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Chien CT, Puhl H, Vogel SS, Molloy JE, Chiu W, Khan S. Hub stability in the calcium calmodulin-dependent protein kinase II. Commun Biol 2024; 7:766. [PMID: 38918547 PMCID: PMC11199487 DOI: 10.1038/s42003-024-06423-y] [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] [Received: 06/20/2023] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
The calcium calmodulin protein kinase II (CaMKII) is a multi-subunit ring assembly with a central hub formed by the association domains. There is evidence for hub polymorphism between and within CaMKII isoforms, but the link between polymorphism and subunit exchange has not been resolved. Here, we present near-atomic resolution cryogenic electron microscopy (cryo-EM) structures revealing that hubs from the α and β isoforms, either standalone or within an β holoenzyme, coexist as 12 and 14 subunit assemblies. Single-molecule fluorescence microscopy of Venus-tagged holoenzymes detects intermediate assemblies and progressive dimer loss due to intrinsic holoenzyme lability, and holoenzyme disassembly into dimers upon mutagenesis of a conserved inter-domain contact. Molecular dynamics (MD) simulations show the flexibility of 4-subunit precursors, extracted in-silico from the β hub polymorphs, encompassing the curvature of both polymorphs. The MD explains how an open hub structure also obtained from the β holoenzyme sample could be created by dimer loss and analysis of its cryo-EM dataset reveals how the gap could open further. An assembly model, considering dimer concentration dependence and strain differences between polymorphs, proposes a mechanism for intrinsic hub lability to fine-tune the stoichiometry of αβ heterooligomers for their dynamic localization within synapses in neurons.
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Affiliation(s)
- Chih-Ta Chien
- Department of Bioengineering, and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD, 20892, USA
| | - Henry Puhl
- Laboratory of Biophotonics and Quantum Biology, National Institutes on Alcohol, Abuse and Alcoholism, National Institutes of Health, Rockville, MD, 208952, USA
| | - Steven S Vogel
- Laboratory of Biophotonics and Quantum Biology, National Institutes on Alcohol, Abuse and Alcoholism, National Institutes of Health, Rockville, MD, 208952, USA
| | - Justin E Molloy
- The Francis Crick Institute, London, UK
- CMCB, Warwick Medical School, Coventry, CV4 7AL, UK
| | - Wah Chiu
- Department of Bioengineering, and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA.
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Light source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA.
| | - Shahid Khan
- Molecular Biology Consortium @ Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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2
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Khan S, Molloy JE, Puhl H, Schulman H, Vogel SS. Real-time single-molecule imaging of CaMKII-calmodulin interactions. Biophys J 2024; 123:824-838. [PMID: 38414237 DOI: 10.1016/j.bpj.2024.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/20/2023] [Accepted: 02/22/2024] [Indexed: 02/29/2024] Open
Abstract
The binding of calcium/calmodulin (CAM) to calcium/calmodulin-dependent protein kinase II (CaMKII) initiates an ATP-driven cascade that triggers CaMKII autophosphorylation. The autophosphorylation in turn increases the CaMKII affinity for CAM. Here, we studied the ATP dependence of CAM association with the actin-binding CaMKIIβ isoform using single-molecule total internal reflection fluorescence microscopy. Rhodamine-CAM associations/dissociations to surface-immobilized Venus-CaMKIIβ were resolved with 0.5 s resolution from video records, batch-processed with a custom algorithm. CAM occupancy was determined simultaneously with spot-photobleaching measurement of CaMKII holoenzyme stoichiometry. We show the ATP-dependent increase of the CAM association requires dimer formation for both the α and β isoforms. The study of mutant β holoenzymes revealed that the ATP-dependent increase in CAM affinity results in two distinct states. The phosphorylation-defective (T287.306-307A) holoenzyme resides only in the low-affinity state. CAM association is further reduced in the T287A holoenzyme relative to T287.306-307A. In the absence of ATP, the affinity of CAM for the T287.306-307A mutant and the wild-type monomer are comparable. The affinity of the ATP-binding impaired (K43R) mutant is even weaker. In ATP, the K43R holoenzyme resides in the low-affinity state. The phosphomimetic mutant (T287D) resides only in a 1000-fold higher-affinity state, with mean CAM occupancy of more than half of the 14-mer holoenzyme stoichiometry in picomolar CAM. ATP promotes T287D holoenzyme disassembly but does not elevate CAM occupancy. Single Poisson distributions characterized the ATP-dependent CAM occupancy of mutant holoenzymes. In contrast, the CAM occupancy of the wild-type population had a two-state distribution with both low- and high-affinity states represented. The low-affinity state was the dominant state, a result different from published in vitro assays. Differences in assay conditions can alter the balance between activating and inhibitory autophosphorylation. Bound ATP could be sufficient for CaMKII structural function, while antagonistic autophosphorylations may tune CaMKII kinase-regulated action-potential frequency decoding in vivo.
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Affiliation(s)
- Shahid Khan
- Molecular Biology Consortium at Lawrence Berkeley National Laboratory, Berkeley, California.
| | | | - Henry Puhl
- Laboratory of Biophotonics and Quantum Biology, National Institutes on Alcohol, Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Howard Schulman
- Panorama Research Institute, Sunnyvale, California; Stanford University School of Medicine, Stanford, California
| | - Steven S Vogel
- Laboratory of Biophotonics and Quantum Biology, National Institutes on Alcohol, Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
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3
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Coutinho A, Poveda JA, Renart ML. Conformational Dynamic Studies of Prokaryotic Potassium Channels Explored by Homo-FRET Methodologies. Methods Mol Biol 2024; 2796:35-72. [PMID: 38856894 DOI: 10.1007/978-1-0716-3818-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Fluorescence techniques have been widely used to shed light over the structure-function relationship of potassium channels for the last 40-50 years. In this chapter, we describe how a Förster resonance energy transfer between identical fluorophores (homo-FRET) approach can be applied to study the gating behavior of the prokaryotic channel KcsA. Two different gates have been described to control the K+ flux across the channel's pore, the helix-bundle crossing and the selectivity filter, located at the opposite sides of the channel transmembrane section. Both gates can be studied individually or by using a double-reporter system. Due to its homotetrameric structural arrangement, KcsA presents a high degree of symmetry that fulfills the first requisite to calculate intersubunit distances through this technique. The results obtained through this work have helped to uncover the conformational plasticity of the selectivity filter under different experimental conditions and the importance of its allosteric coupling to the opening of the activation (inner) gate. This biophysical approach usually requires low protein concentration and presents high sensitivity and reproducibility, complementing the high-resolution structural information provided by X-ray crystallography, cryo-EM, and NMR studies.
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Affiliation(s)
- Ana Coutinho
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Elche, Spain
| | - María Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Elche, Spain.
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4
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Nguyen TA, Puhl HL, Hines K, Liput DJ, Vogel SS. Binary-FRET reveals transient excited-state structure associated with activity-dependent CaMKII - NR2B binding and adaptation. Nat Commun 2022; 13:6335. [PMID: 36284097 PMCID: PMC9596428 DOI: 10.1038/s41467-022-33795-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/03/2022] [Indexed: 12/25/2022] Open
Abstract
Synaptic functions are mediated and modulated by a coordinated choreography of protein conformational changes and interactions in response to intracellular calcium dynamics. Time-lapse Förster resonance energy transfer can be used to study the dynamics of both conformational changes and protein-protein interactions simultaneously under physiological conditions if two resonance energy transfer reactions can be multiplexed. Binary-FRET is a technique developed to independently monitor the dynamics of calcium-calmodulin dependent protein kinase-II catalytic-domain pair separation in the holoenzyme, and its role in establishing activity-dependent holoenzyme affinity for the NR2B binding fragment of the N-methyl-D-aspartate receptor. Here we show that a transient excited-state intermediate exists where paired catalytic-domains in the holoenzyme first separate prior to subsequent NR2B association. Additionally, at non-saturating free calcium concentrations, our multiplexed approach reveals that the holoenzyme exhibits a biochemical form of plasticity, calcium dependent adaptation of T-site ligand binding affinity.
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Affiliation(s)
- Tuan A Nguyen
- Laboratory of Biophotonics and Quantum Biology, NIAAA, NIH, Bethesda, USA
| | - Henry L Puhl
- Laboratory of Biophotonics and Quantum Biology, NIAAA, NIH, Bethesda, USA
| | - Kirk Hines
- Laboratory of Biophotonics and Quantum Biology, NIAAA, NIH, Bethesda, USA
| | - Daniel J Liput
- Laboratory for Integrative Neuroscience, NIAAA, NIH, Bethesda, USA
| | - Steven S Vogel
- Laboratory of Biophotonics and Quantum Biology, NIAAA, NIH, Bethesda, USA.
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5
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Angert I, Karuka SR, Mansky LM, Mueller JD. Partitioning of ribonucleoprotein complexes from the cellular actin cortex. SCIENCE ADVANCES 2022; 8:eabj3236. [PMID: 35984883 PMCID: PMC9390997 DOI: 10.1126/sciadv.abj3236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
The cell cortex plays a crucial role in cell mechanics, signaling, and development. However, little is known about the influence of the cortical meshwork on the spatial distribution of cytoplasmic biomolecules. Here, we describe a fluorescence microscopy method with the capacity to infer the intracellular distribution of labeled biomolecules with subresolution accuracy. Unexpectedly, we find that RNA binding proteins are partially excluded from the cytoplasmic volume adjacent to the plasma membrane that corresponds to the actin cortex. Complementary diffusion measurements of RNA-protein complexes suggest that a rudimentary model based on excluded volume interactions can explain this partitioning effect. Our results suggest the actin cortex meshwork may play a role in regulating the biomolecular content of the volume immediately adjacent to the plasma membrane.
