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Biggs BW, de Paz AM, Bhan NJ, Cybulski TR, Church GM, Tyo KEJ. Engineering Ca 2+-Dependent DNA Polymerase Activity. ACS Synth Biol 2023; 12:3301-3311. [PMID: 37856140 DOI: 10.1021/acssynbio.3c00302] [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: 10/20/2023]
Abstract
Advancements in synthetic biology have provided new opportunities in biosensing, with applications ranging from genetic programming to diagnostics. Next generation biosensors aim to expand the number of accessible environments for measurements, increase the number of measurable phenomena, and improve the quality of the measurement. To this end, an emerging area in the field has been the integration of DNA as an information storage medium within biosensor outputs, leveraging nucleic acids to record the biosensor state over time. However, slow signal transduction steps, due to the time scales of transcription and translation, bottleneck many sensing-DNA recording approaches. DNA polymerases (DNAPs) have been proposed as a solution to the signal transduction problem by operating as both the sensor and responder, but there is presently a lack of DNAPs with functional sensitivity to many desirable target ligands. Here, we engineer components of the Pol δ replicative polymerase complex of Saccharomyces cerevisiae to sense and respond to Ca2+, a metal cofactor relevant to numerous biological phenomena. Through domain insertion and binding site grafting to Pol δ subunits, we demonstrate functional allosteric sensitivity to Ca2+. Together, this work provides an important foundation for future efforts in the development of DNAP-based biosensors.
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Affiliation(s)
- Bradley W Biggs
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexandra M de Paz
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Namita J Bhan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Thaddeus R Cybulski
- Interdepartmental Neuroscience Program, Northwestern University, Chicago, Illinois 60611, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
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2
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Valiente-Gabioud AA, Garteizgogeascoa Suñer I, Idziak A, Fabritius A, Basquin J, Angibaud J, Nägerl UV, Singh SP, Griesbeck O. Fluorescent sensors for imaging of interstitial calcium. Nat Commun 2023; 14:6220. [PMID: 37798285 PMCID: PMC10556026 DOI: 10.1038/s41467-023-41928-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 09/22/2023] [Indexed: 10/07/2023] Open
Abstract
Calcium in interstitial fluids is central to systemic physiology and a crucial ion pool for entry into cells through numerous plasma membrane channels. Its study has been limited by the scarcity of methods that allow monitoring in tight inter-cell spaces of living tissues. Here we present high performance ultra-low affinity genetically encoded calcium biosensors named GreenT-ECs. GreenT-ECs combine large fluorescence changes upon calcium binding and binding affinities (Kds) ranging from 0.8 mM to 2.9 mM, making them tuned to calcium concentrations in extracellular organismal fluids. We validated GreenT-ECs in rodent hippocampal neurons and transgenic zebrafish in vivo, where the sensors enabled monitoring homeostatic regulation of tissue interstitial calcium. GreenT-ECs may become useful for recording very large calcium transients and for imaging calcium homeostasis in inter-cell structures in live tissues and organisms.
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Affiliation(s)
- Ariel A Valiente-Gabioud
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Inés Garteizgogeascoa Suñer
- Institute de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), 808 Route de Lennik, Université Libre de Bruxelles (ULB), 1070, Brussels, Belgium
| | - Agata Idziak
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - Arne Fabritius
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Jérome Basquin
- Structural Cell Biology, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Julie Angibaud
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - U Valentin Nägerl
- Institut Interdisciplinaire de Neurosciences, Synaptic Plasticity and Super-Resolution Microscopy, CNRS - Université de Bordeaux - 146 rue Léo-Saignat, Bordeaux, France
| | - Sumeet Pal Singh
- Institute de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), 808 Route de Lennik, Université Libre de Bruxelles (ULB), 1070, Brussels, Belgium
| | - Oliver Griesbeck
- Max Planck Institute for Biological Intelligence, Tools for Bio-Imaging, Am Klopferspitz 18, 82152, Martinsried, Germany.
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3
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Valiente-Gabioud AA, Fabritius A, Griesbeck O. Probing the interstitial calcium compartment. J Physiol 2023; 601:4217-4226. [PMID: 36073135 DOI: 10.1113/jp279510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022] Open
Abstract
Calcium in interstitial fluids is a crucial ion pool for entry into cells through a plethora of calcium-permeable channels. It is also sensed actively by dedicated receptors. While the mechanisms of global calcium homeostasis and regulation in body fluids appear well understood, more efforts and new technology are needed to elucidate local calcium handling in the small and relatively isolated interstitial spaces between cells. Here we review current methodology for monitoring interstitial calcium and highlight the potential of new approaches for its study. In particular, new generations of high-performance low-affinity genetically encoded calcium indicators could allow imaging of calcium in relatively inaccessible intercellular structures in live tissues and organisms.
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Affiliation(s)
- Ariel A Valiente-Gabioud
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence (i.F.), Martinsried, Germany
| | - Arne Fabritius
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence (i.F.), Martinsried, Germany
| | - Oliver Griesbeck
- Tools for Bio-Imaging, Max-Planck-Institute for Biological Intelligence (i.F.), Martinsried, Germany
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4
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Okkelman IA, McGarrigle R, O’Carroll S, Berrio DC, Schenke-Layland K, Hynes J, Dmitriev RI. Extracellular Ca2+-Sensing Fluorescent Protein Biosensor Based on a Collagen-Binding Domain. ACS APPLIED BIO MATERIALS 2020; 3:5310-5321. [DOI: 10.1021/acsabm.0c00649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Irina A. Okkelman
- Metabolic Imaging Group, Laboratory of Biophysics and Bioanalysis, ABCRF, University College Cork, College Road, Cork T12 YN60, Ireland
| | - Ryan McGarrigle
- Agilent Technologies Ireland Limited, Little
Island T45 WK12, Cork, Ireland
| | - Shane O’Carroll
- Metabolic Imaging Group, Laboratory of Biophysics and Bioanalysis, ABCRF, University College Cork, College Road, Cork T12 YN60, Ireland
| | - Daniel Carvajal Berrio
- Department of Women’s Health, Research Institute for Women’s Health, Eberhard Karls University Tübingen, Tübingen 72074, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies” (iFIT), Eberhard Karls University Tübingen, Geschwister-Scholl-Platz, Tübingen 72074, Germany
| | - Katja Schenke-Layland
- Department of Women’s Health, Research Institute for Women’s Health, Eberhard Karls University Tübingen, Tübingen 72074, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies” (iFIT), Eberhard Karls University Tübingen, Geschwister-Scholl-Platz, Tübingen 72074, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen 72770, Germany
- Department of Medicine/Cardiology, Cardiovascular Research Laboratories, David Geffen School of Medicine at UCLA, Los Angeles 90095, California, United States
| | - James Hynes
- Agilent Technologies Ireland Limited, Little
Island T45 WK12, Cork, Ireland
| | - Ruslan I. Dmitriev
- Metabolic Imaging Group, Laboratory of Biophysics and Bioanalysis, ABCRF, University College Cork, College Road, Cork T12 YN60, Ireland
- I.M. Sechenov First Moscow State University, Institute for Regenerative Medicine, Moscow 119992, Russian Federation
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium
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5
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Tang S, Deng X, Jiang J, Kirberger M, Yang JJ. Design of Calcium-Binding Proteins to Sense Calcium. Molecules 2020; 25:molecules25092148. [PMID: 32375353 PMCID: PMC7248937 DOI: 10.3390/molecules25092148] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 01/25/2023] Open
Abstract
Calcium controls numerous biological processes by interacting with different classes of calcium binding proteins (CaBP’s), with different affinities, metal selectivities, kinetics, and calcium dependent conformational changes. Due to the diverse coordination chemistry of calcium, and complexity associated with protein folding and binding cooperativity, the rational design of CaBP’s was anticipated to present multiple challenges. In this paper we will first discuss applications of statistical analysis of calcium binding sites in proteins and subsequent development of algorithms to predict and identify calcium binding proteins. Next, we report efforts to identify key determinants for calcium binding affinity, cooperativity and calcium dependent conformational changes using grafting and protein design. Finally, we report recent advances in designing protein calcium sensors to capture calcium dynamics in various cellular environments.
