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Struts AV, Barmasov AV, Fried SDE, Hewage KSK, Perera SMDC, Brown MF. Osmotic stress studies of G-protein-coupled receptor rhodopsin activation. Biophys Chem 2024; 304:107112. [PMID: 37952496 DOI: 10.1016/j.bpc.2023.107112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 11/14/2023]
Abstract
We summarize and critically review osmotic stress studies of the G-protein-coupled receptor rhodopsin. Although small amounts of structural water are present in these receptors, the effect of bulk water on their function remains uncertain. Studies of the influences of osmotic stress on the GPCR archetype rhodopsin have given insights into the functional role of water in receptor activation. Experimental work has discovered that osmolytes shift the metarhodopsin equilibrium after photoactivation, either to the active or inactive conformations according to their molar mass. At least 80 water molecules are found to enter rhodopsin in the transition to the photoreceptor active state. We infer that this movement of water is both necessary and sufficient for receptor activation. If the water influx is prevented, e.g., by large polymer osmolytes or by dehydration, then the receptor functional transition is back shifted. These findings imply a new paradigm in which rhodopsin becomes solvent swollen in the activation mechanism. Water thus acts as an allosteric modulator of function for rhodopsin-like receptors in lipid membranes.
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Affiliation(s)
- Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA; Laboratory of Biomolecular NMR, St.-Petersburg State University, 199034 St.-Petersburg, Russia
| | - Alexander V Barmasov
- Department of Biophysics, St.-Petersburg State Pediatric Medical University, 194100 St.-Petersburg, Russia; Department of Physics, St.-Petersburg State University, 199034 St.-Petersburg, Russia
| | - Steven D E Fried
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Kushani S K Hewage
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | | | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA; Department of Physics, University of Arizona, Tucson, AZ 85721, USA.
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2
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Day CA, Kang M. The Utility of Fluorescence Recovery after Photobleaching (FRAP) to Study the Plasma Membrane. MEMBRANES 2023; 13:membranes13050492. [PMID: 37233553 DOI: 10.3390/membranes13050492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/01/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023]
Abstract
The plasma membrane of mammalian cells is involved in a wide variety of cellular processes, including, but not limited to, endocytosis and exocytosis, adhesion and migration, and signaling. The regulation of these processes requires the plasma membrane to be highly organized and dynamic. Much of the plasma membrane organization exists at temporal and spatial scales that cannot be directly observed with fluorescence microscopy. Therefore, approaches that report on the membrane's physical parameters must often be utilized to infer membrane organization. As discussed here, diffusion measurements are one such approach that has allowed researchers to understand the subresolution organization of the plasma membrane. Fluorescence recovery after photobleaching (or FRAP) is the most widely accessible method for measuring diffusion in a living cell and has proven to be a powerful tool in cell biology research. Here, we discuss the theoretical underpinnings that allow diffusion measurements to be used in elucidating the organization of the plasma membrane. We also discuss the basic FRAP methodology and the mathematical approaches for deriving quantitative measurements from FRAP recovery curves. FRAP is one of many methods used to measure diffusion in live cell membranes; thus, we compare FRAP with two other popular methods: fluorescence correlation microscopy and single-particle tracking. Lastly, we discuss various plasma membrane organization models developed and tested using diffusion measurements.
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Affiliation(s)
- Charles A Day
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
- Mayo Clinic, Rochester, MN 55902, USA
| | - Minchul Kang
- Department of Mathematics, Texas A&M-Commerce, Commerce, TX 75428, USA
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3
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Hofmann KP, Lamb TD. Rhodopsin, light-sensor of vision. Prog Retin Eye Res 2023; 93:101116. [PMID: 36273969 DOI: 10.1016/j.preteyeres.2022.101116] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/06/2022]
Abstract
The light sensor of vertebrate scotopic (low-light) vision, rhodopsin, is a G-protein-coupled receptor comprising a polypeptide chain with bound chromophore, 11-cis-retinal, that exhibits remarkable physicochemical properties. This photopigment is extremely stable in the dark, yet its chromophore isomerises upon photon absorption with 70% efficiency, enabling the activation of its G-protein, transducin, with high efficiency. Rhodopsin's photochemical and biochemical activities occur over very different time-scales: the energy of retinaldehyde's excited state is stored in <1 ps in retinal-protein interactions, but it takes milliseconds for the catalytically active state to form, and many tens of minutes for the resting state to be restored. In this review, we describe the properties of rhodopsin and its role in rod phototransduction. We first introduce rhodopsin's gross structural features, its evolution, and the basic mechanisms of its activation. We then discuss light absorption and spectral sensitivity, photoreceptor electrical responses that result from the activity of individual rhodopsin molecules, and recovery of rhodopsin and the visual system from intense bleaching exposures. We then provide a detailed examination of rhodopsin's molecular structure and function, first in its dark state, and then in the active Meta states that govern its interactions with transducin, rhodopsin kinase and arrestin. While it is clear that rhodopsin's molecular properties are exquisitely honed for phototransduction, from starlight to dawn/dusk intensity levels, our understanding of how its molecular interactions determine the properties of scotopic vision remains incomplete. We describe potential future directions of research, and outline several major problems that remain to be solved.
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Affiliation(s)
- Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik (CC2), Charité, and, Zentrum für Biophysik und Bioinformatik, Humboldt-Unversität zu Berlin, Berlin, 10117, Germany.
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia.
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4
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Park J, Jin S, Jang J, Seo D. Single-Molecule Imaging of Membrane Proteins on Vascular Endothelial Cells. J Lipid Atheroscler 2023; 12:58-72. [PMID: 36761059 PMCID: PMC9884557 DOI: 10.12997/jla.2023.12.1.58] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 01/26/2023] Open
Abstract
Transporting substances such as gases, nutrients, waste, and cells is the primary function of blood vessels. Vascular cells use membrane proteins to perform crucial endothelial functions, including molecular transport, immune cell infiltration, and angiogenesis. A thorough understanding of these membrane receptors from a clinical perspective is warranted to gain insights into the pathogenesis of vascular diseases and to develop effective methods for drug delivery through the vascular endothelium. This review summarizes state-of-the-art single-molecule imaging techniques, such as super-resolution microscopy, single-molecule tracking, and protein-protein interaction analysis, for observing and studying membrane proteins. Furthermore, recent single-molecule studies of membrane proteins such as cadherins, integrins, caveolins, transferrin receptors, vesicle-associated protein-1, and vascular endothelial growth factor receptor are discussed.
