as many as 17 channels of fluorescence, several angles of scattered light, and other non-optical parameters such as particle impedance. More specialized flow cytometers can provide even greater analysis power, such as single molecule detection, imaging, and full spectral collection, at reduced rates. These capabilities have made flow cytometers an invaluable tool for numerous applications including cellular immunophenotyping, CD4+ T-cell counting, multiplex microsphere analysis, high-throughput screening, and rare cell analysis and sorting. Many bio-analytical techniques have been influenced by the advent of microfluidics as a component in analytical tools and flow cytometry is no exception. Here we detail the functions and uses of a modern flow cytometer, review the recent and historical contributions of microfluidics and microfabricated devices to field of flow cytometry, examine current application areas, and suggest opportunities for the synergistic application of microfabrication approaches to modern flow cytometry.
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Affiliation(s)
- Menake E. Piyasena
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM USA
- Department of Chemistry, New Mexico Tech, Socorro, NM USA
| | - Steven W. Graves
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM USA
- Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM USA, FAX: 15052771979; TEL:15052772043
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15
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Sridharan R, Zuber J, Connelly SM, Mathew E, Dumont ME. Fluorescent approaches for understanding interactions of ligands with G protein coupled receptors. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1838:15-33. [PMID: 24055822 PMCID: PMC3926105 DOI: 10.1016/j.bbamem.2013.09.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 09/03/2013] [Accepted: 09/08/2013] [Indexed: 11/18/2022]
Abstract
G protein coupled receptors are responsible for a wide variety of signaling responses in diverse cell types. Despite major advances in the determination of structures of this class of receptors, the underlying mechanisms by which binding of different types of ligands specifically elicits particular signaling responses remain unclear. The use of fluorescence spectroscopy can provide important information about the process of ligand binding and ligand dependent conformational changes in receptors, especially kinetic aspects of these processes that can be difficult to extract from X-ray structures. We present an overview of the extensive array of fluorescent ligands that have been used in studies of G protein coupled receptors and describe spectroscopic approaches for assaying binding and probing the environment of receptor-bound ligands with particular attention to examples involving yeast pheromone receptors. In addition, we discuss the use of fluorescence spectroscopy for detecting and characterizing conformational changes in receptors induced by the binding of ligands. Such studies have provided strong evidence for diversity of receptor conformations elicited by different ligands, consistent with the idea that GPCRs are not simple on and off switches. This diversity of states constitutes an underlying mechanistic basis for biased agonism, the observation that different stimuli can produce different responses from a single receptor. It is likely that continued technical advances will allow fluorescence spectroscopy to play an important role in continued probing of structural transitions in G protein coupled receptors. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.
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Affiliation(s)
- Rajashri Sridharan
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
| | - Jeffrey Zuber
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
| | - Sara M. Connelly
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
| | - Elizabeth Mathew
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
| | - Mark E. Dumont
- Department of Biochemistry and Biophysics, P.O. Box 712, University of Rochester Medical Center, Rochester, NY 14642
- Department of Pediatrics, P.O. Box 777, University of Rochester Medical Center, Rochester, NY 14642
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16
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Abstract
The use of fluidics is implicit in a technology named "flow cytometry," which flows a cell or particle through a sensing volume to obtain serial analysis of particles on a one by one basis. This flow of particles enables flow cytometry to collect information on multiple particle populations, giving it a distinct advantage over bulk analysis approaches. Moreover, flow cytometers can analyze thousands of particles per second in a single flowing stream. Additionally, use of volumetric sample delivery makes it possible for flow cytometers to accurately count cells and particles. Furthermore, the analysis results can be coupled with a fluidic diversion mechanism to sort and collect particles based on desired properties. Finally, when high-throughput sampling technologies are employed to rapidly change the input of the sample stream, a flow cytometer can become an integral tool for high-throughput screening. The above properties have made flow cytometry useful in a wide range of biomedical applications. In this unit we will present an overview of fluidic systems that make flow cytometry possible. This will introduce historical approaches, explanations of the commonly implemented current fluidics, and brief discussions of potential future fluidics where appropriate.
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Affiliation(s)
| | - Steven W Graves
- Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, New Mexico
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17
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Matusica D, Skeldal S, Sykes AM, Palstra N, Sharma A, Coulson EJ. An intracellular domain fragment of the p75 neurotrophin receptor (p75(NTR)) enhances tropomyosin receptor kinase A (TrkA) receptor function. J Biol Chem 2013; 288:11144-54. [PMID: 23471969 PMCID: PMC3630867 DOI: 10.1074/jbc.m112.436469] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/17/2013] [Indexed: 11/06/2022] Open
Abstract
Facilitation of nerve growth factor (NGF) signaling by the p75 neurotrophin receptor (p75(NTR)) is critical for neuronal survival and differentiation. However, the interaction between p75(NTR) and TrkA receptors required for this activity is not understood. Here, we report that a specific 29-amino acid peptide derived from the intracellular domain fragment of p75(NTR) interacts with and potentiates binding of NGF to TrkA-expressing cells, leading to increased neurite outgrowth in sympathetic neurons as a result of enhanced Erk1/2 and Akt signaling. An endogenous intracellular domain fragment of p75(NTR) (p75(ICD)) containing these 29 amino acids is produced by regulated proteolysis of the full-length receptor. We demonstrate that generation of this fragment is a requirement for p75(NTR) to facilitate TrkA signaling in neurons and propose that the juxtamembrane region of p75(ICD) acts to cause a conformational change within the extracellular domain of TrkA. This finding provides new insight into the mechanism by which p75(NTR) and TrkA interact to enhance neurotrophic signaling.