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Affiliation(s)
- Isaac Angert
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Siddarth Reddy Karuka
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Louis M. Mansky
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joachim D. Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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6
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Zernov N, Bezprozvanny I, Popugaeva E. CaMKIIβ knockdown decreases store-operated calcium entry in hippocampal dendritic spines. IBRO Neurosci Rep 2022; 12:90-97. [PMID: 35079728 PMCID: PMC8777283 DOI: 10.1016/j.ibneur.2022.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 01/13/2023] Open
Abstract
Calcium/calmodulin-dependent protein kinase II (CaMKII) and neuronal store-operated calcium entry (nSOCE) have been implicated in the development of Alzheimer's disease (AD). nSOCE is involved in regulation of dendritic spine shape, particularly in stability of mushroom spines that play role in formation of strong synapses. CaMKII is involved in regulation of induction of long-term potentiation, that is needed for shaping of memory. In the present study, we demonstrated that inhibition of kinase activity of CaMKII by KN-62 decreases nSOCE amplitude in soma of primary hippocampal neurons. We have shown that knockdown of CaMKIIβ leads to the downregulation of nSOCE in dendritic spines. In agreement with previously published data, we have also observed that CaMKIIβ knockdown causes mushroom spine loss in primary hippocampal culture. The effect of CaMKIIβ knockdown on the nSOCE may be associated with a decrease of dendritic spine head size.
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Affiliation(s)
- Nikita Zernov
- Peter the Great St.Petersburg Polytechnic University, Laboratory of Molecular Neurodegeneration, St.Petersburg, Russia
| | - Ilya Bezprozvanny
- Peter the Great St.Petersburg Polytechnic University, Laboratory of Molecular Neurodegeneration, St.Petersburg, Russia
- UT Southwestern Medical Center, Department of Physiology, Dallas, USA
| | - Elena Popugaeva
- Peter the Great St.Petersburg Polytechnic University, Laboratory of Molecular Neurodegeneration, St.Petersburg, Russia
- Corresponding author.
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7
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Khan S. Conformational spread drives the evolution of the calcium-calmodulin protein kinase II. Sci Rep 2022; 12:8499. [PMID: 35589775 PMCID: PMC9120016 DOI: 10.1038/s41598-022-12090-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 05/03/2022] [Indexed: 11/17/2022] Open
Abstract
The calcium calmodulin (Ca2+/CaM) dependent protein kinase II (CaMKII) decodes Ca2+ frequency oscillations. The CaMKIIα isoform is predominantly expressed in the brain and has a central role in learning. I matched residue and organismal evolution with collective motions deduced from the atomic structure of the human CaMKIIα holoenzyme to learn how its ring architecture abets function. Protein dynamic simulations showed its peripheral kinase domains (KDs) are conformationally coupled via lateral spread along the central hub. The underlying β-sheet motions in the hub or association domain (AD) were deconvolved into dynamic couplings based on mutual information. They mapped onto a coevolved residue network to partition the AD into two distinct sectors. A second, energetically stressed sector was added to ancient bacterial enzyme dimers for assembly of the ringed hub. The continued evolution of the holoenzyme after AD–KD fusion targeted the sector’s ring contacts coupled to the KD. Among isoforms, the α isoform emerged last and, it alone, mutated rapidly after the poikilotherm–homeotherm jump to match the evolution of memory. The correlation between dynamics and evolution of the CaMKII AD argues single residue substitutions fine-tune hub conformational spread. The fine-tuning could increase CaMKIIα Ca2+ frequency response range for complex learning functions.
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Affiliation(s)
- Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,SBA School of Science and Engineering, LUMS, Lahore, Pakistan. .,Laboratory of Cell Biology, NINDS, NIH, Bethesda, MD, 20892, USA.
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8
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Weidtkamp-Peters S, Rehwald S, Stahl Y. Homo-FRET Imaging to Study Protein-Protein Interaction and Complex Formation in Plants. Methods Mol Biol 2022; 2379:197-208. [PMID: 35188664 DOI: 10.1007/978-1-0716-1791-5_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein-protein interactions in living plant cells can be measured by changes in fluorescence anisotropy due to homo-FRET (Förster Resonance Energy Transfer). Here, the energy transfer between identical fluorophores, e.g., enhanced green fluorescent protein (EGFP) fused to a protein of interest, serves as a read-out for protein interaction and clustering. By applying homo-FRET imaging, not only dimeric complexes, but also bigger homomeric complex formation can be followed in vivo at high spatial and temporal resolution. Therefore, this method provides a powerful tool to investigate changes in complex formation over time in their natural environment with high precision at a subcellular level. Here, we describe the necessary theoretical background and how homo-FRET imaging is practically carried out. We also discuss potential pitfalls and points of consideration.
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Affiliation(s)
| | | | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany.
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9
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Buonarati OR, Miller AP, Coultrap SJ, Bayer KU, Reichow SL. Conserved and divergent features of neuronal CaMKII holoenzyme structure, function, and high-order assembly. Cell Rep 2021; 37:110168. [PMID: 34965414 PMCID: PMC8985225 DOI: 10.1016/j.celrep.2021.110168] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/30/2021] [Accepted: 12/03/2021] [Indexed: 11/23/2022] Open
Abstract
Neuronal CaMKII holoenzymes (α and β isoforms) enable molecular signal computation underlying learning and memory but also mediate excitotoxic neuronal death. Here, we provide a comparative analysis of these signaling devices, using single-particle electron microscopy (EM) in combination with biochemical and live-cell imaging studies. In the basal state, both isoforms assemble mainly as 12-mers (but also 14-mers and even 16-mers for the β isoform). CaMKIIα and β isoforms adopt an ensemble of extended activatable states (with average radius of 12.6 versus 16.8 nm, respectively), characterized by multiple transient intra- and inter-holoenzyme interactions associated with distinct functional properties. The extended state of CaMKIIβ allows direct resolution of intra-holoenzyme kinase domain dimers. These dimers could enable cooperative activation by calmodulin, which is observed for both isoforms. High-order CaMKII clustering mediated by inter-holoenzyme kinase domain dimerization is reduced for the β isoform for both basal and excitotoxicity-induced clusters, both in vitro and in neurons. The CaMKII holoenzyme enables neuronal signal computation. In a comparative structure-function analysis of the neuronal α and β isoforms, Buonarati et al. find evidence for kinase domain dimers within the holoenzyme that enable a cooperative activation mechanism in both isoforms and inter-holoenzyme interactions that enable high-order aggregate formation under ischemic conditions.
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Affiliation(s)
- Olivia R Buonarati
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Adam P Miller
- Department of Chemistry, Portland State University, Portland, OR 97201, USA
| | - Steven J Coultrap
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - K Ulrich Bayer
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Steve L Reichow
- Department of Chemistry, Portland State University, Portland, OR 97201, USA.
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10
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Díaz-García C, Renart ML, Poveda JA, Giudici AM, González-Ros JM, Prieto M, Coutinho A. Probing the Structural Dynamics of the Activation Gate of KcsA Using Homo-FRET Measurements. Int J Mol Sci 2021; 22:ijms222111954. [PMID: 34769384 PMCID: PMC8584343 DOI: 10.3390/ijms222111954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/18/2021] [Accepted: 10/29/2021] [Indexed: 12/16/2022] Open
Abstract
The allosteric coupling between activation and inactivation processes is a common feature observed in K+ channels. Particularly, in the prokaryotic KcsA channel the K+ conduction process is controlled by the inner gate, which is activated by acidic pH, and by the selectivity filter (SF) or outer gate, which can adopt non-conductive or conductive states. In a previous study, a single tryptophan mutant channel (W67 KcsA) enabled us to investigate the SF dynamics using time-resolved homo-Förster Resonance Energy Transfer (homo-FRET) measurements. Here, the conformational changes of both gates were simultaneously monitored after labelling the G116C position with tetramethylrhodamine (TMR) within a W67 KcsA background. At a high degree of protein labeling, fluorescence anisotropy measurements showed that the pH-induced KcsA gating elicited a variation in the homo-FRET efficiency among the conjugated TMR dyes (TMR homo-FRET), while the conformation of the SF was simultaneously tracked (W67 homo-FRET). The dependence of the activation pKa of the inner gate with the ion occupancy of the SF unequivocally confirmed the allosteric communication between the two gates of KcsA. This simple TMR homo-FRET based ratiometric assay can be easily extended to study the conformational dynamics associated with the gating of other ion channels and their modulation.
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Affiliation(s)
- Clara Díaz-García
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Maria Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
- Correspondence: (M.L.R.); (A.C.)
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - Ana Marcela Giudici
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - José M. González-Ros
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - Manuel Prieto
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Ana Coutinho
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: (M.L.R.); (A.C.)
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11
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Zoidl GR, Spray DC. The Roles of Calmodulin and CaMKII in Cx36 Plasticity. Int J Mol Sci 2021; 22:4473. [PMID: 33922931 PMCID: PMC8123330 DOI: 10.3390/ijms22094473] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/17/2021] [Accepted: 04/20/2021] [Indexed: 01/07/2023] Open
Abstract
Anatomical and electrophysiological evidence that gap junctions and electrical coupling occur between neurons was initially confined to invertebrates and nonmammals and was thought to be a primitive form of synaptic transmission. More recent studies revealed that electrical communication is common in the mammalian central nervous system (CNS), often coexisting with chemical synaptic transmission. The subsequent progress indicated that electrical synapses formed by the gap junction protein connexin-36 (Cx36) and its paralogs in nonmammals constitute vital elements in mammalian and fish synaptic circuitry. They govern the collective activity of ensembles of coupled neurons, and Cx36 gap junctions endow them with enormous adaptive plasticity, like that seen at chemical synapses. Moreover, they orchestrate the synchronized neuronal network activity and rhythmic oscillations that underlie the fundamental integrative processes, such as memory and learning. Here, we review the available mechanistic evidence and models that argue for the essential roles of calcium, calmodulin, and the Ca2+/calmodulin-dependent protein kinase II in integrating calcium signals to modulate the strength of electrical synapses through interactions with the gap junction protein Cx36.
