1
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Sampieri A, Padilla-Flores T, Thawani AR, Lam PY, Fuchter MJ, Peterson R, Vaca L. The conducting state of TRPA1 modulates channel lateral mobility. Cell Calcium 2023; 116:102800. [PMID: 37776645 DOI: 10.1016/j.ceca.2023.102800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/04/2023] [Accepted: 09/16/2023] [Indexed: 10/02/2023]
Abstract
We have studied Danio rerio (Zebrafish) TRPA1 channel using a method that combines single channel electrophysiological and optical recordings to evaluate lateral mobility and channel gating simultaneously in single channels. TRPA1 channel activation by two distinct chemical ligands: allyl isothiocyanate (AITC) and TRPswitch B, results in substantial reduction of channel lateral mobility at the plasma membrane. Incubation with the cholesterol sequestering agent methyl-β-cyclodextrin (MβCD), prevents the reduction on lateral mobility induced by the two chemical agonists. This results strongly suggest that the open conformation of TRPA1 modulates channel lateral mobility probably by facilitating the insertion of the channel into cholesterol-enriched domains at the plasma membrane.
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Affiliation(s)
- Alicia Sampieri
- Instituto de Fisiología Celular. Departamento de Biología Celular y del desarrollo. Universidad Nacional Autónoma de México. México, CDMX 04510, Mexico
| | - Teresa Padilla-Flores
- Instituto de Fisiología Celular. Departamento de Biología Celular y del desarrollo. Universidad Nacional Autónoma de México. México, CDMX 04510, Mexico
| | - Aditya R Thawani
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, London W12 OBZ, United Kingdom
| | - Pui-Ying Lam
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 West Watertown Plank Rd., Milwaukee, Wisconsin 53226, USA; Neuroscience Research Center, Medical College of Wisconsin, 8701 West Watertown Plank Rd., Milwaukee, Wisconsin, 53226, USA
| | - Matthew J Fuchter
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, London W12 OBZ, United Kingdom
| | - Randall Peterson
- College of Pharmacy, University of Utah, 30 South 2000 East, Salt Lake City, Utah, 84112, USA
| | - Luis Vaca
- Instituto de Fisiología Celular. Departamento de Biología Celular y del desarrollo. Universidad Nacional Autónoma de México. México, CDMX 04510, Mexico.
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2
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Luo MB, Hua DY. Simulation Study on the Mechanism of Intermediate Subdiffusion of Diffusive Particles in Crowded Systems. ACS OMEGA 2023; 8:34188-34195. [PMID: 37744832 PMCID: PMC10515404 DOI: 10.1021/acsomega.3c05945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023]
Abstract
The intermediate subdiffusion of diffusive particles in crowded systems is studied for two model systems: the continuous time random walk (CTRW) model and the obstruction-binding model. For the CTRW model with an arbitrarily given longest waiting time τmax, we find that the diffusive particle exhibits subdiffusion below τmax and recovers normal diffusion above τmax. For the obstruction-binding model with randomly distributed attractive obstacles, the diffusion of the diffusive particle is dependent on the binding energy and the density of obstacles. Interestingly, diffusion curves for different binding strengths can be overlapped by rescaling the simulation time, indicating that the diffusive particle in the obstruction-binding model can change from the intermediate subdiffusion to the normal diffusion at a long-term simulation scale. The results of the two model systems show that the diffusive particles only exhibit intermediate subdiffusion below the longest waiting time. Therefore, long timescale subdiffusion would only be observed in the CTRW model with an infinitely long waiting time and in the obstruction-binding model with an infinitely large binding strength.
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Affiliation(s)
- Meng-Bo Luo
- School of Physics, Zhejiang University, Hangzhou 310027, China
| | - Dao-Yang Hua
- School of Physics, Zhejiang University, Hangzhou 310027, China
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3
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Ambattu LA, Yeo LY. Sonomechanobiology: Vibrational stimulation of cells and its therapeutic implications. BIOPHYSICS REVIEWS 2023; 4:021301. [PMID: 38504927 PMCID: PMC10903386 DOI: 10.1063/5.0127122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/27/2023] [Indexed: 03/21/2024]
Abstract
All cells possess an innate ability to respond to a range of mechanical stimuli through their complex internal machinery. This comprises various mechanosensory elements that detect these mechanical cues and diverse cytoskeletal structures that transmit the force to different parts of the cell, where they are transcribed into complex transcriptomic and signaling events that determine their response and fate. In contrast to static (or steady) mechanostimuli primarily involving constant-force loading such as compression, tension, and shear (or forces applied at very low oscillatory frequencies (≤ 1 Hz) that essentially render their effects quasi-static), dynamic mechanostimuli comprising more complex vibrational forms (e.g., time-dependent, i.e., periodic, forcing) at higher frequencies are less well understood in comparison. We review the mechanotransductive processes associated with such acoustic forcing, typically at ultrasonic frequencies (> 20 kHz), and discuss the various applications that arise from the cellular responses that are generated, particularly for regenerative therapeutics, such as exosome biogenesis, stem cell differentiation, and endothelial barrier modulation. Finally, we offer perspectives on the possible existence of a universal mechanism that is common across all forms of acoustically driven mechanostimuli that underscores the central role of the cell membrane as the key effector, and calcium as the dominant second messenger, in the mechanotransduction process.
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Affiliation(s)
- Lizebona August Ambattu
- Micro/Nanophysics Research Laboratory, School of Engineering, RMIT University, Melbourne VIC 3000, Australia
| | - Leslie Y. Yeo
- Micro/Nanophysics Research Laboratory, School of Engineering, RMIT University, Melbourne VIC 3000, Australia
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4
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Suzuki KGN, Komura N, Ando H. Recently developed glycosphingolipid probes and their dynamic behavior in cell plasma membranes as revealed by single-molecule imaging. Glycoconj J 2023; 40:305-314. [PMID: 37133616 DOI: 10.1007/s10719-023-10116-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2023] [Indexed: 05/04/2023]
Abstract
Glycosphingolipids, including gangliosides, are representative lipid raft markers that perform a variety of physiological roles in cell membranes. However, studies aimed at revealing their dynamic behavior in living cells are rare, mostly due to a lack of suitable fluorescent probes. Recently, the ganglio-series, lacto-series, and globo-series glycosphingolipid probes, which mimic the behavior of the parental molecules in terms of partitioning to the raft fraction, were developed by conjugating hydrophilic dyes to the terminal glycans of glycosphingolipids using state-of-art entirely chemical-based synthetic techniques. High-speed, single-molecule observation of these fluorescent probes revealed that gangliosides were scarcely trapped in small domains (100 nm in diameter) for more than 5 ms in steady-state cells, suggesting that rafts including gangliosides were always moving and very small. Furthermore, dual-color, single-molecule observations clearly showed that homodimers and clusters of GPI-anchored proteins were stabilized by transiently recruiting sphingolipids, including gangliosides, to form homodimer rafts and the cluster rafts, respectively. In this review, we briefly summarize recent studies, the development of a variety of glycosphingolipid probes as well as the identification of the raft structures including gangliosides in living cells by single-molecule imaging.
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Affiliation(s)
- Kenichi G N Suzuki
- Institute for Glyco-core Research (iGCORE), Gifu University, 501-1193, Gifu, Japan.
| | - Naoko Komura
- Institute for Glyco-core Research (iGCORE), Gifu University, 501-1193, Gifu, Japan.
| | - Hiromune Ando
- Institute for Glyco-core Research (iGCORE), Gifu University, 501-1193, Gifu, Japan.
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5
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Takebayashi K, Kamimura Y, Ueda M. Field model for multistate lateral diffusion of various transmembrane proteins observed in living Dictyostelium cells. J Cell Sci 2023; 136:286715. [PMID: 36655427 PMCID: PMC10022678 DOI: 10.1242/jcs.260280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
The lateral diffusion of transmembrane proteins on plasma membranes is a fundamental process for various cellular functions. Diffusion properties specific for individual protein species have been extensively studied, but the common features among protein species are poorly understood. Here, we systematically studied the lateral diffusion of various transmembrane proteins in the lower eukaryote Dictyostelium discoideum cells using a hidden Markov model for single-molecule trajectories obtained experimentally. As common features, all membrane proteins that had from one to ten transmembrane regions adopted three free diffusion states with similar diffusion coefficients regardless of their structural variability. All protein species reduced their mobility similarly upon the inhibition of microtubule or actin cytoskeleton dynamics, or myosin II. The relationship between protein size and the diffusion coefficient was consistent with the Saffman-Delbrück model, meaning that membrane viscosity is a major determinant of lateral diffusion, but protein size is not. These protein species-independent properties of multistate free diffusion were explained simply and quantitatively by free diffusion on the three membrane regions with different viscosities, which is in sharp contrast to the complex diffusion behavior of transmembrane proteins in higher eukaryotes.
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Affiliation(s)
- Kazutoshi Takebayashi
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.,Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Yoichiro Kamimura
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Masahiro Ueda
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.,Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
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6
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Refinement of Singer-Nicolson fluid-mosaic model by microscopy imaging: Lipid rafts and actin-induced membrane compartmentalization. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184093. [PMID: 36423676 DOI: 10.1016/j.bbamem.2022.184093] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022]
Abstract
This year celebrates the 50th anniversary of the Singer-Nicolson fluid mosaic model for biological membranes. The next level of sophistication we have achieved for understanding plasma membrane (PM) structures, dynamics, and functions during these 50 years includes the PM interactions with cortical actin filaments and the partial demixing of membrane constituent molecules in the PM, particularly raft domains. Here, first, we summarize our current knowledge of these two structures and emphasize that they are interrelated. Second, we review the structure, molecular dynamics, and function of raft domains, with main focuses on raftophilic glycosylphosphatidylinositol-anchored proteins (GPI-APs) and their signal transduction mechanisms. We pay special attention to the results obtained by single-molecule imaging techniques and other advanced microscopy methods. We also clarify the limitations of present optical microscopy methods for visualizing raft domains, but emphasize that single-molecule imaging techniques can "detect" raft domains associated with molecules of interest in the PM.