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Affiliation(s)
- Dusan Matusica
- From the Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sune Skeldal
- From the Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Alex M. Sykes
- From the Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nickless Palstra
- From the Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Aanchal Sharma
- From the Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Elizabeth J. Coulson
- From the Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
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18
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Mathew E, Ding FX, Naider F, Dumont ME. Functional fusions of T4 lysozyme in the third intracellular loop of a G protein-coupled receptor identified by a random screening approach in yeast. Protein Eng Des Sel 2012; 26:59-71. [PMID: 23077276 DOI: 10.1093/protein/gzs070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The insertion of a stable soluble protein into loops of transmembrane proteins has proved to be a successful approach for enhancing their stabilities and crystallization, and may also be useful in contexts where the inserted proteins can modulate or report on the activities of membrane proteins. While the use of T4 lysozyme to replace portions of the third intracellular loops of G protein-coupled receptors (GPCRs) has allowed determination of the structures of members of this important class of receptors, the creation of such fusion proteins generally leads to loss of signaling function of the resulting fusion protein, since the third intracellular loops of GPCRs play critical roles in their interactions with G proteins. We describe here a random screening approach allowing insertion of T4 lysozyme into diverse positions in the third loop of the yeast α-pheromone receptor, a GPCR encoded by the yeast STE2 gene. Insertions were accompanied by varying extents of deletion or duplication of the loop. A set of phenotypic screens allow detection of potentially rare variant receptors that are expressed, bind to agonist and are capable of signal transduction via activation of the cognate G protein. A large fraction of screened full-length receptor variants containing at least partial duplications of the loop on either side of the inserted T4 lysozyme retain the ability to activate the downstream signaling pathway in response to binding of ligand. However, we were unable to identify any receptors with truncated C-termini that retain significant signaling function in the presence of inserted T4 lysozyme. Our results establish the feasibility of creating functional receptors containing insertions of T4 lysozyme in their third intracellular loops.
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Affiliation(s)
- Elizabeth Mathew
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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19
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Vigerust DJ, Vick S, Shepherd VL. Characterization of functional mannose receptor in a continuous hybridoma cell line. BMC Immunol 2012; 13:51. [PMID: 22967244 PMCID: PMC3495026 DOI: 10.1186/1471-2172-13-51] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 08/30/2012] [Indexed: 12/29/2022] Open
Abstract
Background The mannose receptor is the best described member of the type I transmembrane C-type lectins; however much remains unanswered about the biology of the receptor. One difficulty has been the inability to consistently express high levels of a functional full length mannose receptor cDNA in mammalian cells. Another difficulty has been the lack of a human macrophage cell line expressing a fully functional receptor. Commonly used human macrophage cell lines such as U937, THP-1, Mono-Mac and HL60 do not express the mannose receptor. We have developed a macrophage hybridoma cell line (43MR cells) created by fusion of U937 cells with primary human monocyte-derived macrophages, resulting in a non-adherent cell line expressing several properties of primary macrophages. The purpose of this study was to identify and select mannose receptor-expressing cells using fluorescence-activated cell sorting and to characterize the expression and function of the receptor. Results In the current study we show that the mannose receptor found on this novel cell has endocytic characteristics consistent with and similar to the mannose receptor found on the surface of monocyte-derived human macrophages and rat bone marrow-derived macrophages. In addition, we demonstrate that these cells engage and internalize pathogen particles such as S. aureus and C. albicans. We further establish the transfectability of these cells via the introduction of a plasmid expressing influenza A hemagglutinin. Conclusions The 43MR cell line represents the first naturally expressed MR-positive cell line derived from a human macrophage background. This cell line provides an important cell model for other researchers for the study of human MR biology and host-pathogen interactions.
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Affiliation(s)
- David J Vigerust
- Department of Veterans Affairs Medical Center, VA Medical Center/Research Service, 1310 24th Ave,, South, Nashville TN 37212, USA
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20
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Gossett DR, Tse HTK, Dudani JS, Goda K, Woods TA, Graves SW, Di Carlo D. Inertial manipulation and transfer of microparticles across laminar fluid streams. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:2757-64. [PMID: 22761059 DOI: 10.1002/smll.201200588] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Indexed: 05/08/2023]
Abstract
A general strategy for controlling particle movement across streams would enable new capabilities in single-cell analysis, solid-phase reaction control, and biophysics research. Transferring cells across streams is difficult to achieve in a well-controlled manner, since it requires precise control of fluid flow along with external force fields or precisely manufactured mechanical structures. Herein a strategy is introduced for particle transfer based on passive inertial lift forces and shifts in the distribution of these forces for channels with shifting aspect ratios. Uniquely, use of the dominant wall-effect lift parallel to the particle rotation direction is explored and utilized to achieve controllable cross-stream motion. In this way, particles are positioned to migrate across laminar streams and enter a new solution without significant disturbance of the interface at rates exceeding 1000 particles per second and sub-millisecond transfer times. The capabilities of rapid inertial solution exchange (RInSE) for preparation of hematological samples and other cellular assays are demonstrated. Lastly, improvements to inline flow cytometry after RInSE of excess fluorescent dye and focusing for downstream analysis are characterized. The described approach is simply applied to manipulating cells and particles and quickly exposing them to or removing them from a reacting solution, with broader applications in control and analysis of low affinity interactions on cells or particles.
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Affiliation(s)
- Daniel R Gossett
- Department of Bioengineering, University of California Los Angeles, 90095-1600, USA
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21
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Multiplex optical sensing with surface-enhanced Raman scattering: a critical review. Anal Chim Acta 2012; 745:10-23. [PMID: 22938601 DOI: 10.1016/j.aca.2012.08.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 08/01/2012] [Accepted: 08/02/2012] [Indexed: 01/25/2023]
Abstract
Multiplex analysis permits the detection of several analytical targets at the same time. This approach may permit to draw a rapid and accurate diagnostic about the health of an individual or an environment. Among the analytical techniques with potential for multiplexing surface-enhanced Raman scattering (SERS) offer unique advantages such as ultrasensitive detection down low the deconvolution times, a unique signature containing all the vibrational information of the target molecules, and the possibility of performing the experiments even in very demanding environments such as natural or biological fluids. Here we review the late advances in multiplex SERS including the direct methods, those aided by the surface functionalization of the plasmonic nanoparticles and the use of SERS encoded particles.