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Affiliation(s)
- Georg R. Zoidl
- Department of Biology & Center for Vision Research (CVR), York University, Toronto, ON M3J 1P3, Canada
| | - David C. Spray
- Dominick P. Purpura Department of Neuroscience & Department of Medicine (Cardiology), Albert Einstein College of Medicine, New York, NY 10461, USA;
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12
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Rivas S, Hanif K, Chakouri N, Ben-Johny M. Probing ion channel macromolecular interactions using fluorescence resonance energy transfer. Methods Enzymol 2021; 653:319-347. [PMID: 34099178 DOI: 10.1016/bs.mie.2021.01.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ion channels are macromolecular complexes whose functions are exquisitely tuned by interacting proteins. Fluorescence resonance energy transfer (FRET) is a powerful methodology that is adept at quantifying ion channel protein-protein interactions in living cells. For FRET experiments, the interacting partners are tagged with appropriate donor and acceptor fluorescent proteins. If the fluorescently-labeled molecules are in close proximity, then photoexcitation of the donor results in non-radiative energy transfer to the acceptor, and subsequent fluorescence emission of the acceptor. The stoichiometry of ion channel interactions and their relative binding affinities can be deduced by quantifying both the FRET efficiency and the total number of donors and acceptors in a given cell. In this chapter, we discuss general considerations for FRET analysis of biological interactions, various strategies for estimating FRET efficiencies, and detailed protocols for construction of binding curves and determination of stoichiometry. We focus on implementation of FRET assays using a flow cytometer given its amenability for high-throughput data acquisition, enhanced accessibility, and robust analysis. This versatile methodology permits mechanistic dissection of dynamic changes in ion channel interactions.
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Affiliation(s)
- Sharen Rivas
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States
| | | | - Nourdine Chakouri
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States
| | - Manu Ben-Johny
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States.
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13
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Liput DJ, Nguyen TA, Augustin SM, Lee JO, Vogel SS. A Guide to Fluorescence Lifetime Microscopy and Förster's Resonance Energy Transfer in Neuroscience. CURRENT PROTOCOLS IN NEUROSCIENCE 2020; 94:e108. [PMID: 33232577 PMCID: PMC8274369 DOI: 10.1002/cpns.108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fluorescence lifetime microscopy (FLIM) and Förster's resonance energy transfer (FRET) are advanced optical tools that neuroscientists can employ to interrogate the structure and function of complex biological systems in vitro and in vivo using light. In neurobiology they are primarily used to study protein-protein interactions, to study conformational changes in protein complexes, and to monitor genetically encoded FRET-based biosensors. These methods are ideally suited to optically monitor changes in neurons that are triggered optogenetically. Utilization of this technique by neuroscientists has been limited, since a broad understanding of FLIM and FRET requires familiarity with the interactions of light and matter on a quantum mechanical level, and because the ultra-fast instrumentation used to measure fluorescent lifetimes and resonance energy transfer are more at home in a physics lab than in a biology lab. In this overview, we aim to help neuroscientists overcome these obstacles and thus feel more comfortable with the FLIM-FRET method. Our goal is to aid researchers in the neuroscience community to achieve a better understanding of the fundamentals of FLIM-FRET and encourage them to fully leverage its powerful ability as a research tool. Published 2020. U.S. Government.
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Affiliation(s)
- Daniel J. Liput
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Tuan A. Nguyen
- Laboratory of Biophotonics and Quantum Biology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Shana M. Augustin
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Jeong Oen Lee
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Steven S. Vogel
- Laboratory of Biophotonics and Quantum Biology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
- Corresponding author:
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14
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Bhattacharyya M, Karandur D, Kuriyan J. Structural Insights into the Regulation of Ca 2+/Calmodulin-Dependent Protein Kinase II (CaMKII). Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035147. [PMID: 31653643 DOI: 10.1101/cshperspect.a035147] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Ca2+/calmodulin-dependent protein kinase II (CaMKII) is a highly conserved serine/threonine kinase that is ubiquitously expressed throughout the human body. Specialized isoforms of CaMKII play key roles in neuronal and cardiac signaling. The distinctive holoenzyme architecture of CaMKII, with 12-14 kinase domains attached by flexible linkers to a central hub, poses formidable challenges for structural characterization. Nevertheless, progress in determining the structural mechanisms underlying CaMKII functions has come from studying the kinase domain and the hub separately, as well as from a recent electron microscopic investigation of the intact holoenzyme. In this review, we discuss our current understanding of the structure of CaMKII. We also discuss the intriguing finding that the CaMKII holoenzyme can undergo activation-triggered subunit exchange, a process that has implications for the potentiation and perpetuation of CaMKII activity.
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Affiliation(s)
- Moitrayee Bhattacharyya
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720.,Howard Hughes Medical Institute, University of California, Berkeley, California 94720
| | - Deepti Karandur
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720.,Howard Hughes Medical Institute, University of California, Berkeley, California 94720
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720.,Howard Hughes Medical Institute, University of California, Berkeley, California 94720.,Department of Chemistry, University of California, Berkeley, California 94720.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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15
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Glu 60 of α-Calcium/calmodulin dependent protein kinase II mediates crosstalk between the regulatory T-site and protein substrate binding region of the active site. Arch Biochem Biophys 2020; 685:108348. [PMID: 32198047 DOI: 10.1016/j.abb.2020.108348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 11/20/2022]
Abstract
Memory formation transpires to be by activation and persistent modification of synapses. A chain of biochemical events accompany synaptic activation and culminate in memory formation. These biochemical events are steered by interplay and modulation of various synaptic proteins, achieved by conformational changes and phosphorylation/dephosphorylation of these proteins. Calcium/calmodulin dependent protein kinase II (CaMKII) and N-methyl-d-aspartate receptors (NMDARs) are synaptic proteins whose interactions play a pivotal role in learning and memory process. Catalytic activity of CaMKII is modulated upon its interaction with the GluN2B subunit of NMDAR. The structural basis of this interaction is not clearly understood. We have investigated the role of Glu60 of α-CaMKII, a conserved residue present in the ATP binding region of kinases, in the regulation of catalysis of CaMKII by GluN2B. Mutation of Glu60 to Gly exerts different effects on the kinetic parameters of phosphorylation of GluN2B and GluN2A, of which only GluN2B binds to the T-site of CaMKII. GluN2B induced modulation of the kinetic parameters of peptide substrate was altered in the E60G mutant. The mutation almost abolished the modulation of the apparent Km value for protein substrate. However, although kinetic parameters for ATP were altered by mutating Glu60, modulation of the apparent Km value for ATP by GluN2B seen in WT was exhibited by the E60G mutant of α-CaMKII. Hence our results posit that the communication of the T-site of CaMKII with protein substrate binding region of active site is mediated through Glu60 while the communication of the T-site with the ATP binding region is not entirely dependent on Glu60.
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16
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Hennen J, Kohler J, Karuka SR, Saunders CA, Luxton GWG, Mueller JD. Differentiating Luminal and Membrane-Associated Nuclear Envelope Proteins. Biophys J 2020; 118:2385-2399. [PMID: 32304637 DOI: 10.1016/j.bpj.2020.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/09/2020] [Accepted: 03/27/2020] [Indexed: 10/24/2022] Open
Abstract
The nuclear envelope (NE) consists of two concentric nuclear membranes separated by the lumen, an ∼40-nm-wide fluid layer. NE proteins are implicated in important cellular processes ranging from gene expression to nuclear positioning. Although recent progress has been achieved in quantifying the assembly states of NE proteins in their native environment with fluorescence fluctuation spectroscopy, these studies raised questions regarding the association of NE proteins with nuclear membranes during the assembly process. Monitoring the interaction of proteins with membranes is important because the binding event is often associated with conformational changes that are critical to cellular signaling pathways. Unfortunately, the close physical proximity of both membranes poses a severe experimental challenge in distinguishing luminal and membrane-associated NE proteins. This study seeks to address this problem by introducing new, to our knowledge, fluorescence-based assays that overcome the restrictions imposed by the NE environment. We found that luminal proteins violate the Stokes-Einstein relation, which eliminates a straightforward use of protein mobility as a marker of membrane association within the NE. However, a surprising anomaly in the temperature-dependent mobility of luminal proteins was observed, which was developed into an assay for distinguishing between soluble and membrane-bound NE proteins. We further introduced a second independent tool for distinguishing both protein populations by harnessing the previously reported undulations of the nuclear membranes. These membrane undulations introduce local volume changes that produce an additional fluorescence fluctuation signal for luminal, but not for membrane-bound, proteins. After testing both methods using simple model systems, we apply the two assays to investigate a previously proposed model of membrane association for the luminal domain of SUN2, a constituent protein of the linker of nucleoskeleton and cytoskeleton complex. Finally, we investigate the effect of C- and N-terminal tagging of the luminal ATPase torsinA on its ability to associate with nuclear membranes.
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Affiliation(s)
- Jared Hennen
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota
| | - John Kohler
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota
| | | | - Cosmo A Saunders
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - G W Gant Luxton
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Joachim D Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota; Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota.
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17
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Imaging of fluorescence anisotropy during photoswitching provides a simple readout for protein self-association. Nat Commun 2020; 11:21. [PMID: 31911590 PMCID: PMC6946710 DOI: 10.1038/s41467-019-13843-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/03/2019] [Indexed: 12/02/2022] Open
Abstract
Monitoring of protein oligomerization has benefited greatly from Förster Resonance Energy Transfer (FRET) measurements. Although donors and acceptors are typically fluorescent molecules with different spectra, homo-FRET can occur between fluorescent molecules of the same type if the emission spectrum overlaps with the absorption spectrum. Here, we describe homo-FRET measurements by monitoring anisotropy changes in photoswitchable fluorescent proteins while photoswitching to the off state. These offer the capability to estimate anisotropy in the same specimen during homo-FRET as well as non-FRET conditions. We demonstrate photoswitching anisotropy FRET (psAFRET) with a number of test chimeras and example oligomeric complexes inside living cells. We also present an equation derived from FRET and anisotropy equations which converts anisotropy changes into a factor we call delta r FRET (drFRET). This is analogous to an energy transfer efficiency and allows experiments performed on a given homo-FRET pair to be more easily compared across different optical configurations. Performing homo-FRET measurements in cells using a fluorescence microscope is challenging, especially when using high numerical aperture objective lenses. Here the authors present a method for improved homo-FRET measurements based on anisotropy changes in photoswitchable fluorescent proteins.