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7
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Single-Molecule Imaging of Ganglioside Probes in Living Cell Plasma Membranes. Methods Mol Biol 2023; 2613:215-227. [PMID: 36587082 DOI: 10.1007/978-1-0716-2910-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Gangliosides play a variety of physiological roles and are one of the most important lipid raft constituents. However, their dynamic behaviors have scarcely been investigated in living cells because of the lack of fluorescent probes that behave like their parental molecules. Recently, fluorescent ganglioside probes that mimic native ganglioside behaviors have been developed. In this chapter, I discuss the recent advances in research related to the lateral localization and dynamic behaviors of gangliosides in the plasma membranes of living cells.
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8
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Lipid Polarization during Cytokinesis. Cells 2022; 11:cells11243977. [PMID: 36552741 PMCID: PMC9776629 DOI: 10.3390/cells11243977] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
The plasma membrane of eukaryotic cells is composed of a large number of lipid species that are laterally segregated into functional domains as well as asymmetrically distributed between the outer and inner leaflets. Additionally, the spatial distribution and organization of these lipids dramatically change in response to various cellular states, such as cell division, differentiation, and apoptosis. Division of one cell into two daughter cells is one of the most fundamental requirements for the sustenance of growth in all living organisms. The successful completion of cytokinesis, the final stage of cell division, is critically dependent on the spatial distribution and organization of specific lipids. In this review, we discuss the properties of various lipid species associated with cytokinesis and the mechanisms involved in their polarization, including forward trafficking, endocytic recycling, local synthesis, and cortical flow models. The differences in lipid species requirements and distribution in mitotic vs. male meiotic cells will be discussed. We will concentrate on sphingolipids and phosphatidylinositols because their transbilayer organization and movement may be linked via the cytoskeleton and thus critically regulate various steps of cytokinesis.
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9
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Chai YJ, Cheng CY, Liao YH, Lin CH, Hsieh CL. Heterogeneous nanoscopic lipid diffusion in the live cell membrane and its dependency on cholesterol. Biophys J 2022; 121:3146-3161. [PMID: 35841144 PMCID: PMC9463655 DOI: 10.1016/j.bpj.2022.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/08/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022] Open
Abstract
Cholesterol plays a unique role in the regulation of membrane organization and dynamics by modulating the membrane phase transition at the nanoscale. Unfortunately, due to their small sizes and dynamic nature, the effects of cholesterol-mediated membrane nanodomains on membrane dynamics remain elusive. Here, using ultrahigh-speed single-molecule tracking with advanced optical microscope techniques, we investigate the diffusive motion of single phospholipids in the live cell plasma membrane at the nanoscale and its dependency on the cholesterol concentration. We find that both saturated and unsaturated phospholipids undergo anomalous subdiffusion on the length scale of 10-100 nm. The diffusion characteristics exhibit considerable variations in space and in time, indicating that the nanoscopic lipid diffusion is highly heterogeneous. Importantly, through the statistical analysis, apparent dual-mobility subdiffusion is observed from the mixed diffusion behaviors. The measured subdiffusion agrees well with the hop diffusion model that represents a diffuser moving in a compartmentalized membrane created by the cytoskeleton meshwork. Cholesterol depletion diminishes the lipid mobility with an apparently smaller compartment size and a stronger confinement strength. Similar results are measured with temperature reduction, suggesting that the more heterogeneous and restricted diffusion is connected to the nanoscopic membrane phase transition. Our conclusion supports the model that cholesterol depletion induces the formation of gel-phase, solid-like membrane nanodomains. These nanodomains undergo restricted diffusion and act as diffusion obstacles to the membrane molecules that are excluded from the nanodomains. This work provides the experimental evidence that the nanoscopic lipid diffusion in the cell plasma membrane is heterogeneous and sensitive to the cholesterol concentration and temperature, shedding new light on the regulation mechanisms of nanoscopic membrane dynamics.
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Affiliation(s)
- Yu-Jo Chai
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - Ching-Ya Cheng
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - Yi-Hung Liao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - Chih-Hsiang Lin
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan.
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10
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Huang SH, Huang BC, Chao L. Development of Cell Membrane Electrophoresis to Measure the Diffusivity of a Native Transmembrane Protein. Anal Chem 2022; 94:4531-4537. [PMID: 35230091 DOI: 10.1021/acs.analchem.2c00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The lateral diffusion of transmembrane proteins in cell membranes is an important process that controls the dynamics and functions of the cell membrane. Several fluorescence-based techniques have been developed to study the diffusivities of transmembrane proteins. However, it is challenging to measure the diffusivity of a transmembrane protein with slow diffusion because of the photobleaching effect caused by long exposure times or multiple exposures to light. In this study, we developed a cell membrane electrophoresis platform to measure diffusivity. We deposited cell membrane vesicles derived from HeLa cells to form supported cell membrane patches. We demonstrated that the electrophoresis platform can be used to drive the movement of not only a lipid probe but also a native transmembrane protein, GLUT1. The movements were halted by the boundaries of the membrane patches and the concentration profiles reached steady states when the diffusion mass flux was balanced with the electrical mass flux. We used the Nernst-Planck equation as the mass balance equation to describe the steady concentration profiles and fitted these equations to our data to obtain the diffusivities. The obtained diffusivities were comparable to those obtained by fluorescence recovery after photobleaching, suggesting the validity of this new method of diffusivity measurement. Only a single snapshot is required for the diffusivity measurement, addressing the problems associated with photobleaching and allowing researchers to measure the diffusivity of transmembrane proteins with slow diffusion.
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Affiliation(s)
- Sin-Han Huang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Bo-Chuan Huang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Ling Chao
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
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11
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Hu B, Liu R, Liu Q, Lin Z, Shi Y, Li J, Wang L, Li L, Xiao X, Wu Y. Engineering surface patterns on nanoparticles: New insights on nano-bio interactions. J Mater Chem B 2022; 10:2357-2383. [DOI: 10.1039/d1tb02549j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The surface properties of nanoparticles affect their fates in biological systems. Based on nanotechnology and methodology, pioneering works have explored the effects of chemical surface patterns on the behavior of...
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12
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Penedo M, Miyazawa K, Okano N, Furusho H, Ichikawa T, Alam MS, Miyata K, Nakamura C, Fukuma T. Visualizing intracellular nanostructures of living cells by nanoendoscopy-AFM. SCIENCE ADVANCES 2021; 7:eabj4990. [PMID: 34936434 PMCID: PMC10954033 DOI: 10.1126/sciadv.abj4990] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/10/2021] [Indexed: 06/14/2023]
Abstract
Atomic force microscopy (AFM) is the only technique that allows label-free imaging of nanoscale biomolecular dynamics, playing a crucial role in solving biological questions that cannot be addressed by other major bioimaging tools (fluorescence or electron microscopy). However, such imaging is possible only for systems either extracted from cells or reconstructed on solid substrates. Thus, nanodynamics inside living cells largely remain inaccessible with the current nanoimaging techniques. Here, we overcome this limitation by nanoendoscopy-AFM, where a needle-like nanoprobe is inserted into a living cell, presenting actin fiber three-dimensional (3D) maps, and 2D nanodynamics of the membrane inner scaffold, resulting in undetectable changes in cell viability. Unlike previous AFM methods, the nanoprobe directly accesses the target intracellular components, exploiting all the AFM capabilities, such as high-resolution imaging, nanomechanical mapping, and molecular recognition. These features should greatly expand the range of intracellular structures observable in living cells.
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Affiliation(s)
- Marcos Penedo
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
| | - Keisuke Miyazawa
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
- Division of Electric Engineering and Computer Science, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- Faculty of Frontier Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Naoko Okano
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
| | - Hirotoshi Furusho
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
| | - Takehiko Ichikawa
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
| | - Mohammad Shahidul Alam
- Division of Nano Life Science, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Kazuki Miyata
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
- Division of Electric Engineering and Computer Science, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- Faculty of Frontier Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- Division of Nano Life Science, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Chikashi Nakamura
- AIST-INDIA Diverse Assets and Applications International Laboratory (DAILAB), Cellular and Molecular Biotechnology Research Institute (CMB), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Takeshi Fukuma
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
- Division of Electric Engineering and Computer Science, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- Faculty of Frontier Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- Division of Nano Life Science, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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13
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Subdiffusive-Brownian crossover in membrane proteins: a generalized Langevin equation-based approach. Biophys J 2021; 120:4722-4737. [PMID: 34592261 DOI: 10.1016/j.bpj.2021.09.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/31/2021] [Accepted: 09/23/2021] [Indexed: 11/22/2022] Open
Abstract
In this work, we propose a generalized Langevin equation-based model to describe the lateral diffusion of a protein in a lipid bilayer. The memory kernel is represented in terms of a viscous (instantaneous) and an elastic (noninstantaneous) component modeled through a Dirac δ function and a three-parameter Mittag-Leffler type function, respectively. By imposing a specific relationship between the parameters of the three-parameter Mittag-Leffler function, the different dynamical regimes-namely ballistic, subdiffusive, and Brownian, as well as the crossover from one regime to another-are retrieved. Within this approach, the transition time from the ballistic to the subdiffusive regime and the spectrum of relaxation times underlying the transition from the subdiffusive to the Brownian regime are given. The reliability of the model is tested by comparing the mean-square displacement derived in the framework of this model and the mean-square displacement of a protein diffusing in a membrane calculated through molecular dynamics simulations.
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14
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Abstract
We investigate particle diffusion in a heterogeneous medium limited by a surface where sorption–desorption processes are governed by a kinetic equation. We consider that the dynamics of the particles present in the medium are governed by a diffusion equation with a spatial dependence on the diffusion coefficient, i.e., K(x) = D|x|−η, with −1 < η and D = const, respectively. This system is analyzed in a semi-infinity region, i.e., the system is defined in the interval [0,∞) for an arbitrary initial condition. The solutions are obtained and display anomalous spreading, that is, the dynamics may be viewed as anomalous diffusion, which in turn is related, and hence, the model can be directly applied to several complex systems ranging from biological fluids to electrolytic cells.