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22
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One-dimensional acoustic standing waves in rectangular channels for flow cytometry. Methods 2012; 57:259-71. [DOI: 10.1016/j.ymeth.2012.02.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 02/22/2012] [Accepted: 02/23/2012] [Indexed: 11/21/2022] Open
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23
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Cummings LJ, Perez-Castillejos R, Mack ET. Analysis of Biochemical Equilibria Relevant to the Immune Response: Finding the Dissociation Constants. Bull Math Biol 2012; 74:1171-1206. [DOI: 10.1007/s11538-012-9716-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2011] [Accepted: 01/05/2012] [Indexed: 12/29/2022]
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24
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Chigaev A, Wu Y, Williams DB, Smagley Y, Sklar LA. Discovery of very late antigen-4 (VLA-4, alpha4beta1 integrin) allosteric antagonists. J Biol Chem 2011; 286:5455-63. [PMID: 21131351 PMCID: PMC3037658 DOI: 10.1074/jbc.m110.162636] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 11/19/2010] [Indexed: 11/06/2022] Open
Abstract
Integrins are cell adhesion receptors that mediate cell-to-cell, or cell-to-extracellular matrix adhesion. They represent an attractive target for treatment of multiple diseases. Two classes of small molecule integrin inhibitors have been developed. Competitive antagonists bind directly to the integrin ligand binding pocket and thus disrupt the ligand-receptor interaction. Allosteric antagonists have been developed primarily for α(L)β(2)- integrin (LFA-1, lymphocyte function-associated antigen-1). Here we present the results of screening the Prestwick Chemical Library using a recently developed assay for the detection of α(4)β(1)-integrin allosteric antagonists. Secondary assays confirmed that the compounds identified: 1) do not behave like competitive (direct) antagonists; 2) decrease ligand binding affinity for VLA-4 ∼2 orders of magnitude; 3) exhibit antagonistic properties at low temperature. In a cell based adhesion assay in vitro, the compounds rapidly disrupted cellular aggregates. In accord with reports that VLA-4 antagonists in vivo induce mobilization of hematopoietic progenitors into the peripheral blood, we found that administration of one of the compounds significantly increased the number of colony-forming units in mice. This effect was comparable to AMD3100, a well known progenitor mobilizing agent. Because all the identified compounds are structurally related, previously used, or currently marketed drugs, this result opens a range of therapeutic possibilities for VLA-4-related pathologies.
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Affiliation(s)
- Alexandre Chigaev
- From the Department of Pathology and Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131
| | - Yang Wu
- From the Department of Pathology and Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131
| | - D. Bart Williams
- From the Department of Pathology and Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131
| | - Yelena Smagley
- From the Department of Pathology and Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131
| | - Larry A. Sklar
- From the Department of Pathology and Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131
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25
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Abstract
Interaction of the integrin receptors with ligands determines the molecular basis of integrin-dependent cell adhesion. Integrin ligands are typically large proteins with relatively low binding affinities. This makes direct ligand-binding kinetic measurements somewhat difficult. Here we examine several real-time methods, aimed to overcome these experimental limitations and to distinguish the regulation of integrin conformation and affinity. This chapter includes: the use of a small ligand-mimetic probe for studies of inside-out regulation of integrin affinity and unbending, real-time cell aggregation and disaggregation kinetics to probe integrin conformational states and the number of integrin-ligand bonds, as well as the real-time monitoring of ligand-induced epitopes under signaling through G-protein-coupled receptors, and others. Experimental data obtained using these novel methods are summarized in terms of the current model of integrin activation.
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Affiliation(s)
- Alexandre Chigaev
- Department of Pathology and Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
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26
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Arterburn JB, Oprea TI, Prossnitz ER, Edwards BS, Sklar LA. Discovery of selective probes and antagonists for G-protein-coupled receptors FPR/FPRL1 and GPR30. Curr Top Med Chem 2010; 9:1227-36. [PMID: 19807662 DOI: 10.2174/156802609789753608] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 07/29/2009] [Indexed: 01/04/2023]
Abstract
Recent technological advances in flow cytometry provide a versatile platform for high throughput screening of compound libraries coupled with high-content biological testing and drug discovery. The G protein-coupled receptors (GPCRs) constitute the largest class of signaling molecules in the human genome with frequent roles in disease pathogenesis, yet many examples of orphan receptors with unknown ligands remain. The complex biology and potential for drug discovery within this class provide strong incentives for chemical biology approaches seeking to develop small molecule probes to facilitate elucidation of mechanistic pathways and enable specific manipulation of the activity of individual receptors. We have initiated small molecule probe development projects targeting two distinct families of GPCRs: the formylpeptide receptors (FPR/FPRL1) and G protein-coupled estrogen receptor (GPR30). In each case the assay for compound screening involved the development of an appropriate small molecule fluorescent probe, and the flow cytometry platform provided inherently biological rich assays that enhanced the process of identification and optimization of novel antagonists. The contributions of cheminformatics analysis tools, virtual screening, and synthetic chemistry in synergy with the biomolecular screening program have yielded valuable new chemical probes with high binding affinity, selectivity for the targeted receptor, and potent antagonist activity. This review describes the discovery of novel small molecule antagonists of FPR and FPRL1, and GPR30, and the associated characterization process involving secondary assays, cell based and in vivo studies to define the selectivity and activity of the resulting chemical probes.
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Affiliation(s)
- Jeffrey B Arterburn
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA.