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Affiliation(s)
- Shen Tang
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
| | - Xiaonan Deng
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
| | - Jie Jiang
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
| | - Michael Kirberger
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA;
| | - Jenny J. Yang
- Department of Chemistry, Center for Diagnostics and Therapeutics and Advanced Translational Imaging Facility, Georgia State University, Atlanta, GA 30303, USA; (S.T.); (X.D.); (J.J.)
- Correspondence: ; Tel.: +1-404-413-5520
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6
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Live cell imaging of signaling and metabolic activities. Pharmacol Ther 2019; 202:98-119. [DOI: 10.1016/j.pharmthera.2019.06.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/31/2019] [Indexed: 12/15/2022]
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Shitashima Y, Shimozawa T, Asahi T, Miyawaki A. A dual-ligand-modulable fluorescent protein based on UnaG and calmodulin. Biochem Biophys Res Commun 2018; 496:872-879. [PMID: 29395087 DOI: 10.1016/j.bbrc.2018.01.134] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 01/20/2018] [Indexed: 11/30/2022]
Abstract
UnaG is a green-emitting fluorescent protein that utilizes unconjugated bilirubin (BR) as its fluorophore. While BR has captured the attention of physiologists as an important antioxidant that scavenges reactive oxygen species in biological membranes, its excessive accumulation causes several clinical symptoms. Although the optimal regulation of BR concentration would result in clinical therapies for aging as well as reduce risks of clinical symptoms, UnaG hardly releases BR owing to its extremely high affinity for BR (Kd = 98 pM). Herein, we engineered the BR binding and fluorescence of UnaG to be Ca2+-sensitive via a genetic insertion of calmodulin (CaM). The resultant UnaG/CaM hybrid protein is a dual-ligand modulable fluorescent protein; binding of the fluorogenic ligand BR is negatively regulated by the other ligand, Ca2+ ion. The affinity for BR differed by three orders of magnitude between the Ca2+-free state (Kd = 9.70 nM) and Ca2+-saturated state (Kd = 9.65 μM). The chimeric protein can release nano- to micro-molar levels of BR with Ca2+ control, and is thus named BReleaCa (BR + releaser + Ca2+). Such a protein hybridization technique will be generally applicable to change the ligand binding properties of a variety of ligand-inducible functional proteins.
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Affiliation(s)
- Yoh Shitashima
- Department of Advanced Science and Engineering, Waseda University, Tokyo, Japan; Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Saitama, Japan
| | - Togo Shimozawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Toru Asahi
- Department of Advanced Science and Engineering, Waseda University, Tokyo, Japan; Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Saitama, Japan; Biotechnological Optics Research Team, Center for Advanced Photonics, RIKEN, Saitama, Japan.
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8
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Barykina NV, Subach OM, Piatkevich KD, Jung EE, Malyshev AY, Smirnov IV, Bogorodskiy AO, Borshchevskiy VI, Varizhuk AM, Pozmogova GE, Boyden ES, Anokhin KV, Enikolopov GN, Subach FV. Green fluorescent genetically encoded calcium indicator based on calmodulin/M13-peptide from fungi. PLoS One 2017; 12:e0183757. [PMID: 28837632 PMCID: PMC5570312 DOI: 10.1371/journal.pone.0183757] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/10/2017] [Indexed: 11/19/2022] Open
Abstract
Currently available genetically encoded calcium indicators (GECIs) utilize calmodulins (CaMs) or troponin C from metazoa such as mammals, birds, and teleosts, as calcium-binding domains. The amino acid sequences of the metazoan calcium-binding domains are highly conserved, which may limit the range of the GECI key parameters and cause undesired interactions with the intracellular environment in mammalian cells. Here we have used fungi, evolutionary distinct organisms, to derive CaM and its binding partner domains and design new GECI with improved properties. We applied iterative rounds of molecular evolution to develop FGCaMP, a novel green calcium indicator. It includes the circularly permuted version of the enhanced green fluorescent protein (EGFP) sandwiched between the fungal CaM and a fragment of CaM-dependent kinase. FGCaMP is an excitation-ratiometric indicator that has a positive and an inverted fluorescence response to calcium ions when excited at 488 and 405 nm, respectively. Compared with the GCaMP6s indicator in vitro, FGCaMP has a similar brightness at 488 nm excitation, 7-fold higher brightness at 405 nm excitation, and 1.3-fold faster calcium ion dissociation kinetics. Using site-directed mutagenesis, we generated variants of FGCaMP with improved binding affinity to calcium ions and increased the magnitude of FGCaMP fluorescence response to low calcium ion concentrations. Using FGCaMP, we have successfully visualized calcium transients in cultured mammalian cells. In contrast to the limited mobility of GCaMP6s and G-GECO1.2 indicators, FGCaMP exhibits practically 100% molecular mobility at physiological concentrations of calcium ion in mammalian cells, as determined by photobleaching experiments with fluorescence recovery. We have successfully monitored the calcium dynamics during spontaneous activity of neuronal cultures using FGCaMP and utilized whole-cell patch clamp recordings to further characterize its behavior in neurons. Finally, we used FGCaMP in vivo to perform structural and functional imaging of zebrafish using wide-field, confocal, and light-sheet microscopy.
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Affiliation(s)
- Natalia V. Barykina
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- P.K. Anokhin Institute of Normal Physiology of RAMS, Moscow, Russia
| | - Oksana M. Subach
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Kiryl D. Piatkevich
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Erica E. Jung
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Aleksey Y. Malyshev
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, Russia
| | - Ivan V. Smirnov
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, Russia
- Medico-Biological Faculty, N.I. Pirogov Russian National Research Medical University, Moscow, Russia
| | | | | | - Anna M. Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
| | - Galina E. Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Edward S. Boyden
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, United States of America
| | - Konstantin V. Anokhin
- P.K. Anokhin Institute of Normal Physiology of RAMS, Moscow, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Grigori N. Enikolopov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Department of Anesthesiology, Stony Brook University Medical Center, Stony Brook, NY, United States of America
- Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, United States of America
| | - Fedor V. Subach
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
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9
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Reddish FN, Miller CL, Gorkhali R, Yang JJ. Monitoring ER/SR Calcium Release with the Targeted Ca2+ Sensor CatchER. J Vis Exp 2017. [PMID: 28570539 DOI: 10.3791/55822] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Intracellular calcium (Ca2+) transients evoked by extracellular stimuli initiate a multitude of biological processes in living organisms. At the center of intracellular calcium release are the major intracellular calcium storage organelles, the endoplasmic reticulum (ER) and the more specialized sarcoplasmic reticulum (SR) in muscle cells. The dynamic release of calcium from these organelles is mediated by the ryanodine receptor (RyR) and the inositol 1,4,5-triphosphate receptor (IP3R) with refilling occurring through the sarco/endoplasmic reticulum calcium ATPase (SERCA) pump. A genetically encoded calcium sensor (GECI) called CatchER was created to monitor the rapid calcium release from the ER/SR. Here, the detailed protocols for the transfection and expression of the improved, ER/SR-targeted GECI CatchER+ in HEK293 and C2C12 cells and its application in monitoring IP3R, RyR, and SERCA pump-mediated calcium transients in HEK293 cells using fluorescence microscopy is outlined. The receptor agonist or inhibitor of choice is dispersed in the chamber solution and the intensity changes are recorded in real time. With this method, a decrease in ER calcium is seen with RyR activation with 4-chloro-m-cresol (4-cmc), the indirect activation of IP3R with adenosine triphosphate (ATP), and inhibition of the SERCA pump with cyclopiazonic acid (CPA). We also discuss protocols for determining the in situ Kd and quantifying basal [Ca2+] in C2C12 cells. In summary, these protocols, used in conjunction with CatchER+, can elicit receptor mediated calcium release from the ER with future application in studying ER/SR calcium related pathologies.