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Affiliation(s)
- Jiseong Park
- Department of Physics and Chemistry, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, Korea
| | - Siwoo Jin
- Department of Physics and Chemistry, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, Korea
| | - Juhee Jang
- Department of Physics and Chemistry, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, Korea
| | - Daeha Seo
- Department of Physics and Chemistry, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, Korea
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5
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Using Fluorescence Recovery After Photobleaching data to uncover filament dynamics. PLoS Comput Biol 2022; 18:e1010573. [PMID: 36156590 PMCID: PMC9536589 DOI: 10.1371/journal.pcbi.1010573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 10/06/2022] [Accepted: 09/14/2022] [Indexed: 11/20/2022] Open
Abstract
Fluorescence Recovery After Photobleaching (FRAP) has been extensively used to understand molecular dynamics in cells. This technique when applied to soluble, globular molecules driven by diffusion is easily interpreted and well understood. However, the classical methods of analysis cannot be applied to anisotropic structures subjected to directed transport, such as cytoskeletal filaments or elongated organelles transported along microtubule tracks. A new mathematical approach is needed to analyze FRAP data in this context and determine what information can be obtain from such experiments. To address these questions, we analyze fluorescence intensity profile curves after photobleaching of fluorescently labelled intermediate filaments anterogradely transported along microtubules. We apply the analysis to intermediate filament data to determine information about the filament motion. Our analysis consists of deriving equations for fluorescence intensity profiles and developing a mathematical model for the motion of filaments and simulating the model. Two closed forms for profile curves were derived, one for filaments of constant length and one for filaments with constant velocity, and three types of simulation were carried out. In the first type of simulation, the filaments have random velocities which are constant for the duration of the simulation. In the second type, filaments have random velocities which instantaneously change at random times. In the third type, filaments have random velocities and exhibit pausing between velocity changes. Our analysis shows: the most important distribution governing the shape of the intensity profile curves obtained from filaments is the distribution of the filament velocity. Furthermore, filament length which is constant during the experiment, had little impact on intensity profile curves. Finally, gamma distributions for the filament velocity with pauses give the best fit to asymmetric fluorescence intensity profiles of intermediate filaments observed in FRAP experiments performed in polarized migrating astrocytes. Our analysis also shows that the majority of filaments are stationary. Overall, our data give new insight into the regulation of intermediate filament dynamics during cell migration. Fluorescence Recovery After Photobleaching (FRAP) is a commonly-used technique to analyze the dynamics of fluorescently-tagged proteins or structures in biology. After photochemical altering the fluorophor in a specific region, fluorescent material from the surrounding region moves into the photobleached region. Usually applied to the diffusion of soluble or membrane associate proteins, the existing models of analysis are not suitable for the elucidation of directional transport of elongated structures. Different modes of motions for the elongated structures with distributed lengths and velocities in cells are considered. First, we observe that filament lengths can be inferred from the level of noisiness. We further show the characteristics of fluorescence profile curves mainly depend on the occurrence of changes in velocities and distributions of velocities; whereas length distributions have negligible impact. Analysis of experimental data using this new framework indicates intermediate filaments transported by kinesins along microtubules in polarized migrating cells have gamma distributed velocities changing over time between pausing. Most filaments are found to be very slow or stationary with a few moving fast. This new computational approach should permit the interpretation of FRAP experimental data obtained with any directionally moving elongated structures of various lengths.
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6
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Leroux M, Soubry N, Reyes-Lamothe R. Dynamics of Proteins and Macromolecular Machines in Escherichia coli. EcoSal Plus 2021; 9:eESP00112020. [PMID: 34060908 PMCID: PMC11163846 DOI: 10.1128/ecosalplus.esp-0011-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/16/2021] [Indexed: 11/20/2022]
Abstract
Proteins are major contributors to the composition and the functions in the cell. They often assemble into larger structures, macromolecular machines, to carry out intricate essential functions. Although huge progress in understanding how macromolecular machines function has been made by reconstituting them in vitro, the role of the intracellular environment is still emerging. The development of fluorescence microscopy techniques in the last 2 decades has allowed us to obtain an increased understanding of proteins and macromolecular machines in cells. Here, we describe how proteins move by diffusion, how they search for their targets, and how they are affected by the intracellular environment. We also describe how proteins assemble into macromolecular machines and provide examples of how frequent subunit turnover is used for them to function and to respond to changes in the intracellular conditions. This review emphasizes the constant movement of molecules in cells, the stochastic nature of reactions, and the dynamic nature of macromolecular machines.
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Affiliation(s)
- Maxime Leroux
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Nicolas Soubry
- Department of Biology, McGill University, Montreal, QC, Canada
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Parameter estimation in fluorescence recovery after photobleaching: quantitative analysis of protein binding reactions and diffusion. J Math Biol 2021; 83:1. [PMID: 34129100 PMCID: PMC8205911 DOI: 10.1007/s00285-021-01616-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 09/15/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
Fluorescence recovery after photobleaching (FRAP) is a common experimental method for investigating rates of molecular redistribution in biological systems. Many mathematical models of FRAP have been developed, the purpose of which is usually the estimation of certain biological parameters such as the diffusivity and chemical reaction rates of a protein, this being accomplished by fitting the model to experimental data. In this article, we consider a two species reaction–diffusion FRAP model. Using asymptotic analysis, we derive new FRAP recovery curve approximation formulae, and formally re-derive existing ones. On the basis of these formulae, invoking the concept of Fisher information, we predict, in terms of biological and experimental parameters, sufficient conditions to ensure that the values all model parameters can be estimated from data. We verify our predictions with extensive computational simulations. We also use computational methods to investigate cases in which some or all biological parameters are theoretically inestimable. In these cases, we propose methods which can be used to extract the maximum possible amount of information from the FRAP data.