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27
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Goddard G, Brown LO, Habbersett R, Brady CI, Martin JC, Graves SW, Freyer JP, Doorn SK. High-resolution spectral analysis of individual SERS-active nanoparticles in flow. J Am Chem Soc 2010; 132:6081-90. [PMID: 20143808 DOI: 10.1021/ja909850s] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nanoparticle spectroscopic tags based on surface enhanced Raman scattering (SERS) are playing an increasingly important role in bioassay and imaging applications. The ability to rapidly characterize large populations of such tags spectroscopically in a high-throughput flow-based platform will open new areas for their application and provide new tools for advancing their development. We demonstrate here a high-resolution spectral flow cytometer capable of acquiring Raman spectra of individual SERS-tags at flow rates of hundreds of particles per second, while maintaining the spectral resolution required to make full use of the detailed information encoded in the Raman signature for advanced multiplexing needs. The approach allows multiple optical parameters to be acquired simultaneously over thousands of individual nanoparticle tags. Characteristics such as tag size, brightness, and spectral uniformity are correlated on a per-particle basis. The tags evaluated here display highly uniform spectral signatures, but with greater variability in brightness. Subpopulations in the SERS response, not apparent in ensemble measurements, are also shown to exist. Relating tag variability to synthesis parameters makes flow-based spectral characterization a powerful tool for advancing particle development through its ability to provide rapid feedback on strategies aimed at constraining desired tag properties. Evidence for single-tag signal saturation at high excitation power densities is also shown, suggesting a role for high-throughput investigation of fundamental properties of the SERS tags as well.
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Affiliation(s)
- Gregory Goddard
- National Flow Cytometry Resource, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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28
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Saunders MJ, Graves SW, Sklar LA, Oprea TI, Edwards BS. High-throughput multiplex flow cytometry screening for botulinum neurotoxin type a light chain protease inhibitors. Assay Drug Dev Technol 2010; 8:37-46. [PMID: 20035615 DOI: 10.1089/adt.2009.0219] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Given their medical importance, proteases have been studied by diverse approaches and screened for small molecule protease inhibitors. Here, we present a multiplexed microsphere-based protease assay that uses high-throughput flow cytometry to screen for inhibitors of the light chain protease of botulinum neurotoxin type A (BoNTALC). Our assay uses a full-length substrate and several deletion mutants screened in parallel to identify small molecule inhibitors. The use of multiplex flow cytometry has the advantage of using full-length substrates, which contain already identified distal-binding elements for the BoNTALC, and could lead to a new class of BoNTALC inhibitors. In this study, we have screened 880 off patent drugs and bioavailable compounds to identify ebselen as an in vitro inhibitor of BoNTALC. This discovery demonstrates the validity of our microsphere-based approach and illustrates its potential for high-throughput screening for inhibitors of proteases in general.
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Affiliation(s)
- Matthew J Saunders
- The Center for Molecular Discovery and Department of Pathology, University of New Mexico, Albuquerque, New Mexico 87131, USA.
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29
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Rolling on E- or P-selectin induces the extended but not high-affinity conformation of LFA-1 in neutrophils. Blood 2010; 116:617-24. [PMID: 20445017 DOI: 10.1182/blood-2010-01-266122] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human blood neutrophils rolling on E- or P-selectin reduced their rolling velocity when intercellular adhesion molecule (ICAM)-1 was available. Similar to mouse neutrophils, this was dependent on P-selectin glycoprotein ligand 1 (PSGL1), alpha(L)beta(2) integrin, the Src family tyrosine kinase FGR and spleen tyrosine kinase SYK. Blocking phospholipase C or p38 MAP kinase attenuated, but did not abolish the velocity reduction. To test expression of integrin activation epitopes, we adapted an immobilized reporter assay and developed a new homogeneous microfluidics-based reporter antibody binding assay. Rolling on E- or P-selectin induced the extension reporter epitopes KIM127 and NKI-L16, but not the high affinity reporter epitope monoclonal antibody (mAb) 24. This enabled rolling neutrophils to bind to immobilized extension reporter, but not activation reporter antibodies and allowed binding of soluble KIM127 during rolling. We conclude that human neutrophil rolling on E- or P-selectin induces the extended alpha(L)beta(2) integrin conformation through signaling triggered by PSGL-1 engagement.
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Chemburu S, Fenton K, Lopez GP, Zeineldin R. Biomimetic silica microspheres in biosensing. Molecules 2010; 15:1932-57. [PMID: 20336023 PMCID: PMC6257317 DOI: 10.3390/molecules15031932] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 03/16/2010] [Accepted: 03/17/2010] [Indexed: 11/16/2022] Open
Abstract
Lipid vesicles spontaneously fuse and assemble into a lipid bilayer on planar or spherical silica surfaces and other substrates. The supported lipid bilayers (SLBs) maintain characteristics of biological membranes, and are thus considered to be biomembrane mimetic systems that are stable because of the underlying substrate. Examples of their shared characteristics with biomembranes include lateral fluidity, barrier formation to ions and molecules, and their ability to incorporate membrane proteins into them. Biomimetic silica microspheres consisting of SLBs on solid or porous silica microspheres have been utilized for different biosensing applications. The advantages of such biomimetic microspheres for biosensing include their increased surface area to volume ratio which improves the detection limits of analytes, and their amenability for miniaturization, multiplexing and high throughput screening. This review presents examples and formats of using such biomimetic solid or porous silica microspheres in biosensing.
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Affiliation(s)
- Sireesha Chemburu
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - Kyle Fenton
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - Gabriel P. Lopez
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM 87131, USA
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Reema Zeineldin
- Department of Pharmaceutical Sciences, Massachusetts College of Pharmacy and Health Sciences, 19 Foster Street, Worcester, MA 01608, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-508-373-5762; Fax: +1- 508-890-5618
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Blazer LL, Roman DL, Muxlow MR, Neubig RR. Use of flow cytometric methods to quantify protein-protein interactions. ACTA ACUST UNITED AC 2010; Chapter 13:Unit 13.11.1-15. [PMID: 20069525 DOI: 10.1002/0471142956.cy1311s51] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A method is described for the quantitative analysis of protein-protein interactions using the flow cytometry protein interaction assay (FCPIA). This method is based upon immobilizing protein on a polystyrene bead, incubating these beads with a fluorescently labeled binding partner, and assessing the sample for bead-associated fluorescence in a flow cytometer. This method can be used to calculate protein-protein interaction affinities or to perform competition experiments with unlabeled binding partners or small molecules. Examples described in this protocol highlight the use of this assay in the quantification of the affinity of binding partners of the regulator of G-protein signaling protein, RGS19, in either a saturation or a competition format. An adaptation of this method that is compatible for high-throughput screening is also provided.
