1
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Choosing the Probe for Single-Molecule Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms232314949. [PMID: 36499276 PMCID: PMC9735909 DOI: 10.3390/ijms232314949] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.
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2
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Guryev EL, Shanwar S, Zvyagin A, Deyev SM, Balalaeva IV. Photoluminescent Nanomaterials for Medical Biotechnology. Acta Naturae 2021; 13:16-31. [PMID: 34377553 PMCID: PMC8327149 DOI: 10.32607/actanaturae.11180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/12/2020] [Indexed: 12/20/2022] Open
Abstract
Creation of various photoluminescent nanomaterials has significantly expanded the arsenal of approaches used in modern biomedicine. Their unique photophysical properties can significantly improve the sensitivity and specificity of diagnostic methods, increase therapy effectiveness, and make a theranostic approach to treatment possible through the application of nanoparticle conjugates with functional macromolecules. The most widely used nanomaterials to date are semiconductor quantum dots; gold nanoclusters; carbon dots; nanodiamonds; semiconductor porous silicon; and up-conversion nanoparticles. This paper considers the promising groups of photoluminescent nanomaterials that can be used in medical biotechnology: in particular, for devising agents for optical diagnostic methods, sensorics, and various types of therapy.
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Affiliation(s)
- E. L. Guryev
- Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022 Russia
| | - S. Shanwar
- Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022 Russia
| | - A.V. Zvyagin
- Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022 Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
- I. M. Sechenov First Moscow State Medical University, Moscow, 119991 Russia
| | - S. M. Deyev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
- I. M. Sechenov First Moscow State Medical University, Moscow, 119991 Russia
| | - I. V. Balalaeva
- Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022 Russia
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3
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Romanazzi T, Zanella D, Cheng MH, Smith B, Carter AM, Galli A, Bahar I, Bossi E. Bile Acids Gate Dopamine Transporter Mediated Currents. Front Chem 2021; 9:753990. [PMID: 34957043 PMCID: PMC8702627 DOI: 10.3389/fchem.2021.753990] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/16/2021] [Indexed: 11/21/2022] Open
Abstract
Bile acids (BAs) are molecules derived from cholesterol that are involved in dietary fat absorption. New evidence supports an additional role for BAs as regulators of brain function. Sterols such as cholesterol interact with monoamine transporters, including the dopamine (DA) transporter (DAT) which plays a key role in DA neurotransmission and reward. This study explores the interactions of the BA, obeticholic acid (OCA), with DAT and characterizes the regulation of DAT activity via both electrophysiology and molecular modeling. We expressed murine DAT (mDAT) in Xenopus laevis oocytes and confirmed its functionality. Next, we showed that OCA promotes a DAT-mediated inward current that is Na+-dependent and not regulated by intracellular calcium. The current induced by OCA was transient in nature, returning to baseline in the continued presence of the BA. OCA also transiently blocked the DAT-mediated Li+-leak current, a feature that parallels DA action and indicates direct binding to the transporter in the absence of Na+. Interestingly, OCA did not alter DA affinity nor the ability of DA to promote a DAT-mediated inward current, suggesting that the interaction of OCA with the transporter is non-competitive, regarding DA. Docking simulations performed for investigating the molecular mechanism of OCA action on DAT activity revealed two potential binding sites. First, in the absence of DA, OCA binds DAT through interactions with D421, a residue normally involved in coordinating the binding of the Na+ ion to the Na2 binding site (Borre et al., J. Biol. Chem., 2014, 289, 25764-25773; Cheng and Bahar, Structure, 2015, 23, 2171-2181). Furthermore, we uncover a separate binding site for OCA on DAT, of equal potential functional impact, that is coordinated by the DAT residues R445 and D436. Binding to that site may stabilize the inward-facing (IF) open state by preventing the re-formation of the IF-gating salt bridges, R60-D436 and R445-E428, that are required for DA transport. This study suggests that BAs may represent novel pharmacological tools to regulate DAT function, and possibly, associated behaviors.