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Affiliation(s)
- Florence N Reddish
- Department of Chemistry, Center of Diagnostics and Therapeutics (CDT), Georgia State University
| | - Cassandra L Miller
- Department of Chemistry, Center of Diagnostics and Therapeutics (CDT), Georgia State University
| | - Rakshya Gorkhali
- Department of Chemistry, Center of Diagnostics and Therapeutics (CDT), Georgia State University
| | - Jenny J Yang
- Department of Chemistry, Center of Diagnostics and Therapeutics (CDT), Georgia State University;
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10
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Molecular Basis for Modulation of Metabotropic Glutamate Receptors and Their Drug Actions by Extracellular Ca 2. Int J Mol Sci 2017; 18:ijms18030672. [PMID: 28335551 PMCID: PMC5372683 DOI: 10.3390/ijms18030672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/13/2017] [Accepted: 03/17/2017] [Indexed: 12/24/2022] Open
Abstract
Metabotropic glutamate receptors (mGluRs) associated with the slow phase of the glutamatergic signaling pathway in neurons of the central nervous system have gained importance as drug targets for chronic neurodegenerative diseases. While extracellular Ca2+ was reported to exhibit direct activation and modulation via an allosteric site, the identification of those binding sites was challenged by weak binding. Herein, we review the discovery of extracellular Ca2+ in regulation of mGluRs, summarize the recent developments in probing Ca2+ binding and its co-regulation of the receptor based on structural and biochemical analysis, and discuss the molecular basis for Ca2+ to regulate various classes of drug action as well as its importance as an allosteric modulator in mGluRs.
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11
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Suzuki J, Kanemaru K, Iino M. Genetically Encoded Fluorescent Indicators for Organellar Calcium Imaging. Biophys J 2016; 111:1119-1131. [PMID: 27477268 DOI: 10.1016/j.bpj.2016.04.054] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 12/14/2022] Open
Abstract
Optical Ca(2+) indicators are powerful tools for investigating intracellular Ca(2+) signals in living cells. Although a variety of Ca(2+) indicators have been developed, deciphering the physiological functions and spatiotemporal dynamics of Ca(2+) in intracellular organelles remains challenging. Genetically encoded Ca(2+) indicators (GECIs) using fluorescent proteins are promising tools for organellar Ca(2+) imaging, and much effort has been devoted to their development. In this review, we first discuss the key points of organellar Ca(2+) imaging and summarize the requirements for optimal organellar Ca(2+) indicators. Then, we highlight some of the recent advances in the engineering of fluorescent GECIs targeted to specific organelles. Finally, we discuss the limitations of currently available GECIs and the requirements for advancing the research on intraorganellar Ca(2+) signaling.
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Affiliation(s)
- Junji Suzuki
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Physiology, University of California San Francisco, San Francisco, California
| | - Kazunori Kanemaru
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masamitsu Iino
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Cellular and Molecular Pharmacology, Nihon University School of Medicine, Tokyo, Japan.
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12
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Bioinspired design of a polymer gel sensor for the realization of extracellular Ca(2+) imaging. Sci Rep 2016; 6:24275. [PMID: 27067646 PMCID: PMC4828671 DOI: 10.1038/srep24275] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/21/2016] [Indexed: 12/20/2022] Open
Abstract
Although the role of extracellular Ca2+ draws increasing attention as a messenger in intercellular communications, there is currently no tool available for imaging Ca2+ dynamics in extracellular regions. Here we report the first solid-state fluorescent Ca2+ sensor that fulfills the essential requirements for realizing extracellular Ca2+ imaging. Inspired by natural extracellular Ca2+-sensing receptors, we designed a particular type of chemically-crosslinked polyacrylic acid gel, which can undergo single-chain aggregation in the presence of Ca2+. By attaching aggregation-induced emission luminogen to the polyacrylic acid as a pendant, the conformational state of the main chain at a given Ca2+ concentration is successfully translated into fluorescence property. The Ca2+ sensor has a millimolar-order apparent dissociation constant compatible with extracellular Ca2+ concentrations, and exhibits sufficient dynamic range and excellent selectivity in the presence of physiological concentrations of biologically relevant ions, thus enabling monitoring of submillimolar fluctuations of Ca2+ in flowing analytes containing millimolar Ca2+ concentrations.
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13
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Tang S, Reddish F, Zhuo Y, Yang JJ. Fast kinetics of calcium signaling and sensor design. Curr Opin Chem Biol 2015; 27:90-7. [PMID: 26151819 DOI: 10.1016/j.cbpa.2015.06.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 06/11/2015] [Accepted: 06/11/2015] [Indexed: 12/25/2022]
Abstract
Fast calcium signaling is regulated by numerous calcium channels exhibiting high spatiotemporal profiles which are currently measured by fluorescent calcium sensors. There is still a strong need to improve the kinetics of genetically encoded calcium indicators (sensors) to capture calcium dynamics in the millisecond time frame. In this review, we summarize several major fast calcium signaling pathways and discuss the recent developments and application of genetically encoded calcium indicators to detect these pathways. A new class of genetically encoded calcium indicators designed with site-directed mutagenesis on the surface of beta-barrel fluorescent proteins to form a pentagonal bipyramidal-like calcium binding domain dramatically accelerates calcium binding kinetics. Furthermore, novel genetically encoded calcium indicators with significantly increased fluorescent lifetime change are advantageous in deep-field imaging with high light-scattering and notable morphology change.
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Affiliation(s)
- Shen Tang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, United States
| | - Florence Reddish
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, United States
| | - You Zhuo
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, United States
| | - Jenny J Yang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, United States.
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14
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Imaging intraorganellar Ca2+ at subcellular resolution using CEPIA. Nat Commun 2014; 5:4153. [PMID: 24923787 PMCID: PMC4082642 DOI: 10.1038/ncomms5153] [Citation(s) in RCA: 330] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 05/16/2014] [Indexed: 12/19/2022] Open
Abstract
The endoplasmic reticulum (ER) and mitochondria accumulate Ca2+ within their lumens to regulate numerous cell functions. However, determining the dynamics of intraorganellar Ca2+ has proven to be difficult. Here we describe a family of genetically encoded Ca2+ indicators, named calcium-measuring organelle-entrapped protein indicators (CEPIA), which can be utilized for intraorganellar Ca2+ imaging. CEPIA, which emit green, red or blue/green fluorescence, are engineered to bind Ca2+ at intraorganellar Ca2+ concentrations. They can be targeted to different organelles and may be used alongside other fluorescent molecular markers, expanding the range of cell functions that can be simultaneously analysed. The spatiotemporal resolution of CEPIA makes it possible to resolve Ca2+ import into individual mitochondria while simultaneously measuring ER and cytosolic Ca2+. We have used these imaging capabilities to reveal differential Ca2+ handling in individual mitochondria. CEPIA imaging is a useful new tool to further the understanding of organellar functions. The use of intracellular calcium sensors provides important information about the dynamics of calcium signalling in cells. Here Suzuki et al. develop organelle-targeted sensors to simultaneously measure calcium concentrations in ER and mitochondria, and uncover novel insights into calcium flux in mitochondria.