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8
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Park PSH. Supramolecular organization of rhodopsin in rod photoreceptor cell membranes. Pflugers Arch 2021; 473:1361-1376. [PMID: 33591421 DOI: 10.1007/s00424-021-02522-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 11/30/2022]
Abstract
Rhodopsin is the light receptor in rod photoreceptor cells that initiates scotopic vision. Studies on the light receptor span well over a century, yet questions about the organization of rhodopsin within the photoreceptor cell membrane still persist and a consensus view on the topic is still elusive. Rhodopsin has been intensely studied for quite some time, and there is a wealth of information to draw from to formulate an organizational picture of the receptor in native membranes. Early experimental evidence in apparent support for a monomeric arrangement of rhodopsin in rod photoreceptor cell membranes is contrasted and reconciled with more recent visual evidence in support of a supramolecular organization of rhodopsin. What is known so far about the determinants of forming a supramolecular structure and possible functional roles for such an organization are also discussed. Many details are still missing on the structural and functional properties of the supramolecular organization of rhodopsin in rod photoreceptor cell membranes. The emerging picture presented here can serve as a springboard towards a more in-depth understanding of the topic.
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Affiliation(s)
- Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
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9
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Membrane Curvature Revisited-the Archetype of Rhodopsin Studied by Time-Resolved Electronic Spectroscopy. Biophys J 2020; 120:440-452. [PMID: 33217383 DOI: 10.1016/j.bpj.2020.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/01/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) comprise the largest and most pharmacologically targeted membrane protein family. Here, we used the visual receptor rhodopsin as an archetype for understanding membrane lipid influences on conformational changes involved in GPCR activation. Visual rhodopsin was recombined with lipids varying in their degree of acyl chain unsaturation and polar headgroup size using 1-palmitoyl-2-oleoyl-sn-glycero- and 1,2-dioleoyl-sn-glycerophospholipids with phosphocholine (PC) or phosphoethanolamine (PE) substituents. The receptor activation profile after light excitation was measured using time-resolved ultraviolet-visible spectroscopy. We discovered that more saturated POPC lipids back shifted the equilibrium to the inactive state, whereas the small-headgroup, highly unsaturated DOPE lipids favored the active state. Increasing unsaturation and decreasing headgroup size have similar effects that combine to yield control of rhodopsin activation, and necessitate factors beyond proteolipid solvation energy and bilayer surface electrostatics. Hence, we consider a balance of curvature free energy with hydrophobic matching and demonstrate how our data support a flexible surface model (FSM) for the coupling between proteins and lipids. The FSM is based on the Helfrich formulation of membrane bending energy as we previously first applied to lipid-protein interactions. Membrane elasticity and curvature strain are induced by lateral pressure imbalances between the constituent lipids and drive key physiological processes at the membrane level. Spontaneous negative monolayer curvature toward water is mediated by unsaturated, small-headgroup lipids and couples directly to GPCR activation upon light absorption by rhodopsin. For the first time to our knowledge, we demonstrate this modulation in both the equilibrium and pre-equilibrium evolving states using a time-resolved approach.
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10
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Position of rhodopsin photoisomerization on the disk surface confers variability to the rising phase of the single photon response in vertebrate rod photoreceptors. PLoS One 2020; 15:e0240527. [PMID: 33052986 PMCID: PMC7556485 DOI: 10.1371/journal.pone.0240527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/29/2020] [Indexed: 11/23/2022] Open
Abstract
Retinal rods function as accurate photon counters to provide for vision under very dim light. To do so, rods must generate highly amplified, reproducible responses to single photons, yet outer segment architecture and randomness in the location of rhodopsin photoisomerization on the surface of an internal disk introduce variability to the rising phase of the photon response. Soon after a photoisomerization at a disk rim, depletion of cGMP near the plasma membrane closes ion channels and hyperpolarizes the rod. But with a photoisomerization in the center of a disk, local depletion of cGMP is distant from the channels in the plasma membrane. Thus, channel closure is delayed by the time required for the reduction of cGMP concentration to reach the plasma membrane. Moreover, the local fall in cGMP dissipates over a larger volume before affecting the channels, so response amplitude is reduced. This source of variability increases with disk radius. Using a fully space-resolved biophysical model of rod phototransduction, we quantified the variability attributable to randomness in the location of photoisomerization as a function of disk structure. In mouse rods that have small disks bearing a single incisure, this variability was negligible in the absence of the incisure. Variability was increased slightly by the incisure, but randomness in the shutoff of rhodopsin emerged as the main source of single photon response variability at all but the earliest times. Variability arising from randomness in the transverse location of photoisomerization increased in magnitude and persisted over a longer period in the photon response of large salamander rods. A symmetric arrangement of multiple incisures in the disks of salamander rods greatly reduced this variability during the rising phase, but the incisures had the opposite effect on variability arising from randomness in rhodopsin shutoff at later times.
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11
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Feldman TB, Ivankov OI, Kuklin AI, Murugova TN, Yakovleva MA, Smitienko OA, Kolchugina IB, Round A, Gordeliy VI, Belushkin AV, Ostrovsky MA. Small-angle neutron and X-ray scattering analysis of the supramolecular organization of rhodopsin in photoreceptor membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183000. [DOI: 10.1016/j.bbamem.2019.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 01/16/2023]
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12
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Hayashi F, Saito N, Tanimoto Y, Okada K, Morigaki K, Seno K, Maekawa S. Raftophilic rhodopsin-clusters offer stochastic platforms for G protein signalling in retinal discs. Commun Biol 2019; 2:209. [PMID: 31240247 PMCID: PMC6570657 DOI: 10.1038/s42003-019-0459-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 05/10/2019] [Indexed: 12/18/2022] Open
Abstract
Rhodopsin is a G protein-coupled receptor (GPCR) that initiates the phototransduction cascade in retinal disc membrane. Recent studies have suggested that rhodopsin forms highly ordered rows of dimers responsible for single-photon detection by rod photoreceptors. Dimerization is also known to confer to rhodopsin a high affinity for ordered lipids (raftophilicity). However, the role of rhodopsin organization and its raftophilicity in phototransduction remains obscure, owing to the lack of direct observation of rhodopsin dynamics and distribution in native discs. Here, we explore the single-molecule and semi-multimolecule behaviour of rhodopsin in native discs. Rhodopsin forms transient meso-scale clusters, even in darkness, which are loosely confined to the disc centre. Cognate G protein transducin co-distributes with rhodopsin, and exhibits lateral translocation to the disc periphery upon activation. We demonstrate that rhodopsin offers inherently distributed and stochastic platforms for G protein signalling by self-organizing raftophilic clusters, which continually repeat generation/extinction in the disc membrane.