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Affiliation(s)
- Tiziana Romanazzi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Daniele Zanella
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Behrgen Smith
- Department of Physics and Chemistry, Biomolecular Engineering, Milwaukee School of Engineering, Milwaukee, WI, United States
| | - Angela M Carter
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Aurelio Galli
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Elena Bossi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,Center for Research in Neuroscience, University of Insubria, Varese, Italy
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4
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Ohtani R, Kawano K, Kinoshita M, Yanaka S, Watanabe H, Hirai K, Futaki S, Matsumori N, Uji-I H, Ohba M, Kato K, Hayami S. Pseudo-Membrane Jackets: Two-Dimensional Coordination Polymers Achieving Visible Phase Separation in Cell Membrane. Angew Chem Int Ed Engl 2020; 59:17931-17937. [PMID: 32608036 DOI: 10.1002/anie.202006600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/29/2020] [Indexed: 11/09/2022]
Abstract
Cell membranes contain lateral systems that consist of various lipid compositions and actin cytoskeleton, providing two-dimensional (2D) platforms for chemical reactions. However, such complex 2D environments have not yet been used as a synthetic platform for artificial 2D nanomaterials. Herein, we demonstrate the direct synthesis of 2D coordination polymers (CPs) at the liquid-cell interface of the plasma membrane of living cells. The coordination-driven self-assembly of networking metal complex lipids produces cyanide-bridged CP layers with metal ions, enabling "pseudo-membrane jackets" that produce long-lived micro-domains with a size of 1-5 μm. The resultant artificial and visible phase separation systems remain stable even in the absence of actin skeletons in cells. Moreover, we show the cell application of the jackets by demonstrating the enhancement of cellular calcium response to ATP.
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Affiliation(s)
- Ryo Ohtani
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kenichi Kawano
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Masanao Kinoshita
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Hikaru Watanabe
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kenji Hirai
- Research Institute for Electronic Science, Hokkaido University, N20W10, Kita-Ward Sapporo, Hokkaido, 001-0020, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hiroshi Uji-I
- Research Institute for Electronic Science, Hokkaido University, N20W10, Kita-Ward Sapporo, Hokkaido, 001-0020, Japan.,Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001, Heverlee, Belgium
| | - Masaaki Ohba
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Shinya Hayami
- Department of Chemistry, Graduate School of Science and Technology and Institute of Pulsed Power Science, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
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5
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Ohtani R, Kawano K, Kinoshita M, Yanaka S, Watanabe H, Hirai K, Futaki S, Matsumori N, Uji‐i H, Ohba M, Kato K, Hayami S. Pseudo‐Membrane Jackets: Two‐Dimensional Coordination Polymers Achieving Visible Phase Separation in Cell Membrane. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ryo Ohtani
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Kenichi Kawano
- Institute for Chemical Research Kyoto University Uji Kyoto 611-0011 Japan
| | - Masanao Kinoshita
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS) National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji Okazaki 444-8787 Japan
- Graduate School of Pharmaceutical Sciences Nagoya City University 3-1 Tanabe-dori, Mizuho-ku Nagoya Aichi 467-8603 Japan
| | - Hikaru Watanabe
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Kenji Hirai
- Research Institute for Electronic Science Hokkaido University N20W10 Kita-Ward Sapporo Hokkaido 001-0020 Japan
| | - Shiroh Futaki
- Institute for Chemical Research Kyoto University Uji Kyoto 611-0011 Japan
| | - Nobuaki Matsumori
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Hiroshi Uji‐i
- Research Institute for Electronic Science Hokkaido University N20W10 Kita-Ward Sapporo Hokkaido 001-0020 Japan
- Department of Chemistry KU Leuven Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Masaaki Ohba
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS) National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji Okazaki 444-8787 Japan
- Graduate School of Pharmaceutical Sciences Nagoya City University 3-1 Tanabe-dori, Mizuho-ku Nagoya Aichi 467-8603 Japan
| | - Shinya Hayami
- Department of Chemistry Graduate School of Science and Technology and Institute of Pulsed Power Science Kumamoto University 2-39-1 Kurokami, Chuo-ku Kumamoto 860-8555 Japan
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6
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Lv X, Wu Y, Tian R, Gu Y, Liu Y, Li J, Du G, Ledesma-Amaro R, Liu L. Synthetic metabolic channel by functional membrane microdomains for compartmentalized flux control. Metab Eng 2020; 59:106-118. [DOI: 10.1016/j.ymben.2020.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 10/24/2022]
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7
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Quantitative Analysis of Single Quantum Dot Trajectories. Methods Mol Biol 2020. [PMID: 32246331 DOI: 10.1007/978-1-0716-0463-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Single quantum dot tracking (SQDT) is a powerful technique for interrogating biomolecular dynamics in living cells and tissue. SQDT has particularly excelled in driving discovery at the single-molecule level in the fields of neuronal communication, plasma membrane organization, viral infection, and immune system response. Here, we briefly characterize various elements of the SQDT analytical framework and provide the reader with a detailed set of executable commands to implement commonly used algorithms for SQDT data processing.
