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Kompella VPS, Romano MC, Stansfield I, Mancera RL. What determines sub-diffusive behavior in crowded protein solutions? Biophys J 2024; 123:134-146. [PMID: 38073154 PMCID: PMC10808025 DOI: 10.1016/j.bpj.2023.12.002] [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: 06/11/2023] [Revised: 10/07/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023] Open
Abstract
The aqueous environment inside cells is densely packed. A typical cell has a macromolecular concentration in the range 90-450 g/L, with 5%-40% of its volume being occupied by macromolecules, resulting in what is known as macromolecular crowding. The space available for the free diffusion of metabolites and other macromolecules is thus greatly reduced, leading to so-called excluded volume effects. The slow diffusion of macromolecules under crowded conditions has been explained using transient complex formation. However, sub-diffusion noted in earlier works is not well characterized, particularly the role played by transient complex formation and excluded volume effects. We have used Brownian dynamics simulations to characterize the diffusion of chymotrypsin inhibitor 2 in protein solutions of bovine serum albumin and lysozyme at concentrations ranging from 50 to 300 g/L. The predicted changes in diffusion coefficient as a function of crowder concentration are consistent with NMR experiments. The sub-diffusive behavior observed in the sub-microsecond timescale can be explained in terms of a so-called cage effect, arising from rattling motion in a local molecular cage as a consequence of excluded volume effects. By selectively manipulating the nature of interactions between protein molecules, we determined that excluded volume effects induce sub-diffusive dynamics at sub-microsecond timescales. These findings may help to explain the diffusion-mediated effects of protein crowding on cellular processes.
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Affiliation(s)
- Vijay Phanindra Srikanth Kompella
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin Institute for Data Science, Curtin University, Perth, Western Australia, Australia; Department of Physics, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom
| | - Maria Carmen Romano
- Department of Physics, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom; Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ian Stansfield
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ricardo L Mancera
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin Institute for Data Science, Curtin University, Perth, Western Australia, Australia.
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2
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Wlodarczyk D, Amilusik M, Kosyl KM, Chrunik M, Lawniczak-Jablonska K, Strankowski M, Zajac M, Tsiumra V, Grochot A, Reszka A, Suchocki A, Giela T, Iwanowski P, Bockowski M, Przybylinska H. Synthesis Attempt and Structural Studies of Novel A 2CeWO 6 Double Perovskites (A 2+ = Ba, Ca) in and outside of Ambient Conditions. ACS OMEGA 2022; 7:18382-18408. [PMID: 35694470 PMCID: PMC9178617 DOI: 10.1021/acsomega.2c00669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/21/2022] [Indexed: 05/25/2023]
Abstract
This comprehensive work showcases two novel, rock-salt-type minerals in the form of amphoteric cerium-tungstate double perovskite and ilmenite powders created via a high-temperature solid-state reaction in inert gases. The presented studies have fundamental meaning and will mainly focus on a detailed synthesis description of undoped structures, researching their possible polymorphism in various conditions and hinting at some nontrivial physicochemical properties like charge transfer for upcoming optical studies after eventual doping with selectively chosen rare-earth ions. The formerly mentioned, targeted A2BB'X6 group of compounds contains mainly divalent alkali cations in the form of XIIA = Ba2+, Ca2+ sharing, here, oxygen-arranged clusters (IIX = O2-) with purposely selected central ions from f-block VIB = Ce4/3+ and d-block VIB' = W4/5/6+ since together they often possess some exotic properties that could be tuned and implemented into futuristic equipment like sensors or energy converters. Techniques like powder XRD, XPS, XAS, EPR, Raman, and FTIR spectroscopies alongside DSC and TG were involved with an intent to thoroughly describe any possible changes within these materials. Mainly, to have a full prospect of any desirable or undesirable phenomena before diving into more complicated subjects like: energy or charge transfer in low temperatures; to reveal whether or not the huge angular tilting generates large enough dislocations within the material's unit cell to change its initial properties; or if temperature and pressure stimuli are responsible for any phase transitions and eventual, irreversible decomposition.