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Affiliation(s)
- Fumio Hayashi
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501 Japan
| | - Natsumi Saito
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501 Japan
| | - Yasushi Tanimoto
- Research Centre for Environmental Genomics, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501 Japan
| | - Keisuke Okada
- Graduate School of Agriculture, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501 Japan
| | - Kenichi Morigaki
- Research Centre for Environmental Genomics, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501 Japan
- Graduate School of Agriculture, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501 Japan
| | - Keiji Seno
- Faculty of Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192 Japan
- International Mass Imaging Centre, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192 Japan
| | - Shohei Maekawa
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501 Japan
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Lippincott-Schwartz J, Snapp EL, Phair RD. The Development and Enhancement of FRAP as a Key Tool for Investigating Protein Dynamics. Biophys J 2018; 115:1146-1155. [PMID: 30219286 DOI: 10.1016/j.bpj.2018.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/27/2018] [Accepted: 08/06/2018] [Indexed: 01/18/2023] Open
Abstract
The saga of fluorescence recovery after photobleaching (FRAP) illustrates how disparate technical developments impact science. Starting with the classic 1976 Axelrod et al. work in Biophysical Journal, FRAP (originally fluorescence photobleaching recovery) opened the door to extraction of quantitative information from photobleaching experiments, laying the experimental and theoretical groundwork for quantifying both the mobility and the mobile fraction of a labeled population of proteins. Over the ensuing years, FRAP's reach dramatically expanded, with new developments in GFP technology and turn-key confocal microscopy, which enabled measurement of protein diffusion and binding/dissociation rates in virtually every compartment within the cell. The FRAP technique and data catalyzed an exchange of ideas between biophysicists studying membrane dynamics, cell biologists focused on intracellular dynamics, and systems biologists modeling the dynamics of cell activity. The outcome transformed the field of cellular biology, leading to a fundamental rethinking of long-held theories of cellular dynamism. Here, we review the pivotal FRAP studies that made these developments and conceptual changes possible, which gave rise to current models of complex cell dynamics.
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Affiliation(s)
| | - Erik Lee Snapp
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia.
| | - Robert D Phair
- Integrative Bioinformatics, Inc., Mountain View, California
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14
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Lee S, Tan HY, Geneva II, Kruglov A, Calvert PD. Actin filaments partition primary cilia membranes into distinct fluid corrals. J Cell Biol 2018; 217:2831-2849. [PMID: 29945903 PMCID: PMC6080922 DOI: 10.1083/jcb.201711104] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/16/2018] [Accepted: 05/22/2018] [Indexed: 12/15/2022] Open
Abstract
Lee et al. examine the dynamics of membrane proteins within the ciliary membrane using quantum dots and 2P Super FRAP. They show that ciliary membrane proteins diffuse rapidly within highly fluid local membrane domains delimited by actin filaments. Physical properties of primary cilia membranes in living cells were examined using two independent, high-spatiotemporal-resolution approaches: fast tracking of single quantum dot–labeled G protein–coupled receptors and a novel two-photon super-resolution fluorescence recovery after photobleaching of protein ensemble. Both approaches demonstrated the cilium membrane to be partitioned into corralled domains spanning 274 ± 20 nm, within which the receptors are transiently confined for 0.71 ± 0.09 s. The mean membrane diffusion coefficient within the corrals, Dm1 = 2.9 ± 0.41 µm2/s, showed that the ciliary membranes were among the most fluid encountered. At longer times, the apparent membrane diffusion coefficient, Dm2 = 0.23 ± 0.05 µm2/s, showed that corral boundaries impeded receptor diffusion 13-fold. Mathematical simulations predict the probability of G protein–coupled receptors crossing corral boundaries to be 1 in 472. Remarkably, latrunculin A, cytochalasin D, and jasplakinolide treatments altered the corral permeability. Ciliary membranes are thus partitioned into highly fluid membrane nanodomains that are delimited by filamentous actin.
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Affiliation(s)
- Sungsu Lee
- Center for Vision Research and Department of Ophthalmology, State University of New York Upstate Medical University, Syracuse, NY.,Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, NY
| | - Han Yen Tan
- Center for Vision Research and Department of Ophthalmology, State University of New York Upstate Medical University, Syracuse, NY
| | - Ivayla I Geneva
- Center for Vision Research and Department of Ophthalmology, State University of New York Upstate Medical University, Syracuse, NY.,Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY
| | - Aleksandr Kruglov
- Center for Vision Research and Department of Ophthalmology, State University of New York Upstate Medical University, Syracuse, NY
| | - Peter D Calvert
- Center for Vision Research and Department of Ophthalmology, State University of New York Upstate Medical University, Syracuse, NY .,Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY.,Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, NY
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15
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Bläßle A, Soh G, Braun T, Mörsdorf D, Preiß H, Jordan BM, Müller P. Quantitative diffusion measurements using the open-source software PyFRAP. Nat Commun 2018; 9:1582. [PMID: 29679054 PMCID: PMC5910415 DOI: 10.1038/s41467-018-03975-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 03/26/2018] [Indexed: 11/18/2022] Open
Abstract
Fluorescence Recovery After Photobleaching (FRAP) and inverse FRAP (iFRAP) assays can be used to assess the mobility of fluorescent molecules. These assays measure diffusion by monitoring the return of fluorescence in bleached regions (FRAP), or the dissipation of fluorescence from photoconverted regions (iFRAP). However, current FRAP/iFRAP analysis methods suffer from simplified assumptions about sample geometry, bleaching/photoconversion inhomogeneities, and the underlying reaction-diffusion kinetics. To address these shortcomings, we developed the software PyFRAP, which fits numerical simulations of three-dimensional models to FRAP/iFRAP data and accounts for bleaching/photoconversion inhomogeneities. Using PyFRAP we determined the diffusivities of fluorescent molecules spanning two orders of magnitude in molecular weight. We measured the tortuous effects that cell-like obstacles exert on effective diffusivity and show that reaction kinetics can be accounted for by model selection. These applications demonstrate the utility of PyFRAP, which can be widely adapted as a new extensible standard for FRAP analysis. FRAP analysis often relies on simplified assumptions that can affect measurement accuracy. Here the authors present a Python-based FRAP analysis software using simulations instead of simplified theoretical models to fit the data, which accounts for complex sample geometries and bleach conditions.