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18
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Kim Y, Puhl HL, Chen E, Taumoefolau GH, Nguyen TA, Kliger DS, Blank PS, Vogel SS. Venus A206 Dimers Behave Coherently at Room Temperature. Biophys J 2019; 116:1918-1930. [PMID: 31060812 DOI: 10.1016/j.bpj.2019.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/28/2019] [Accepted: 04/16/2019] [Indexed: 12/11/2022] Open
Abstract
Fluorescent proteins (FPs) have revolutionized cell biology by allowing genetic tagging of specific proteins inside living cells. In conjunction with Förster's resonance energy transfer (FRET) measurements, FP-tagged proteins can be used to study protein-protein interactions and estimate distances between tagged proteins. FRET is mediated by weak Coulombic dipole-dipole coupling of donor and acceptor fluorophores that behave independently, with energy hopping discretely and incoherently between fluorophores. Stronger dipole-dipole coupling can mediate excitonic coupling in which excitation energy is distributed near instantaneously between coherently interacting excited states that behave as a single quantum entity. The interpretation of FP energy transfer measurements to estimate separation often assumes that donors and acceptors are very weakly coupled and therefore use a FRET mechanism. This assumption is considered reasonable as close fluorophore proximity, typically associated with strong excitonic coupling, is limited by the FP β-barrel structure. Furthermore, physiological temperatures promote rapid vibrational dephasing associated with a rapid decoherence of fluorophore-excited states. Recently, FP dephasing times that are 50 times slower than traditional organic fluorophores have been measured, raising the possibility that evolution has shaped FPs to allow stronger than expected coupling under physiological conditions. In this study, we test if excitonic coupling between FPs is possible at physiological temperatures. FRET and excitonic coupling can be distinguished by monitoring spectral changes associated with fluorophore dimerization. The weak coupling mediating FRET should not cause a change in fluorophore absorption, whereas strong excitonic coupling causes Davydov splitting. Circular dichroism spectroscopy revealed Davydov splitting when the yellow FP VenusA206 dimerizes, and a novel approach combining photon antibunching and fluorescence correlation spectroscopy was used to confirm that the two fluorophores in a VenusA206 homodimer behave as a single-photon emitter. We conclude that excitonic coupling between VenusA206 fluorophores is possible at physiological temperatures.
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Affiliation(s)
- Youngchan Kim
- Section on Cellular Biophotonics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Henry L Puhl
- Section on Cellular Biophotonics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Eefei Chen
- Chemistry and Biochemistry Department, University of California Santa Cruz, Santa Cruz, California
| | - Grace H Taumoefolau
- Section on Cellular Biophotonics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Tuan A Nguyen
- Section on Cellular Biophotonics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - David S Kliger
- Chemistry and Biochemistry Department, University of California Santa Cruz, Santa Cruz, California
| | - Paul S Blank
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Steven S Vogel
- Section on Cellular Biophotonics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland.
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19
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Conformational plasticity in the KcsA potassium channel pore helix revealed by homo-FRET studies. Sci Rep 2019; 9:6215. [PMID: 30996281 PMCID: PMC6470172 DOI: 10.1038/s41598-019-42405-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/29/2019] [Indexed: 11/24/2022] Open
Abstract
Potassium channels selectivity filter (SF) conformation is modulated by several factors, including ion-protein and protein-protein interactions. Here, we investigate the SF dynamics of a single Trp mutant of the potassium channel KcsA (W67) using polarized time-resolved fluorescence measurements. For the first time, an analytical framework is reported to analyze the homo-Förster resonance energy transfer (homo-FRET) within a symmetric tetrameric protein with a square geometry. We found that in the closed state (pH 7), the W67-W67 intersubunit distances become shorter as the average ion occupancy of the SF increases according to cation type and concentration. The hypothesis that the inactivated SF at pH 4 is structurally similar to its collapsed state, detected at low K+, pH 7, was ruled out, emphasizing the critical role played by the S2 binding site in the inactivation process of KcsA. This homo-FRET approach provides complementary information to X-ray crystallography in which the protein conformational dynamics is usually compromised.
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20
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Leopold HJ, Leighton R, Schwarz J, Boersma AJ, Sheets ED, Heikal AA. Crowding Effects on Energy-Transfer Efficiencies of Hetero-FRET Probes As Measured Using Time-Resolved Fluorescence Anisotropy. J Phys Chem B 2019; 123:379-393. [PMID: 30571116 DOI: 10.1021/acs.jpcb.8b09829] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Macromolecular crowding is prevalent in all living cells due to the presence of large biomolecules and organelles. Cellular crowding is heterogeneous and is known to influence biomolecular transport, biochemical reactions, and protein folding. Emerging evidence suggests that some cell pathologies may be correlated with compartmentalized crowding. As a result, there is a need for robust biosensors that are sensitive to crowding as well as quantitative, noninvasive fluorescence methods that are compatible with living cells studies. Here, we have developed a model that describes the rotational dynamics of hetero-Förster resonance energy transfer (FRET) biosensors as a means to determine the energy-transfer efficiency and donor-acceptor distance. The model was tested on wavelength-dependent time-resolved fluorescence anisotropy of hetero-FRET probes (mCerulean3-linker-mCitrine) with variable linkers in both crowded (Ficoll-70) and viscous (glycerol) solutions at room temperature. Our results indicate that the energy-transfer efficiencies of these FRET probes increase as the linker becomes shorter and more flexible in pure buffer at room temperature. In addition, the FRET probes favor compact structures with enhanced energy-transfer efficiencies and a shorter donor-acceptor distance in the heterogeneous, polymer-crowded environment due to steric hindrance. In contrast, the extended conformation of these FRET probes is more favorable in viscous, homogeneous environments with a reduced energy-transfer efficiency compared to those in pure buffer, which we attribute to reduced structural fluctuations of the mCerulean3-mCitrine FRET pair in the glycerol-enriched buffer. Our results represent an important step toward the application of quantitative and noninvasive time-resolved fluorescence anisotropy of hetero-FRET probes to investigate compartmentalized macromolecular crowding and protein-protein interactions in living cells as well as in controlled environments.
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Affiliation(s)
- Hannah J Leopold
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Ryan Leighton
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Jacob Schwarz
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Arnold J Boersma
- DW1-Leibniz Institute for Interactive Materials , Forckenbeckstr. 50 , 52056 Aachen , Germany
| | - Erin D Sheets
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Ahmed A Heikal
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
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21
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Snell NE, Rao VP, Seckinger KM, Liang J, Leser J, Mancini AE, Rizzo MA. Homotransfer of FRET Reporters for Live Cell Imaging. BIOSENSORS-BASEL 2018; 8:bios8040089. [PMID: 30314323 PMCID: PMC6316388 DOI: 10.3390/bios8040089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 09/27/2018] [Accepted: 10/10/2018] [Indexed: 01/01/2023]
Abstract
Förster resonance energy transfer (FRET) between fluorophores of the same species was recognized in the early to mid-1900s, well before modern heterotransfer applications. Recently, homotransfer FRET principles have re-emerged in biosensors that incorporate genetically encoded fluorescent proteins. Homotransfer offers distinct advantages over the standard heterotransfer FRET method, some of which are related to the use of fluorescence polarization microscopy to quantify FRET between two fluorophores of identical color. These include enhanced signal-to-noise, greater compatibility with other optical sensors and modulators, and new design strategies based upon the clustering or dimerization of singly-labeled sensors. Here, we discuss the theoretical basis for measuring homotransfer using polarization microscopy, procedures for data collection and processing, and we review the existing genetically-encoded homotransfer biosensors.
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Affiliation(s)
- Nicole E Snell
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Vishnu P Rao
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Kendra M Seckinger
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Junyi Liang
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Jenna Leser
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Allison E Mancini
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - M A Rizzo
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
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22
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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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23
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Park SW, Persaud SD, Ogokeh S, Meyers TA, Townsend D, Wei LN. CRABP1 protects the heart from isoproterenol-induced acute and chronic remodeling. J Endocrinol 2018; 236:151-165. [PMID: 29371236 PMCID: PMC5815894 DOI: 10.1530/joe-17-0613] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 01/25/2018] [Indexed: 01/09/2023]
Abstract
Excessive and/or persistent activation of calcium-calmodulin protein kinase II (CaMKII) is detrimental in acute and chronic cardiac injury. However, intrinsic regulators of CaMKII activity are poorly understood. We find that cellular retinoic acid-binding protein 1 (CRABP1) directly interacts with CaMKII and uncover a functional role for CRABP1 in regulating CaMKII activation. We generated Crabp1-null mice (CKO) in C57BL/6J background for pathophysiological studies. CKO mice develop hypertrophy as adults, exhibiting significant left ventricular dilation with reduced ejection fraction at the baseline cardiac function. Interestingly, CKO mice have elevated basal CaMKII phosphorylation at T287, and phosphorylation on its substrate phospholamban (PLN) at T17. Acute isoproterenol (ISO) challenge (80 mg/kg two doses in 1 day) causes more severe apoptosis and necrosis in CKO hearts, and treatment with a CaMKII inhibitor KN-93 protects CKO mice from this injury. Chronic (30 mg/kg/day) ISO challenge also significantly increases hypertrophy and fibrosis in CKO mice as compared to WT. In wild-type mice, CRABP1 expression is increased in early stages of ISO challenge and eventually reduces to the basal level. Mechanistically, CRABP1 directly inhibits CaMKII by competing with calmodulin (CaM) for CaMKII interaction. This study demonstrates increased susceptibility of CKO mice to ISO-induced acute and chronic cardiac injury due to, at least in part, elevated CaMKII activity. Deleting Crabp1 results in reduced baseline cardiac function and aggravated damage challenged with acute and persistent β-adrenergic stimulation. This is the first report of a physiological role of CRABP1 as an endogenous regulator of CaMKII, which protects the heart from ISO-induced damage.
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Affiliation(s)
- Sung Wook Park
- Department of PharmacologyUniversity of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Shawna D Persaud
- Department of PharmacologyUniversity of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Stanislas Ogokeh
- Department of PharmacologyUniversity of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Tatyana A Meyers
- Department of Integrative Biology and PhysiologyUniversity of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - DeWayne Townsend
- Department of Integrative Biology and PhysiologyUniversity of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Li-Na Wei
- Department of PharmacologyUniversity of Minnesota Medical School, Minneapolis, Minnesota, USA
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24
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Samodelov SL, Zurbriggen MD. Quantitatively Understanding Plant Signaling: Novel Theoretical-Experimental Approaches. TRENDS IN PLANT SCIENCE 2017; 22:685-704. [PMID: 28668509 DOI: 10.1016/j.tplants.2017.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
With the need to respond to and integrate a multitude of external and internal stimuli, plant signaling is highly complex, exhibiting signaling component redundancy and high interconnectedness between individual pathways. We review here novel theoretical-experimental approaches in manipulating plant signaling towards the goal of a comprehensive understanding and targeted quantitative control of plant processes. We highlight approaches taken in the field of synthetic biology used in other systems and discuss their applicability in plants. Finally, we introduce existing tools for the quantitative analysis and monitoring of plant signaling and the integration of experimentally obtained quantitative data into mathematical models. Incorporating principles of synthetic biology into plant sciences more widely will lead this field forward in both fundamental and applied research.