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Zhang Y, Reddish F, Tang S, Zhuo Y, Wang YF, Yang JJ, Weber IT. Structural basis for a hand-like site in the calcium sensor CatchER with fast kinetics. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2309-19. [PMID: 24311573 PMCID: PMC3852649 DOI: 10.1107/s0907444913021306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/30/2013] [Indexed: 11/10/2022]
Abstract
Calcium ions, which are important signaling molecules, can be detected in the endoplasmic reticulum by an engineered mutant of green fluorescent protein (GFP) designated CatchER with a fast off-rate. High resolution (1.78-1.20 Å) crystal structures were analyzed for CatchER in the apo form and in complexes with calcium or gadolinium to probe the binding site for metal ions. While CatchER exhibits a 1:1 binding stoichiometry in solution, two positions were observed for each of the metal ions bound within the hand-like site formed by the carboxylate side chains of the mutated residues S147E, S202D, Q204E, F223E and T225E that may be responsible for its fast kinetic properties. Comparison of the structures of CatchER, wild-type GFP and enhanced GFP confirmed that different conformations of Thr203 and Glu222 are associated with the two forms of Tyr66 of the chromophore which are responsible for the absorbance wavelengths of the different proteins. Calcium binding to CatchER may shift the equilibrium for conformational population of the Glu222 side chain and lead to further changes in its optical properties.
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Affiliation(s)
- Ying Zhang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Florence Reddish
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Shen Tang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - You Zhuo
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Jenny J. Yang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
- Centre for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Irene T. Weber
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
- Centre for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
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16
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Ca2+ homeostasis in the endoplasmic reticulum measured with a new low-Ca2+-affinity targeted aequorin. Cell Calcium 2013; 54:37-45. [DOI: 10.1016/j.ceca.2013.04.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 02/27/2013] [Accepted: 04/04/2013] [Indexed: 11/18/2022]
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17
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Shaw SL, Ehrhardt DW. Smaller, faster, brighter: advances in optical imaging of living plant cells. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:351-75. [PMID: 23506334 DOI: 10.1146/annurev-arplant-042110-103843] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The advent of fluorescent proteins and access to modern imaging technologies have dramatically accelerated the pace of discovery in plant cell biology. Remarkable new insights into such diverse areas as plant pathogenesis, cytoskeletal dynamics, sugar transport, cell wall synthesis, secretory control, and hormone signaling have come from careful examination of living cells using advanced optical probes. New technologies, both commercially available and on the horizon, promise a continued march toward more quantitative methods for imaging and for extending the optical exploration of biological structure and activity to molecular scales. In this review, we lay out fundamental issues in imaging plant specimens and look ahead to several technological innovations in molecular tools, instrumentation, imaging methods, and specimen handling that show promise for shaping the coming era of plant cell biology.
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Affiliation(s)
- Sidney L Shaw
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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18
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Liu Q, Bian W, Shi H, Fan L, Shuang S, Dong C, Choi MMF. A novel ratiometric emission probe for Ca2+in living cells. Org Biomol Chem 2013. [DOI: 10.1039/c2ob26888d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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19
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Weber E, Guth C, Weiss IM. GFP facilitates native purification of recombinant perlucin derivatives and delays the precipitation of calcium carbonate. PLoS One 2012; 7:e46653. [PMID: 23056388 PMCID: PMC3463529 DOI: 10.1371/journal.pone.0046653] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/03/2012] [Indexed: 12/02/2022] Open
Abstract
Insolubility is one of the possible functions of proteins involved in biomineralization, which often limits their native purification. This becomes a major problem especially when recombinant expression systems are required to obtain larger amounts. For example, the mollusc shell provides a rich source of unconventional proteins, which can interfere in manifold ways with different mineral phases and interfaces. Therefore, the relevance of such proteins for biotechnological processes is still in its infancy. Here we report a simple and reproducible purification procedure for a GFP-tagged lectin involved in biomineralization, originally isolated from mother-of-pearl in abalone shells. An optimization of E. coli host cell culture conditions was the key to obtain reasonable yields and high degrees of purity by using simple one-step affinity chromatography. We identified a dual functional role for the GFP domain when it became part of a mineralizing system in vitro. First, the GFP domain improved the solubility of an otherwise insoluble protein, in this case recombinant perlucin derivatives. Second, GFP inhibited calcium carbonate precipitation in a concentration dependent manner. This was demonstrated here using a simple bulk assay over a time period of 400 seconds. At concentrations of 2 µg/ml and higher, the inhibitory effect was observed predominantly for HCO(3) (-) as the first ionic interaction partner, but not necessarily for Ca(2+). The interference of GFP-tagged perlucin derivatives with the precipitation of calcium carbonate generated different types of GFP-fluorescent composite calcite crystals. GFP-tagging offers therefore a genetically tunable tool to gently modify mechanical and optical properties of synthetic biocomposite minerals.
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Affiliation(s)
- Eva Weber
- INM – Leibniz Institute for New Materials gGmbH, Saarbruecken, Germany
| | - Christina Guth
- INM – Leibniz Institute for New Materials gGmbH, Saarbruecken, Germany
| | - Ingrid M. Weiss
- INM – Leibniz Institute for New Materials gGmbH, Saarbruecken, Germany
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20
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Zhao K, Wang X, Wong HC, Wohlhueter R, Kirberger MP, Chen G, Yang JJ. Predicting Ca2+ -binding sites using refined carbon clusters. Proteins 2012; 80:2666-79. [PMID: 22821762 DOI: 10.1002/prot.24149] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Revised: 06/14/2012] [Accepted: 07/11/2012] [Indexed: 12/13/2022]
Abstract
Identifying Ca(2+) -binding sites in proteins is the first step toward understanding the molecular basis of diseases related to Ca(2+) -binding proteins. Currently, these sites are identified in structures either through X-ray crystallography or NMR analysis. However, Ca(2+) -binding sites are not always visible in X-ray structures due to flexibility in the binding region or low occupancy in a Ca(2+) -binding site. Similarly, both Ca(2+) and its ligand oxygens are not directly observed in NMR structures. To improve our ability to predict Ca(2+) -binding sites in both X-ray and NMR structures, we report a new graph theory algorithm (MUG(C) ) to predict Ca(2+) -binding sites. Using carbon atoms covalently bonded to the chelating oxygen atoms, and without explicit reference to side-chain oxygen ligand co-ordinates, MUG(C) is able to achieve 94% sensitivity with 76% selectivity on a dataset of X-ray structures composed of 43 Ca(2+) -binding proteins. Additionally, prediction of Ca(2+) -binding sites in NMR structures was obtained by MUG(C) using a different set of parameters, which were determined by the analysis of both Ca(2+) -constrained and unconstrained Ca(2+) -loaded structures derived from NMR data. MUG(C) identified 20 of 21 Ca(2+) -binding sites in NMR structures inferred without the use of Ca(2+) constraints. MUG(C) predictions are also highly selective for Ca(2+) -binding sites as analyses of binding sites for Mg(2+) , Zn(2+) , and Pb(2+) were not identified as Ca(2+) -binding sites. These results indicate that the geometric arrangement of the second-shell carbon cluster is sufficient not only for accurate identification of Ca(2+) -binding sites in NMR and X-ray structures but also for selective differentiation between Ca(2+) and other relevant divalent cations.