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Affiliation(s)
- Alexander Bläßle
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Gary Soh
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Theresa Braun
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany.,University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - David Mörsdorf
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Hannes Preiß
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Ben M Jordan
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany.
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16
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Abstract
Morphogens are signaling molecules that provide positional information to cells during development. They must move through embryonic tissues in order to coordinate patterning. The rate of a morphogen's movement through a tissue-its effective diffusivity-affects the morphogen's distribution and therefore influences patterning. Fluorescence recovery after photobleaching (FRAP) is a powerful method to measure the effective diffusion of molecules through cells and tissues, and has been successfully employed to examine morphogen mobility and gain important insights into embryogenesis. Here, we provide detailed protocols for FRAP assays in vitro and in living zebrafish embryos, and we explain how to analyze FRAP data using the open-source software PyFRAP to determine effective diffusion coefficients.
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Affiliation(s)
- Gary H Soh
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.
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17
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Abstract
Retinal photoreceptor cells contain a specialized outer segment (OS) compartment that functions in the capture of light and its conversion into electrical signals in a process known as phototransduction. In rods, photoisomerization of 11-cis to all-trans retinal within rhodopsin triggers a biochemical cascade culminating in the closure of cGMP-gated channels and hyperpolarization of the cell. Biochemical reactions return the cell to its 'dark state' and the visual cycle converts all-trans retinal back to 11-cis retinal for rhodopsin regeneration. OS are continuously renewed, with aged membrane removed at the distal end by phagocytosis and new membrane added at the proximal end through OS disk morphogenesis linked to protein trafficking. The molecular basis for disk morphogenesis remains to be defined in detail although several models have been proposed, and molecular mechanisms underlying protein trafficking are under active investigation. The aim of this Cell Science at a Glance article and the accompanying poster is to highlight our current understanding of photoreceptor structure, phototransduction, the visual cycle, OS renewal, protein trafficking and retinal degenerative diseases.
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Affiliation(s)
- Robert S Molday
- Department of Biochemistry and Molecular Biology, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3 Department of Ophthalmology and Visual Sciences, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia, Canada V5Z 3N9
| | - Orson L Moritz
- Department of Ophthalmology and Visual Sciences, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia, Canada V5Z 3N9
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18
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Quaternary structures of opsin in live cells revealed by FRET spectrometry. Biochem J 2016; 473:3819-3836. [PMID: 27623775 DOI: 10.1042/bcj20160422] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 09/12/2016] [Indexed: 02/06/2023]
Abstract
Rhodopsin is a prototypical G-protein-coupled receptor (GPCR) that initiates phototransduction in the retina. The receptor consists of the apoprotein opsin covalently linked to the inverse agonist 11-cis retinal. Rhodopsin and opsin have been shown to form oligomers within the outer segment disc membranes of rod photoreceptor cells. However, the physiological relevance of the observed oligomers has been questioned since observations were made on samples prepared from the retina at low temperatures. To investigate the oligomeric status of opsin in live cells at body temperatures, we utilized a novel approach called Förster resonance energy transfer spectrometry, which previously has allowed the determination of the stoichiometry and geometry (i.e. quaternary structure) of various GPCRs. In the current study, we have extended the method to additionally determine whether or not a mixture of oligomeric forms of opsin exists and in what proportion. The application of this improved method revealed that opsin expressed in live Chinese hamster ovary (CHO) cells at 37°C exists as oligomers of various sizes. At lower concentrations, opsin existed in an equilibrium of dimers and tetramers. The tetramers were in the shape of a near-rhombus. At higher concentrations of the receptor, higher-order oligomers began to form. Thus, a mixture of different oligomeric forms of opsin is present in the membrane of live CHO cells and oligomerization occurs in a concentration-dependent manner. The general principles underlying the concentration-dependent oligomerization of opsin may be universal and apply to other GPCRs as well.
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19
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Hanke-Gogokhia C, Wu Z, Gerstner CD, Frederick JM, Zhang H, Baehr W. Arf-like Protein 3 (ARL3) Regulates Protein Trafficking and Ciliogenesis in Mouse Photoreceptors. J Biol Chem 2016; 291:7142-55. [PMID: 26814127 DOI: 10.1074/jbc.m115.710954] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Indexed: 12/22/2022] Open
Abstract
Arf-like protein 3 (ARL3) is a ubiquitous small GTPase expressed in ciliated cells of plants and animals. Germline deletion ofArl3in mice causes multiorgan ciliopathy reminiscent of Bardet-Biedl or Joubert syndromes. As photoreceptors are elegantly compartmentalized and have cilia, we probed the function of ARL3 (ADP-ribosylation factor (Arf)-like 3 protein) by generating rod photoreceptor-specific (prefix(rod)) and retina-specific (prefix(ret))Arl3deletions. In predegenerate(rod)Arl3(-/-)mice, lipidated phototransduction proteins showed trafficking deficiencies, consistent with the role of ARL3 as a cargo displacement factor for lipid-binding proteins. By contrast,(ret)Arl3(-/-)rods and cones expressing Cre recombinase during embryonic development formed neither connecting cilia nor outer segments and degenerated rapidly. Absence of cilia infers participation of ARL3 in ciliogenesis and axoneme formation. Ciliogenesis was rescued, and degeneration was reversed in part by subretinal injection of adeno-associated virus particles expressing ARL3-EGFP. The conditional knock-out phenotypes permitted identification of two ARL3 functions, both in the GTP-bound form as follows: one as a regulator of intraflagellar transport participating in photoreceptor ciliogenesis and the other as a cargo displacement factor transporting lipidated protein to the outer segment. Surprisingly, a farnesylated inositol polyphosphate phosphatase only trafficked from the endoplasmic reticulum to the Golgi, thereby excluding it from a role in photoreceptor cilia physiology.