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Affiliation(s)
- Sophia L Samodelov
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany.
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25
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Deciphering CaMKII Multimerization Using Fluorescence Correlation Spectroscopy and Homo-FRET Analysis. Biophys J 2017; 112:1270-1281. [PMID: 28355553 DOI: 10.1016/j.bpj.2017.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/03/2017] [Accepted: 02/03/2017] [Indexed: 11/20/2022] Open
Abstract
While kinases are typically composed of one or two subunits, calcium-calmodulin (CaM)-dependent protein kinase II (CaMKII) is composed of 8-14 subunits arranged as pairs around a central core. It is not clear if the CaMKII holoenzyme functions as an assembly of independent subunits, as catalytic pairs, or as a single unit. One strategy to address this question is to genetically engineer monomeric and dimeric CaMKII and evaluate how their activity compares to the wild-type (WT) holoenzyme. Here a technique that combines fluorescence correlation spectroscopy and homo-FRET analysis was used to characterize assembly mutants of Venus-tagged CaMKIIα to identify a dimeric CaMKII. Spectroscopy was then used to compare how holoenzyme structure and function changes in response to activation with CaM in the dimeric mutant, WT-holoenzyme, and a monomeric CaMKII oligomerization-domain deletion mutant control. CaM triggered an increase in hydrodynamic volume in both WT and dimeric CaMKII without altering subunit stoichiometry or the net homo-FRET between Venus-tagged catalytic domains. Biochemical analysis revealed that the dimeric mutant also functioned like WT holoenzyme in terms of its kinase activity with an exogenous substrate, and for endogenous T286 autophosphorylation. We conclude that the fundamental functional units of CaMKII holoenzyme are paired catalytic-domains.
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The CaMKII holoenzyme structure in activation-competent conformations. Nat Commun 2017; 8:15742. [PMID: 28589927 PMCID: PMC5467236 DOI: 10.1038/ncomms15742] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 04/25/2017] [Indexed: 12/18/2022] Open
Abstract
The Ca2+/calmodulin-dependent protein kinase II (CaMKII) assembles into large 12-meric holoenzymes, which is thought to enable regulatory processes required for synaptic plasticity underlying learning, memory and cognition. Here we used single particle electron microscopy (EM) to determine a pseudoatomic model of the CaMKIIα holoenzyme in an extended and activation-competent conformation. The holoenzyme is organized by a rigid central hub complex, while positioning of the kinase domains is highly flexible, revealing dynamic holoenzymes ranging from 15–35 nm in diameter. While most kinase domains are ordered independently, ∼20% appear to form dimers and <3% are consistent with a compact conformation. An additional level of plasticity is revealed by a small fraction of bona-fide 14-mers (<4%) that may enable subunit exchange. Biochemical and cellular FRET studies confirm that the extended state of CaMKIIα resolved by EM is the predominant form of the holoenzyme, even under molecular crowding conditions. Ca2+/calmodulin-dependent protein kinase II (CaMKII) forms a 12 subunit holoenzyme central to synaptic plasticity. Here the authors report a 3D structure of the CaMKII holoenzyme in an activation-competent state obtained by single particle EM, and suggest a role for the intrinsically disordered linker domain in facilitating cooperative activation.
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Currie M, Leopold H, Schwarz J, Boersma AJ, Sheets ED, Heikal AA. Fluorescence Dynamics of a FRET Probe Designed for Crowding Studies. J Phys Chem B 2017; 121:5688-5698. [DOI: 10.1021/acs.jpcb.7b01306] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Megan Currie
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Hannah Leopold
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Jacob Schwarz
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Arnold J. Boersma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Erin D. Sheets
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
| | - Ahmed A. Heikal
- Department
of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, Minnesota 55812, United States
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Khan S, Conte I, Carter T, Bayer KU, Molloy JE. Multiple CaMKII Binding Modes to the Actin Cytoskeleton Revealed by Single-Molecule Imaging. Biophys J 2016; 111:395-408. [PMID: 27463141 PMCID: PMC4968397 DOI: 10.1016/j.bpj.2016.06.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 06/07/2016] [Accepted: 06/09/2016] [Indexed: 11/22/2022] Open
Abstract
Localization of the Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) to dendritic spine synapses is determined in part by the actin cytoskeleton. We determined binding of GFP-tagged CaMKII to tag-RFP-labeled actin cytoskeleton within live cells using total internal reflection fluorescence microscopy and single-molecule tracking. Stepwise photobleaching showed that CaMKII formed oligomeric complexes. Photoactivation experiments demonstrated that diffusion out of the evanescent field determined the track lifetimes. Latrunculin treatment triggered a coupled loss of actin stress fibers and the colocalized, long-lived CaMKII tracks. The CaMKIIα (α) isoform, which was previously thought to lack F-actin interactions, also showed binding, but this was threefold weaker than that observed for CaMKIIβ (β). The βE' splice variant bound more weakly than α, showing that binding by β depends critically on the interdomain linker. The mutations βT287D and αT286D, which mimic autophosphorylation states, also abolished F-actin binding. Autophosphorylation triggers autonomous CaMKII activity, but does not impair GluN2B binding, another important synaptic protein interaction of CaMKII. The CaMKII inhibitor tatCN21 or CaMKII mutations that inhibit GluN2B association by blocking binding of ATP (βK43R and αK42M) or Ca(2+)/calmodulin (βA303R) had no effect on the interaction with F-actin. These results provide the first rationale for the reduced synaptic spine localization of the αT286D mutant, indicating that transient F-actin binding contributes to the synaptic localization of the CaMKIIα isoform. The track lifetime distributions had a stretched exponential form consistent with a heterogeneously diffusing population. This heterogeneity suggests that CaMKII adopts different F-actin binding modes, which is most easily rationalized by multiple subunit contacts between the CaMKII dodecamer and the F-actin cytoskeleton that stabilize the initial weak (micromolar) monovalent interaction.
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Affiliation(s)
- Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, California.
| | - Ianina Conte
- Cardiovascular and Cell Science Research Institute, St. George's University of London, London, UK
| | - Tom Carter
- Cell Biology and Genetics, St. George's University of London, London, UK
| | - K Ulrich Bayer
- Department of Pharmacology, University of Colorado Denver, Aurora, Colorado
| | - Justin E Molloy
- The Francis Crick Institute, Mill Hill Laboratory, London, UK
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Nguyen TA, Sarkar P, Veetil JV, Davis KA, Puhl HL, Vogel SS. Covert Changes in CaMKII Holoenzyme Structure Identified for Activation and Subsequent Interactions. Biophys J 2016; 108:2158-70. [PMID: 25954874 DOI: 10.1016/j.bpj.2015.03.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/18/2015] [Accepted: 03/10/2015] [Indexed: 11/29/2022] Open
Abstract
Between 8 to 14 calcium-calmodulin (Ca(2+)/CaM) dependent protein kinase-II (CaMKII) subunits form a complex that modulates synaptic activity. In living cells, the autoinhibited holoenzyme is organized as catalytic-domain pairs distributed around a central oligomerization-domain core. The functional significance of catalytic-domain pairing is not known. In a provocative model, catalytic-domain pairing was hypothesized to prevent ATP access to catalytic sites. If correct, kinase-activity would require catalytic-domain pair separation. Simultaneous homo-FRET and fluorescence correlation spectroscopy was used to detect structural changes correlated with kinase activation under physiological conditions. Saturating Ca(2+)/CaM triggered Threonine-286 autophosphorylation and a large increase in CaMKII holoenzyme hydrodynamic volume without any appreciable change in catalytic-domain pair proximity or subunit stoichiometry. An alternative hypothesis is that two appropriately positioned Threonine-286 interaction-sites (T-sites), each located on the catalytic-domain of a pair, are required for holoenzyme interactions with target proteins. Addition of a T-site ligand, in the presence of Ca(2+)/CaM, elicited a large decrease in catalytic-domain homo-FRET, which was blocked by mutating the T-site (I205K). Apparently catalytic-domain pairing is altered to allow T-site interactions.
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Affiliation(s)
- Tuan A Nguyen
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Pabak Sarkar
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Jithesh V Veetil
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Kaitlin A Davis
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Henry L Puhl
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - Steven S Vogel
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland.
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Levitt JA, Morton PE, Fruhwirth GO, Santis G, Chung PH, Parsons M, Suhling K. Simultaneous FRAP, FLIM and FAIM for measurements of protein mobility and interaction in living cells. BIOMEDICAL OPTICS EXPRESS 2015; 6:3842-54. [PMID: 26504635 PMCID: PMC4605044 DOI: 10.1364/boe.6.003842] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/16/2015] [Accepted: 08/18/2015] [Indexed: 05/23/2023]
Abstract
We present a novel integrated multimodal fluorescence microscopy technique for simultaneous fluorescence recovery after photobleaching (FRAP), fluorescence lifetime imaging (FLIM) and fluorescence anisotropy imaging (FAIM). This approach captures a series of polarization-resolved fluorescence lifetime images during a FRAP recovery, maximizing the information available from a limited photon budget. We have applied this method to analyse the behaviour of GFP-labelled coxsackievirus and adenovirus receptor (CAR) in living human epithelial cells. Our data reveal that CAR exists in oligomeric states throughout the cell, and that these complexes occur in conjunction with high immobile fractions of the receptor at cell-cell junctions. These findings shed light on previously unknown molecular associations between CAR receptors in intact cells and demonstrate the power of combined FRAP, FLIM and FAIM microscopy as a robust method to analyse complex multi-component dynamics in living cells.