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15
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Chattopadhyay M, Krok E, Orlikowska H, Schwille P, Franquelim HG, Piatkowski L. Hydration Layer of Only a Few Molecules Controls Lipid Mobility in Biomimetic Membranes. J Am Chem Soc 2021; 143:14551-14562. [PMID: 34342967 PMCID: PMC8447254 DOI: 10.1021/jacs.1c04314] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Self-assembly of
biomembranes results from the intricate interactions
between water and the lipids’ hydrophilic head groups. Therefore,
the lipid–water interplay strongly contributes to modulating
membrane architecture, lipid diffusion, and chemical activity. Here,
we introduce a new method of obtaining dehydrated, phase-separated,
supported lipid bilayers (SLBs) solely by controlling the decrease
of their environment’s relative humidity. This facilitates
the study of the structure and dynamics of SLBs over a wide range
of hydration states. We show that the lipid domain structure of phase-separated
SLBs is largely insensitive to the presence of the hydration layer.
In stark contrast, lipid mobility is drastically affected by dehydration,
showing a 6-fold decrease in lateral diffusion. At the same time,
the diffusion activation energy increases approximately 2-fold for
the dehydrated membrane. The obtained results, correlated with the
hydration structure of a lipid molecule, revealed that about six to
seven water molecules directly hydrating the phosphocholine moiety
play a pivotal role in modulating lipid diffusion. These findings
could provide deeper insights into the fundamental reactions where
local dehydration occurs, for instance during cell–cell fusion,
and help us better understand the survivability of anhydrobiotic organisms.
Finally, the strong dependence of lipid mobility on the number of
hydrating water molecules opens up an application potential for SLBs
as very precise, nanoscale hydration sensors.
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Affiliation(s)
- Madhurima Chattopadhyay
- Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznan, Poland
| | - Emilia Krok
- Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznan, Poland
| | - Hanna Orlikowska
- Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznan, Poland
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Henri G Franquelim
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Lukasz Piatkowski
- Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznan, Poland
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16
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Hernández-Adame PL, Meza U, Rodríguez-Menchaca AA, Sánchez-Armass S, Ruiz-García J, Gomez E. Determination of the size of lipid rafts studied through single-molecule FRET simulations. Biophys J 2021; 120:2287-2295. [PMID: 33864789 DOI: 10.1016/j.bpj.2021.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/16/2021] [Accepted: 04/08/2021] [Indexed: 11/16/2022] Open
Abstract
Fluorescence resonance energy transfer (FRET) is a high-resolution technique that allows the characterization of spatial and temporal properties of biological structures and mechanisms. In this work, we developed an in silico single-molecule FRET methodology to study the dynamics of fluorophores inside lipid rafts. We monitored the fluorescence of a single acceptor molecule in the presence of several donor molecules. By looking at the average fluorescence, we selected events with single acceptor and donor molecules, and we used them to determine the raft size in the range of 5-16 nm. We conclude that our method is robust and insensitive to variations in the diffusion coefficient, donor density, or selected fluorescence threshold.
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Affiliation(s)
| | - Ulises Meza
- Department of Physiology and Biophysics, School of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Aldo A Rodríguez-Menchaca
- Department of Physiology and Biophysics, School of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Sergio Sánchez-Armass
- Department of Physiology and Biophysics, School of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Jaime Ruiz-García
- Biological Physics Laboratory, Physics Institute, San Luis Potosí, Mexico.
| | - Eduardo Gomez
- Biological Physics Laboratory, Physics Institute, San Luis Potosí, Mexico.
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17
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Fernandes M, Lenzi E, Evangelista L, Li Q, Zola R, de Souza R. Diffusion and adsorption-desorption phenomena in confined systems with periodically varying medium. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2020.116386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Koyama-Honda I, Fujiwara TK, Kasai RS, Suzuki KGN, Kajikawa E, Tsuboi H, Tsunoyama TA, Kusumi A. High-speed single-molecule imaging reveals signal transduction by induced transbilayer raft phases. J Cell Biol 2021; 219:211461. [PMID: 33053147 PMCID: PMC7563750 DOI: 10.1083/jcb.202006125] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/09/2020] [Accepted: 09/14/2020] [Indexed: 12/21/2022] Open
Abstract
Using single-molecule imaging with enhanced time resolutions down to 5 ms, we found that CD59 cluster rafts and GM1 cluster rafts were stably induced in the outer leaflet of the plasma membrane (PM), which triggered the activation of Lyn, H-Ras, and ERK and continually recruited Lyn and H-Ras right beneath them in the inner leaflet with dwell lifetimes <0.1 s. The detection was possible due to the enhanced time resolutions employed here. The recruitment depended on the PM cholesterol and saturated alkyl chains of Lyn and H-Ras, whereas it was blocked by the nonraftophilic transmembrane protein moiety and unsaturated alkyl chains linked to the inner-leaflet molecules. Because GM1 cluster rafts recruited Lyn and H-Ras as efficiently as CD59 cluster rafts, and because the protein moieties of Lyn and H-Ras were not required for the recruitment, we conclude that the transbilayer raft phases induced by the outer-leaflet stabilized rafts recruit lipid-anchored signaling molecules by lateral raft-lipid interactions and thus serve as a key signal transduction platform.
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Affiliation(s)
- Ikuko Koyama-Honda
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, University of Tokyo, Tokyo, Japan
| | - Takahiro K Fujiwara
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
| | - Rinshi S Kasai
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kenichi G N Suzuki
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan.,Institute for Glyco-core Research, Gifu University, Nagoya, Japan.,Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University, Gifu, Japan
| | - Eriko Kajikawa
- Laboratory for Organismal Patterning, Center for Biosystems Dynamics Research, RIKEN Kobe, Kobe, Japan
| | - Hisae Tsuboi
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Taka A Tsunoyama
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Akihiro Kusumi
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
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19
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Ślęzak J, Burov S. From diffusion in compartmentalized media to non-Gaussian random walks. Sci Rep 2021; 11:5101. [PMID: 33658556 PMCID: PMC7930099 DOI: 10.1038/s41598-021-83364-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 12/18/2020] [Indexed: 01/31/2023] Open
Abstract
In this work we establish a link between two different phenomena that were studied in a large and growing number of biological, composite and soft media: the diffusion in compartmentalized environment and the non-Gaussian diffusion that exhibits linear or power-law growth of the mean square displacement joined by the exponential shape of the positional probability density. We explore a microscopic model that gives rise to transient confinement, similar to the one observed for hop-diffusion on top of a cellular membrane. The compartmentalization of the media is achieved by introducing randomly placed, identical barriers. Using this model of a heterogeneous medium we derive a general class of random walks with simple jump rules that are dictated by the geometry of the compartments. Exponential decay of positional probability density is observed and we also quantify the significant decrease of the long time diffusion constant. Our results suggest that the observed exponential decay is a general feature of the transient regime in compartmentalized media.
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Affiliation(s)
- Jakub Ślęzak
- Physics Department, Bar-Ilan University, Ramat Gan, 5290002 Israel
| | - Stanislav Burov
- Physics Department, Bar-Ilan University, Ramat Gan, 5290002 Israel
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20
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Nussinov R, Jang H, Gursoy A, Keskin O, Gaponenko V. Inhibition of Nonfunctional Ras. Cell Chem Biol 2021; 28:121-133. [PMID: 33440168 PMCID: PMC7897307 DOI: 10.1016/j.chembiol.2020.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Intuitively, functional states should be targeted; not nonfunctional ones. So why could drugging the inactive K-Ras4BG12Cwork-but drugging the inactive kinase will likely not? The reason is the distinct oncogenic mechanisms. Kinase driver mutations work by stabilizing the active state and/or destabilizing the inactive state. Either way, oncogenic kinases are mostly in the active state. Ras driver mutations work by quelling its deactivation mechanisms, GTP hydrolysis, and nucleotide exchange. Covalent inhibitors that bind to the inactive GDP-bound K-Ras4BG12C conformation can thus work. By contrast, in kinases, allosteric inhibitors work by altering the active-site conformation to favor orthosteric drugs. From the translational standpoint this distinction is vital: it expedites effective pharmaceutical development and extends the drug classification based on the mechanism of action. Collectively, here we postulate that drug action relates to blocking the mechanism of activation, not to whether the protein is in the active or inactive state.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul 34450, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.
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21
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Calebiro D, Koszegi Z, Lanoiselée Y, Miljus T, O'Brien S. G protein-coupled receptor-G protein interactions: a single-molecule perspective. Physiol Rev 2020; 101:857-906. [PMID: 33331229 DOI: 10.1152/physrev.00021.2020] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) regulate many cellular and physiological processes, responding to a diverse range of extracellular stimuli including hormones, neurotransmitters, odorants, and light. Decades of biochemical and pharmacological studies have provided fundamental insights into the mechanisms of GPCR signaling. Thanks to recent advances in structural biology, we now possess an atomistic understanding of receptor activation and G protein coupling. However, how GPCRs and G proteins interact in living cells to confer signaling efficiency and specificity remains insufficiently understood. The development of advanced optical methods, including single-molecule microscopy, has provided the means to study receptors and G proteins in living cells with unprecedented spatio-temporal resolution. The results of these studies reveal an unexpected level of complexity, whereby GPCRs undergo transient interactions among themselves as well as with G proteins and structural elements of the plasma membrane to form short-lived signaling nanodomains that likely confer both rapidity and specificity to GPCR signaling. These findings may provide new strategies to pharmaceutically modulate GPCR function, which might eventually pave the way to innovative drugs for common diseases such as diabetes or heart failure.