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Affiliation(s)
- Kun Zhao
- Department of Mathematics and Statistics, Georgia State University, Atlanta, GA 30303, USA
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21
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Marvin JS, Schreiter ER, Echevarría IM, Looger LL. A genetically encoded, high-signal-to-noise maltose sensor. Proteins 2012; 79:3025-36. [PMID: 21989929 PMCID: PMC3265398 DOI: 10.1002/prot.23118] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes.
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Affiliation(s)
- Jonathan S Marvin
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA.
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22
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Wang ZM, Tang S, Messi ML, Yang JJ, Delbono O. Residual sarcoplasmic reticulum Ca2+ concentration after Ca2+ release in skeletal myofibers from young adult and old mice. Pflugers Arch 2012; 463:615-24. [PMID: 22249494 DOI: 10.1007/s00424-012-1073-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 12/31/2011] [Accepted: 01/02/2012] [Indexed: 10/14/2022]
Abstract
Contrasting information suggests either almost complete depletion of sarcoplasmic reticulum (SR) Ca(2+) or significant residual Ca(2+) concentration after prolonged depolarization of the skeletal muscle fiber. The primary obstacle to resolving this controversy is the lack of genetically encoded Ca(2+) indicators targeted to the SR that exhibit low-Ca(2+) affinity, a fast biosensor: Ca(2+) off-rate reaction, and can be expressed in myofibers from adult and older adult mammalian species. This work used the recently designed low-affinity Ca(2+) sensor (Kd = 1.66 mM in the myofiber) CatchER (calcium sensor for detecting high concentrations in the ER) targeted to the SR, to investigate whether prolonged skeletal muscle fiber depolarization significantly alters residual SR Ca(2+) with aging. We found CatchER a proper tool to investigate SR Ca(2+) depletion in young adult and older adult mice, consistently tracking SR luminal Ca(2+) release in response to brief and repetitive stimulation. We evoked SR Ca(2+) release in whole-cell voltage-clamped flexor digitorum brevis muscle fibers from young and old FVB mice and tested the maximal SR Ca(2+) release by directly activating the ryanodine receptor (RyR1) with 4-chloro-m-cresol in the same myofibers. Here, we report for the first time that the Ca(2+) remaining in the SR after prolonged depolarization (2 s) in myofibers from aging (~220 μM) was larger than young (~132 μM) mice. These experiments indicate that SR Ca(2+) is far from fully depleted under physiological conditions throughout life, and support the concept of excitation-contraction uncoupling in functional senescent myofibers.
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Affiliation(s)
- Zhong-Min Wang
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, 1 Medical Center Boulevard, Winston-Salem, NC, 27157, USA
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23
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Abstract
The development of novel fluorescence methods for the detection of key biomolecules is of great interest, both in basic research and in drug discovery. Particularly relevant and widespread molecules in cells are ADP and GDP, which are the products of a large number of cellular reactions, including reactions catalysed by nucleoside triphosphatases and kinases. Previously, biosensors for ADP were developed in this laboratory, based on fluorophore adducts with the bacterial actin homologue ParM. It is shown in the present study that one of these biosensors, tetramethylrhodamine–ParM, can also monitor GDP. The biosensor can be used to measure micromolar concentrations of GDP on the background of millimolar concentrations of GTP. The fluorescence response of the biosensor is fast, the response time being <0.2 s. Thus the biosensor allows real-time measurements of GTPase and GTP-dependent kinase reactions. Applications of the GDP biosensor are exemplified with two different GTPases, measuring the rates of GTP hydrolysis and nucleotide exchange.
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24
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Veselov AA, Abraham BG, Lemmetyinen H, Karp MT, Tkachenko NV. Photochemical properties and sensor applications of modified yellow fluorescent protein (YFP) covalently attached to the surfaces of etched optical fibers (EOFs). Anal Bioanal Chem 2011; 402:1149-58. [PMID: 22116380 DOI: 10.1007/s00216-011-5564-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 11/07/2011] [Indexed: 01/14/2023]
Abstract
Fluorescent proteins have the inherent ability to act as sensing components which function both in vitro and inside living cells. We describe here a novel study on a covalent site-specific bonding of fluorescent proteins to form self-assembled monolayers (SAMs) on the surface of etched optical fibers (EOFs). Deposition of fluorescent proteins on EOFs gives the opportunity to increase the interaction of guided light with deposited molecules relative to plane glass surfaces. The EOF modification is carried out by surface activation using 3-aminopropylthrimethoxysilane (APTMS) and bifunctional crosslinker sulfosuccinimidyl 4-[N-maleimidomethyl]cyclohexane-1-carboxylate (sulfo-SMCC) which exposes sulfhydryl-reactive maleimide groups followed by covalent site-specific coupling of modified yellow fluorescent protein (YFP). Steady-state and fluorescence lifetime measurements confirm the formation of SAM. The sensor applications of YPF SAMs on EOF are demonstrated by the gradual increase of emission intensity upon addition of Ca(2+) ions in the concentration range from a few tens of micromolars up to a few tens of millimolars. The studies on the effect of pH, divalent cations, denaturing agents, and proteases reveal the stability of YFP on EOFs at normal physiological conditions. However, treatments with 0.5% SDS at pH 8.5 and protease trypsin are found to denaturate or cleave the YFP from fiber surfaces.
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Affiliation(s)
- Alexey A Veselov
- Department of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, 33101 Tampere, Finland.
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25
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Design and application of a class of sensors to monitor Ca2+ dynamics in high Ca2+ concentration cellular compartments. Proc Natl Acad Sci U S A 2011; 108:16265-70. [PMID: 21914846 DOI: 10.1073/pnas.1103015108] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Quantitative analysis of Ca(2+) fluctuations in the endoplasmic/sarcoplasmic reticulum (ER/SR) is essential to defining the mechanisms of Ca(2+)-dependent signaling under physiological and pathological conditions. Here, we developed a unique class of genetically encoded indicators by designing a Ca(2+) binding site in the EGFP. One of them, calcium sensor for detecting high concentration in the ER, exhibits unprecedented Ca(2+) release kinetics with an off-rate estimated at around 700 s(-1) and appropriate Ca(2+) binding affinity, likely attributable to local Ca(2+)-induced conformational changes around the designed Ca(2+) binding site and reduced chemical exchange between two chromophore states. Calcium sensor for detecting high concentration in the ER reported considerable differences in ER Ca(2+) dynamics and concentration among human epithelial carcinoma cells (HeLa), human embryonic kidney 293 cells (HEK-293), and mouse myoblast cells (C2C12), enabling us to monitor SR luminal Ca(2+) in flexor digitorum brevis muscle fibers to determine the mechanism of diminished SR Ca(2+) release in aging mice. This sensor will be invaluable in examining pathogenesis characterized by alterations in Ca(2+) homeostasis.
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26
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Wang X, Zhao K, Kirberger M, Wong H, Chen G, Yang JJ. Analysis and prediction of calcium-binding pockets from apo-protein structures exhibiting calcium-induced localized conformational changes. Protein Sci 2010; 19:1180-90. [PMID: 20512971 DOI: 10.1002/pro.394] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Calcium binding in proteins exhibits a wide range of polygonal geometries that relate directly to an equally diverse set of biological functions. The binding process stabilizes protein structures and typically results in local conformational change and/or global restructuring of the backbone. Previously, we established the MUG program, which utilized multiple geometries in the Ca(2+)-binding pockets of holoproteins to identify such pockets, ignoring possible Ca(2+)-induced conformational change. In this article, we first report our progress in the analysis of Ca(2+)-induced conformational changes followed by improved prediction of Ca(2+)-binding sites in the large group of Ca(2+)-binding proteins that exhibit only localized conformational changes. The MUG(SR) algorithm was devised to incorporate side chain torsional rotation as a predictor. The output from MUG(SR) presents groups of residues where each group, typically containing two to five residues, is a potential binding pocket. MUG(SR) was applied to both X-ray apo structures and NMR holo structures, which did not use calcium distance constraints in structure calculations. Predicted pockets were validated by comparison with homologous holo structures. Defining a "correct hit" as a group of residues containing at least two true ligand residues, the sensitivity was at least 90%; whereas for a "correct hit" defined as a group of residues containing at least three true ligand residues, the sensitivity was at least 78%. These data suggest that Ca(2+)-binding pockets are at least partially prepositioned to chelate the ion in the apo form of the protein.