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Affiliation(s)
- James A. Levitt
- Department of Physics, King’s College London, Strand, London WC2R 2LS, UK
| | - Penny E. Morton
- Division of Asthma, Allergy, and Lung Biology, Guys Campus, King’s College London, London, UK
- Randall Division of Cell and Molecular Biophysics, Guys Campus, King’s College London, London, SE1 1UL, UK
| | - Gilbert O. Fruhwirth
- Department of Imaging Chemsitry and Biology, Division of Imaging Sciences and Biomedical Engineering, St. Thomas Hospital, King's College London, SE1 7EH, UK
| | - George Santis
- Division of Asthma, Allergy, and Lung Biology, Guys Campus, King’s College London, London, UK
| | - Pei-Hua Chung
- Department of Physics, King’s College London, Strand, London WC2R 2LS, UK
| | - Maddy Parsons
- Randall Division of Cell and Molecular Biophysics, Guys Campus, King’s College London, London, SE1 1UL, UK
| | - Klaus Suhling
- Department of Physics, King’s College London, Strand, London WC2R 2LS, UK
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31
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Warren SC, Margineanu A, Katan M, Dunsby C, French PMW. Homo-FRET Based Biosensors and Their Application to Multiplexed Imaging of Signalling Events in Live Cells. Int J Mol Sci 2015; 16:14695-716. [PMID: 26133241 PMCID: PMC4519867 DOI: 10.3390/ijms160714695] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 12/20/2022] Open
Abstract
Multiplexed imaging of Förster Resonance Energy Transfer (FRET)-based biosensors potentially presents a powerful approach to monitoring the spatio-temporal correlation of signalling pathways within a single live cell. Here, we discuss the potential of homo-FRET based biosensors to facilitate multiplexed imaging. We demonstrate that the homo-FRET between pleckstrin homology domains of Akt (Akt-PH) labelled with mCherry may be used to monitor 3'-phosphoinositide accumulation in live cells and show how global analysis of time resolved fluorescence anisotropy measurements can be used to quantify this accumulation. We further present multiplexed imaging readouts of calcium concentration, using fluorescence lifetime measurements of TN-L15-a CFP/YFP based hetero-FRET calcium biosensor-with 3'-phosphoinositide accumulation.
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Affiliation(s)
- Sean C Warren
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
| | - Anca Margineanu
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
| | - Matilda Katan
- Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
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33
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Michalski PJ. The delicate bistability of CaMKII. Biophys J 2014; 105:794-806. [PMID: 23931327 DOI: 10.1016/j.bpj.2013.06.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/13/2013] [Accepted: 06/25/2013] [Indexed: 01/08/2023] Open
Abstract
Calcium/calmodulin-dependent protein kinase II (CaMKII) is a synaptic, autophosphorylating kinase that is essential for learning and memory. Previous models have suggested that CaMKII functions as a bistable switch that could be the molecular correlate of long-term memory, but experiments have failed to validate these predictions. These models involved significant approximations to overcome the combinatorial complexity inherent in a multisubunit, multistate system. Here, we develop a stochastic particle-based model of CaMKII activation and dynamics that overcomes combinatorial complexity without significant approximations. We report four major findings. First, the CaMKII model system is never bistable at resting calcium concentrations, which suggests that CaMKII activity does not function as the biochemical switch underlying long-term memory. Second, the steady-state activation curves are either laserlike or steplike. Both are characterized by a well-defined threshold for activation, which suggests that thresholding is a robust feature of this system. Third, transiently activated CaMKII can maintain its activity over the time course of many experiments, and such slow deactivation may account for the few reports of bistability in the literature. And fourth, under in vivo conditions, increases in phosphatase activity can increase CaMKII activity. This is a surprising and counterintuitive effect, as dephosphorylation is generally associated with CaMKII deactivation.
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Affiliation(s)
- P J Michalski
- Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, Connecticut, USA.
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Kraft LJ, Nguyen TA, Vogel SS, Kenworthy AK. Size, stoichiometry, and organization of soluble LC3-associated complexes. Autophagy 2014; 10:861-77. [PMID: 24646892 PMCID: PMC4768459 DOI: 10.4161/auto.28175] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
MAP1LC3B, an ortholog of yeast Atg8 and a member of the family of proteins formerly also known as ATG8 in mammals (LC3B henceforth in the text), functions in autophagosome formation and autophagy substrate recruitment. LC3 exists in both a soluble (autophagosome-independent) form as well as a lipid modified form that becomes tightly incorporated into autophagosomal membranes. Although LC3 is known to associate with tens of proteins, relatively little is known about soluble LC3 aside from its interactions with the LC3 lipid conjugation machinery. In previous studies we found autophagosome-independent GFP-LC3B diffuses unusually slowly for a protein of its size, suggesting it may constitutively associate with a high molecular weight complex, form homo-oligomers or aggregates, or reversibly bind microtubules or membranes. To distinguish between these possibilities, we characterized the size, stoichiometry, and organization of autophagosome-independent LC3B in living cells and in cytoplasmic extracts using fluorescence recovery after photobleaching (FRAP) and fluorescence polarization fluctuation analysis (FPFA). We found that the diffusion of LC3B was unaffected by either mutational disruption of its lipid modification or microtubule depolymerization. Brightness and homo-FRET analysis indicate LC3B does not homo-oligomerize. However, mutation of specific residues on LC3B required for binding other proteins and mRNA altered the effective hydrodynamic radius of the protein as well as its stoichiometry. We conclude that when not bound to autophagosomes, LC3B associates with a multicomponent complex with an effective size of ~500 kDa in the cytoplasm. These findings provide new insights into the nature of soluble LC3B and illustrate the power of FRAP and FPFA to investigate the emergent properties of protein complexes in the autophagy pathway.
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Affiliation(s)
- Lewis J Kraft
- Chemical and Physical Biology Program; Department of Molecular Physiology and Biophysics; Department of Cell and Developmental Biology; Vanderbilt University Medical Center; Nashville, TN USA
| | - Tuan A Nguyen
- Section on Cellular Biophotonics, Laboratory of Molecular Physiology; National Institute on Alcohol Abuse and Alcoholism; National Institutes of Health; Rockville, MD USA
| | - Steven S Vogel
- Section on Cellular Biophotonics, Laboratory of Molecular Physiology; National Institute on Alcohol Abuse and Alcoholism; National Institutes of Health; Rockville, MD USA
| | - Anne K Kenworthy
- Chemical and Physical Biology Program; Department of Molecular Physiology and Biophysics; Department of Cell and Developmental Biology; Vanderbilt University Medical Center; Nashville, TN USA
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Yu K, Zhu J, Qu Z, Cui YY, Hartzell HC. Activation of the Ano1 (TMEM16A) chloride channel by calcium is not mediated by calmodulin. ACTA ACUST UNITED AC 2014; 143:253-67. [PMID: 24420770 PMCID: PMC4001774 DOI: 10.1085/jgp.201311047] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Calcium-mediated activation of the TMEM16A chloride channel does not depend on changes in phosphorylation status or the calcium-binding protein calmodulin. The Ca2+-activated Cl channel anoctamin-1 (Ano1; Tmem16A) plays a variety of physiological roles, including epithelial fluid secretion. Ano1 is activated by increases in intracellular Ca2+, but there is uncertainty whether Ca2+ binds directly to Ano1 or whether phosphorylation or additional Ca2+-binding subunits like calmodulin (CaM) are required. Here we show that CaM is not necessary for activation of Ano1 by Ca2+ for the following reasons. (a) Exogenous CaM has no effect on Ano1 currents in inside-out excised patches. (b) Overexpression of Ca2+-insensitive mutants of CaM have no effect on Ano1 currents, whereas they eliminate the current mediated by the small-conductance Ca2+-activated K+ (SK2) channel. (c) Ano1 does not coimmunoprecipitate with CaM, whereas SK2 does. Furthermore, Ano1 binds very weakly to CaM in pull-down assays. (d) Ano1 is activated in excised patches by low concentrations of Ba2+, which does not activate CaM. In addition, we conclude that reversible phosphorylation/dephosphorylation is not required for current activation by Ca2+ because the current can be repeatedly activated in excised patches in the absence of ATP or other high-energy compounds. Although Ano1 is blocked by the CaM inhibitor trifluoperazine (TFP), we propose that TFP inhibits the channel in a CaM-independent manner because TFP does not inhibit Ano1 when applied to the cytoplasmic side of excised patches. These experiments lead us to conclude that CaM is not required for activation of Ano1 by Ca2+. Although CaM is not required for channel opening by Ca2+, work of other investigators suggests that CaM may have effects in modulating the biophysical properties of the channel.
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Affiliation(s)
- Kuai Yu
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
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36
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Abstract
Fluorescence can be characterized by its intensity, position, wavelength, lifetime, and polarization. The more of these features are acquired in a single measurement, the more can be learned about the sample, i.e., the microenvironment of the fluorescence probe. Polarization-resolved fluorescence lifetime imaging-time-resolved fluorescence anisotropy imaging, TR-FAIM-allows mapping of viscosity or binding or of homo-FRET which can indicate dimerization or generally oligomerization.
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Affiliation(s)
- Klaus Suhling
- Department of Physics, King's College London, London, UK
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37
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Kato KI, Iwamoto T, Kida S. Interactions between αCaMKII and calmodulin in living cells: conformational changes arising from CaM-dependent and -independent relationships. Mol Brain 2013; 6:37. [PMID: 23958294 PMCID: PMC3765210 DOI: 10.1186/1756-6606-6-37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/14/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND αCaMKII plays central and essential roles in long-term potentiation (LTP), learning and memory. αCaMKII is activated via binding with Ca²⁺/CaM in response to elevated Ca²⁺ concentration. Furthermore, prolonged increase in Ca²⁺ concentration leads to the auto-phosphorylation of αCaMKII at T286, maintaining the activation of αCaMKII even after Ca²⁺/CaM dissociation. Importantly, the active form of αCaMKII is thought to exhibit conformational change. In order to elucidate the relationships between the interaction of αCaMKII with CaM and the conformational change of αCaMKII, we generated molecular probes (YFP-αCaMKII with CFP-CaM and YFP-αCaMKII-CFP) and performed time-lapse imaging of the interaction with CaM and the conformational change, respectively, in living cells using FRET. RESULTS The interaction of YFP-αCaMKII with CFP-CaM and the conformational change of YFP-αCaMKII-CFP were induced simultaneously in response to increased concentrations of Ca²⁺. Consistent with previous predictions, high levels of Ca²⁺ signaling maintained the conformational change of YFP-αCaMKII-CFP at the time when CFP-CaM was released from YFP-αCaMKII. These observations indicated the transfer of αCaMKII conformational change from CaM-dependence to CaM-independence. Furthermore, analyses using αCaMKII mutants showed that phosphorylation at T286 and T305/306 played positive and negative roles, respectively, during in vivo interaction with CaM and further suggested that CaM-dependent and CaM-independent conformational changed forms displays similar but distinct structures. CONCLUSIONS Importantly, these structual differences between CaM-dependent and -independent forms of αCaMKII may exhibit differential functions for αCaMKII, such as interactions with other molecules required for LTP and memory. Our molecular probes could thus be used to identify therapeutic targets for cognitive disorders that are associated with the misregulation of αCaMKII.