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Affiliation(s)
- Davide Calebiro
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Zsombor Koszegi
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Yann Lanoiselée
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Tamara Miljus
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Shannon O'Brien
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
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22
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Tamura T, Fujisawa A, Tsuchiya M, Shen Y, Nagao K, Kawano S, Tamura Y, Endo T, Umeda M, Hamachi I. Organelle membrane-specific chemical labeling and dynamic imaging in living cells. Nat Chem Biol 2020; 16:1361-1367. [PMID: 32958953 DOI: 10.1038/s41589-020-00651-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/14/2020] [Indexed: 12/22/2022]
Abstract
Lipids play crucial roles as structural elements, signaling molecules and material transporters in cells. However, the functions and dynamics of lipids within cells remain unclear because of a lack of methods to selectively label lipids in specific organelles and trace their movement by live-cell imaging. We describe here a technology for the selective labeling and fluorescence imaging (microscopic or nanoscopic) of phosphatidylcholine in target organelles. This approach involves the metabolic incorporation of azido-choline, followed by a spatially limited bioorthogonal reaction that enables the visualization and quantitative analysis of interorganelle lipid transport in live cells. More importantly, with live-cell imaging, we obtained direct evidence that the autophagosomal membrane originates from the endoplasmic reticulum. This method is simple and robust and is thus powerful for real-time tracing of interorganelle lipid trafficking.
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Affiliation(s)
- Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto, Japan
| | - Alma Fujisawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto, Japan
| | - Masaki Tsuchiya
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto, Japan
| | - Yuying Shen
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kohjiro Nagao
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Shin Kawano
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Yasushi Tamura
- Faculty of Science, Yamagata University, Yamagata, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Masato Umeda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto, Japan.
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23
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Detergent Resistant Membrane Domains in Broccoli Plasma Membrane Associated to the Response to Salinity Stress. Int J Mol Sci 2020; 21:ijms21207694. [PMID: 33080920 PMCID: PMC7588934 DOI: 10.3390/ijms21207694] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 10/13/2020] [Indexed: 01/09/2023] Open
Abstract
Detergent-resistant membranes (DRMs) microdomains, or “raft lipids”, are key components of the plasma membrane (PM), being involved in membrane trafficking, signal transduction, cell wall metabolism or endocytosis. Proteins imbibed in these domains play important roles in these cellular functions, but there are few studies concerning DRMs under abiotic stress. In this work, we determine DRMs from the PM of broccoli roots, the lipid and protein content, the vesicles structure, their water osmotic permeability and a proteomic characterization focused mainly in aquaporin isoforms under salinity (80 mM NaCl). Based on biochemical lipid composition, higher fatty acid saturation and enriched sterol content under stress resulted in membranes, which decreased osmotic water permeability with regard to other PM vesicles, but this permeability was maintained under control and saline conditions; this maintenance may be related to a lower amount of total PIP1 and PIP2. Selective aquaporin isoforms related to the stress response such as PIP1;2 and PIP2;7 were found in DRMs and this protein partitioning may act as a mechanism to regulate aquaporins involved in the response to salt stress. Other proteins related to protein synthesis, metabolism and energy were identified in DRMs independently of the treatment, indicating their preference to organize in DMRs.
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24
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Górska K, Horzela A, Lenzi EK, Pagnini G, Sandev T. Generalized Cattaneo (telegrapher's) equations in modeling anomalous diffusion phenomena. Phys Rev E 2020; 102:022128. [PMID: 32942420 DOI: 10.1103/physreve.102.022128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/20/2020] [Indexed: 11/07/2022]
Abstract
We study generalized Cattaneo (telegrapher's) equations involving memory effects introduced by smearing the time derivatives. Consistency conditions where the smearing functions obey restrict freedom in their choice but the proposed scheme goes beyond the approach based on using fractional derivatives. We find conditions under which solutions of the equations considered so far can be recognized as probability distributions, i.e., are normalizable and nonnegative on their domains. Nonnegativity of solutions is demonstrated by methods of positive definite and completely monotonic functions with the Bernstein theorem being the cornerstone of the ongoing proofs. Analysis of exactly solvable examples and relevant mean-squared displacements enables us to classify diffusion processes described by such got solutions and to identify them with either ordinary or anomalous diffusion which character may change over time. To complete the present research we compare our results with those obtained using the continuous-time random-walk and the continuous-time persistent random-walk approaches.
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Affiliation(s)
- K Górska
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
| | - A Horzela
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Kraków, Poland
| | - E K Lenzi
- Departamento de Fisica, Universidade Estadual de Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
| | - G Pagnini
- BCAM-Basque Centre for Applied Mathematics, 48009 Bilbao, Basque Country Spain and Ikerbasque-Basque Foundation for Science, 48013 Bilbao, Basque Country, Spain
| | - T Sandev
- Research Center for Computer Science and Information Technologies, Macedonian Academy of Sciences and Arts, 1000 Skopje, Macedonia, Institute of Physics & Astronomy, University of Potsdam, D-14776 Potsdam-Golm, Germany and Institute of Physics, Faculty of Natural Sciences and Mathematics, Ss Cyril and Methodius University, 1000 Skopje, Macedonia
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25
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Cheetham M, Griffiths J, Nijs BD, Heath GR, Evans SD, Baumberg JJ, Chikkaraddy R. Out-of-Plane Nanoscale Reorganization of Lipid Molecules and Nanoparticles Revealed by Plasmonic Spectroscopy. J Phys Chem Lett 2020; 11:2875-2882. [PMID: 32191487 PMCID: PMC7168604 DOI: 10.1021/acs.jpclett.0c00182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/19/2020] [Indexed: 05/25/2023]
Abstract
Lipid bilayers assembled on solid substrates have been extensively studied with single-molecule resolution as the constituent molecules diffuse in 2D; however, the out-of-plane motion is typically ignored. Here we present the subnanometer out-of-plane diffusion of nanoparticles attached to hybrid lipid bilayers (HBLs) assembled on metal surfaces. The nanoscale cavity formed between the Au nanoparticle and Au film provides strongly enhanced optical fields capable of locally probing HBLs assembled in the gaps. This allows us to spectroscopically resolve the nanoparticles assembled on bilayers, near edges, and in membrane defects, showing the strong influence of charged lipid rafts. Nanoparticles sitting on the edges of the HBL are observed to flip onto and off of the bilayer, with flip energies of ∼10 meV showing how thermal energies dynamically modify lipid arrangements around a nanoparticle. We further resolve the movement of individual lipid molecules by doping the HBL with low concentrations of Texas Red (TxR) dye-labeled lipids.
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Affiliation(s)
- Matthew
R. Cheetham
- NanoPhotonics
Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Jack Griffiths
- NanoPhotonics
Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Bart de Nijs
- NanoPhotonics
Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
| | - George R. Heath
- School
of Physics and Astronomy, University of
Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Stephen D. Evans
- School
of Physics and Astronomy, University of
Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Jeremy J. Baumberg
- NanoPhotonics
Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Rohit Chikkaraddy
- NanoPhotonics
Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
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26
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Gentzsch C, Seier K, Drakopoulos A, Jobin M, Lanoiselée Y, Koszegi Z, Maurel D, Sounier R, Hübner H, Gmeiner P, Granier S, Calebiro D, Decker M. Selective and Wash-Resistant Fluorescent Dihydrocodeinone Derivatives Allow Single-Molecule Imaging of μ-Opioid Receptor Dimerization. Angew Chem Int Ed Engl 2020; 59:5958-5964. [PMID: 31808251 PMCID: PMC7125027 DOI: 10.1002/anie.201912683] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Indexed: 12/21/2022]
Abstract
μ-Opioid receptors (μ-ORs) play a critical role in the modulation of pain and mediate the effects of the most powerful analgesic drugs. Despite extensive efforts, it remains insufficiently understood how μ-ORs produce specific effects in living cells. We developed new fluorescent ligands based on the μ-OR antagonist E-p-nitrocinnamoylamino-dihydrocodeinone (CACO), that display high affinity, long residence time and pronounced selectivity. Using these ligands, we achieved single-molecule imaging of μ-ORs on the surface of living cells at physiological expression levels. Our results reveal a high heterogeneity in the diffusion of μ-ORs, with a relevant immobile fraction. Using a pair of fluorescent ligands of different color, we provide evidence that μ-ORs interact with each other to form short-lived homodimers on the plasma membrane. This approach provides a new strategy to investigate μ-OR pharmacology at single-molecule level.
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Affiliation(s)
- Christian Gentzsch
- Pharmaceutical and Medicinal ChemistryInstitute of Pharmacy and Food ChemistryJulius Maximilian University of WürzburgAm Hubland97074WürzburgGermany
| | - Kerstin Seier
- Institute of Pharmacology and ToxicologyJulius Maximilian University of WürzburgVersbacher Strasse 997078WürzburgGermany
| | - Antonios Drakopoulos
- Pharmaceutical and Medicinal ChemistryInstitute of Pharmacy and Food ChemistryJulius Maximilian University of WürzburgAm Hubland97074WürzburgGermany
| | - Marie‐Lise Jobin
- Institute of Pharmacology and ToxicologyJulius Maximilian University of WürzburgVersbacher Strasse 997078WürzburgGermany
| | - Yann Lanoiselée
- Institute of Metabolism and Systems Research & Centre of Membrane Proteins and ReceptorsUniversity of BirminghamIBR Tower, Level 2, EdgbastonBirminghamB152TTUK
| | - Zsombor Koszegi
- Institute of Metabolism and Systems Research & Centre of Membrane Proteins and ReceptorsUniversity of BirminghamIBR Tower, Level 2, EdgbastonBirminghamB152TTUK
| | - Damien Maurel
- ARPEGE (Pharmacology Screening Interactome) platform facilityInstitut de Génomique FonctionnelleUniversité de Montpellier, CNRS, INSERM141, rue de la Cardonille34094Montpellier Cedex 05France
| | - Rémy Sounier
- Institut de Génomique FonctionnelleUniversité de Montpellier, CNRS, INSERM141, rue de la Cardonille34094Montpellier Cedex 05France
| | - Harald Hübner
- Medicinal ChemistryDepartment of Chemistry and PharmacyFriedrich-Alexander University of Erlangen-Nuremberg91058ErlangenGermany
| | - Peter Gmeiner
- Medicinal ChemistryDepartment of Chemistry and PharmacyFriedrich-Alexander University of Erlangen-Nuremberg91058ErlangenGermany
| | - Sébastien Granier
- Institut de Génomique FonctionnelleUniversité de Montpellier, CNRS, INSERM141, rue de la Cardonille34094Montpellier Cedex 05France
| | - Davide Calebiro
- Institute of Pharmacology and ToxicologyJulius Maximilian University of WürzburgVersbacher Strasse 997078WürzburgGermany
- Institute of Metabolism and Systems Research & Centre of Membrane Proteins and ReceptorsUniversity of BirminghamIBR Tower, Level 2, EdgbastonBirminghamB152TTUK
| | - Michael Decker
- Pharmaceutical and Medicinal ChemistryInstitute of Pharmacy and Food ChemistryJulius Maximilian University of WürzburgAm Hubland97074WürzburgGermany
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27
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Zhu K, Su H. Unraveling Dynamic Transitions in Time-Resolved Biomolecular Motions by A Dressed Diffusion Model. J Phys Chem A 2020; 124:613-617. [PMID: 31589443 DOI: 10.1021/acs.jpca.9b08142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent experimental data reveal the complexity of diffusion dynamics beyond the scope of classical Brownian dynamics. The particles exhibit diverse diffusive motions from the anomalous toward classical diffusion over a wide range of temporal scales. Here a dressed diffusion model is developed to account for non-Brownian phenomena. By coupling the particle dynamics with a local field, the dressed diffusion model generalizes the Langevin equation through coupled damping kernels and generates the salient feature of time-dependent diffusion dynamics reported in the experimental measurements of biomolecules. The dressed diffusion model provides one quantitative aspect for future endeavors in this rapid-growing field.