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Affiliation(s)
- Christin Hanke-Gogokhia
- From the Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, and the Department of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Zhijian Wu
- the NEI, National Institutes of Health, Bethesda, Maryland 20892
| | - Cecilia D Gerstner
- From the Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, and
| | - Jeanne M Frederick
- From the Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, and
| | - Houbin Zhang
- the Sichuan Provincial Key Laboratory for Human Disease Gene Study, Institute of Laboratory Medicine, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, 610072 Sichuan, China, the School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072 Sichuan, China, and
| | - Wolfgang Baehr
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, Utah 84132, From the Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, and the Department of Biology, University of Utah, Salt Lake City, Utah 84112
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20
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Najafi M, Calvert PD. Measurements of rhodopsin diffusion within signaling membrane microcompartments in live photoreceptors. Methods Mol Biol 2015; 1271:309-23. [PMID: 25697532 DOI: 10.1007/978-1-4939-2330-4_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
High-resolution multiphoton imaging of live cells has become an invaluable method to study protein dynamics in highly compartmentalized subcellular environments. Here we describe procedures that we recently developed to quantify rhodopsin mobility within and between retinal rod photoreceptor light signaling microcompartments, the disc membrane lobules, using multiphoton fluorescence relaxation after photoconversion.
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Affiliation(s)
- Mehdi Najafi
- Department of Ophthalmology and the Center for Vision Research, State University of New York Upstate Medical University, Syracuse, NY, USA
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21
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Tanimoto Y, Okada K, Hayashi F, Morigaki K. Evaluating the Raftophilicity of Rhodopsin Photoreceptor in a Patterned Model Membrane. Biophys J 2015; 109:2307-16. [PMID: 26636942 PMCID: PMC4675817 DOI: 10.1016/j.bpj.2015.10.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 10/07/2015] [Accepted: 10/08/2015] [Indexed: 01/09/2023] Open
Abstract
Lipid rafts in the cell membrane are believed to affect various membrane functions, including the signaling by G-protein coupled receptors (GPCRs). However, the regulatory roles of lipid rafts on GPCRs' functions are still poorly understood, partially owing to the lack of the methods to quantitatively evaluate the affinity of membrane proteins to lipid raft (raftophilicity). Here, we describe a methodology to gauge the raftophilicity of a representative GPCR in vertebrate photoreceptor, i.e., rhodopsin (Rh), and its cognate G protein transducin (Gt) by using a patterned model membrane. We generated a substrate-supported planar lipid bilayer that has patterned regions of liquid-ordered (Lo) and liquid-disordered (Ld) membrane domains. We reconstituted Rh and Gt into the patterned membrane and observed their lateral distribution and diffusion. Mobile and functional Rh molecules could be reconstituted through the rapid dilution of solubilized Rh, by optimizing the reconstitution conditions including the chamber design, protein/detergent concentrations, and solution mixing. We determined the partition and diffusion coefficients of Rh and Gt in the Lo-rich and Ld-rich regions. Both Rh and Gt were predominantly localized in the Ld phase, suggesting their low affinity to lipid rafts. Patterned model membrane offers a robust and scalable platform for systematically and quantitatively studying the functional roles of lipid rafts in biological membranes including retinal disk membranes.
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Affiliation(s)
- Yasushi Tanimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Keisuke Okada
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Fumio Hayashi
- Graduate School of Science, Kobe University, Kobe, Japan.
| | - Kenichi Morigaki
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan; Research Center for Environmental Genomics, Kobe University, Kobe, Japan.
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22
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Koch KW, Dell'Orco D. Protein and Signaling Networks in Vertebrate Photoreceptor Cells. Front Mol Neurosci 2015; 8:67. [PMID: 26635520 PMCID: PMC4646965 DOI: 10.3389/fnmol.2015.00067] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 10/26/2015] [Indexed: 01/10/2023] Open
Abstract
Vertebrate photoreceptor cells are exquisite light detectors operating under very dim and bright illumination. The photoexcitation and adaptation machinery in photoreceptor cells consists of protein complexes that can form highly ordered supramolecular structures and control the homeostasis and mutual dependence of the secondary messengers cyclic guanosine monophosphate (cGMP) and Ca2+. The visual pigment in rod photoreceptors, the G protein-coupled receptor rhodopsin is organized in tracks of dimers thereby providing a signaling platform for the dynamic scaffolding of the G protein transducin. Illuminated rhodopsin is turned off by phosphorylation catalyzed by rhodopsin kinase (GRK1) under control of Ca2+-recoverin. The GRK1 protein complex partly assembles in lipid raft structures, where shutting off rhodopsin seems to be more effective. Re-synthesis of cGMP is another crucial step in the recovery of the photoresponse after illumination. It is catalyzed by membrane bound sensory guanylate cyclases (GCs) and is regulated by specific neuronal Ca2+-sensor proteins called guanylate cyclase-activating proteins (GCAPs). At least one GC (ROS-GC1) was shown to be part of a multiprotein complex having strong interactions with the cytoskeleton and being controlled in a multimodal Ca2+-dependent fashion. The final target of the cGMP signaling cascade is a cyclic nucleotide-gated (CNG) channel that is a hetero-oligomeric protein located in the plasma membrane and interacting with accessory proteins in highly organized microdomains. We summarize results and interpretations of findings related to the inhomogeneous organization of signaling units in photoreceptor outer segments.