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Affiliation(s)
- Damian Wlodarczyk
- Institute
of Physics, Polish Academy of Sciences, Ave. Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Mikolaj Amilusik
- Institute
of High Pressure, Polish Academy of Sciences, Sokolowska 29/37, PL-01142 Warsaw, Poland
| | - Katarzyna M. Kosyl
- Institute
of Physics, Polish Academy of Sciences, Ave. Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Maciej Chrunik
- Military
University of Technology, Gen. Sylwestra Kaliskiego 2, PL-00908 Warsaw, Poland
| | | | - Michal Strankowski
- Chemical
Faculty, Gdansk University of Technology, G. Narutowicza 11/12, PL-80233 Gdansk, Poland
| | - Marcin Zajac
- Solaris
Synchrotron NSRC, Jagiellonian University, Czerwone Maki 98, PL-30392 Cracow, Poland
| | - Volodymyr Tsiumra
- Institute
of Physics, Polish Academy of Sciences, Ave. Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Aneta Grochot
- Institute
of Physics, Polish Academy of Sciences, Ave. Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Anna Reszka
- Institute
of Physics, Polish Academy of Sciences, Ave. Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Andrzej Suchocki
- Institute
of Physics, Polish Academy of Sciences, Ave. Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Tomasz Giela
- Solaris
Synchrotron NSRC, Jagiellonian University, Czerwone Maki 98, PL-30392 Cracow, Poland
| | - Przemyslaw Iwanowski
- Institute
of Physics, Polish Academy of Sciences, Ave. Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Michal Bockowski
- Institute
of High Pressure, Polish Academy of Sciences, Sokolowska 29/37, PL-01142 Warsaw, Poland
| | - Hanka Przybylinska
- Institute
of Physics, Polish Academy of Sciences, Ave. Lotnikow 32/46, PL-02668 Warsaw, Poland
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3
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Liu A, Huang X, He W, Xue F, Yang Y, Liu J, Chen L, Yuan L, Xu P. pHmScarlet is a pH-sensitive red fluorescent protein to monitor exocytosis docking and fusion steps. Nat Commun 2021; 12:1413. [PMID: 33658493 PMCID: PMC7930027 DOI: 10.1038/s41467-021-21666-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/05/2021] [Indexed: 12/21/2022] Open
Abstract
pH-sensitive fluorescent proteins (FPs) are highly advantageous for the non-invasive monitoring of exocytosis events. Superecliptic pHluorin (SEP), a green pH-sensitive FP, has been widely used for imaging single-vesicle exocytosis. However, the docking step cannot be visualized using this FP, since the fluorescence signal inside vesicles is too low to be observed during docking process. Among the available red pH-sensitive FPs, none is comparable to SEP for practical applications due to unoptimized pH-sensitivity and fluorescence brightness or severe photochromic behavior. In this study, we engineer a bright and photostable red pH-sensitive FP, named pHmScarlet, which compared to other red FPs has higher pH sensitivity and enables the simultaneous detection of vesicle docking and fusion. pHmScarlet can also be combined with SEP for dual-color imaging of two individual secretory events. Furthermore, although the emission wavelength of pHmScarlet is red-shifted compared to that of SEP, its spatial resolution is high enough to show the ring structure of vesicle fusion pores using Hessian structured illumination microscopy (Hessian-SIM).
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Affiliation(s)
- Anyuan Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaoshuai Huang
- Biomedical Engineering Department, Peking University, Beijing, China
| | - Wenting He
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fudong Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yanrui Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, China
| | - Jiajia Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Lin Yuan
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Pingyong Xu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Department of Clinical Laboratory, Children's Hospital of Chongqing Medical University, Chongqing, China.
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4
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Line-FRAP, A Versatile Method to Measure Diffusion Rates In Vitro and In Vivo. J Mol Biol 2021; 433:166898. [PMID: 33647289 DOI: 10.1016/j.jmb.2021.166898] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022]
Abstract
The crowded cellular milieu affect molecular diffusion through hard (occluded space) and soft (weak, non-specific) interactions. Multiple methods have been developed to measure diffusion coefficients at physiological protein concentrations within cells, each with its limitations. Here, we show that Line-FRAP, combined with rigours data analysis, is able to determine diffusion coefficients in a variety of environments, from in vitro to in vivo. The use of Line mode greatly improves time resolution of FRAP data acquisition, from 20-100 Hz in the classical mode to 800 Hz in the line mode. This improves data analysis, as intensity and radius of the bleach at the first post-bleach frame is critical. We evaluated the method on different proteins labelled chemically or fused to YFP in a wide range of environments. The diffusion coefficients measured in HeLa and in E. coli were ~2.5-fold and 15-fold slower than in buffer, and were comparable to previously published data. Increasing the osmotic pressure on E. coli further decreases diffusion, to the point at which proteins virtually stop moving. The method presented here, which requires a confocal microscope equipped with dual scanners, can be applied to study a large range of molecules with different sizes, and provides robust results in a wide range of environments and protein concentrations for fast diffusing molecules.