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Affiliation(s)
- Kaicheng Zhu
- Department of Chemistry , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong
| | - Haibin Su
- Department of Chemistry , The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon , Hong Kong
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28
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Gentzsch C, Seier K, Drakopoulos A, Jobin M, Lanoiselée Y, Koszegi Z, Maurel D, Sounier R, Hübner H, Gmeiner P, Granier S, Calebiro D, Decker M. Selective and Wash‐Resistant Fluorescent Dihydrocodeinone Derivatives Allow Single‐Molecule Imaging of μ‐Opioid Receptor Dimerization. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201912683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Christian Gentzsch
- Pharmaceutical and Medicinal ChemistryInstitute of Pharmacy and Food ChemistryJulius Maximilian University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Kerstin Seier
- Institute of Pharmacology and ToxicologyJulius Maximilian University of Würzburg Versbacher Strasse 9 97078 Würzburg Germany
| | - Antonios Drakopoulos
- Pharmaceutical and Medicinal ChemistryInstitute of Pharmacy and Food ChemistryJulius Maximilian University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Marie‐Lise Jobin
- Institute of Pharmacology and ToxicologyJulius Maximilian University of Würzburg Versbacher Strasse 9 97078 Würzburg Germany
| | - Yann Lanoiselée
- Institute of Metabolism and Systems Research & Centre of Membrane Proteins and ReceptorsUniversity of Birmingham IBR Tower, Level 2, Edgbaston Birmingham B152TT UK
| | - Zsombor Koszegi
- Institute of Metabolism and Systems Research & Centre of Membrane Proteins and ReceptorsUniversity of Birmingham IBR Tower, Level 2, Edgbaston Birmingham B152TT UK
| | - Damien Maurel
- ARPEGE (Pharmacology Screening Interactome) platform facilityInstitut de Génomique FonctionnelleUniversité de Montpellier, CNRS, INSERM 141, rue de la Cardonille 34094 Montpellier Cedex 05 France
| | - Rémy Sounier
- Institut de Génomique FonctionnelleUniversité de Montpellier, CNRS, INSERM 141, rue de la Cardonille 34094 Montpellier Cedex 05 France
| | - Harald Hübner
- Medicinal ChemistryDepartment of Chemistry and PharmacyFriedrich-Alexander University of Erlangen-Nuremberg 91058 Erlangen Germany
| | - Peter Gmeiner
- Medicinal ChemistryDepartment of Chemistry and PharmacyFriedrich-Alexander University of Erlangen-Nuremberg 91058 Erlangen Germany
| | - Sébastien Granier
- Institut de Génomique FonctionnelleUniversité de Montpellier, CNRS, INSERM 141, rue de la Cardonille 34094 Montpellier Cedex 05 France
| | - Davide Calebiro
- Institute of Pharmacology and ToxicologyJulius Maximilian University of Würzburg Versbacher Strasse 9 97078 Würzburg Germany
- Institute of Metabolism and Systems Research & Centre of Membrane Proteins and ReceptorsUniversity of Birmingham IBR Tower, Level 2, Edgbaston Birmingham B152TT UK
| | - Michael Decker
- Pharmaceutical and Medicinal ChemistryInstitute of Pharmacy and Food ChemistryJulius Maximilian University of Würzburg Am Hubland 97074 Würzburg Germany
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29
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Martinac B, Nikolaev YA, Silvani G, Bavi N, Romanov V, Nakayama Y, Martinac AD, Rohde P, Bavi O, Cox CD. Cell membrane mechanics and mechanosensory transduction. CURRENT TOPICS IN MEMBRANES 2020; 86:83-141. [DOI: 10.1016/bs.ctm.2020.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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30
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Cohen AE, Shi Z. Do Cell Membranes Flow Like Honey or Jiggle Like Jello? Bioessays 2019; 42:e1900142. [DOI: 10.1002/bies.201900142] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 10/31/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Adam E. Cohen
- Departments of Chemistry and Chemical Biology and PhysicsHarvard University Cambridge MA USA
- Howard Hughes Medical Institute Chevy Chase MD USA
| | - Zheng Shi
- Departments of Chemistry and Chemical Biology and PhysicsHarvard University Cambridge MA USA
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31
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Yu Y, Li M, Yu Y. Tracking Single Molecules in Biomembranes: Is Seeing Always Believing? ACS NANO 2019; 13:10860-10868. [PMID: 31589406 PMCID: PMC7179047 DOI: 10.1021/acsnano.9b07445] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The spatial organization of molecules in cell membranes and their dynamic interactions play a central role in regulating cell functions. Single-particle tracking (SPT), a technique in which single molecules are imaged and tracked in real time, has led to breakthrough discoveries regarding these spatiotemporal complexities of cell membranes. There are, however, emerging concerns about factors that might produce misleading interpretations of SPT results. Here, we briefly review the application of SPT to understanding the nanoscale heterogeneities of plasma membranes, with a focus on the unique challenges, pitfalls, and limitations that confront the use of nanoparticles as imaging probes for tracking the dynamics of single molecules in cell membranes.
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32
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Sil P, Mateos N, Nath S, Buschow S, Manzo C, Suzuki KGN, Fujiwara T, Kusumi A, Garcia-Parajo MF, Mayor S. Dynamic actin-mediated nano-scale clustering of CD44 regulates its meso-scale organization at the plasma membrane. Mol Biol Cell 2019; 31:561-579. [PMID: 31577524 PMCID: PMC7202065 DOI: 10.1091/mbc.e18-11-0715] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transmembrane adhesion receptors at the cell surface, such as CD44, are often equipped with modules to interact with the extracellular matrix (ECM) and the intracellular cytoskeletal machinery. CD44 has been recently shown to compartmentalize the membrane into domains by acting as membrane pickets, facilitating the function of signaling receptors. While spatial organization and diffusion studies of membrane proteins are usually conducted separately, here we combine observations of organization and diffusion by using high spatio-temporal resolution imaging on living cells to reveal a hierarchical organization of CD44. CD44 is present in a meso-scale meshwork pattern where it exhibits enhanced confinement and is enriched in nanoclusters of CD44 along its boundaries. This nanoclustering is orchestrated by the underlying cortical actin dynamics. Interaction with actin is mediated by specific segments of the intracellular domain. This influences the organization of the protein at the nano-scale, generating a selective requirement for formin over Arp2/3-based actin-nucleation machinery. The extracellular domain and its interaction with elements of ECM do not influence the meso-scale organization, but may serve to reposition the meshwork with respect to the ECM. Taken together, our results capture the hierarchical nature of CD44 organization at the cell surface, with active cytoskeleton-templated nanoclusters localized to a meso-scale meshwork pattern.
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Affiliation(s)
- Parijat Sil
- National Centre for Biological Sciences (NCBS)
| | - Nicolas Mateos
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona 08860, Spain
| | - Sangeeta Nath
- Institute of Stem Cell and Regenerative Medicine.,Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education, Bangalore 560065, India
| | - Sonja Buschow
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, Rotterdam 3015 GD Rotterdam, The Netherlands
| | - Carlo Manzo
- Facultat de Ciències i Tecnologia, Universitat de Vic-Universitat Central de Catalunya, Vic 08500, Spain
| | - Kenichi G N Suzuki
- Centre for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Takahiro Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Akihiro Kusumi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan.,Okinawa Institute of Science and Technology, Graduate University, Okinawa 904-0412, Japan
| | - Maria F Garcia-Parajo
- Institute of Stem Cell and Regenerative Medicine.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Satyajit Mayor
- National Centre for Biological Sciences (NCBS).,Institute of Stem Cell and Regenerative Medicine
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33
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Goiko M, de Bruyn JR, Heit B. Membrane Diffusion Occurs by Continuous-Time Random Walk Sustained by Vesicular Trafficking. Biophys J 2019; 114:2887-2899. [PMID: 29925025 DOI: 10.1016/j.bpj.2018.04.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/06/2018] [Accepted: 04/16/2018] [Indexed: 10/28/2022] Open
Abstract
Diffusion in cellular membranes is regulated by processes that occur over a range of spatial and temporal scales. These processes include membrane fluidity, interprotein and interlipid interactions, interactions with membrane microdomains, interactions with the underlying cytoskeleton, and cellular processes that result in net membrane movement. The complex, non-Brownian diffusion that results from these processes has been difficult to characterize, and moreover, the impact of factors such as membrane recycling on membrane diffusion remains largely unexplored. We have used a careful statistical analysis of single-particle tracking data of the single-pass plasma membrane protein CD93 to show that the diffusion of this protein is well described by a continuous-time random walk in parallel with an aging process mediated by membrane corrals. The overall result is an evolution in the diffusion of CD93: proteins initially diffuse freely on the cell surface but over time become increasingly trapped within diffusion-limiting membrane corrals. Stable populations of freely diffusing and corralled CD93 are maintained by an endocytic/exocytic process in which corralled CD93 is selectively endocytosed, whereas freely diffusing CD93 is replenished by exocytosis of newly synthesized and recycled CD93. This trafficking not only maintained CD93 diffusivity but also maintained the heterogeneous distribution of CD93 in the plasma membrane. These results provide insight into the nature of the biological and biophysical processes that can lead to significantly non-Brownian diffusion of membrane proteins and demonstrate that ongoing membrane recycling is critical to maintaining steady-state diffusion and distribution of proteins in the plasma membrane.