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Affiliation(s)
- Levi L Blazer
- Department of Pharmacology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
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Jayakumar D, Marathe DD, Neelamegham S. Detection of site-specific glycosylation in proteins using flow cytometry. Cytometry A 2010; 75:866-73. [PMID: 19735085 DOI: 10.1002/cyto.a.20773] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We tested the possibility that we may express unique peptide probes on cell surfaces, and detect site-specific glycosylation on these peptides using flow cytometry. Such development can enhance the application of flow cytometry to detect and quantify post-translational modifications in proteins. To this end, the N-terminal section of the human leukocyte glycoprotein PSGL-1 (P-selectin glycoprotein ligand-1) was modified to contain a poly-histidine tag followed by a proteolytic cleavage site. Amino acids preceding the cleavage site have a single O-linked glycosylation site. The recombinant protein called PSGL-1 (HT) was expressed on the surface of two mammalian cell lines, CHO and HL-60, using a lentiviral delivery approach. Results demonstrate that the N-terminal portion of PSGL-1 (HT) can be released from these cells by protease, and the resulting peptide can be readily captured and detected using cytometry-bead assays. Using this strategy, the peptide was immunoprecipitated onto beads bearing mAbs against either the poly-histidine sequence or the human PSGL-1. The carbohydrate epitope associated with the released peptide was detected using HECA-452 and CSLEX-1, monoclonal antibodies that recognize the sialyl Lewis-X epitope. Finally, the peptide released from cells could be separated and enriched using nickel chelate beads. Overall, such an approach that combines recombinant protein expression with flow cytometry may be useful to quantify changes in site-specific glycosylation for basic science and clinical applications.
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Affiliation(s)
- Deepak Jayakumar
- Chemical and Biological Engineering, State University of New York, Buffalo, New York 14260, USA
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Roman DL, Ota S, Neubig RR. Polyplexed flow cytometry protein interaction assay: a novel high-throughput screening paradigm for RGS protein inhibitors. JOURNAL OF BIOMOLECULAR SCREENING 2009; 14:610-9. [PMID: 19531661 PMCID: PMC2908316 DOI: 10.1177/1087057109336590] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Intracellular signaling cascades are a series of regulated protein-protein interactions that may provide a number of targets for potential drug discovery. Here, the authors examine the interaction of regulators of G-protein signaling (RGS) proteins with the G-protein Galphao, using a flow cytometry protein interaction assay (FCPIA). FCPIA accurately measures nanomolar binding constants of this protein-protein interaction and has been used in high-throughput screening. This report focuses on 5 RGS proteins (4, 6, 7, 8, and 16). To increase the content of screens, the authors assessed high-throughput screening of these RGS proteins in multiplex, by establishing binding constants of each RGS with Galphao in isolation, and then in a multiplex format with 5 RGS proteins present. To use this methodology as a higher-content multiplex protein-protein interaction screen, they established Z-factor values for RGS proteins in multiplex of 0.73 to 0.92, indicating this method is suitable for screening using FCPIA. To increase throughput, they also compressed a set of 8000 compounds by combining 4 compounds in a single assay well. Subsequent deconvolution of the compounds mixtures verified the identification of active compounds at specific RGS targets in their mixtures using the polyplexed FCPIA method.
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Affiliation(s)
- David L Roman
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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34
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Heng BC, Cowan CM, Basu S. Comparison of enzymatic and non-enzymatic means of dissociating adherent monolayers of mesenchymal stem cells. Biol Proced Online 2009; 11:161-9. [PMID: 19495917 PMCID: PMC3055293 DOI: 10.1007/s12575-009-9001-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 01/30/2009] [Indexed: 12/24/2022] Open
Abstract
The dissociation of adherent mesenchymal stem cell (MSC) monolayers with trypsin and enzyme-free dissociation buffer was compared. A significantly lower proportion of viable cells were obtained with enzyme-free dissociation buffers compared to trypsin. Subsequently, the dissociated cells were re-seeded on new cell culture dishes and were subjected to the MTT assay 24 h later. The proportion of viable cells that reattached was significantly lower for cells obtained by dissociation with enzyme-free dissociation buffer compared to trypsin. Frozen–thawed MSC displayed a similar trend, yielding consistently higher cell viability and reattachment rates when dissociated with trypsin compared to enzyme-free dissociation buffer. It was also demonstrated that exposure of trypsin-dissociated MSC to enzyme-free dissociation buffer for 1 h had no significant detrimental effect on cell viability.
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Chigaev A, Waller A, Amit O, Halip L, Bologa CG, Sklar LA. Real-time analysis of conformation-sensitive antibody binding provides new insights into integrin conformational regulation. J Biol Chem 2009; 284:14337-46. [PMID: 19251697 PMCID: PMC2682882 DOI: 10.1074/jbc.m901178200] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Integrins are heterodimeric adhesion receptors that regulate immune cell
adhesion. Integrin-dependent adhesion is controlled by multiple conformational
states that include states with different affinity to the ligand, states with
various degrees of molecule unbending, and others. Affinity change and
molecule unbending play major roles in the regulation of cell adhesion. The
relationship between different conformational states of the integrin is
unclear. Here we have used conformationally sensitive antibodies and a small
LDV-containing ligand to study the role of the inside-out signaling through
formyl peptide receptor and CXCR4 in the regulation of
α4β1 integrin conformation. We found that in
the absence of ligand, activation by formyl peptide or SDF-1 did not result in
a significant exposure of HUTS-21 epitope. Occupancy of the ligand binding
pocket without cell activation was sufficient to induce epitope exposure.