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5
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Casarotto PC, Girych M, Fred SM, Kovaleva V, Moliner R, Enkavi G, Biojone C, Cannarozzo C, Sahu MP, Kaurinkoski K, Brunello CA, Steinzeig A, Winkel F, Patil S, Vestring S, Serchov T, Diniz CRAF, Laukkanen L, Cardon I, Antila H, Rog T, Piepponen TP, Bramham CR, Normann C, Lauri SE, Saarma M, Vattulainen I, Castrén E. Antidepressant drugs act by directly binding to TRKB neurotrophin receptors. Cell 2021; 184:1299-1313.e19. [PMID: 33606976 PMCID: PMC7938888 DOI: 10.1016/j.cell.2021.01.034] [Citation(s) in RCA: 318] [Impact Index Per Article: 106.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 12/22/2020] [Accepted: 01/21/2021] [Indexed: 12/11/2022]
Abstract
It is unclear how binding of antidepressant drugs to their targets gives rise to the clinical antidepressant effect. We discovered that the transmembrane domain of tyrosine kinase receptor 2 (TRKB), the brain-derived neurotrophic factor (BDNF) receptor that promotes neuronal plasticity and antidepressant responses, has a cholesterol-sensing function that mediates synaptic effects of cholesterol. We then found that both typical and fast-acting antidepressants directly bind to TRKB, thereby facilitating synaptic localization of TRKB and its activation by BDNF. Extensive computational approaches including atomistic molecular dynamics simulations revealed a binding site at the transmembrane region of TRKB dimers. Mutation of the TRKB antidepressant-binding motif impaired cellular, behavioral, and plasticity-promoting responses to antidepressants in vitro and in vivo. We suggest that binding to TRKB and allosteric facilitation of BDNF signaling is the common mechanism for antidepressant action, which may explain why typical antidepressants act slowly and how molecular effects of antidepressants are translated into clinical mood recovery.
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Affiliation(s)
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Senem M Fred
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | - Vera Kovaleva
- Institute of Biotechnology-HILIFE, University of Helsinki, Helsinki, Finland
| | - Rafael Moliner
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | - Giray Enkavi
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Caroline Biojone
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | | | | | - Katja Kaurinkoski
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | | | - Anna Steinzeig
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | - Frederike Winkel
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | - Sudarshan Patil
- Department of Biomedicine and KG Jebsen Center for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Stefan Vestring
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Berta-Ottenstein-Programme for Clinician Scientists, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tsvetan Serchov
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Cassiano R A F Diniz
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland; Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, São Paul, Brazil
| | - Liina Laukkanen
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland
| | - Iseline Cardon
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland; Brain Master Program, Faculty of Science, Aix-Marseille Université, Marseille, France; Department of Psychiatry, University of Regensburg, Regenburg, Germany
| | - Hanna Antila
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland; Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tomasz Rog
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Timo Petteri Piepponen
- Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Clive R Bramham
- Department of Biomedicine and KG Jebsen Center for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Claus Normann
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Basics in Neuromodulation (NeuroModul Basics), University of Freiburg, Freiburg, Germany
| | - Sari E Lauri
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland; Molecular and Integrative Biosciences Research Program, University of Helsinki, Helsinki, Finland
| | - Mart Saarma
- Institute of Biotechnology-HILIFE, University of Helsinki, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland; Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Eero Castrén
- Neuroscience Center-HILIFE, University of Helsinki, Helsinki, Finland.