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Affiliation(s)
- Maria Goiko
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada; Department of Physics and Astronomy, The University of Western Ontario, London, Ontario, Canada
| | - John R de Bruyn
- Department of Physics and Astronomy, The University of Western Ontario, London, Ontario, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada; Centre for Human Immunology, The University of Western Ontario, London, Ontario, Canada.
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34
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de Wit G, Albrecht D, Ewers H, Kukura P. Revealing Compartmentalized Diffusion in Living Cells with Interferometric Scattering Microscopy. Biophys J 2019; 114:2945-2950. [PMID: 29925030 DOI: 10.1016/j.bpj.2018.05.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/08/2018] [Accepted: 05/02/2018] [Indexed: 12/19/2022] Open
Abstract
The spatiotemporal organization and dynamics of the plasma membrane and its constituents are central to cellular function. Fluorescence-based single-particle tracking has emerged as a powerful approach for studying the single molecule behavior of plasma-membrane-associated events because of its excellent background suppression, at the expense of imaging speed and observation time. Here, we show that interferometric scattering microscopy combined with 40 nm gold nanoparticle labeling can be used to follow the motion of membrane proteins in the plasma membrane of live cultured mammalian cell lines and hippocampal neurons with up to 3 nm precision and 25 μs temporal resolution. The achievable spatiotemporal precision enabled us to reveal signatures of compartmentalization in neurons likely caused by the actin cytoskeleton.
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Affiliation(s)
- Gabrielle de Wit
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - David Albrecht
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Helge Ewers
- Department of Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Philipp Kukura
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom.
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35
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Le Roux AL, Quiroga X, Walani N, Arroyo M, Roca-Cusachs P. The plasma membrane as a mechanochemical transducer. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180221. [PMID: 31431176 PMCID: PMC6627014 DOI: 10.1098/rstb.2018.0221] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
Cells are constantly submitted to external mechanical stresses, which they must withstand and respond to. By forming a physical boundary between cells and their environment that is also a biochemical platform, the plasma membrane (PM) is a key interface mediating both cellular response to mechanical stimuli, and subsequent biochemical responses. Here, we review the role of the PM as a mechanosensing structure. We first analyse how the PM responds to mechanical stresses, and then discuss how this mechanical response triggers downstream biochemical responses. The molecular players involved in PM mechanochemical transduction include sensors of membrane unfolding, membrane tension, membrane curvature or membrane domain rearrangement. These sensors trigger signalling cascades fundamental both in healthy scenarios and in diseases such as cancer, which cells harness to maintain integrity, keep or restore homeostasis and adapt to their external environment. This article is part of a discussion meeting issue 'Forces in cancer: interdisciplinary approaches in tumour mechanobiology'.
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Affiliation(s)
- Anabel-Lise Le Roux
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona 08028, Spain
| | - Xarxa Quiroga
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona 08028, Spain
| | - Nikhil Walani
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, Spain
| | - Marino Arroyo
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona 08028, Spain
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, Spain
| | - Pere Roca-Cusachs
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona 08028, Spain
- Department of Biomedical Sciences, Universitat de Barcelona, Barcelona 08036, Spain
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36
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Koerdt SN, Ashraf APK, Gerke V. Annexins and plasma membrane repair. CURRENT TOPICS IN MEMBRANES 2019; 84:43-65. [PMID: 31610865 DOI: 10.1016/bs.ctm.2019.07.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Plasma membrane wound repair is a cell-autonomous process that is triggered by Ca2+ entering through the site of injury and involves membrane resealing, i.e., re-establishment of a continuous plasma membrane, as well as remodeling of the cortical actin cytoskeleton. Among other things, the injury-induced Ca2+ elevation initiates the wound site recruitment of Ca2+-regulated proteins that function in the course of repair. Annexins are a class of such Ca2+-regulated proteins. They associate with acidic phospholipids of cellular membranes in their Ca2+ bound conformation with Ca2+ sensitivities ranging from the low to high micromolar range depending on the respective annexin protein. Annexins accumulate at sites of plasma membrane injury in a temporally controlled manner and are thought to function by controlling membrane rearrangements at the wound site, most likely in conjunction with other repair proteins such as dysferlin. Their role in membrane repair, which has been evidenced in several model systems, will be discussed in this chapter.
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Affiliation(s)
- Sophia N Koerdt
- Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Arsila P K Ashraf
- Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Volker Gerke
- Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation, University of Münster, Münster, Germany.
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37
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Clarkson CG, Johnson A, Leggett GJ, Geoghegan M. Slow polymer diffusion on brush-patterned surfaces in aqueous solution. NANOSCALE 2019; 11:6052-6061. [PMID: 30869707 DOI: 10.1039/c9nr00341j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A model system for the investigation of diffusional transport in compartmentalized nanosystems is described. Arrays of "corrals" enclosed within poly[oligo(ethylene glycol)methyl ether methacrylate] (POEGMA) "walls" were fabricated using double-exposure interferometric lithography to deprotect aminosilane films protected by a nitrophenyl group. In exposed regions, removal of the nitrophenyl group enabled attachment of an initiator for the atom-transfer radical polymerization of end-grafted POEGMA (brushes). Diffusion coefficients for poly(ethylene glycol) in these corrals were obtained by fluorescence correlation spectroscopy. Two modes of surface diffusion were observed: one which is similar to diffusion on the unpatterned surface and a very slow mode of surface diffusion that becomes increasingly important as confinement increases. Diffusion within the POEGMA brushes does not significantly contribute to the results.
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38
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Calebiro D, Koszegi Z. The subcellular dynamics of GPCR signaling. Mol Cell Endocrinol 2019; 483:24-30. [PMID: 30610913 DOI: 10.1016/j.mce.2018.12.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/26/2018] [Accepted: 12/27/2018] [Indexed: 01/20/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of membrane receptors and mediate the effects of a multitude of extracellular cues, such as hormones, neurotransmitters, odorants and light. Because of their involvement in numerous physiological and pathological processes and their accessibility, they are extensively exploited as pharmacological targets. Biochemical and structural biology investigations have clarified the molecular basis of GPCR signaling to a high level of detail. In spite of this, how GPCRs can efficiently and precisely translate extracellular signals into specific and well-orchestrated biological responses in the complexity of a living cell or organism remains insufficiently understood. To explain the high efficiency and specificity observed in GPCR signaling, it has been suggested that GPCR might signal in discrete nanodomains on the plasma membrane or even form stable complexes with G proteins and effectors. However, directly testing these hypotheses has proven a major challenge. Recent studies taking advantage of innovative optical methods such as fluorescence resonance energy transfer (FRET) and single-molecule microscopy have begun to dig into the organization of GPCR signaling in living cells on the spatial (nm) and temporal (ms) scales on which cell signaling events are taking place. The results of these studies are revealing a complex and highly dynamic picture, whereby GPCRs undergo transient interaction with their signaling partners, membrane lipids and the cytoskeleton to form short-lived signaling nanodomains both on the plasma membrane and at intracellular sites. Continuous exchanges among such nanodomains via later diffusion as well as via membrane trafficking might provide a highly sophisticated way of controlling the timing and location of GPCR signaling. Here, we will review the most recent advances in our understanding of the organization of GPCR signaling in living cells, with a particular focus on its dynamics.
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Affiliation(s)
- Davide Calebiro
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, UK.
| | - Zsombor Koszegi
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, UK
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39
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Coker HLE, Cheetham MR, Kattnig DR, Wang YJ, Garcia-Manyes S, Wallace MI. Controlling Anomalous Diffusion in Lipid Membranes. Biophys J 2019; 116:1085-1094. [PMID: 30846364 DOI: 10.1016/j.bpj.2018.12.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/21/2018] [Accepted: 12/14/2018] [Indexed: 12/24/2022] Open
Abstract
Diffusion in cell membranes is not just simple two-dimensional Brownian motion but typically depends on the timescale of the observation. The physical origins of this anomalous subdiffusion are unresolved, and model systems capable of quantitative and reproducible control of membrane diffusion have been recognized as a key experimental bottleneck. Here, we control anomalous diffusion using supported lipid bilayers containing lipids derivatized with polyethylene glycol (PEG) headgroups. Bilayers with specific excluded area fractions are formed by control of PEG lipid mole fraction. These bilayers exhibit a switch in diffusive behavior, becoming anomalous as bilayer continuity is disrupted. Using a combination of single-molecule fluorescence and interferometric imaging, we measure the anomalous behavior in this model over four orders of magnitude in time. Diffusion in these bilayers is well described by a power-law dependence of the mean-square displacement with observation time. Anomaleity in this system can be tailored by simply controlling the mole fraction of PEG lipid, producing bilayers with diffusion parameters similar to those observed for anomalous diffusion in biological membranes.
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Affiliation(s)
- Helena L E Coker
- Department of Chemistry, King's College London, London, United Kingdom; Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Matthew R Cheetham
- Department of Chemistry, King's College London, London, United Kingdom; Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Daniel R Kattnig
- Living Systems Institute & Department of Physics, University of Exeter, Exeter, United Kingdom
| | - Yong J Wang
- Department of Physics, King's College London, London, United Kingdom
| | | | - Mark I Wallace
- Department of Chemistry, King's College London, London, United Kingdom.