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8
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Hoferer M, Bonfanti S, Taloni A, La Porta CAM, Zapperi S. Protein-driven lipid domain nucleation in biological membranes. Phys Rev E 2019; 100:042410. [PMID: 31770996 DOI: 10.1103/physreve.100.042410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Indexed: 06/10/2023]
Abstract
Lipid rafts are heterogeneous dynamic lipid domains of the cell membranes that are involved in several biological processes, such as protein and lipid specific transport and signaling. Our understanding of lipid raft formation is still limited due to the transient and elusive nature of these domains in vivo, in contrast with the stable phase-separated domains observed in artificial membranes. Inspired by experimental findings highlighting the relevance of transmembrane proteins for lipid rafts, we investigate lipid domain nucleation by coarse-grained molecular dynamics and Ising-model simulations. We find that the presence of a transmembrane protein can trigger lipid domain nucleation in a flat membrane from an otherwise mixed lipid phase. Furthermore, we study the role of the lipid domain in the diffusion of the protein showing that its mobility is hindered by the presence of the raft. The results of our coarse-grained molecular-dynamics and Ising-model simulations thus coherently support the important role played by transmembrane proteins in lipid domain formation and stability.
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Affiliation(s)
- Moritz Hoferer
- ETH Zurich, Zürichbergstrasse 18, 8092 Zurich, Switzerland
| | - Silvia Bonfanti
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Via Celoria 16, 20133 Milano, Italy
| | - Alessandro Taloni
- CNR - Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, via dei Taurini 19, 00185 Roma, Italy
| | - Caterina A M La Porta
- Center for Complexity and Biosystems, Department of Environmental Science and Policy, University of Milan, via Celoria 26, 20133 Milano, Italy
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Biofisica, Via Celoria 26, 20133 Milano, Italy
| | - Stefano Zapperi
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Via Celoria 16, 20133 Milano, Italy
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica della Materia Condensata e di Tecnologie per l'Energia, Via R. Cozzi 53, 20125 Milano, Italy
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9
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Bailey DM, Catron MA, Kovtun O, Macdonald RL, Zhang Q, Rosenthal SJ. Single Quantum Dot Tracking Reveals Serotonin Transporter Diffusion Dynamics are Correlated with Cholesterol-Sensitive Threonine 276 Phosphorylation Status in Primary Midbrain Neurons. ACS Chem Neurosci 2018; 9:2534-2541. [PMID: 29787674 DOI: 10.1021/acschemneuro.8b00214] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Serotonin transporter (SERT) terminates serotonin signaling in the brain by enabling rapid clearance of the neurotransmitter. SERT dysfunction has been associated with a variety of psychiatric disorders, including depression, anxiety, and autism. Visualizing SERT behavior at the single molecule level in endogenous systems remains a challenge. In this study, we utilize quantum dot (QD) single particle tracking (SPT) to capture SERT dynamics in primary rat midbrain neurons. Membrane microenvironment, specifically membrane cholesterol, plays a key role in SERT regulation and has been found to affect SERT conformational state. We sought to determine how reduced cholesterol content affects both lateral mobility and phosphorylation of conformationally sensitive threonine 276 (Thr276) in endogenous SERT using two different methods of cholesterol manipulation, statins and methyl-β-cyclodextrin. Both chronic and acute cholesterol depletion increased SERT lateral diffusion, radial displacement along the membrane, mobile fraction, and Thr276 phosphorylation levels. Overall, this work has provided new insights about endogenous neuronal SERT mobility and its associations with membrane cholesterol and SERT phosphorylation status.
