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Liu Y, Bafaro EM, Dempski RE. Single-molecule quantification of the oligomeric state of ZIP transporters in mammalian cells with fluorescence correlation spectroscopy. Methods Enzymol 2023; 687:103-137. [PMID: 37666629 DOI: 10.1016/bs.mie.2023.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The SLC39 family of transporters, otherwise known as ZIPs for Zrt and Irt-like Proteins, function to increase cytosolic levels of transition metals. ZIP transporters have been identified at all phylogenetic levels and are members of the SoLute Carrier (SLC) superfamily. There are fourteen ZIP transporters encoded in the human genome. ZIP transmembrane proteins are expressed in the plasma membrane or membranes of intracellular organelles and have unique expression profiles across cell types. While direct structural efforts including x-ray crystallography, NMR and ab initio approaches have been effective tools in elucidating the structure of ZIPs, direct elucidation of the oligomeric state of these proteins is essential in understanding how wild type ZIP proteins function and whether mutations alter the oligomeric state of ZIPs. Unfortunately, several tools to quantify oligomeric states of proteins require overexpression of proteins which can lead to artifacts in experimental results. In contrast, fluorescence correlation spectroscopy (FCS) is a single-molecule technique which can be used to quantify the oligomeric state of transmembrane proteins. FCS takes advantage of the observation that the molecular brightness of a cluster of fluorescent molecules is directly proportional to the number of fluorescent molecules within the protein complex. This chapter describes how to implement FCS, focused on ZIP transporters, to quantify the oligomeric state of transmembrane in vivo. Included within this chapter are procedures to design constructs for experiments, transfection of mammalian cells as well as data acquisition and analysis. Taken together, FCS is a powerful mechanism to investigate the oligomeric state of proteins embedded within membranes of cells.
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Affiliation(s)
- Yuting Liu
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Elizabeth M Bafaro
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Robert E Dempski
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, United States.
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Kroeck KG, Qiu W, Catalano C, Trinh TKH, Guo Y. Native Cell Membrane Nanoparticles System for Membrane Protein-Protein Interaction Analysis. J Vis Exp 2020. [PMID: 32744521 DOI: 10.3791/61298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Protein-protein interactions in cell membrane systems play crucial roles in a wide range of biological processes- from cell-to-cell interactions to signal transduction; from sensing environmental signals to biological response; from metabolic regulation to developmental control. Accurate structural information of protein-protein interactions is crucial for understanding the molecular mechanisms of membrane protein complexes and for the design of highly specific molecules to modulate these proteins. Many in vivo and in vitro approaches have been developed for the detection and analysis of protein-protein interactions. Among them the structural biology approach is unique in that it can provide direct structural information of protein-protein interactions at the atomic level. However, current membrane protein structural biology is still largely limited to detergent-based methods. The major drawback of detergent-based methods is that they often dissociate or denature membrane protein complexes once their native lipid bilayer environment is removed by detergent molecules. We have been developing a native cell membrane nanoparticle system for membrane protein structural biology. Here, we demonstrate the use of this system in the analysis of protein-protein interactions on the cell membrane with a case study of the oligomeric state of AcrB.
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Affiliation(s)
- Kyle G Kroeck
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University
| | - Weihua Qiu
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University
| | - Claudio Catalano
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University
| | - Thi Kim Hoang Trinh
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University
| | - Youzhong Guo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University; Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University;
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Nguyen TA, Puhl HL, Pham AK, Vogel SS. Auto-FPFA: An Automated Microscope for Characterizing Genetically Encoded Biosensors. Sci Rep 2018; 8:7374. [PMID: 29743504 PMCID: PMC5943267 DOI: 10.1038/s41598-018-25689-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/26/2018] [Indexed: 12/14/2022] Open
Abstract
Genetically encoded biosensors function by linking structural change in a protein construct, typically tagged with one or more fluorescent proteins, to changes in a biological parameter of interest (such as calcium concentration, pH, phosphorylation-state, etc.). Typically, the structural change triggered by alterations in the bio-parameter is monitored as a change in either fluorescent intensity, or lifetime. Potentially, other photo-physical properties of fluorophores, such as fluorescence anisotropy, molecular brightness, concentration, and lateral and/or rotational diffusion could also be used. Furthermore, while it is likely that multiple photo-physical attributes of a biosensor might be altered as a function of the bio-parameter, standard measurements monitor only a single photo-physical trait. This limits how biosensors are designed, as well as the accuracy and interpretation of biosensor measurements. Here we describe the design and construction of an automated multimodal-microscope. This system can autonomously analyze 96 samples in a micro-titer dish and for each sample simultaneously measure intensity (photon count), fluorescence lifetime, time-resolved anisotropy, molecular brightness, lateral diffusion time, and concentration. We characterize the accuracy and precision of this instrument, and then demonstrate its utility by characterizing three types of genetically encoded calcium sensors as well as a negative control.