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40
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Adler J, Sintorn IM, Strand R, Parmryd I. Conventional analysis of movement on non-flat surfaces like the plasma membrane makes Brownian motion appear anomalous. Commun Biol 2019; 2:12. [PMID: 30652124 PMCID: PMC6325064 DOI: 10.1038/s42003-018-0240-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 11/26/2018] [Indexed: 01/09/2023] Open
Abstract
Cells are neither flat nor smooth, which has serious implications for prevailing plasma membrane models and cellular processes like cell signalling, adhesion and molecular clustering. Using probability distributions from diffusion simulations, we demonstrate that 2D and 3D Euclidean distance measurements substantially underestimate diffusion on non-flat surfaces. Intuitively, the shortest within surface distance (SWSD), the geodesic distance, should reduce this problem. The SWSD is accurate for foldable surfaces but, although it outperforms 2D and 3D Euclidean measurements, it still underestimates movement on deformed surfaces. We demonstrate that the reason behind the underestimation is that topographical features themselves can produce both super- and subdiffusion, i.e. the appearance of anomalous diffusion. Differentiating between topography-induced and genuine anomalous diffusion requires characterising the surface by simulating Brownian motion on high-resolution cell surface images and a comparison with the experimental data.
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Affiliation(s)
- Jeremy Adler
- Science for Life Laboratory, Medical Cell Biology, Uppsala University, Uppsala University, Box 571, 751 21 Uppsala, Sweden
| | - Ida-Maria Sintorn
- Department of Information Technology, Uppsala University, Box 331, 751 05 Uppsala, Sweden
| | - Robin Strand
- Department of Information Technology, Uppsala University, Box 331, 751 05 Uppsala, Sweden
| | - Ingela Parmryd
- Science for Life Laboratory, Medical Cell Biology, Uppsala University, Uppsala University, Box 571, 751 21 Uppsala, Sweden
- Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
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41
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Weatherill EE, Coker HLE, Cheetham MR, Wallace MI. Urea-mediated anomalous diffusion in supported lipid bilayers. Interface Focus 2018; 8:20180028. [PMID: 30443327 PMCID: PMC6227775 DOI: 10.1098/rsfs.2018.0028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2018] [Indexed: 12/16/2022] Open
Abstract
Diffusion in biological membranes is seldom simply Brownian motion; instead, the rate of diffusion is dependent on the time scale of observation and so is often described as anomalous. In order to help better understand this phenomenon, model systems are needed where the anomalous diffusion of the lipid bilayer can be tuned and quantified. We recently demonstrated one such model by controlling the excluded area fraction in supported lipid bilayers (SLBs) through the incorporation of lipids derivatized with polyethylene glycol. Here, we extend this work, using urea to induce anomalous diffusion in SLBs. By tuning incubation time and urea concentration, we produce bilayers that exhibit anomalous behaviour on the same scale as that observed in biological membranes.
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Affiliation(s)
- E. E. Weatherill
- Department of Chemistry, Britannia House, King's College London, 7 Trinity Street, London SE1 1DB, UK
| | - H. L. E. Coker
- Department of Chemistry, Britannia House, King's College London, 7 Trinity Street, London SE1 1DB, UK
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - M. R. Cheetham
- Department of Chemistry, Britannia House, King's College London, 7 Trinity Street, London SE1 1DB, UK
- Cavendish Laboratory, Department of Physics, NanoPhotonics Centre, University of Cambridge, Cambridge CB3 0HE, UK
| | - M. I. Wallace
- Department of Chemistry, Britannia House, King's College London, 7 Trinity Street, London SE1 1DB, UK
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42
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A Rationale for Mesoscopic Domain Formation in Biomembranes. Biomolecules 2018; 8:biom8040104. [PMID: 30274275 PMCID: PMC6316292 DOI: 10.3390/biom8040104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/04/2018] [Accepted: 09/06/2018] [Indexed: 12/25/2022] Open
Abstract
Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also be observed in vitro on model systems such as supported membranes or lipid vesicles. Lipid mixtures separating in liquid-ordered and liquid-disordered phases below a demixing temperature play a pivotal role in this context. Protein-protein and protein-lipid interactions also contribute to membrane shaping by promoting small domains or clusters. Such phase separations displaying characteristic length-scales falling in-between the nanoscopic, molecular scale on the one hand and the macroscopic scale on the other hand, are named mesophases in soft condensed matter physics. In this review, we propose a classification of the diverse mechanisms leading to mesophase separation in biomembranes. We distinguish between mechanisms relying upon equilibrium thermodynamics and those involving out-of-equilibrium mechanisms, notably active membrane recycling. In equilibrium, we especially focus on the many mechanisms that dwell on an up-down symmetry breaking between the upper and lower bilayer leaflets. Symmetry breaking is an ubiquitous mechanism in condensed matter physics at the heart of several important phenomena. In the present case, it can be either spontaneous (domain buckling) or explicit, i.e., due to an external cause (global or local vesicle bending properties). Whenever possible, theoretical predictions and simulation results are confronted to experiments on model systems or living cells, which enables us to identify the most realistic mechanisms from a biological perspective.
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43
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Grosjean K, Der C, Robert F, Thomas D, Mongrand S, Simon-Plas F, Gerbeau-Pissot P. Interactions between lipids and proteins are critical for organization of plasma membrane-ordered domains in tobacco BY-2 cells. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3545-3557. [PMID: 29722895 PMCID: PMC6022670 DOI: 10.1093/jxb/ery152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 04/16/2018] [Indexed: 05/20/2023]
Abstract
The laterally heterogeneous plant plasma membrane (PM) is organized into finely controlled specialized areas that include membrane-ordered domains. Recently, the spatial distribution of such domains within the PM has been identified as playing a key role in cell responses to environmental challenges. To examine membrane order at a local level, BY-2 tobacco suspension cell PMs were labelled with an environment-sensitive probe (di-4-ANEPPDHQ). Four experimental models were compared to identify mechanisms and cell components involved in short-term (1 h) maintenance of the ordered domain organization in steady-state cell PMs: modulation of the cytoskeleton or the cell wall integrity of tobacco BY-2 cells; and formation of giant vesicles using either a lipid mixture of tobacco BY-2 cell PMs or the original lipid and protein combinations of the tobacco BY-2 cell PM. Whilst inhibiting phosphorylation or disrupting either the cytoskeleton or the cell wall had no observable effects, we found that lipids and proteins significantly modified both the abundance and spatial distribution of ordered domains. This indicates the involvement of intrinsic membrane components in the local physical state of the plant PM. Our findings support a major role for the 'lipid raft' model, defined as the sterol-dependent ordered assemblies of specific lipids and proteins in plant PM organization.
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Affiliation(s)
- Kevin Grosjean
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Christophe Der
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Franck Robert
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Dominique Thomas
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR, CNRS, Université de Bordeaux, Bordeaux, France
| | - Françoise Simon-Plas
- Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, Dijon, France
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44
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Fan N, Jiang H, Ye Z, Wu G, Kang Y, Wang Q, Ran X, Guo J, Zhang G, Wang G, Peng B. The Insertion Mechanism of a Living Cell Determined by the Stress Segmentation Effect of the Cell Membrane during the Tip-Cell Interaction. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1703868. [PMID: 29717805 DOI: 10.1002/smll.201703868] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/11/2018] [Indexed: 06/08/2023]
Abstract
Atomic force microscopy probes are proved to be powerful tools to measure and manipulate the individual cell, providing potential applications for the controlled drug/protein delivery. However, the measured insertion efficiency varies dramatically from 20 to 80%, in some cases, the nanotip can never penetrate the cell membrane no matter how much force is applied to it. Thus, the insertion mechanism of a living cell during the tip-cell interaction must be thoroughly investigated before this technology comes into practical applications. In this work, a multistructural cell model is established to study the tip-membrane interaction. The simulation results show that the stress of the cell membrane can be divided into two stages by the stress segmentation point S. After point S, the stress of the cell membrane increases slightly and most of the indentation force is allocated to the cytoskeleton. This phenomenon is called "stress segmentation effect of the cell membrane," which confirms the hypothesis based on the experimental studies. Moreover, according to the experimental and numerical studies, the hypothesis of the stress segmentation effect also explains the reason that modifying the cell membrane or using the manmade sharpened nanotip can increase the insertion efficiency.
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Affiliation(s)
- Na Fan
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, 611731, P. R. China
| | - Hai Jiang
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, 611731, P. R. China
| | - Zhiyi Ye
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Guiyong Wu
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, 611731, P. R. China
| | - Yuejun Kang
- Institute for Clean Energy & Advanced Materials, Southwest University, Chongqing, 400715, P. R. China
| | - Qun Wang
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, 611731, P. R. China
| | - Xiaolin Ran
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Jian Guo
- School of Mechanical Engineering, University of South China, Hengyang, Hunan, 421001, P. R. China
| | - Guocheng Zhang
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, 611731, P. R. China
| | - Guixue Wang
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Bei Peng
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, 611731, P. R. China
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45
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Jin W, Simsek MF, Pralle A. Quantifying spatial and temporal variations of the cell membrane ultra-structure by bimFCS. Methods 2018. [PMID: 29530504 DOI: 10.1016/j.ymeth.2018.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
It has been long recognized that the cell membrane is heterogeneous on scales ranging from a couple of molecules to micrometers in size and hence diffusion of receptors is length scale dependent. This heterogeneity modulates many cell-membrane-associated processes requiring transient spatiotemporal separation of components. The transient increase in local concentration of interacting signal components enables robust signaling in an otherwise thermally noisy system. Understanding how lipids and proteins self-organize and interact with the cell cortex requires quantifying the motion of the components. Multi-length scale diffusion measurements by single particle tracking, fluorescence correlation spectroscopy (FCS) or related techniques are able to identify components being transiently trapped in nanodomains, from freely moving one and from ones with reduced long-scale diffusion due to interaction with the cell cortex. One particular implementation of multi-length scale diffusion measurements is the combination of FCS with a spatially resolved detector, such as a camera and two-dimensional extended excitation profile. The main advantages of this approach are that all length scales are interrogated simultaneously, uniquely permits quantifying changes to the membrane structure caused by extrenal or internal perturbations. Here, we review how combining total internal reflection microscopy (TIRF) with FC resolves the membrane organization in living cells. We show how to implement the method, which requires only a few seconds of data acquisition to quantify membrane nanodomains, or the spacing of membrane fences caused by the actin cortex. The choice of diffusing fluorescent probe determines which membrane heterogeneity is detected. We review the instrument, sample preparation, experimental and computational requirements to perform such measurements, and discuss the potential and limitations. The discussion includes examples of spatial and temporal comparisons of the membrane structure in response to perturbations demonstrating the complex cell physiology.