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10
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Kovtun O, Tomlinson ID, Bailey DM, Thal LB, Ross EJ, Harris L, Frankland MP, Ferguson RS, Glaser Z, Greer J, Rosenthal SJ. Single Quantum Dot Tracking Illuminates Neuroscience at the Nanoscale. Chem Phys Lett 2018; 706:741-752. [PMID: 30270931 PMCID: PMC6157616 DOI: 10.1016/j.cplett.2018.06.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The use of nanometer-sized semiconductor crystals, known as quantum dots, allows us to directly observe individual biomolecular transactions through a fluorescence microscope. Here, we review the evolution of single quantum dot tracking over the past two decades, highlight key biophysical discoveries facilitated by quantum dots, briefly discuss biochemical and optical implementation strategies for a single quantum dot tracking experiment, and report recent accomplishments of our group at the interface of molecular neuroscience and nanoscience.
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Affiliation(s)
- Oleg Kovtun
- Departments of Chemistry, Chemical Biology, Vanderbilt University
- Departments of Vanderbilt Institute of Nanoscale Science and Engineering
| | - Ian D. Tomlinson
- Departments of Chemistry, Chemical Biology, Vanderbilt University
- Departments of Vanderbilt Institute of Nanoscale Science and Engineering
| | - Danielle M. Bailey
- Departments of Chemistry, Chemical Biology, Vanderbilt University
- Departments of Pharmacology, Chemical Biology, Vanderbilt University
- Departments of Vanderbilt Institute of Nanoscale Science and Engineering
| | - Lucas B. Thal
- Departments of Chemistry, Chemical Biology, Vanderbilt University
- Departments of Vanderbilt Institute of Nanoscale Science and Engineering
- Departments of Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN
| | - Emily J. Ross
- Departments of Hudson Alpha Institute for Biotechnology, Huntsville, AL
| | - Lauren Harris
- Departments of Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN
| | | | | | - Zachary Glaser
- Departments of Chemistry, Chemical Biology, Vanderbilt University
| | - Jonathan Greer
- Departments of Chemistry, Chemical Biology, Vanderbilt University
| | - Sandra J. Rosenthal
- Departments of Chemistry, Chemical Biology, Vanderbilt University
- Departments of Pharmacology, Chemical Biology, Vanderbilt University
- Departments of Chemical and Biomolecular Engineering, Chemical Biology, Vanderbilt University
- Departments of Physics and Astronomy, Chemical Biology, Vanderbilt University
- Departments of Vanderbilt Institute of Nanoscale Science and Engineering
- Departments of Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN
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11
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Zeppelin T, Ladefoged LK, Sinning S, Periole X, Schiøtt B. A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition. PLoS Comput Biol 2018; 14:e1005907. [PMID: 29329285 PMCID: PMC5811071 DOI: 10.1371/journal.pcbi.1005907] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 02/13/2018] [Accepted: 11/29/2017] [Indexed: 01/30/2023] Open
Abstract
Monoamine transporters (MATs) carry out neurotransmitter reuptake from the synaptic cleft, a key step in neurotransmission, which is targeted in the treatment of neurological disorders. Cholesterol (CHOL), a major component of the synaptic plasma membrane, has been shown to exhibit a modulatory effect on MATs. Recent crystal structures of the dopamine transporter (DAT) revealed the presence of two conserved CHOL-like molecules, suggesting a functional protein-CHOL direct interaction. Here, we present extensive atomistic molecular dynamics (MD) simulations of DAT in an outward-facing conformation. In the absence of bound CHOL, DAT undergoes structural changes reflecting early events of dopamine transport: transition to an inward-facing conformation. In contrast, in the presence of bound CHOL, these conformational changes are inhibited, seemingly by an immobilization of the intracellular interface of transmembrane helix 1a and 5 by CHOL. We also provide evidence, from coarse grain MD simulations that the CHOL sites observed in the DAT crystal structures are preserved in all human monoamine transporters (dopamine, serotonin and norepinephrine), suggesting that our findings might extend to the entire family.