EC50 for HUTS-21 binding in the presence of LDV was identical to a
previously reported ligand equilibrium dissociation constant at rest and after
activation. Furthermore, the rate of HUTS-21 binding was also related to the
VLA-4 activation state even at saturating ligand concentration. We propose
that the unbending of the integrin molecule after guanine nucleotide-binding
protein-coupled receptor-induced signaling accounts for the enhanced rate of
HUTS-21 binding. Taken together, current results support the existence of
multiple conformational states independently regulated by both inside-out
signaling and ligand binding. Our data suggest that VLA-4 integrin hybrid
domain movement does not depend on the affinity state of the ligand binding
pocket.
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Affiliation(s)
- Alexandre Chigaev
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, USA.
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36
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Buranda T, Wu Y, Sklar LA. Chapter 11. Subsecond analyses of G-protein coupled-receptor ternary complex dynamics by rapid mix flow cytometry. Methods Enzymol 2009; 461:227-47. [PMID: 19480922 PMCID: PMC4476792 DOI: 10.1016/s0076-6879(09)05411-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2024]
Abstract
The binding of full and partial agonist ligands (L) to G-protein-coupled receptors (GPCRs) initiates the formation of ternary complexes with G-proteins (LRG complexes). We describe the assembly of detergent-solubilized LRG complexes on beads. Rapid mix flow cytometry is used to analyze the subsecond dynamics of guanine nucleotide-mediated ternary complex disassembly. Ternary complexes were assembled with three formyl peptide receptor constructs (wild type, FPR-Galpha(i2) fusion, and FPR-GFP fusion) and two isotypes of the alpha subunit (alpha(i2) and alpha(i3)) and betagamma dimer (beta(i)(1)gamma(2) and beta(4)gamma(2)). Experimental evidence suggests that thermodynamic stability of ternary complexes depends on subunit isotype. Comparison of assemblies derived from the three constructs of FPR and G-protein heterotrimers composed of the available subunit isotypes demonstrate that the fast step is associated with the separation of receptor and G-protein and that the dissociation of the ligand or of the alpha and betagamma subunits was slower. These results are compatible with a cell activation model involving G-protein conformational changes rather than disassembly of Galphabetagamma heterotrimer.
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Affiliation(s)
- Tione Buranda
- Department of Pathology and Cancer Center, University of New Mexico Health Science Center, Albuquerque, New Mexico, USA
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Chapter 11 Identification of Ligands Targeting RGS Proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 86:335-56. [DOI: 10.1016/s1877-1173(09)86011-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
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38
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Bernsteel DJ, Roman DL, Neubig RR. In vitro protein kinase activity measurement by flow cytometry. Anal Biochem 2008; 383:180-5. [DOI: 10.1016/j.ab.2008.08.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Revised: 08/18/2008] [Accepted: 08/27/2008] [Indexed: 10/21/2022]
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Woods TA, Graves SW, Nolan JP. Microsphere surface protein determination using flow cytometry. ACTA ACUST UNITED AC 2008; Chapter 13:Unit13.2. [PMID: 18770818 DOI: 10.1002/0471142956.cy1302s34] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This unit describes an extrinsic staining protocol using the amine-reactive CBQCA dye to measure the amount of protein on the surface of a microsphere. This approach is novel in that it allows microspheres bearing proteins without known binding partners to be accurately quantified on a flow cytometer.
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Affiliation(s)
- Travis A Woods
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
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40
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Biosensors based on release of compounds upon disruption of lipid bilayers supported on porous microspheres. Biointerphases 2008; 3:38. [DOI: 10.1116/1.2918743] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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41
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Dai M, Temirov J, Pesavento E, Kiss C, Velappan N, Pavlik P, Werner JH, Bradbury ARM. Using T7 phage display to select GFP-based binders. Protein Eng Des Sel 2008; 21:413-24. [PMID: 18469345 DOI: 10.1093/protein/gzn016] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Filamentous phage do not display cytoplasmic proteins very effectively. As T7 is a cytoplasmic phage, released by cell lysis, it has been prospected as being more efficient for the display of such proteins. Here we investigate this proposition, using a family of GFP-based cytoplasmic proteins that are poorly expressed by traditional phage display. Using two single-molecule detection techniques, fluorescence correlation spectroscopy and anti-bunching, we show that the number of displayed fluorescent proteins ranges from one to three. The GFP derivatives displayed on T7 contain binding loops able to recognize specific targets. By mixing these in a large background of non-binders, these derivatives were used to optimize selection conditions. Using the optimal selection conditions determined in these experiments, we then demonstrated the selection of specific binders from a library of GFP clones containing heavy chain CDR3 antibody binding loops derived from normal donors inserted at a single site. The selected GFP-based binders were successfully used to detect binding without the use of secondary reagents in flow cytometry, fluorescence-linked immunosorbant assays and immunoblotting. These results demonstrate that specific GFP-based affinity reagents, selected from T7-based libraries, can be used in applications in which only the intrinsic fluorescence is used for detection.