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Affiliation(s)
- Karl-Wilhelm Koch
- Department of Neurosciences, Biochemistry Group, University of Oldenburg Oldenburg, Germany
| | - Daniele Dell'Orco
- Department of Neurological, Biomedical and Movement Sciences, Section of Biological Chemistry and Center for BioMedical Computing (CBMC), University of Verona Verona, Italy
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23
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Schöneberg J, Heck M, Hofmann KP, Noé F. Explicit spatiotemporal simulation of receptor-G protein coupling in rod cell disk membranes. Biophys J 2015; 107:1042-1053. [PMID: 25185540 DOI: 10.1016/j.bpj.2014.05.050] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/13/2014] [Accepted: 05/19/2014] [Indexed: 12/11/2022] Open
Abstract
Dim-light vision is mediated by retinal rod cells. Rhodopsin (R), a G-protein-coupled receptor, switches to its active form (R(∗)) in response to absorbing a single photon and activates multiple copies of the G-protein transducin (G) that trigger further downstream reactions of the phototransduction cascade. The classical assumption is that R and G are uniformly distributed and freely diffusing on disk membranes. Recent experimental findings have challenged this view by showing specific R architectures, including RG precomplexes, nonuniform R density, specific R arrangements, and immobile fractions of R. Here, we derive a physical model that describes the first steps of the photoactivation cascade in spatiotemporal detail and single-molecule resolution. The model was implemented in the ReaDDy software for particle-based reaction-diffusion simulations. Detailed kinetic in vitro experiments are used to parametrize the reaction rates and diffusion constants of R and G. Particle diffusion and G activation are then studied under different conditions of R-R interaction. It is found that the classical free-diffusion model is consistent with the available kinetic data. The existence of precomplexes between inactive R and G is only consistent with the data if these precomplexes are weak, with much larger dissociation rates than suggested elsewhere. Microarchitectures of R, such as dimer racks, would effectively immobilize R but have little impact on the diffusivity of G and on the overall amplification of the cascade at the level of the G protein.
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Affiliation(s)
- Johannes Schöneberg
- Department of Mathematics, Computer Science and Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Martin Heck
- Institut für Medizinische Physik und Biophysik, Charité, Universitätsmedizin Berlin, Berlin, Germany.
| | - Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Frank Noé
- Department of Mathematics, Computer Science and Bioinformatics, Freie Universität Berlin, Berlin, Germany.
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24
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Gunkel M, Schöneberg J, Alkhaldi W, Irsen S, Noé F, Kaupp UB, Al-Amoudi A. Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. Structure 2015; 23:628-38. [PMID: 25728926 DOI: 10.1016/j.str.2015.01.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/16/2015] [Accepted: 01/22/2015] [Indexed: 12/23/2022]
Abstract
The visual pigment rhodopsin belongs to the family of G protein-coupled receptors that can form higher oligomers. It is controversial whether rhodopsin forms oligomers and whether oligomers are functionally relevant. Here, we study rhodopsin organization in cryosections of dark-adapted mouse rod photoreceptors by cryoelectron tomography. We identify four hierarchical levels of organization. Rhodopsin forms dimers; at least ten dimers form a row. Rows form pairs (tracks) that are aligned parallel to the disk incisures. Particle-based simulation shows that the combination of tracks with fast precomplex formation, i.e. rapid association and dissociation between inactive rhodopsin and the G protein transducin, leads to kinetic trapping: rhodopsin first activates transducin from its own track, whereas recruitment of transducin from other tracks proceeds more slowly. The trap mechanism could produce uniform single-photon responses independent of rhodopsin lifetime. In general, tracks might provide a platform that coordinates the spatiotemporal interaction of signaling molecules.
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Affiliation(s)
- Monika Gunkel
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Johannes Schöneberg
- Computational Molecular Biology Group, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Weaam Alkhaldi
- German Center of Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Stephan Irsen
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Frank Noé
- Computational Molecular Biology Group, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - U Benjamin Kaupp
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.
| | - Ashraf Al-Amoudi
- German Center of Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.
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25
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Billings N, Birjiniuk A, Samad TS, Doyle PS, Ribbeck K. Material properties of biofilms-a review of methods for understanding permeability and mechanics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:036601. [PMID: 25719969 PMCID: PMC4504244 DOI: 10.1088/0034-4885/78/3/036601] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Microorganisms can form biofilms, which are multicellular communities surrounded by a hydrated extracellular matrix of polymers. Central properties of the biofilm are governed by this extracellular matrix, which provides mechanical stability to the 3D biofilm structure, regulates the ability of the biofilm to adhere to surfaces, and determines the ability of the biofilm to adsorb gases, solutes, and foreign cells. Despite their critical relevance for understanding and eliminating of biofilms, the materials properties of the extracellular matrix are understudied. Here, we offer the reader a guide to current technologies that can be utilized to specifically assess the permeability and mechanical properties of the biofilm matrix and its interacting components. In particular, we highlight technological advances in instrumentation and interactions between multiple disciplines that have broadened the spectrum of methods available to conduct these studies. We review pioneering work that furthers our understanding of the material properties of biofilms.
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Affiliation(s)
- Nicole Billings
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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26
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Whited AM, Park PSH. Nanodomain organization of rhodopsin in native human and murine rod outer segment disc membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:26-34. [PMID: 25305340 DOI: 10.1016/j.bbamem.2014.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/25/2014] [Accepted: 10/01/2014] [Indexed: 01/31/2023]
Abstract
Biological membranes display distinct domains that organize membrane proteins and signaling molecules to facilitate efficient and reliable signaling. The organization of rhodopsin, a G protein-coupled receptor, in native rod outer segment disc membranes was investigated by atomic force microscopy. Atomic force microscopy revealed that rhodopsin is arranged into domains of variable size, which we refer to herein as nanodomains, in native membranes. Quantitative analysis of 150 disc membranes revealed that the physical properties of nanodomains are conserved in humans and mice and that the properties of individual disc membranes can be variable. Examining the variable properties of disc membranes revealed some of the factors contributing to the size of rod outer segment discs and the formation of nanodomains in the membrane. The diameter of rod outer segment discs was dependent on the number of rhodopsin molecules incorporated into the membrane but independent of the spatial density of rhodopsin. The number of nanodomains present in a single disc was also dependent on the number of rhodopsin molecules incorporated into the membrane. The size of the nanodomains was largely independent of the number or spatial density of rhodopsin in the membrane.