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Affiliation(s)
- Talia Zeppelin
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Lucy Kate Ladefoged
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, Denmark
| | - Steffen Sinning
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus C, Denmark
| | - Xavier Periole
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, Denmark
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12
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Kuech EM, Brogden G, Naim HY. Alterations in membrane trafficking and pathophysiological implications in lysosomal storage disorders. Biochimie 2016; 130:152-162. [DOI: 10.1016/j.biochi.2016.09.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/19/2016] [Accepted: 09/19/2016] [Indexed: 12/11/2022]
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13
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Quantum Dot-Based Nanotools for Bioimaging, Diagnostics, and Drug Delivery. Chembiochem 2016; 17:2103-2114. [DOI: 10.1002/cbic.201600357] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Indexed: 12/12/2022]
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14
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Villar VAM, Cuevas S, Zheng X, Jose PA. Localization and signaling of GPCRs in lipid rafts. Methods Cell Biol 2016; 132:3-23. [DOI: 10.1016/bs.mcb.2015.11.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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15
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Schengrund CL. Gangliosides: glycosphingolipids essential for normal neural development and function. Trends Biochem Sci 2015; 40:397-406. [DOI: 10.1016/j.tibs.2015.03.007] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 11/25/2022]
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16
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Paramelle D, Nieves D, Brun B, Kraut RS, Fernig DG. Targeting Cell Membrane Lipid Rafts by Stoichiometric Functionalization of Gold Nanoparticles With a Sphingolipid-Binding Domain Peptide. Adv Healthc Mater 2015; 4:911-7. [PMID: 25650337 DOI: 10.1002/adhm.201400730] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/14/2015] [Indexed: 01/15/2023]
Abstract
A non-membrane protein-based nanoparticle agent for the tracking of lipid rafts on live cells is produced by stoichiometric functionalization of gold nanoparticles with a previously characterized sphingolipid- and cell membrane microdomain-binding domain peptide (SBD). The SBD peptide is inserted in a self-assembled monolayer of peptidol and alkane thiol ethylene glycol, on gold nanoparticles surface. The stoichiometric functionalization of nanoparticles with the SBD peptide, essential for single molecule tracking, is achieved by means of non-affinity nanoparticle purification. The SBD-nanoparticles have remarkable long-term resistance to electrolyte-induced aggregation and ligand-exchange and have no detectable non-specific binding to live cells. Binding and diffusion of SBD-nanoparticles bound to the membrane of live cells is measured by real-time photothermal microscopy and shows the dynamics of sphingolipid-enriched microdomains on cells membrane, with evidence for clustering, splitting, and diffusion over time of the SBD-nanoparticle labeled membrane domains. The monofunctionalized SBD-nanoparticle is a promising targeting agent for the tracking of lipid rafts independently of their protein composition and the labelling requires no prior modification of the cells. This approach has potential for further functionalization of the particles to manipulate the organization of, or targeting to microdomains that control signaling events and thereby lead to novel diagnostics and therapeutics.