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Affiliation(s)
- Ken-ichi Kato
- Department of Bioscience, Faculty of Applied Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan.
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Warren SC, Margineanu A, Alibhai D, Kelly DJ, Talbot C, Alexandrov Y, Munro I, Katan M, Dunsby C, French PMW. Rapid global fitting of large fluorescence lifetime imaging microscopy datasets. PLoS One 2013; 8:e70687. [PMID: 23940626 PMCID: PMC3734241 DOI: 10.1371/journal.pone.0070687] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/20/2013] [Indexed: 12/18/2022] Open
Abstract
Fluorescence lifetime imaging (FLIM) is widely applied to obtain quantitative information from fluorescence signals, particularly using Förster Resonant Energy Transfer (FRET) measurements to map, for example, protein-protein interactions. Extracting FRET efficiencies or population fractions typically entails fitting data to complex fluorescence decay models but such experiments are frequently photon constrained, particularly for live cell or in vivo imaging, and this leads to unacceptable errors when analysing data on a pixel-wise basis. Lifetimes and population fractions may, however, be more robustly extracted using global analysis to simultaneously fit the fluorescence decay data of all pixels in an image or dataset to a multi-exponential model under the assumption that the lifetime components are invariant across the image (dataset). This approach is often considered to be prohibitively slow and/or computationally expensive but we present here a computationally efficient global analysis algorithm for the analysis of time-correlated single photon counting (TCSPC) or time-gated FLIM data based on variable projection. It makes efficient use of both computer processor and memory resources, requiring less than a minute to analyse time series and multiwell plate datasets with hundreds of FLIM images on standard personal computers. This lifetime analysis takes account of repetitive excitation, including fluorescence photons excited by earlier pulses contributing to the fit, and is able to accommodate time-varying backgrounds and instrument response functions. We demonstrate that this global approach allows us to readily fit time-resolved fluorescence data to complex models including a four-exponential model of a FRET system, for which the FRET efficiencies of the two species of a bi-exponential donor are linked, and polarisation-resolved lifetime data, where a fluorescence intensity and bi-exponential anisotropy decay model is applied to the analysis of live cell homo-FRET data. A software package implementing this algorithm, FLIMfit, is available under an open source licence through the Open Microscopy Environment.
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Affiliation(s)
- Sean C Warren
- Department of Chemistry, Institute for Chemical Biology, Imperial College London, London, United Kingdom.
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40
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Sun Y, Rombola C, Jyothikumar V, Periasamy A. Förster resonance energy transfer microscopy and spectroscopy for localizing protein-protein interactions in living cells. Cytometry A 2013; 83:780-93. [PMID: 23813736 DOI: 10.1002/cyto.a.22321] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 04/08/2013] [Accepted: 05/23/2013] [Indexed: 12/15/2022]
Abstract
The fundamental theory of Förster resonance energy transfer (FRET) was established in the 1940s. Its great power was only realized in the past 20 years after different techniques were developed and applied to biological experiments. This success was made possible by the availability of suitable fluorescent probes, advanced optics, detectors, microscopy instrumentation, and analytical tools. Combined with state-of-the-art microscopy and spectroscopy, FRET imaging allows scientists to study a variety of phenomena that produce changes in molecular proximity, thereby leading to many significant findings in the life sciences. In this review, we outline various FRET imaging techniques and their strengths and limitations; we also provide a biological model to demonstrate how to investigate protein-protein interactions in living cells using both intensity- and fluorescence lifetime-based FRET microscopy methods.
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Affiliation(s)
- Yuansheng Sun
- The W.M. Keck Center for Cellular Imaging (KCCI), Department of Biology, Physical and Life Sciences Building, University of Virginia, Charlottesville, Virginia
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41
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Stratton MM, Chao LH, Schulman H, Kuriyan J. Structural studies on the regulation of Ca2+/calmodulin dependent protein kinase II. Curr Opin Struct Biol 2013; 23:292-301. [PMID: 23632248 DOI: 10.1016/j.sbi.2013.04.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/24/2013] [Accepted: 04/02/2013] [Indexed: 11/15/2022]
Abstract
Ca(2+)/calmodulin dependent protein kinase II (CaMKII) is a broadly distributed metazoan Ser/Thr protein kinase that is important in neuronal and cardiac signaling. CaMKII forms oligomeric assemblies, typically dodecameric, in which the calcium-responsive kinase domains are organized around a central hub. We review the results of crystallographic analyses of CaMKII, including the recently determined structure of a full-length and autoinhibited form of the holoenzyme. These structures, when combined with other data, allow informed speculation about how CaMKII escapes calcium-dependence when calcium spikes exceed threshold frequencies.
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Affiliation(s)
- Margaret M Stratton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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Broussard JA, Rappaz B, Webb DJ, Brown CM. Fluorescence resonance energy transfer microscopy as demonstrated by measuring the activation of the serine/threonine kinase Akt. Nat Protoc 2013; 8:265-81. [PMID: 23306460 DOI: 10.1038/nprot.2012.147] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes procedures for performing fluorescence resonance energy transfer (FRET) microscopy analysis by three different methods: acceptor photobleaching, sensitized emission and spectral imaging. We also discuss anisotropy and fluorescence lifetime imaging microscopy-based FRET techniques. By using the specific example of the FRET probe Akind (Akt indicator), which is a version of Akt modified such that FRET occurs when the probe is activated by phosphorylation, indicating Akt activation. The protocol provides a detailed step-by-step description of sample preparation, image acquisition and analysis, including control samples, image corrections and the generation of quantitative FRET/CFP ratio images for both sensitized emission and spectral imaging. The sample preparation takes 2 d, equipment setup takes 2-3 h and image acquisition and analysis take 6-8 h.
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Affiliation(s)
- Joshua A Broussard
- Department of Biological Sciences and Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, Tennessee, USA
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Vogel SS, Nguyen TA, van der Meer BW, Blank PS. The impact of heterogeneity and dark acceptor states on FRET: implications for using fluorescent protein donors and acceptors. PLoS One 2012; 7:e49593. [PMID: 23152925 PMCID: PMC3496711 DOI: 10.1371/journal.pone.0049593] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 10/15/2012] [Indexed: 11/18/2022] Open
Abstract
Förster resonance energy transfer (FRET) microscopy is widely used to study protein interactions in living cells. Typically, spectral variants of the Green Fluorescent Protein (FPs) are incorporated into proteins expressed in cells, and FRET between donor and acceptor FPs is assayed. As appreciable FRET occurs only when donors and acceptors are within 10 nm of each other, the presence of FRET can be indicative of aggregation that may denote association of interacting species. By monitoring the excited-state (fluorescence) decay of the donor in the presence and absence of acceptors, dual-component decay analysis has been used to reveal the fraction of donors that are FRET positive (i.e., in aggregates)._However, control experiments using constructs containing both a donor and an acceptor FP on the same protein repeatedly indicate that a large fraction of these donors are FRET negative, thus rendering the interpretation of dual-component analysis for aggregates between separately donor-containing and acceptor-containing proteins problematic. Using Monte-Carlo simulations and analytical expressions, two possible sources for such anomalous behavior are explored: 1) conformational heterogeneity of the proteins, such that variations in the distance separating donor and acceptor FPs and/or their relative orientations persist on time-scales long in comparison with the excited-state lifetime, and 2) FP dark states.
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Affiliation(s)
- Steven S Vogel
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, United States of America.
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44
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Devauges V, Marquer C, Lécart S, Cossec JC, Potier MC, Fort E, Suhling K, Lévêque-Fort S. Homodimerization of amyloid precursor protein at the plasma membrane: a homoFRET study by time-resolved fluorescence anisotropy imaging. PLoS One 2012; 7:e44434. [PMID: 22973448 PMCID: PMC3433432 DOI: 10.1371/journal.pone.0044434] [Citation(s) in RCA: 31] [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: 03/05/2012] [Accepted: 08/03/2012] [Indexed: 11/18/2022] Open
Abstract
Classical FRET (Förster Resonance Energy Transfer) using two fluorescent labels (one for the donor and another one for the acceptor) is not efficient for studying the homodimerization of a protein as only half of the homodimers formed can be identified by this technique. We thus resorted to homoFRET detected by time-resolved Fluorescence Anisotropy IMaging (tr-FAIM). To specifically image the plasma membrane of living cells, an original combination of tr-FAIM and Total Internal Reflection Fluorescence Lifetime Imaging Microscope (TIRFLIM) was implemented. The correcting factor accounting for the depolarization due to the high numerical aperture (NA) objective, mandatory for TIRF microscopy, was quantified on fluorescein solutions and on HEK293 cells expressing enhanced Green Fluorescence Protein (eGFP). Homodimerization of Amyloid Precursor Protein (APP), a key mechanism in the etiology of Alzheimer’s disease, was measured on this original set-up. We showed, both in epifluorescence and under TIRF excitation, different energy transfer rates associated with the homodimerization of wild type APP-eGFP or of a mutated APP-eGFP, which forms constitutive dimers. This original set-up thus offers promising prospects for future studies of protein homodimerization in living cells in control and pathological conditions.