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Affiliation(s)
- Xue Wang
- Department of Computer Science, Georgia State University, Atlanta, Georgia 30303, USA
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27
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Carlson HJ, Cotton DW, Campbell RE. Circularly permuted monomeric red fluorescent proteins with new termini in the beta-sheet. Protein Sci 2010; 19:1490-9. [PMID: 20521333 PMCID: PMC2923502 DOI: 10.1002/pro.428] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 05/18/2010] [Indexed: 11/10/2022]
Abstract
Circularly permuted fluorescent proteins (FPs) have a growing number of uses in live cell fluorescence biosensing applications. Most notably, they enable the construction of single fluorescent protein-based biosensors for Ca(2+) and other analytes of interest. Circularly permuted FPs are also of great utility in the optimization of fluorescence resonance energy transfer (FRET)-based biosensors by providing a means for varying the critical dipole-dipole orientation. We have previously reported on our efforts to create circularly permuted variants of a monomeric red FP (RFP) known as mCherry. In our previous work, we had identified six distinct locations within mCherry that tolerated the insertion of a short peptide sequence. Creation of circularly permuted variants with new termini at the locations corresponding to the sites of insertion led to the discovery of three permuted variants that retained no more than 18% of the brightness of mCherry. We now report the extensive directed evolution of the variant with new termini at position 193 of the protein sequence for improved fluorescent brightness. The resulting variant, known as cp193g7, has 61% of the intrinsic brightness of mCherry and was found to be highly tolerant of circular permutation at other locations within the sequence. We have exploited this property to engineer an expanded series of circularly permuted variants with new termini located along the length of the 10th beta-strand of mCherry. These new variants may ultimately prove useful for the creation of single FP-based Ca(2+) biosensors.
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Affiliation(s)
| | | | - Robert E Campbell
- Department of Chemistry, University of AlbertaEdmonton, Alberta, Canada T6G 2G2
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28
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Contreras L, Drago I, Zampese E, Pozzan T. Mitochondria: the calcium connection. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:607-18. [PMID: 20470749 DOI: 10.1016/j.bbabio.2010.05.005] [Citation(s) in RCA: 252] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 05/04/2010] [Accepted: 05/04/2010] [Indexed: 12/21/2022]
Abstract
Calcium handling by mitochondria is a key feature in cell life. It is involved in energy production for cell activity, in buffering and shaping cytosolic calcium rises and also in determining cell fate by triggering or preventing apoptosis. Both mitochondria and the mechanisms involved in the control of calcium homeostasis have been extensively studied, but they still provide researchers with long-standing or even new challenges. Technical improvements in the tools employed for the investigation of calcium dynamics have been-and are still-opening new perspectives in this field, and more prominently for mitochondria. In this review we present a state-of-the-art toolkit for calcium measurements, with major emphasis on the advantages of genetically encoded indicators. These indicators can be efficiently and selectively targeted to specific cellular sub-compartments, allowing previously unavailable high-definition calcium dynamic studies. We also summarize the main features of cellular and, in more detail, mitochondrial calcium handling, especially focusing on the latest breakthroughs in the field, such as the recent direct characterization of the calcium microdomains that occur on the mitochondrial surface upon cellular stimulation. Additionally, we provide a major example of the key role played by calcium in patho-physiology by briefly describing the extensively reported-albeit highly controversial-alterations of calcium homeostasis in Alzheimer's disease, casting lights on the possible alterations in mitochondrial calcium handling in this pathology.
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Affiliation(s)
- Laura Contreras
- Department of Biomedical Sciences, University of Padua, Italy.
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29
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Kirberger M, Wang X, Zhao K, Tang S, Chen G, Yang JJ. Integration of Diverse Research Methods to Analyze and Engineer Ca-Binding Proteins: From Prediction to Production. Curr Bioinform 2010; 5:68-80. [PMID: 20802832 PMCID: PMC2927018 DOI: 10.2174/157489310790596358] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In recent years, increasingly sophisticated computational and bioinformatics tools have evolved for the analyses of protein structure, function, ligand interactions, modeling and energetics. This includes the development of algorithms to recursively evaluate side-chain rotamer permutations, identify regions in a 3D structure that meet some set of search parameters, calculate and minimize energy values, and provide high-resolution visual tools for theoretical modeling. Here we discuss the interdependency between different areas of bioinformatics, the evolution of different algorithm design approaches, and finally the transition from theoretical models to real-world design and application as they relate to Ca(2+)-binding proteins. Within this context, it has become evident that significant pre-experimental design and calculations can be modeled through computational methods, thus eliminating potentially unproductive research and increasing our confidence in the correlation between real and theoretical models. Moving from prediction to production, it is anticipated that bioinformatics tools will play an increasingly significant role in research and development, improving our ability to both understand the physiological roles of Ca(2+) and other metals and to extend that knowledge to the design of function-specific synthetic proteins capable of fulfilling different roles in medical diagnostics and therapeutics.
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Affiliation(s)
- Michael Kirberger
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Xue Wang
- Department of Computer Science, Georgia State University, Atlanta, Georgia
| | - Kun Zhao
- Department of Mathematics and Statistics, Georgia State University, Atlanta, Georgia, USA
| | - Shen Tang
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Guantao Chen
- Department of Computer Science, Georgia State University, Atlanta, Georgia
- Department of Mathematics and Statistics, Georgia State University, Atlanta, Georgia, USA
| | - Jenny J. Yang
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
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30
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Abstract
The sarcoplasmic reticulum (SR) of smooth muscles presents many intriguing facets and questions concerning its roles, especially as these change with development, disease, and modulation of physiological activity. The SR's function was originally perceived to be synthetic and then that of a Ca store for the contractile proteins, acting as a Ca amplification mechanism as it does in striated muscles. Gradually, as investigators have struggled to find a convincing role for Ca-induced Ca release in many smooth muscles, a role in controlling excitability has emerged. This is the Ca spark/spontaneous transient outward current coupling mechanism which reduces excitability and limits contraction. Release of SR Ca occurs in response to inositol 1,4,5-trisphosphate, Ca, and nicotinic acid adenine dinucleotide phosphate, and depletion of SR Ca can initiate Ca entry, the mechanism of which is being investigated but seems to involve Stim and Orai as found in nonexcitable cells. The contribution of the elemental Ca signals from the SR, sparks and puffs, to global Ca signals, i.e., Ca waves and oscillations, is becoming clearer but is far from established. The dynamics of SR Ca release and uptake mechanisms are reviewed along with the control of luminal Ca. We review the growing list of the SR's functions that still includes Ca storage, contraction, and relaxation but has been expanded to encompass Ca homeostasis, generating local and global Ca signals, and contributing to cellular microdomains and signaling in other organelles, including mitochondria, lysosomes, and the nucleus. For an integrated approach, a review of aspects of the SR in health and disease and during development and aging are also included. While the sheer versatility of smooth muscle makes it foolish to have a "one model fits all" approach to this subject, we have tried to synthesize conclusions wherever possible.