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6
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Sánchez MF, Murad F, Gülcüler Balta GS, Martin-Villalba A, García-Sáez AJ, Carrer DC. Early activation of CD95 is limited and localized to the cytotoxic synapse. FEBS J 2018; 285:2813-2827. [PMID: 29797791 DOI: 10.1111/febs.14518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 04/28/2018] [Accepted: 05/22/2018] [Indexed: 01/13/2023]
Abstract
The cytotoxic synapse formed between cytotoxic T lymphocytes or natural killer cells expressing CD95L and target cells with CD95 on their surface is a key pathway for apoptosis induction by the immune system. Despite similarities with the immune synapse in antigen presenting cells, little is known about the role of the spatiotemporal organization of agonistic proteins/receptor interactions for CD95 signaling. Here, we have developed an artificial cytotoxic synapse to examine how mobility and geometry of an anti-CD95 agonistic antibody affect receptor aggregation and mobility, ie the first step of receptor activation. By measuring the distribution, diffusion coefficient, and fraction of immobile CD95 receptor in living cells, we show that at short times, the initial activation of CD95 occurs locally and is limited to the contact region of the cytotoxic synapse. This anisotropic activation of apoptotic signaling supports a role for confined interactions on the efficiency of signal transduction that may have implications for biomedical applications of extrinsic apoptosis induction.
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Affiliation(s)
- María Florencia Sánchez
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC), CONICET-Universidad Nacional de Córdoba, Argentina
| | - Fabronia Murad
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Gülce S Gülcüler Balta
- Department of Molecular Neurobiology, German Cancer Research Center (DFKZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Germany
| | - Ana Martin-Villalba
- Department of Molecular Neurobiology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Ana J García-Sáez
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Dolores C Carrer
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC), CONICET-Universidad Nacional de Córdoba, Argentina
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7
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Dynamic microtubule association of Doublecortin X (DCX) is regulated by its C-terminus. Sci Rep 2017; 7:5245. [PMID: 28701724 PMCID: PMC5507856 DOI: 10.1038/s41598-017-05340-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/25/2017] [Indexed: 12/14/2022] Open
Abstract
Doublecortin X (DCX), known to be essential for neuronal migration and cortical layering in the developing brain, is a 40 kDa microtubule (MT)-associated protein. DCX directly interacts with MTs via its two structured doublecortin (DC) domains, but the dynamics of this association and the possible regulatory roles played by the flanking unstructured regions remain poorly defined. Here, we employ quantitative fluorescence recovery after photobleaching (FRAP) protocols in living cells to reveal that DCX shows remarkably rapid and complete exchange within the MT network but that the removal of the C-terminal region significantly slows this exchange. We further probed how MT organization or external stimuli could additionally modulate DCX exchange dynamics. MT depolymerisation (nocodazole treatment) or stabilization (taxol treatment) further enhanced DCX exchange rates, however the exchange rates for the C-terminal truncated DCX protein were resistant to the impact of taxol-induced stabilization. Furthermore, in response to a hyperosmotic stress stimulus, DCX exchange dynamics were slowed, and again the C-terminal truncated DCX protein was resistant to the stimulus. Thus, the DCX dynamically associates with MTs in living cells and its C-terminal region plays important roles in the MT-DCX association.
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8
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Verdugo M, Ogra Y, Quiroz W. Mechanisms underlying the toxic effects of antimony species in human embryonic kidney cells (HEK-293) and their comparison with arsenic species. J Toxicol Sci 2017; 41:783-792. [PMID: 27853107 DOI: 10.2131/jts.41.783] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Antimony cytotoxicity was assessed in human embryonic kidney cells (HEK-293). Uptake, mitochondrial respiratory activity, ROS generation and diffusional kinetics were measured using fluorescence recovery after photobleaching (FRAP). Furthermore, the toxic effect induced by Sb was compared with As toxicity in regard to ROS generation and diffusional kinetics, which provides information on the protein aggregation process. Our results show a favored uptake of Sb(III) and a more severe effect, decreasing the mitochondrial activity more than in the presence of Sb(V). In comparison with As, the Sb species did not generate a significant increase in ROS generation, which was observed with As(III) and As(V). FRAP analysis yielded important information on the diffusion and binding dynamics of live cells in presence of these metalloids. The mobile fraction showed a strong decrease with the As species and Sb(III). The diffusion rate and the koff-rate were significantly decreased for the As and Sb species but were more strong in the presence of As(III).