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Affiliation(s)
- M Dai
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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42
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43
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Goddard GR, Sanders CK, Martin JC, Kaduchak G, Graves SW. Analytical Performance of an Ultrasonic Particle Focusing Flow Cytometer. Anal Chem 2007; 79:8740-6. [DOI: 10.1021/ac071402t] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gregory R. Goddard
- National Flow Cytometry Resource, Mail Stop M888, Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, New Mexico 87545
| | - Claire K. Sanders
- National Flow Cytometry Resource, Mail Stop M888, Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, New Mexico 87545
| | - John C. Martin
- National Flow Cytometry Resource, Mail Stop M888, Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, New Mexico 87545
| | - Gregory Kaduchak
- National Flow Cytometry Resource, Mail Stop M888, Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, New Mexico 87545
| | - Steven W. Graves
- National Flow Cytometry Resource, Mail Stop M888, Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, New Mexico 87545
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44
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Sklar LA, Carter MB, Edwards BS. Flow cytometry for drug discovery, receptor pharmacology and high-throughput screening. Curr Opin Pharmacol 2007; 7:527-34. [PMID: 17652026 PMCID: PMC2230635 DOI: 10.1016/j.coph.2007.06.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 06/06/2007] [Accepted: 06/15/2007] [Indexed: 12/16/2022]
Abstract
Although flow cytometry is viewed as a mature technology, there have been dramatic advances in analysis capabilities, sorting, sample handling and sensitivity in the past decade. These advances contribute to its application in biological and chemical diversity, sample throughput, high content, and complex systems biology. This article will evaluate the new opportunities for flow cytometry relating to receptor assembly and pharmacology, as well as a range of screening applications.
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Affiliation(s)
- Larry A Sklar
- The New Mexico Molecular Libraries Screening Center, Cancer Research and Treatment Center, The University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
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45
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Simons PC, Young SM, Gibaja V, Lee WC, Josiah S, Edwards BS, Sklar LA. Duplexed, bead-based competitive assay for inhibitors of protein kinases. Cytometry A 2007; 71:451-9. [PMID: 17542028 DOI: 10.1002/cyto.a.20398] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Many cellular signal transduction cascades have protein kinases as critical components. Small molecule protein kinase inhibitors can be effective as laboratory probes and drugs. Methods that allow two or more kinases to be evaluated simultaneously for inhibition by a small molecule would allow unequivocal tests of specificity and selectivity of action of the small molecule. METHODS Two hexahistidine-tagged activin receptor-like kinases were expressed in E. coli, purified, and bound to nickel beads. A fluorescent kinase ligand (F-KL) that binds to the ATP-binding site of these kinases with nanomolar affinity was developed. Binding of F-KL with kinase on the bead made the beads bright, and inhibitors decreased the brightness. RESULTS A test panel of 17 nonfluorescent kinase inhibitors, spanning two orders of magnitude affinity for the kinases, gave K(d) values for the kinases that correlated well with a fluorescence polarization assay. Results were obtained for the kinases in duplex, using an autosampler to send beads from a 96-well plate to a flow cytometer in a format suitable for high throughput screening. CONCLUSIONS Inhibitors of kinases can be measured in duplex in a high throughput format by flow cytometry, if a suitable fluorescent ligand is available.
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Affiliation(s)
- Peter C Simons
- New Mexico Molecular Libraries Screening Center, University of New Mexico, Health Sciences Center, Albuquerque, New Mexico 87131, USA
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46
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47
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Buranda T, Waller A, Wu Y, Simons PC, Biggs S, Prossnitz ER, Sklar LA. Some mechanistic insights into GPCR activation from detergent-solubilized ternary complexes on beads. ADVANCES IN PROTEIN CHEMISTRY 2007; 74:95-135. [PMID: 17854656 DOI: 10.1016/s0065-3233(07)74003-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The binding of full and partial agonist ligands (L) to G protein-coupled receptors (GPCRs) initiates the formation of ternary complexes with G proteins [ligand-receptor-G protein (LRG) complexes]. Cyclic ternary complex models are required to account for the thermodynamically plausible complexes. It has recently become possible to assemble solubilized formyl peptide receptor (FPR) and beta(2)-adrenergic receptor (beta(2)AR) ternary complexes for flow cytometric bead-based assays. In these systems, soluble ternary complex formation of the receptors with G proteins allows direct quantitative measurements which can be analyzed in terms of three-dimensional concentrations (molarity). In contrast to the difficulty of analyzing comparable measurements in two-dimensional membrane systems, the output of these flow cytometric experiments can be analyzed via ternary complex simulations in which all of the parameters can be estimated. An outcome from such analysis yielded lower affinity for soluble ternary complex assembly by partial agonists compared with full agonists for the beta(2)AR. In the four-sided ternary complex model, this behavior is consistent with distinct ligand-induced conformational states for full and partial agonists. Rapid mix flow cytometry is used to analyze the subsecond dynamics of guanine nucleotide-mediated ternary complex disassembly. The modular breakup of ternary complex components is highlighted by the finding that the fastest step involves the departure of the ligand-activated GPCR from the intact G protein heterotrimer. The data also show that, under these experimental conditions, G protein subunit dissociation does not occur within the time frame relevant to signaling. The data and concepts are discussed in the context of a review of current literature on signaling mechanism based on structural and spectroscopic (FRET) studies of ternary complex components.
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Affiliation(s)
- Tione Buranda
- Department of Pathology and Cancer Center, University of New Mexico Health Science Center, Albuquerque, New Mexico 87131, USA
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48
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Kiss C, Fisher H, Pesavento E, Dai M, Valero R, Ovecka M, Nolan R, Phipps ML, Velappan N, Chasteen L, Martinez JS, Waldo GS, Pavlik P, Bradbury AR. Antibody binding loop insertions as diversity elements. Nucleic Acids Res 2006; 34:e132. [PMID: 17023486 PMCID: PMC1635297 DOI: 10.1093/nar/gkl681] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Accepted: 09/03/2006] [Indexed: 11/13/2022] Open
Abstract
In the use of non-antibody proteins as affinity reagents, diversity has generally been derived from oligonucleotide-encoded random amino acids. Although specific binders of high-affinity have been selected from such libraries, random oligonucleotides often encode stop codons and amino acid combinations that affect protein folding. Recently it has been shown that specific antibody binding loops grafted into heterologous proteins can confer the specific antibody binding activity to the created chimeric protein. In this paper, we examine the use of such antibody binding loops as diversity elements. We first show that we are able to graft a lysozyme-binding antibody loop into green fluorescent protein (GFP), creating a fluorescent protein with lysozyme-binding activity. Subsequently we have developed a PCR method to harvest random binding loops from antibodies and insert them at predefined sites in any protein, using GFP as an example. The majority of such GFP chimeras remain fluorescent, indicating that binding loops do not disrupt folding. This method can be adapted to the creation of other nucleic acid libraries where diversity is flanked by regions of relative sequence conservation, and its availability sets the stage for the use of antibody loop libraries as diversity elements for selection experiments.