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Affiliation(s)
- Susan Wray
- Department of Physiology, School of Biomedical Sciences, University of Liverpool, Liverpool, Merseyside L69 3BX, United Kingdom.
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31
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Chen N, Huang Y, Yang L, Liu R, Yang JJ. Designing caspase-3 sensors for imaging of apoptosis in living cells. Chemistry 2010; 15:9311-4. [PMID: 19655355 DOI: 10.1002/chem.200901439] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ning Chen
- Department of Chemistry, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
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Webb SE, Rogers KL, Karplus E, Miller AL. The use of aequorins to record and visualize Ca(2+) dynamics: from subcellular microdomains to whole organisms. Methods Cell Biol 2010; 99:263-300. [PMID: 21035690 DOI: 10.1016/b978-0-12-374841-6.00010-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this chapter, we describe the practical aspects of measuring [Ca(2+)] transients that are generated in a particular cytoplasmic domain, or within a specific organelle or its periorganellar environment, using bioluminescent, genetically encoded and targeted Ca(2+) reporters, especially those based on apoaequorin. We also list examples of the organisms, tissues, and cells that have been transfected with apoaequorin or an apoaequorin-BRET complex, as well as of the organelles and subcellular domains that have been specifically targeted with these bioluminescent Ca(2+) reporters. In addition, we summarize the various techniques used to load the apoaequorin cofactor, coelenterazine, and its analogs into cells, tissues, and intact organisms, and we describe recent advances in the detection and imaging technologies that are currently being used to measure and visualize the luminescence generated by the aequorin-Ca(2+) reaction within these various cytoplasmic domains and subcellular compartments.
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Affiliation(s)
- Sarah E Webb
- Biochemistry and Cell Biology Section and State Key Laboratory of Molecular Neuroscience, Division of Life Science, HKUST, Clear Water Bay, Kowloon, Hong Kong, PR China
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Abstract
Small, fluorescent, calcium-sensing molecules have been enormously useful in mapping intracellular calcium signals in time and space, as chapters in this volume attest. Despite their widespread adoption and utility, they suffer some disadvantages. Genetically encoded calcium sensors that can be expressed inside cells by transfection or transgenesis are desirable. The last 10 years have been marked by a rapid evolution in the laboratory of genetically encoded calcium sensors both figuratively and literally, resulting in 11 distinct configurations of fluorescent proteins and their attendant calcium sensor modules. Here, the design logic and performance of this abundant collection of sensors and their in vitro and in vivo use and performance are described. Genetically encoded calcium sensors have proved valuable in the measurement of calcium concentration in cellular organelles, for the most part in single cells in vitro. Their success as quantitative calcium sensors in tissues in vitro and in vivo is qualified, but they have proved valuable in imaging the pattern of calcium signals within tissues in whole animals. Some branches of the calcium sensor evolutionary tree continue to evolve rapidly and the steady progress in optimizing sensor parameters leads to the certain hope that these drawbacks will eventually be overcome by further genetic engineering.
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Affiliation(s)
- Michael Whitaker
- Institute of Cell and Molecular Biosciences Medical School, Newcastle University, Framlington Place Newcastle upon Tyne, United Kingdom
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Balla T. Green light to illuminate signal transduction events. Trends Cell Biol 2009; 19:575-86. [PMID: 19818623 DOI: 10.1016/j.tcb.2009.08.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 08/03/2009] [Accepted: 08/11/2009] [Indexed: 11/17/2022]
Abstract
When cells are exposed to hormones that act on cell surface receptors, information is processed through the plasma membrane into the cell interior via second messengers generated in the inner leaflet of the plasma membrane. Individual biochemical steps along this cascade have been characterized from ligand binding to receptors through to activation of guanine nucleotide binding proteins and their downstream effectors such as adenylate cyclase or phospholipase C. However, the complexity of temporal and spatial integration of these molecular events requires that they are studied in intact cells. The great expansion of fluorescent techniques and improved imaging technologies such as confocal and TIRF microscopy combined with genetically-engineered protein modules has provided a completely new approach to signal transduction research. Spatial definition of biochemical events followed with real-time temporal resolution has become a standard goal, and several new techniques are now breaking the resolution barrier of light microscopy.
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Affiliation(s)
- Tamas Balla
- Section on Molecular Signal Transduction, Program on Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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35
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Fluorescence complementation via EF-hand interactions. J Biotechnol 2009; 142:205-13. [PMID: 19500621 DOI: 10.1016/j.jbiotec.2009.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 05/06/2009] [Accepted: 05/12/2009] [Indexed: 11/20/2022]
Abstract
Fluorescence complementation technology with fluorescent proteins is a powerful approach to investigate molecular recognition by monitoring fluorescence enhancement when non-fluorescent fragments of fluorescent proteins are fused with target proteins, resulting in a new fluorescent complex. Extension of the technology to calcium-dependent protein-protein interactions has, however, rarely been reported. Here, a linker containing trypsin cleavage sites was grafted onto enhanced green fluorescent protein (EGFP). Under physiological conditions, a modified fluorescent protein, EGFP-T1, was cleaved into two major fragments which continue to interact with each other, exhibiting strong optical and fluorescence signals. The larger fragment, comprised of amino acids 1-172, including the chromophore, retains only weak fluorescence. Strong green fluorescence was observed when plasmid DNA encoding complementary EGFP fragments fused to the EF-hand motifs of calbindin D9k (EF1 and EF2) were co-transfected into HeLa cells, suggesting that chromophore maturation and fluorescence complementation from EGFP fragments can be accomplished intracellularly by reassembly of EF-hand motifs, which have a strong tendency for dimerization. Moreover, an intracellular calcium increase upon addition of a calcium ionophore, ionomycin in living cells, results in an increase of fluorescence signal. This novel application of calcium-dependent fluorescence complementation has the potential to monitor protein-protein interactions triggered by calcium signalling pathways in living cells.
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Holder AN, Ellis AL, Zou J, Chen N, Yang JJ. Facilitating chromophore formation of engineered Ca(2+) binding green fluorescent proteins. Arch Biochem Biophys 2009; 486:27-34. [PMID: 19358822 PMCID: PMC2774846 DOI: 10.1016/j.abb.2009.03.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 03/26/2009] [Accepted: 03/28/2009] [Indexed: 01/24/2023]
Abstract
Green fluorescent protein (GFP) containing a self-coded chromophore has been applied in protein trafficking and folding, gene expression, and as sensors in living cells. While the "cycle3" mutation denoted as C3 mutation (F99S/M153T/V163A) offers the ability to increase GFP fluorescence at 37 degrees C, it is not clear whether such mutations will also be able to assist the folding and formation of the chromophore upon the addition of metal ion binding sites. Here, we investigate in both bacterial and mammalian systems, the effect of C2 (M153T/V163A) and C3 (F99S/M153T/V163A) mutations on the folding of enhanced GFP (EGFP, includes F64L/S65T) and its variants engineered with two types of Ca(2+) binding sites: (1) a designed discontinuous Ca(2+) binding site and (2) a grafted continuous Ca(2+) binding motif. We show that, for the constructed EGFP variants, the C2 mutation is sufficient to facilitate the production of fluorescence in both bacterial and mammalian cells. Further addition of the mutation F99S decreases the folding efficiency of these variants although a similar effect is not detectable for EGFP, likely due to the already greatly enhanced mutation F64L/S65T from the original GFP, which hastens the chromophore formation. The extinction coefficient and quantum yield of purified proteins of each construct were also examined to compare the effects of both C2 and C3 mutations on protein spectroscopic properties. Our quantitative analyses of the effect of C2 and C3 mutations on the folding and formation of GFP chromophore that undergoes different folding trajectories in bacterial versus mammalian cells provide insights into the development of fluorescent protein-based analytical sensors.