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Affiliation(s)
- Marcelo Verdugo
- Laboratory of Toxicology and Environmental Health, Graduate School of Pharmaceutical Sciences, Chiba University
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9
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Vasilyeva NA, Murzina GB, Kireev II, Pivovarov AS. Influence of Membrane Receptor Lateral Diffusion on the Short-Term Depression of Acetylcholine-Induced Current in Helix Neurons. Cell Mol Neurobiol 2017; 37:1443-1455. [PMID: 28236056 DOI: 10.1007/s10571-017-0475-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/16/2017] [Indexed: 11/29/2022]
Abstract
We have studied how various drugs increasing the rate of nicotinic acetylcholine receptors (nAChRs) lateral diffusion affect the depression of ACh-induced current in land snail Helix lucorum neurons responsible for defensive behavior. The acetylcholine (ACh) iontophoretic application protocol imitated the behavioral habituation protocol for the intact animal. We found that the drugs decreasing cholesterol level in cell membranes as methyl-β-cyclodextrin 1 mM and Ro 48-8071 2 µM, and polyclonal antibodies to actin-binding proteins as spectrin 5 µg/ml and merlin 2.5 µg/ml have changed the dynamic of ACh-current depression. The nAChRs lateral diffusion coefficient was obtained by fluorescence recovery after photobleaching. A curve fitting model specially created for analysis of short-term choline sensitivity depression in snail neurons helped us evaluate separately the contribution of nAChRs lateral diffusion, their endocytosis and exocytosis to observed effects during electrophysiological experiments. Taken together, we hypothesize that nAChRs lateral diffusion plays an important role in the cellular correlate of habituation in land snail Helix lucorum neurons.
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Affiliation(s)
- Natalia A Vasilyeva
- Department of Higher Nervous Activity, Lomonosov Moscow State University, Leninskie Gory, 1, building 12, Moscow, Russia, 119234.,Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Butlerova, 5a, Moscow, Russia, 117485
| | - Galina B Murzina
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Butlerova, 5a, Moscow, Russia, 117485
| | - Igor I Kireev
- A.N.Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 1, building 40, Moscow, Russia, 119234
| | - Arkady S Pivovarov
- Department of Higher Nervous Activity, Lomonosov Moscow State University, Leninskie Gory, 1, building 12, Moscow, Russia, 119234.
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10
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A Quick-responsive DNA Nanotechnology Device for Bio-molecular Homeostasis Regulation. Sci Rep 2016; 6:31379. [PMID: 27506964 PMCID: PMC4979213 DOI: 10.1038/srep31379] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/12/2016] [Indexed: 01/01/2023] Open
Abstract
Physiological processes such as metabolism, cell apoptosis and immune responses, must be strictly regulated to maintain their homeostasis and achieve their normal physiological functions. The speed with which bio-molecular homeostatic regulation occurs directly determines the ability of an organism to adapt to conditional changes. To produce a quick-responsive regulatory system that can be easily utilized for various types of homeostasis, a device called nano-fingers that facilitates the regulation of physiological processes was constructed using DNA origami nanotechnology. This nano-fingers device functioned in linked open and closed phases using two types of DNA tweezers, which were covalently coupled with aptamers that captured specific molecules when the tweezer arms were sufficiently close. Via this specific interaction mechanism, certain physiological processes could be simultaneously regulated from two directions by capturing one biofactor and releasing the other to enhance the regulatory capacity of the device. To validate the universal application of this device, regulation of the homeostasis of the blood coagulant thrombin was attempted using the nano-fingers device. It was successfully demonstrated that this nano-fingers device achieved coagulation buffering upon the input of fuel DNA. This nano-device could also be utilized to regulate the homeostasis of other types of bio-molecules.