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Affiliation(s)
- Weixiang Jin
- Dept. of Physics, 239 Fronczak Hall, University at Buffalo, SUNY, Buffalo, NY 14260-1500, United States
| | - M Fethullah Simsek
- Dept. of Physics, 239 Fronczak Hall, University at Buffalo, SUNY, Buffalo, NY 14260-1500, United States
| | - Arnd Pralle
- Dept. of Physics, 239 Fronczak Hall, University at Buffalo, SUNY, Buffalo, NY 14260-1500, United States.
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46
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Lu SM, Fairn GD. Mesoscale organization of domains in the plasma membrane - beyond the lipid raft. Crit Rev Biochem Mol Biol 2018; 53:192-207. [PMID: 29457544 DOI: 10.1080/10409238.2018.1436515] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The plasma membrane is compartmentalized into several distinct regions or domains, which show a broad diversity in both size and lifetime. The segregation of lipids and membrane proteins is thought to be driven by the lipid composition itself, lipid-protein interactions and diffusional barriers. With regards to the lipid composition, the immiscibility of certain classes of lipids underlies the "lipid raft" concept of plasmalemmal compartmentalization. Historically, lipid rafts have been described as cholesterol and (glyco)sphingolipid-rich regions of the plasma membrane that exist as a liquid-ordered phase that are resistant to extraction with non-ionic detergents. Over the years the interest in lipid rafts grew as did the challenges with studying these nanodomains. The term lipid raft has fallen out of favor with many scientists and instead the terms "membrane raft" or "membrane nanodomain" are preferred as they connote the heterogeneity and dynamic nature of the lipid-protein assemblies. In this article, we will discuss the classical lipid raft hypothesis and its limitations. This review will also discuss alternative models of lipid-protein interactions, annular lipid shells, and larger membrane clusters. We will also discuss the mesoscale organization of plasmalemmal domains including visible structures such as clathrin-coated pits and caveolae.
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Affiliation(s)
- Stella M Lu
- a Keenan Research Centre for Biomedical Science, St. Michael's Hospital , Toronto , Canada.,b Department of Biochemistry , University of Toronto , Toronto , Canada
| | - Gregory D Fairn
- a Keenan Research Centre for Biomedical Science, St. Michael's Hospital , Toronto , Canada.,b Department of Biochemistry , University of Toronto , Toronto , Canada.,c Department of Surgery , University of Toronto , Toronto , Canada
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47
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Abstract
How do Ras isoforms attain oncogenic specificity at the membrane? Oncogenic KRas, HRas, and NRas (K-Ras, H-Ras, and N-Ras) differentially populate distinct cancers. How they selectively activate effectors and why is KRas4B the most prevalent are highly significant questions. Here, we consider determinants that may bias isoform-specific effector activation and signaling at the membrane. We merge functional data with a conformational view to provide mechanistic insight. Cell-specific expression levels, pathway cross-talk, and distinct interactions are the key, but conformational trends can modulate selectivity. There are two major pathways in oncogenic Ras-driven proliferation: MAPK (Raf/MEK/ERK) and PI3Kα/Akt/mTOR. All membrane-anchored, proximally located, oncogenic Ras isoforms can promote Raf dimerization and fully activate MAPK signaling. So why the differential statistics of oncogenic isoforms in distinct cancers and what makes KRas so highly oncogenic? Many cell-specific factors may be at play, including higher KRAS mRNA levels. As a key factor, we suggest that because only KRas4B binds calmodulin, only KRas can fully activate PI3Kα/Akt signaling. We propose that full activation of both MAPK and PI3Kα/Akt proliferative pathways by oncogenic KRas4B-but not by HRas or NRas-may help explain why the KRas4B isoform is especially highly populated in certain cancers. We further discuss pharmacologic implications. Cancer Res; 78(3); 593-602. ©2017 AACR.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland. .,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
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48
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Nussinov R, Tsai CJ, Jang H. Oncogenic Ras Isoforms Signaling Specificity at the Membrane. Cancer Res 2018; 78:593-602. [PMID: 29273632 PMCID: PMC5811325 DOI: 10.1158/0008-5472.can-17-2727] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/13/2017] [Accepted: 11/10/2017] [Indexed: 01/21/2023]
Abstract
How do Ras isoforms attain oncogenic specificity at the membrane? Oncogenic KRas, HRas, and NRas (K-Ras, H-Ras, and N-Ras) differentially populate distinct cancers. How they selectively activate effectors and why is KRas4B the most prevalent are highly significant questions. Here, we consider determinants that may bias isoform-specific effector activation and signaling at the membrane. We merge functional data with a conformational view to provide mechanistic insight. Cell-specific expression levels, pathway cross-talk, and distinct interactions are the key, but conformational trends can modulate selectivity. There are two major pathways in oncogenic Ras-driven proliferation: MAPK (Raf/MEK/ERK) and PI3Kα/Akt/mTOR. All membrane-anchored, proximally located, oncogenic Ras isoforms can promote Raf dimerization and fully activate MAPK signaling. So why the differential statistics of oncogenic isoforms in distinct cancers and what makes KRas so highly oncogenic? Many cell-specific factors may be at play, including higher KRAS mRNA levels. As a key factor, we suggest that because only KRas4B binds calmodulin, only KRas can fully activate PI3Kα/Akt signaling. We propose that full activation of both MAPK and PI3Kα/Akt proliferative pathways by oncogenic KRas4B-but not by HRas or NRas-may help explain why the KRas4B isoform is especially highly populated in certain cancers. We further discuss pharmacologic implications. Cancer Res; 78(3); 593-602. ©2017 AACR.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
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49
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Rey I, Garcia DA, Wheatley BA, Song W, Upadhyaya A. Biophysical Techniques to Study B Cell Activation: Single-Molecule Imaging and Force Measurements. Methods Mol Biol 2018; 1707:51-68. [PMID: 29388099 DOI: 10.1007/978-1-4939-7474-0_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cells of the adaptive immune system recognize pathogenic peptides through specialized receptors on their membranes. The engagement of these receptors with antigen leads to cell activation, which induces profound changes in the cell including cytoskeleton remodeling and membrane deformation. During this process, receptors and signaling molecules undergo spatiotemporal reorganization to form signaling microclusters and the immunological synapse. The cytoskeletal and membrane dynamics also leads to exertion of forces on the cell-substrate interface. In this chapter we describe two techniques-one for single-molecule imaging of B cell receptors to measure their diffusive properties as cells get activated on supported lipid bilayers; and the second for visualizing and quantifying cellular forces using elastic surfaces to stimulate T and B cells.
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Affiliation(s)
- Ivan Rey
- Biophysics Program, University of Maryland, College Park, MD, 20742, USA
| | - David A Garcia
- Department of Physics, University of Maryland, College Park, MD, 20742, USA
| | | | - Wenxia Song
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Arpita Upadhyaya
- Biophysics Program, University of Maryland, College Park, MD, 20742, USA. .,Department of Physics, University of Maryland, College Park, MD, 20742, USA. .,Institute for Physical Science and Technology, University of Maryland, 1151, PSC Bldg., College Park, MD, 20742, USA.
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50
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Veerapathiran S, Wohland T. The imaging FCS diffusion law in the presence of multiple diffusive modes. Methods 2017; 140-141:140-150. [PMID: 29203404 DOI: 10.1016/j.ymeth.2017.11.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 01/21/2023] Open
Abstract
The cellular plasma membrane is the barrier over which cells exchange materials and communicate with their surroundings, and thus plays the central role in cellular sensing and metabolism. Therefore, the investigation of plasma membrane organization and dynamics is required for understanding of cellular functions. The plasma membrane is a heterogeneous matrix. The presence of structures such as lipid and protein domains and the cytoskeleton meshwork poses a hindrance to the free diffusion of membrane associated biomolecules. However, these domains and the cytoskeleton meshwork barriers are below the optical diffraction limit with potentially short lifetimes and are not easily detected even in super-resolution microscopy. Therefore, dynamic measurements are often used to indirectly prove the existence of domains and barriers by analyzing the mode of diffusion of probe molecules. One of these tools is the Fluorescence Correlation Spectroscopy (FCS) diffusion law. The FCS diffusion law is a plot of diffusion time (τd) versus observation area. For at least three different diffusive modes - free, domain confined, and meshwork hindered hop diffusion - the expected plots have been characterized, typically by its y-intercept (τ0) when fit with a linear model, and have been verified in many cases. However, a description of τ0 has only been given for pure diffusive modes. But in many experimental cases it is not evident that a protein will undergo only one kind of diffusion, and thus the interpretation of the τ0 value is problematic. Here, we therefore address the question about the absolute value of τ0 in the case of complex diffusive modes, i.e. when either one molecule is domain confined and cytoskeleton hindered or when two molecules exhibit different diffusive behavior at the same position in a sample. In addition, we investigate how τ0 changes when the diffusive mode of a probe alters upon disruption of domains or the cytoskeleton by drug treatments. By a combination of experimental studies and simulations, we show that τ0 is not influenced equally by the different diffusive modes as typically found in cellular environments, and that it is the relative change of τ0 rather than its absolute value that provides information on the mode of diffusion.
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Affiliation(s)
- Sapthaswaran Veerapathiran
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore, Singapore; Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore, Singapore.
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