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Affiliation(s)
- Angela N. Holder
- Department of Chemistry and Center for Drug Design and Advanced Biotechnology, Georgia State University, 50 Decatur Street, Atlanta, GA 30302, USA
| | - April L. Ellis
- Department of Chemistry and Center for Drug Design and Advanced Biotechnology, Georgia State University, 50 Decatur Street, Atlanta, GA 30302, USA
| | - Jin Zou
- Department of Chemistry and Center for Drug Design and Advanced Biotechnology, Georgia State University, 50 Decatur Street, Atlanta, GA 30302, USA
| | - Ning Chen
- Department of Chemistry and Center for Drug Design and Advanced Biotechnology, Georgia State University, 50 Decatur Street, Atlanta, GA 30302, USA
| | - Jenny J. Yang
- Department of Chemistry and Center for Drug Design and Advanced Biotechnology, Georgia State University, 50 Decatur Street, Atlanta, GA 30302, USA
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Chen N, Zou J, Wang S, Ye Y, Huang Y, Gadda G, Yang JJ. Designing protease sensors for real-time imaging of trypsin activation in pancreatic cancer cells. Biochemistry 2009; 48:3519-26. [PMID: 19271729 PMCID: PMC2739378 DOI: 10.1021/bi802289v] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Acute pancreatitis is a serious and potentially fatal disease caused by intracellular trypsinogen activation. Although protease detection has been greatly facilitated by the development of protease probes capable of monitoring protease activation and inhibition, real-time quantitative measurement of protease activity in living cells remains a challenge, and the identification of the cellular compartment for trypsinogen activation is inconclusive. Here we report a novel strategy for developing trypsin sensors by grafting an enzymatic cleavage site into a sensitive location for optical change of chromophore in a single enhanced green fluorescent protein (EGFP). Our designed trypsin sensor exhibits rapid kinetic responses for protease activation and inhibition with a large ratiometric optical signal change. In addition, it has strong specificity, as enzymatic cleavage is not observed with other proteases such as thrombin, cathepsin B, tryptase, and tissue plasminogen activator. Moreover, the developed trypsin sensor allows us for the first time to observe, in real time, trypsinogen activation by caerulein in the pancreatic cancer cell line, MIA PaCa-2 without zymogen granules. These developed protease sensors will facilitate improved understanding of mechanisms and locations of protease activation and further provide screening of protease inhibitors with therapeutic effects.
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Affiliation(s)
- Ning Chen
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Jin Zou
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Siming Wang
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Yiming Ye
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Yun Huang
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Giovanni Gadda
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
| | - Jenny J. Yang
- Department of Chemistry, Center for Drug Design and Biotechnology, Georgia State University, Atlanta, GA 30303, USA
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Kim SB, Sato M, Tao H. Split Gaussia Luciferase-Based Bioluminescence Template for Tracing Protein Dynamics in Living Cells. Anal Chem 2008; 81:67-74. [DOI: 10.1021/ac801658y] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sung Bae Kim
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 305-8569, Japan, and Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Moritoshi Sato
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 305-8569, Japan, and Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hiroaki Tao
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 305-8569, Japan, and Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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39
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McCombs JE, Palmer AE. Measuring calcium dynamics in living cells with genetically encodable calcium indicators. Methods 2008; 46:152-9. [PMID: 18848629 DOI: 10.1016/j.ymeth.2008.09.015] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Accepted: 09/12/2008] [Indexed: 01/25/2023] Open
Abstract
Genetically encoded calcium indicators (GECIs) allow researchers to measure calcium dynamics in specific targeted locations within living cells. Such indicators enable dissection of the spatial and temporal control of calcium signaling processes. Here we review recent progress in the development of GECIs, highlighting which indicators are most appropriate for measuring calcium in specific organelles and localized domains in mammalian tissue culture cells. An overview of recent approaches that have been undertaken to ensure that the GECIs are minimally perturbed by the cellular environment is provided. Additionally, the procedures for introducing GECIs into mammalian cells, conducting calcium imaging experiments, and analyzing data are discussed. Because organelle-targeted indicators often pose an additional challenge, we underscore strategies for calibrating GECIs in these locations.
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Affiliation(s)
- Janet E McCombs
- Department of Chemistry and Biochemistry, University of Colorado, UCB 215, 76 Chemistry, Boulder, CO 80309-0215, USA
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40
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Sabouri-Ghomi M, Wu Y, Hahn K, Danuser G. Visualizing and quantifying adhesive signals. Curr Opin Cell Biol 2008; 20:541-50. [PMID: 18586481 PMCID: PMC2661108 DOI: 10.1016/j.ceb.2008.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Revised: 05/15/2008] [Accepted: 05/19/2008] [Indexed: 12/17/2022]
Abstract
Understanding the structural adaptation and signaling of adhesion sites in response to mechanical stimuli requires in situ characterization of the dynamic activation of a large number of adhesion components. Here, we review high-resolution live cell imaging approaches to measure forces, assembly, and interaction of adhesion components, and the activation of adhesion-mediated signals. We conclude by outlining computational multiplexing as a framework for the integration of these data into comprehensive models of adhesion signaling pathways.
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Affiliation(s)
- Mohsen Sabouri-Ghomi
- Department of Cell Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Yi Wu
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Klaus Hahn
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Gaudenz Danuser
- Department of Cell Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
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41
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Breitwieser GE. Extracellular calcium as an integrator of tissue function. Int J Biochem Cell Biol 2008; 40:1467-80. [PMID: 18328773 PMCID: PMC2441573 DOI: 10.1016/j.biocel.2008.01.019] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 01/16/2008] [Accepted: 01/18/2008] [Indexed: 12/23/2022]
Abstract
The past several decades of research into calcium signaling have focused on intracellular calcium (Ca(i)(2+)), revealing both exquisite spatial and dynamic control of this potent second messenger. Our understanding of Ca(i)(2+) signaling has benefited from the evolution of cell culture methods, development of high affinity fluorescent calcium indicators (both membrane-permeant small molecules and genetically encoded proteins), and high-resolution fluorescence microscopy. As our understanding of single cell calcium dynamics has increased, translational efforts have attempted to push calcium signaling studies back into tissues, organs and whole animals. Emerging results from these more complicated, diffusion-limited systems have begun to define a role for extracellular calcium (Ca(o)(2+)) as an agonist, spurred by the cloning and characterization of a G protein-coupled receptor activated by Ca(o)(2+) (the calcium sensing receptor, CaR). Here, we review the current state-of-the art for measurement of Ca(o)(2+) fluctuations, and the evidence that fluctuations in Ca(o)(2+) can act as primary signals regulating cell function. Current results suggest that Ca(o)(2+) in bone and epidermis may act as a chemotactic homing signal, targeting cells to the appropriate tissue locations prior to initiation of the differentiation program. Ca(i)(2+) signaling-mediated Ca(o)(2+) fluctuations in interstitial spaces may integrate cell signaling responses in multicellular networks through activation of CaR. Appreciation of the importance of Ca(o)(2+) fluctuations in coordinating cell function will likely spur identification of additional, niche-specific Ca(2+) sensors, and provide unique insights into the regulation of multicellular signaling networks.
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Affiliation(s)
- Gerda E Breitwieser
- Weis Center for Research, Geisinger Clinic, 100 N. Academy Avenue, Danville, PA 17822, United States.
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