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11
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Kneussel M, Hausrat TJ. Postsynaptic Neurotransmitter Receptor Reserve Pools for Synaptic Potentiation. Trends Neurosci 2016; 39:170-182. [PMID: 26833258 DOI: 10.1016/j.tins.2016.01.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 11/18/2022]
Abstract
At excitatory and inhibitory synapses, an immediate transfer of additional neurotransmitter receptors from non-synaptic positions to the synapse mediates synaptic long-term potentiation (LTP). Different types of non-synaptic reserve pools permit the rapid supply of transmembrane neurotransmitter receptors. Recycling endosomes (REs) serve as an intracellular reservoir of receptors that is delivered to the plasma membrane on LTP induction. Furthermore, AMPA receptors at the non-synaptic plasma membrane provide an extrasynaptic reserve pool that is also important to potentiate synapse function. Finally, bidirectional synaptic versus extrasynaptic trapping of freely diffusing plasma membrane GABAA receptors (GABAARs) by scaffolding proteins modulates synaptic transmission. Here we discuss novel findings regarding neurotransmitter receptor reservoirs and potential reserve pool mechanisms for synaptic potentiation.
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Affiliation(s)
- Matthias Kneussel
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany.
| | - Torben Johann Hausrat
- Department of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany
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12
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Abstract
The study of polarized protein trafficking in live neurons is critical for understanding neuronal structure and function. Given the complex anatomy of neurons and the numerous trafficking pathways that are active in them, however, visualization of specific vesicle populations leaving the Golgi complex presents unique challenges. Indeed, several approaches used in non-polarized cells, and even in polarized epithelial cells, have been less successful in neurons. Here, we describe an adaptation of the recently developed Retention Using Selective Hooks (RUSH) system (Boncompain et al., Nat Methods 9:493-498, 2012), previously used in non-polarized cells, to analyze the polarized sorting of proteins from the Golgi complex to dendrites and axons in live neurons. The RUSH system involves the retention of a fluorescently tagged cargo protein fused to the streptavidin-binding peptide (SBP) in the endoplasmic reticulum (ER) through the expression of an ER-hook protein fused to streptavidin. Upon D-biotin addition, the cargo protein is released and its traffic to dendrites and axons can be analyzed in live neurons.
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13
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Fluorescence recovery after photobleaching in material and life sciences: putting theory into practice. Q Rev Biophys 2015; 48:323-87. [PMID: 26314367 DOI: 10.1017/s0033583515000013] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
AbstractFluorescence recovery after photobleaching (FRAP) is a versatile tool for determining diffusion and interaction/binding properties in biological and material sciences. An understanding of the mechanisms controlling the diffusion requires a deep understanding of structure–interaction–diffusion relationships. In cell biology, for instance, this applies to the movement of proteins and lipids in the plasma membrane, cytoplasm and nucleus. In industrial applications related to pharmaceutics, foods, textiles, hygiene products and cosmetics, the diffusion of solutes and solvent molecules contributes strongly to the properties and functionality of the final product. All these systems are heterogeneous, and accurate quantification of the mass transport processes at the local level is therefore essential to the understanding of the properties of soft (bio)materials. FRAP is a commonly used fluorescence microscopy-based technique to determine local molecular transport at the micrometer scale. A brief high-intensity laser pulse is locally applied to the sample, causing substantial photobleaching of the fluorescent molecules within the illuminated area. This causes a local concentration gradient of fluorescent molecules, leading to diffusional influx of intact fluorophores from the local surroundings into the bleached area. Quantitative information on the molecular transport can be extracted from the time evolution of the fluorescence recovery in the bleached area using a suitable model. A multitude of FRAP models has been developed over the years, each based on specific assumptions. This makes it challenging for the non-specialist to decide which model is best suited for a particular application. Furthermore, there are many subtleties in performing accurate FRAP experiments. For these reasons, this review aims to provide an extensive tutorial covering the essential theoretical and practical aspects so as to enable accurate quantitative FRAP experiments for molecular transport measurements in soft (bio)materials.