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Affiliation(s)
- David Paramelle
- Institute of Materials Research and Engineering; A*STAR (Agency for Science Technology and Research); 3 Research Link 117602 Singapore
| | - Daniel Nieves
- Department of Biochemistry; Institute of Integrative Biology; University of Liverpool; Liverpool L69 7ZB UK
| | - Benjamin Brun
- Institute of Materials Research and Engineering; A*STAR (Agency for Science Technology and Research); 3 Research Link 117602 Singapore
| | - Rachel S. Kraut
- School of Biological Sciences; Nanyang Technological University; 50 Nanyang Ave 639798 Singapore
| | - David G. Fernig
- Department of Biochemistry; Institute of Integrative Biology; University of Liverpool; Liverpool L69 7ZB UK
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17
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Kovtun O, Sakrikar D, Tomlinson ID, Chang JC, Arzeta-Ferrer X, Blakely RD, Rosenthal SJ. Single-quantum-dot tracking reveals altered membrane dynamics of an attention-deficit/hyperactivity-disorder-derived dopamine transporter coding variant. ACS Chem Neurosci 2015; 6:526-34. [PMID: 25747272 PMCID: PMC5530757 DOI: 10.1021/cn500202c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The presynaptic, cocaine- and amphetamine-sensitive dopamine (DA) transporter (DAT, SLC6A3) controls the intensity and duration of synaptic dopamine signals by rapid clearance of DA back into presynaptic nerve terminals. Abnormalities in DAT-mediated DA clearance have been linked to a variety of neuropsychiatric disorders, including addiction, autism, and attention deficit/hyperactivity disorder (ADHD). Membrane trafficking of DAT appears to be an important, albeit incompletely understood, post-translational regulatory mechanism; its dysregulation has been recently proposed as a potential risk determinant of these disorders. In this study, we demonstrate a link between an ADHD-associated DAT mutation (Arg615Cys, R615C) and variation on DAT transporter cell surface dynamics, a combination only previously studied with ensemble biochemical and optical approaches that featured limited spatiotemporal resolution. Here, we utilize high-affinity, DAT-specific antagonist-conjugated quantum dot (QD) probes to establish the dynamic mobility of wild-type and mutant DATs at the plasma membrane of living cells. Single DAT-QD complex trajectory analysis revealed that the DAT 615C variant exhibited increased membrane mobility relative to DAT 615R, with diffusion rates comparable to those observed after lipid raft disruption. This phenomenon was accompanied by a loss of transporter mobilization triggered by amphetamine, a common component of ADHD medications. Together, our data provides the first dynamic imaging of single DAT proteins, providing new insights into the relationship between surface dynamics and trafficking of both wild-type and disease-associated transporters. Our approach should be generalizable to future studies that explore the possibilities of perturbed surface DAT dynamics that may arise as a consequence of genetic alterations, regulatory changes, and drug use that contribute to the etiology or treatment of neuropsychiatric disorders.
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Affiliation(s)
- Oleg Kovtun
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- McCoy & McCoy Laboratories, Inc, Madisonville, Kentucky 42431, United States
| | - Dhananjay Sakrikar
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ian D. Tomlinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jerry C. Chang
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, New York 10065, United States
| | - Xochitl Arzeta-Ferrer
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Randy D. Blakely
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Silvio O. Conte Center for Neuroscience Research, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Sandra J. Rosenthal
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Nanoscale Science and Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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18
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Vu TQ, Lam WY, Hatch EW, Lidke DS. Quantum dots for quantitative imaging: from single molecules to tissue. Cell Tissue Res 2015; 360:71-86. [PMID: 25620410 DOI: 10.1007/s00441-014-2087-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/04/2014] [Indexed: 10/24/2022]
Abstract
Since their introduction to biological imaging, quantum dots (QDs) have progressed from a little known, but attractive, technology to one that has gained broad application in many areas of biology. The versatile properties of these fluorescent nanoparticles have allowed investigators to conduct biological studies with extended spatiotemporal capabilities that were previously not possible. In this review, we focus on QD applications that provide enhanced quantitative information concerning protein dynamics and localization, including single particle tracking and immunohistochemistry, and finish by examining the prospects of upcoming applications, such as correlative light and electron microscopy and super-resolution. Advances in single molecule imaging, including multi-color and three-dimensional QD tracking, have provided new insights into the mechanisms of cell signaling and protein trafficking. New forms of QD tracking in vivo have allowed the observation of biological processes at molecular level resolution in the physiological context of the whole animal. Further methodological development of multiplexed QD-based immunohistochemistry assays should enable more quantitative analysis of key proteins in tissue samples. These advances highlight the unique quantitative data sets that QDs can provide to further our understanding of biological and disease processes.
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Affiliation(s)
- Tania Q Vu
- Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, Ore., USA,
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19
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Wegner KD, Hildebrandt N. Quantum dots: bright and versatile in vitro and in vivo fluorescence imaging biosensors. Chem Soc Rev 2015; 44:4792-4834. [DOI: 10.1039/c4cs00532e] [Citation(s) in RCA: 562] [Impact Index Per Article: 62.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Colourful cells and tissues: semiconductor quantum dots and their versatile applications in multiplexed bioimaging research.