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Affiliation(s)
- Viviane Devauges
- Institut des Sciences Moléculaires d’Orsay, CNRS UMR 8214, Univ. Paris Sud, Orsay, France
- Laboratoire Charles Fabry, CNRS UMR 8501, Institut d’Optique, Univ. Paris Sud, Palaiseau, France
- Centre de Photonique Biomédicale, Univ. Paris Sud, CLUPS/LUMAT FR2764, Orsay, France
| | | | - Sandrine Lécart
- Centre de Photonique Biomédicale, Univ. Paris Sud, CLUPS/LUMAT FR2764, Orsay, France
| | | | | | - Emmanuel Fort
- Institut Langevin, ESPCI ParisTech, Univ. Paris Diderot, UMR 7587, Paris, France
| | - Klaus Suhling
- Department of Physics, King’s College London, Strand, London, United Kingdom
| | - Sandrine Lévêque-Fort
- Institut des Sciences Moléculaires d’Orsay, CNRS UMR 8214, Univ. Paris Sud, Orsay, France
- Centre de Photonique Biomédicale, Univ. Paris Sud, CLUPS/LUMAT FR2764, Orsay, France
- * E-mail:
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45
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Michalski PJ, Loew LM. CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation. Phys Biol 2012; 9:036010. [PMID: 22683827 DOI: 10.1088/1478-3975/9/3/036010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The combinatorial explosion produced by the multi-state, multi-subunit character of CaMKII has made analysis and modeling of this key signaling protein a significant challenge. Using rule-based and particle-based approaches, we construct exact models of CaMKII holoenzyme dynamics and study these models as a function of the number of subunits per holoenzyme, N. Without phosphatases the dynamics of activation are independent of the holoenzyme structure unless phosphorylation significantly alters the kinase activity of a subunit. With phosphatases the model is independent of holoenzyme size for N > 6. We introduce an infinite subunit holoenzyme approximation (ISHA), which simplifies the modeling by eliminating the combinatorial complexities encountered in any finite holoenzyme model. The ISHA is an excellent approximation to the full system over a broad range of physiologically relevant parameters. Finally, we demonstrate that the ISHA reproduces the behavior of exact models during synaptic plasticity protocols, which justifies its use as a module in large models of synaptic plasticity.
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Affiliation(s)
- P J Michalski
- Richard D Berlin Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT 06030, USA.
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Nguyen TA, Sarkar P, Veetil JV, Koushik SV, Vogel SS. Fluorescence polarization and fluctuation analysis monitors subunit proximity, stoichiometry, and protein complex hydrodynamics. PLoS One 2012; 7:e38209. [PMID: 22666486 PMCID: PMC3364239 DOI: 10.1371/journal.pone.0038209] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/01/2012] [Indexed: 11/19/2022] Open
Abstract
Förster resonance energy transfer (FRET) microscopy is frequently used to study protein interactions and conformational changes in living cells. The utility of FRET is limited by false positive and negative signals. To overcome these limitations we have developed Fluorescence Polarization and Fluctuation Analysis (FPFA), a hybrid single-molecule based method combining time-resolved fluorescence anisotropy (homo-FRET) and fluorescence correlation spectroscopy. Using FPFA, homo-FRET (a 1–10 nm proximity gauge), brightness (a measure of the number of fluorescent subunits in a complex), and correlation time (an attribute sensitive to the mass and shape of a protein complex) can be simultaneously measured. These measurements together rigorously constrain the interpretation of FRET signals. Venus based control-constructs were used to validate FPFA. The utility of FPFA was demonstrated by measuring in living cells the number of subunits in the α-isoform of Venus-tagged calcium-calmodulin dependent protein kinase-II (CaMKIIα) holoenzyme. Brightness analysis revealed that the holoenzyme has, on average, 11.9±1.2 subunit, but values ranged from 10–14 in individual cells. Homo-FRET analysis simultaneously detected that catalytic domains were arranged as dimers in the dodecameric holoenzyme, and this paired organization was confirmed by quantitative hetero-FRET analysis. In freshly prepared cell homogenates FPFA detected only 10.2±1.3 subunits in the holoenzyme with values ranging from 9–12. Despite the reduction in subunit number, catalytic domains were still arranged as pairs in homogenates. Thus, FPFA suggests that while the absolute number of subunits in an auto-inhibited holoenzyme might vary from cell to cell, the organization of catalytic domains into pairs is preserved.
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Affiliation(s)
- Tuan A. Nguyen
- Section on Cellular Biophotonics, Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland, United States of America
| | - Pabak Sarkar
- Section on Cellular Biophotonics, Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland, United States of America
| | - Jithesh V. Veetil
- Section on Cellular Biophotonics, Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland, United States of America
| | - Srinagesh V. Koushik
- Section on Cellular Biophotonics, Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland, United States of America
| | - Steven S. Vogel
- Section on Cellular Biophotonics, Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail:
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Hunt J, Keeble AH, Dale RE, Corbett MK, Beavil RL, Levitt J, Swann MJ, Suhling K, Ameer-Beg S, Sutton BJ, Beavil AJ. A fluorescent biosensor reveals conformational changes in human immunoglobulin E Fc: implications for mechanisms of receptor binding, inhibition, and allergen recognition. J Biol Chem 2012; 287:17459-17470. [PMID: 22442150 PMCID: PMC3366799 DOI: 10.1074/jbc.m111.331967] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 03/08/2012] [Indexed: 11/06/2022] Open
Abstract
IgE binding to its high affinity receptor FcεRI on mast cells and basophils is a key step in the mechanism of allergic disease and a target for therapeutic intervention. Early indications that IgE adopts a bent structure in solution have been confirmed by recent x-ray crystallographic studies of IgEFc, which further showed that the bend, contrary to expectation, is enhanced in the crystal structure of the complex with receptor. To investigate the structure of IgEFc and its conformational changes that accompany receptor binding in solution, we created a Förster resonance energy transfer (FRET) biosensor using biologically encoded fluorescent proteins fused to the N- and C-terminal IgEFc domains (Cε2 and Cε4, respectively) together with the theoretical basis for quantitating its behavior. This revealed not only that the IgEFc exists in a bent conformation in solution but also that the bend is indeed enhanced upon FcεRI binding. No change in the degree of bending was seen upon binding to the B cell receptor for IgE, CD23 (FcεRII), but in contrast, binding of the anti-IgE therapeutic antibody omalizumab decreases the extent of the bend, implying a conformational change that opposes FcεRI engagement. HomoFRET measurements further revealed that the (Cε2)(2) and (Cε4)(2) domain pairs behave as rigid units flanking the conformational change in the Cε3 domains. Finally, modeling of the accessible conformations of the two Fab arms in FcεRI-bound IgE revealed a mutual exclusion not seen in IgG and Fab orientations relative to the membrane that may predispose receptor-bound IgE to cross-linking by allergens.
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Affiliation(s)
- James Hunt
- MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, Guy's Hospital Campus, London SE1 1UL; The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL; The Division of Asthma Allergy and Lung Biology, King's College London, Guy's Hospital Campus, London SE1 1UL
| | - Anthony H Keeble
- MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, Guy's Hospital Campus, London SE1 1UL; The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL; The Division of Asthma Allergy and Lung Biology, King's College London, Guy's Hospital Campus, London SE1 1UL
| | - Robert E Dale
- The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL
| | - Melissa K Corbett
- The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL
| | - Rebecca L Beavil
- MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, Guy's Hospital Campus, London SE1 1UL; The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL; The Division of Asthma Allergy and Lung Biology, King's College London, Guy's Hospital Campus, London SE1 1UL
| | - James Levitt
- The Department of Physics, King's College London, Strand, London WC2R 2LS
| | - Marcus J Swann
- Farfield Group Limited, Voyager, Chicago Avenue, Manchester Airport, Manchester, M90 3DQ, United Kingdom
| | - Klaus Suhling
- The Department of Physics, King's College London, Strand, London WC2R 2LS
| | - Simon Ameer-Beg
- The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL
| | - Brian J Sutton
- MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, Guy's Hospital Campus, London SE1 1UL; The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL
| | - Andrew J Beavil
- MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, Guy's Hospital Campus, London SE1 1UL; The Randall Division of Cell and Molecular Biophysics, Guy's Hospital Campus, London SE1 1UL; The Division of Asthma Allergy and Lung Biology, King's College London, Guy's Hospital Campus, London SE1 1UL.
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48
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González-Vera JA. Probing the kinome in real time with fluorescent peptides. Chem Soc Rev 2012; 41:1652-64. [DOI: 10.1039/c1cs15198c] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Chao LH, Stratton MM, Lee IH, Rosenberg OS, Levitz J, Mandell DJ, Kortemme T, Groves JT, Schulman H, Kuriyan J. A mechanism for tunable autoinhibition in the structure of a human Ca2+/calmodulin- dependent kinase II holoenzyme. Cell 2011; 146:732-45. [PMID: 21884935 DOI: 10.1016/j.cell.2011.07.038] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 05/11/2011] [Accepted: 07/29/2011] [Indexed: 01/16/2023]
Abstract
Calcium/calmodulin-dependent kinase II (CaMKII) forms a highly conserved dodecameric assembly that is sensitive to the frequency of calcium pulse trains. Neither the structure of the dodecameric assembly nor how it regulates CaMKII are known. We present the crystal structure of an autoinhibited full-length human CaMKII holoenzyme, revealing an unexpected compact arrangement of kinase domains docked against a central hub, with the calmodulin-binding sites completely inaccessible. We show that this compact docking is important for the autoinhibition of the kinase domains and for setting the calcium response of the holoenzyme. Comparison of CaMKII isoforms, which differ in the length of the linker between the kinase domain and the hub, demonstrates that these interactions can be strengthened or weakened by changes in linker length. This equilibrium between autoinhibited states provides a simple mechanism for tuning the calcium response without changes in either the hub or the kinase domains.
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Affiliation(s)
- Luke H Chao
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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50
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Quantitative microscopy and imaging tools for the mechanical analysis of morphogenesis. Curr Opin Genet Dev 2011; 21:664-70. [PMID: 21893407 DOI: 10.1016/j.gde.2011.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 08/10/2011] [Accepted: 08/11/2011] [Indexed: 11/20/2022]
Abstract
The importance of mechanical signals during embryogenesis and development, through both intercellular and extracellular signals, is coming into focus. It is widely hypothesized that physical forces help to guide the shape, cellular differentiation and the patterning of tissues. To test these ideas many classical engineering principles and imaging technologies are being adapted. Recent advances in microscopy, mechanical testing and genetic and pharmacological techniques, alongside computational models are helping to dissect the activity of mechanical signals in development at the cellular and molecular level. These inroads are providing maps of mechanical changes in tissue structure and stiffness, and will permit deeper insights into the role of mechanics in both developmental biology and disease.
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