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Shen Y, Rosendale M, Campbell RE, Perrais D. pHuji, a pH-sensitive red fluorescent protein for imaging of exo- and endocytosis. J Cell Biol 2014; 207:419-32. [PMID: 25385186 PMCID: PMC4226733 DOI: 10.1083/jcb.201404107] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 10/07/2014] [Indexed: 11/22/2022] Open
Abstract
Fluorescent proteins with pH-sensitive fluorescence are valuable tools for the imaging of exocytosis and endocytosis. The Aequorea green fluorescent protein mutant superecliptic pHluorin (SEP) is particularly well suited to these applications. Here we describe pHuji, a red fluorescent protein with a pH sensitivity that approaches that of SEP, making it amenable for detection of single exocytosis and endocytosis events. To demonstrate the utility of the pHuji plus SEP pair, we perform simultaneous two-color imaging of clathrin-mediated internalization of both the transferrin receptor and the β2 adrenergic receptor. These experiments reveal that the two receptors are differentially sorted at the time of endocytic vesicle formation.
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Affiliation(s)
- Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Morgane Rosendale
- University of Bordeaux and Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000 Bordeaux, France University of Bordeaux and Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000 Bordeaux, France
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - David Perrais
- University of Bordeaux and Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000 Bordeaux, France University of Bordeaux and Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000 Bordeaux, France
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Bauer NC, Corbett AH, Doetsch PW. Automated quantification of the subcellular localization of multicompartment proteins via Q-SCAn. Traffic 2013; 14:1200-8. [PMID: 24034606 PMCID: PMC3836439 DOI: 10.1111/tra.12118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/06/2013] [Accepted: 09/11/2013] [Indexed: 01/19/2023]
Abstract
In eukaryotic cells, proteins can occupy multiple intracellular compartments and even move between compartments to fulfill critical biological functions or respond to cellular signals. Examples include transcription factors that reside in the cytoplasm but are mobilized to the nucleus as well as dual-purpose DNA repair proteins that are charged with simultaneously maintaining the integrity of both the nuclear and mitochondrial genomes. While numerous methods exist to study protein localization and dynamics, automated methods to quantify the relative amounts of proteins that occupy multiple subcellular compartments have not been extensively developed. To address this need, we present a rapid, automated method termed quantitative subcellular compartmentalization analysis (Q-SCAn). To develop this method, we exploited the facile molecular biology of the budding yeast, Saccharomyces cerevisiae. Individual subcellular compartments are defined by a fluorescent marker protein and the intensity of a target GFP-tagged protein is then quantified within each compartment. To validate Q-SCAn, we analyzed relocalization of the transcription factor Yap1 following oxidative stress and then extended the approach to multicompartment localization by examining two DNA repair proteins critical for the base excision repair pathway, Ntg1 and Ung1. Our findings demonstrate the utility of Q-SCAn for quantitative analysis of the subcellular distribution of multicompartment proteins.
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Affiliation(s)
- Nicholas C. Bauer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Anita H. Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, United States
| | - Paul W. Doetsch
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, United States
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, 30322, United States
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, United States
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González-González IM, Henley JM. Postsynaptic kainate receptor recycling and surface expression are regulated by metabotropic autoreceptor signalling. Traffic 2013; 14:810-22. [PMID: 23556457 PMCID: PMC3744763 DOI: 10.1111/tra.12071] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 04/02/2013] [Accepted: 04/04/2013] [Indexed: 01/01/2023]
Abstract
Kainate receptors (KARs) play fundamentally important roles in controlling synaptic function and regulating neuronal excitability. Postsynaptic KARs contribute to excitatory neurotransmission but the molecular mechanisms underlying their activity-dependent surface expression are not well understood. Strong activation of KARs in cultured hippocampal neurons leads to the downregulation of postsynaptic KARs via endocytosis and degradation. In contrast, low-level activation augments postsynaptic KAR surface expression. Here, we show that this increase in KARs is due to enhanced recycling via the recruitment of Rab11-dependent, transferrin-positive endosomes into spines. Dominant-negative Rab11 or the recycling inhibitor primaquine prevents the kainate-evoked increase in surface KARs. Moreover, we show that the increase in surface expression is mediated via a metabotropic KAR signalling pathway, which is blocked by the protein kinase C inhibitor chelerythrine, the calcium chelator BAPTA and the G-protein inhibitor pertussis toxin. Thus, we report a previously uncharacterized positive feedback system that increases postsynaptic KARs in response to low- or moderate-level agonist activation and can provide additional flexibility to synaptic regulation.
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Affiliation(s)
| | - Jeremy M Henley
- School of Biochemistry, University of Bristol, Medical Sciences Building, University WalkBristol, BS8 1TD, UK
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