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Affiliation(s)
- K. David Wegner
- NanoBioPhotonics
- Institut d'Electronique Fondamentale
- Université Paris-Sud
- 91405 Orsay Cedex
- France
| | - Niko Hildebrandt
- NanoBioPhotonics
- Institut d'Electronique Fondamentale
- Université Paris-Sud
- 91405 Orsay Cedex
- France
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20
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Liang Q, Wu QY, Wang ZY. Effect of hydrophobic mismatch on domain formation and peptide sorting in the multicomponent lipid bilayers in the presence of immobilized peptides. J Chem Phys 2014; 141:074702. [DOI: 10.1063/1.4891931] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Qing Liang
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, People's Republic of China
- Department of Physics, Ningbo University, Ningbo 315211, People's Republic of China
| | - Qing-Yan Wu
- Center for Statistical and Theoretical Condensed Matter Physics and Department of Physics, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Zhi-Yong Wang
- School of Optoelectronic Information, Chongqing University of Technology, Chongqing 400054, People's Republic of China
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21
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Affiliation(s)
- Wei Wang
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Nongjian Tao
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Electrical Engineering, Arizona State University, Tempe, AZ 85287, USA
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22
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Abstract
This article describes a procedure to prepare a raft-like intracellular membrane fraction enriched for the trans-Golgi network (TGN) and endosomal compartments. The initial step in this technique involves cell disruption by homogenization, followed by clearance of the plasma membrane, late endosomes, mitochondria and the endoplasmic reticulum by differential sedimentation. Carbonate treatment, sonication and sucrose density-gradient ultracentrifugation are subsequently used to isolate the target membranes. The isolated subcellular fraction contains less than 1% of the total cellular proteins, but it is highly enriched for syntaxin-6 and Rab11. Typically, 40-60% of the cellular pool of GM1 glycosphingolipid and 10-20% of the total cellular cholesterol cofractionate with this buoyant membrane fraction. Given the role of GM1 as a cell-surface receptor for the cholera toxin and that levels of both GM1 and cholesterol in the TGN-endosomal compartment are upregulated in some inherited diseases, this protocol can potentially be applied to the analysis of disease-associated changes to GM1-enriched intracellular membranes. The isolated membranes are very well separated from caveolin-rich domains of the plasma membrane, the TGN and recycling endosomes. The entire protocol can be completed in as little as 1 d.
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Affiliation(s)
- Mark G Waugh
- Institute for Liver and Digestive Health, University College London, Royal Free Campus, London, UK
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23
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Chang JC, Rosenthal SJ. A Bright Light to Reveal Mobility: Single Quantum Dot Tracking Reveals Membrane Dynamics and Cellular Mechanisms. J Phys Chem Lett 2013; 4:2858-2866. [PMID: 28626534 PMCID: PMC5473254 DOI: 10.1021/jz401071g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This perspective describes recent progress in single quantum dot techniques, with an emphasis on their applications in exploring membrane dynamics and cellular mechanisms. In these cases, conventional population measurements, such as fluorescence recovery after photobleaching, yield only a mean value on an ensemble or bulk collection of molecules, where the behavior of individual proteins and vehicles is missing. In recent years, the single quantum dot imaging approach has been introduced as a sub-category of single molecule fluorescent techniques to reveal single protein/vehicle dynamics in real-time. One of the major advantages of using single quantum dots is the high signal-to-noise ratio originating from their unique photophysical properties such as extraordinarily high molar extinction coefficients and large effective Stokes shifts. In addition to a brief overview on the principle of single quantum dot imaging techniques, we highlight recent discoveries and discuss future directions in the field.
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Affiliation(s)
- Jerry C. Chang
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Sandra J. Rosenthal
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
- Department of Pharmacology, Chemical and Biomolecular Engineering, Physics and Astronomy, and Vanderbilt Institute of Nanoscale Science and Engineering, Vanderbilt University, Nashville, TN 37235
- Department of Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
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