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Affiliation(s)
- Tuan A Nguyen
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Rockville, Maryland, USA
| | - Henry L Puhl
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Rockville, Maryland, USA
| | - An K Pham
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Rockville, Maryland, USA
| | - Steven S Vogel
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Rockville, Maryland, USA.
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Abstract
The ligand-regulated structure and biochemistry of nuclear receptor complexes are commonly determined by in vitro studies of isolated receptors, cofactors, and their fragments. However, in the living cell, the complexes that form are governed not just by the relative affinities of isolated cofactors for the receptor but also by the cell-specific sequestration or concentration of subsets of competing or cooperating cofactors, receptors, and other effectors into distinct subcellular domains and/or their temporary diversion into other cellular activities. Most methods developed to understand nuclear receptor function in the cellular environment involve the direct tagging of the nuclear receptor or its cofactors with fluorescent proteins (FPs) and the tracking of those FP-tagged factors by fluorescence microscopy. One of those approaches, Förster resonance energy transfer (FRET) microscopy, quantifies the transfer of energy from a higher energy "donor" FP to a lower energy "acceptor" FP attached to a single protein or to interacting proteins. The amount of FRET is influenced by the ligand-induced changes in the proximities and orientations of the FPs within the tagged nuclear receptor complexes, which is an indicator of the structure of the complexes, and by the kinetics of the interaction between FP-tagged factors. Here, we provide a guide for parsing information about the structure and biochemistry of nuclear receptor complexes from FRET measurements in living cells.
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Affiliation(s)
- Fred Schaufele
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94143-0540, USA.
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Bailey K, Yazdi T, Masharani U, Tyrrell B, Butch A, Schaufele F. Advantages and Limitations of Androgen Receptor-Based Methods for Detecting Anabolic Androgenic Steroid Abuse as Performance Enhancing Drugs. PLoS One 2016; 11:e0151860. [PMID: 26998755 PMCID: PMC4801337 DOI: 10.1371/journal.pone.0151860] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/04/2016] [Indexed: 12/19/2022] Open
Abstract
Testosterone (T) and related androgens are performance enhancing drugs (PEDs) abused by some athletes to gain competitive advantage. To monitor unauthorized androgen abuse, doping control programs use mass spectrometry (MS) to detect androgens, synthetic anabolic-androgenic steroids (AASs) and their metabolites in an athlete’s urine. AASs of unknown composition will not be detected by these procedures. Since AASs achieve their anabolic effects by activating the Androgen Receptor (AR), cell-based bioassays that measure the effect of a urine sample on AR activity are under investigation as complementary, pan-androgen detection methods. We evaluated an AR BioAssay as a monitor for androgen activity in urine pre-treated with glucuronidase, which releases T from the inactive T-glucuronide that predominates in urine. AR BioAssay activity levels were expressed as ‘T-equivalent’ concentrations by comparison to a T dose response curve. The T-equivalent concentrations of androgens in the urine of hypogonadal participants supplemented with T (in whom all androgenic activity should arise from T) were quantitatively identical to the T measurements conducted by MS at the UCLA Olympic Analytical Laboratory (0.96 ± 0.22). All 17 AASs studied were active in the AR BioAssay; other steroids were inactive. 12 metabolites of 10 commonly abused AASs, which are used for MS monitoring of AAS doping because of their prolonged presence in urine, had reduced or no AR BioAssay activity. Thus, the AR BioAssay can accurately and inexpensively monitor T, but its ability to monitor urinary AASs will be limited to a period immediately following doping in which the active AASs remain intact.
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Affiliation(s)
- Kathy Bailey
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Tahmineh Yazdi
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Umesh Masharani
- Division of Endocrinology, University of California San Francisco, San Francisco, California, United States of America
| | - Blake Tyrrell
- Division of Endocrinology, University of California San Francisco, San Francisco, California, United States of America
| | - Anthony Butch
- Department of Pathology and Laboratory Medicine, Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Fred Schaufele
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America.,Department of Obstetrics and Gynecology, University of California San Francisco, San Francisco, California, United States of America
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Affiliation(s)
- Ammasi Periasamy
- University of Virginia, W.M. Keck Center for Cellular Imaging, Charlottesville, VA, USA.
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