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Affiliation(s)
- Csaba Kiss
- HCDR3s as diversity elements, Los Alamos National LaboratoryLos Alamos, NM, USA
| | - Hugh Fisher
- HCDR3s as diversity elements, Los Alamos National LaboratoryLos Alamos, NM, USA
| | - Emanuele Pesavento
- HCDR3s as diversity elements, Los Alamos National LaboratoryLos Alamos, NM, USA
| | - Minghua Dai
- HCDR3s as diversity elements, Los Alamos National LaboratoryLos Alamos, NM, USA
| | - Rosa Valero
- HCDR3s as diversity elements, Los Alamos National LaboratoryLos Alamos, NM, USA
| | - Milan Ovecka
- HCDR3s as diversity elements, Los Alamos National LaboratoryLos Alamos, NM, USA
| | - Rhiannon Nolan
- HCDR3s as diversity elements, Los Alamos National LaboratoryLos Alamos, NM, USA
| | - M. Lisa Phipps
- HCDR3s as diversity elements, Los Alamos National LaboratoryLos Alamos, NM, USA
| | - Nileena Velappan
- HCDR3s as diversity elements, Los Alamos National LaboratoryLos Alamos, NM, USA
| | - Leslie Chasteen
- HCDR3s as diversity elements, Los Alamos National LaboratoryLos Alamos, NM, USA
| | | | - Geoffrey S. Waldo
- HCDR3s as diversity elements, Los Alamos National LaboratoryLos Alamos, NM, USA
| | - Peter Pavlik
- HCDR3s as diversity elements, Los Alamos National LaboratoryLos Alamos, NM, USA
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49
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Roman DL, Talbot JN, Roof RA, Sunahara RK, Traynor JR, Neubig RR. Identification of small-molecule inhibitors of RGS4 using a high-throughput flow cytometry protein interaction assay. Mol Pharmacol 2006; 71:169-75. [PMID: 17012620 DOI: 10.1124/mol.106.028670] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Regulators of G-protein signaling (RGS) proteins are important components of signal transduction pathways initiated through G-protein-coupled receptors (GPCRs). RGS proteins accelerate the intrinsic GTPase activity of G-protein alpha-subunits (Galpha) and thus shorten the time course and reduce the magnitude of G-protein alpha- and betagamma-subunit signaling. Inhibiting RGS action has been proposed as a means to enhance the activity and specificity of GPCR agonist drugs, but pharmacological targeting of protein-protein interactions has typically been difficult. The aim of this project was to identify inhibitors of RGS4. Using a Luminex 96-well plate bead analyzer and a novel flow-cytometric protein interaction assay to assess Galpha-RGS interactions in a high-throughput screen, we identified the first small-molecule inhibitor of an RGS protein. Of 3028 compounds screened, 1, methyl N-[(4-chlorophenyl)sulfonyl]-4-nitrobenzenesulfinimidoate (CCG-4986), inhibited RGS4/Galpha(o) binding with 3 to 5 muM potency. It binds to RGS4, inhibits RGS4 stimulation of Galpha(o) GTPase activity in vitro, and prevents RGS4 regulation of mu-opioid-inhibited adenylyl cyclase activity in permeabilized cells. Furthermore, CCG-4986 is selective for RGS4 and does not inhibit RGS8. Thus, we demonstrate the feasibility of targeting RGS/Galpha protein-protein interactions with small molecules as a novel means to modulate GPCR-mediated signaling processes.
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Affiliation(s)
- David L Roman
- Department of Pharmacology, University of Michigan Medical School, 1150 W. Medical Center Drive, 1303 MSRB III, Ann Arbor, MI 41809, USA
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50
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Edwards BS, Young SM, Oprea TI, Bologa CG, Prossnitz ER, Sklar LA. Biomolecular screening of formylpeptide receptor ligands with a sensitive, quantitative, high-throughput flow cytometry platform. Nat Protoc 2006; 1:59-66. [PMID: 17406212 DOI: 10.1038/nprot.2006.9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The formylpeptide receptor (FPR) family of G protein-coupled receptors contributes to the localization and activation of tissue-damaging leukocytes at sites of chronic inflammation. Here we describe a high-throughput flow cytometry screening approach that has successfully identified multiple families of previously unknown FPR ligands. The assay detects active structures that block the binding of a fluorescent ligand to membrane FPR of intact cells, thus detecting both agonists and antagonists. It is homogeneous in that assay reagents are added in sequence and the wells are subsequently analyzed without intervening wash steps. Microplate wells are routinely processed at a rate of 40 wells per minute, requiring a volume of only 2 microl to be sampled from each. This screening approach has recently been extended to identify a high-affinity, selective agonist for the intracellular estrogen-binding G protein-coupled receptor GPR30. With the development of appropriate assay reagents, it may be generally adaptable to a wide range of receptors. The total time required for the assay ranges between 1.5 and 2.5 h. The time required for flow cytometry analysis of a 96-well plate at the end of the procedure is less than 2.5 min. By comparison, manual processing of 96 samples will typically require 40-50 min, and a fast commercial automated sampler processes 96-well plates in less than 15 min, requiring the aspiration of 22 microl per sample for an analysis volume of 2 microl.
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Affiliation(s)
- Bruce S Edwards
- Cytometry, Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, USA.
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