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Affiliation(s)
- Allison M Whited
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.
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27
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Submembrane assembly and renewal of rod photoreceptor cGMP-gated channel: insight into the actin-dependent process of outer segment morphogenesis. J Neurosci 2014; 34:8164-74. [PMID: 24920621 DOI: 10.1523/jneurosci.1282-14.2014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The photoreceptor outer segment (OS) is comprised of two compartments: plasma membrane (PM) and disk membranes. It is unknown how the PM renewal is coordinated with that of the disk membranes. Here we visualized the localization and trafficking process of rod cyclic nucleotide-gated channel α-subunit (CNGA1), a PM component essential for phototransduction. The localization was visualized by fusing CNGA1 to a fluorescent protein Dendra2 and expressing in Xenopus laevis rod photoreceptors. Dendra2 allowed us to label CNGA1 in a spatiotemporal manner and therefore discriminate between old and newly trafficked CNGA1-Dendra2 in the OS PM. Newly synthesized CNGA1 was preferentially trafficked to the basal region of the lateral OS PM where newly formed and matured disks are also added. Unique trafficking pattern and diffusion barrier excluded CNGA1 from the PM domains, which are the proposed site of disk membrane maturation. Such distinct compartmentalization allows the confinement of cyclic nucleotide-gated channel in the PM, while preventing the disk membrane incorporation. Cytochalasin D and latrunculin A treatments, which are known to disrupt F-actin-dependent disk membrane morphogenesis, prevented the entrance of newly synthesized CNGA1 to the OS PM, but did not prevent the entrance of rhodopsin and peripherin/rds to the membrane evaginations believed to be disk membrane precursors. Uptake of rhodopsin and peripherin/rds coincided with the overgrowth of the evaginations at the base of the OS. Thus F-actin is essential for the trafficking of CNGA1 to the ciliary PM, and coordinates the formations of disk membrane rim region and OS PM.
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28
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Kwiatek JM, Hinde E, Gaus K. Microscopy approaches to investigate protein dynamics and lipid organization. Mol Membr Biol 2014; 31:141-51. [DOI: 10.3109/09687688.2014.937469] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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29
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Comar W, Schubert SM, Jastrzebska B, Palczewski K, Smith AW. Time-resolved fluorescence spectroscopy measures clustering and mobility of a G protein-coupled receptor opsin in live cell membranes. J Am Chem Soc 2014; 136:8342-9. [PMID: 24831851 PMCID: PMC4063175 DOI: 10.1021/ja501948w] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Indexed: 01/31/2023]
Abstract
Determining membrane protein quaternary structure is extremely challenging, especially in live cell membranes. We measured the oligomerization of opsin, a prototypical G protein-coupled receptor with pulsed-interleaved excitation fluorescence cross-correlation spectroscopy (PIE-FCCS). Individual cell measurements revealed that opsin is predominantly organized into dimeric clusters. At low concentrations, we observed that the population of oligomers increased linearly with the square of the individual monomer populations. This finding supports a monomer-dimer equilibrium and provides an experimental measurement of the equilibrium constant.
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Affiliation(s)
- William
D. Comar
- The
University of Akron Department of Chemistry, 190 Buchtel Common, Akron, Ohio 44303-3601, United States
| | - Sarah M. Schubert
- The
University of Akron Department of Chemistry, 190 Buchtel Common, Akron, Ohio 44303-3601, United States
| | - Beata Jastrzebska
- Department
of Pharmacology, School of Medicine, Case
Western Reserve University, 2109 Adelbert Road, Cleveland, Ohio 44106-4965, United States
| | - Krzysztof Palczewski
- Department
of Pharmacology, School of Medicine, Case
Western Reserve University, 2109 Adelbert Road, Cleveland, Ohio 44106-4965, United States
| | - Adam W. Smith
- The
University of Akron Department of Chemistry, 190 Buchtel Common, Akron, Ohio 44303-3601, United States
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30
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Liebman PA. A historical perspective on the lateral diffusion model of GTPase activation and related coupling of membrane signaling proteins. CELLULAR LOGISTICS 2014; 4:e29389. [PMID: 25279248 PMCID: PMC4160331 DOI: 10.4161/cl.29389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 05/28/2014] [Indexed: 12/03/2022]
Abstract
Aspects of our discovery of lateral diffusion of the G protein coupled receptor (GPCR) rhodopsin and that a single activated rhodopsin can non-covalently catalyze GTP binding to thousands of GTPases per second on rod disk membranes via this diffusion are summarized herein. Rapid GTPase coupling to membrane-bound phosphodiesterase (PDE) further amplifies the signal via cGMP hydrolysis, essential to visual transduction. Important generalizations from this work are that biomembranes can uniquely concentrate, orient for reaction and provide a solvent appropriate to rapid, powerful and appropriately controlled sequential interaction of signaling proteins. Of equal importance to function is timely control and termination of such powerful amplification via receptor phosphorylation (quenching) and arrestin binding. Downstream kinetic modulation by GTPase activating proteins (GAPs) and regulators of G protein signaling (RGS) and related mechanisms as well as limitations set by membrane domain fencing, structural protein binding etc. can be essential in relevant systems.
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Affiliation(s)
- Paul A Liebman
- Department of Biochemistry and Biophysics; University of Pennsylvania; Philadelphia, PA USA
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Johansson B, Höök F, Klenerman D, Jönsson P. Label-free measurements of the diffusivity of molecules in lipid membranes. Chemphyschem 2014; 15:486-91. [PMID: 24402971 DOI: 10.1002/cphc.201301136] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Indexed: 11/05/2022]
Abstract
An important and characteristic property of a cell membrane is the lateral mobility of protein molecules in the lipid bilayer. This has conventionally been measured by labeling the molecules with fluorescent markers and monitoring their mobility by different fluorescence-based techniques. However, adding the label to the studied molecule may affect the system, so it is an assumption in almost all experiments that the measured mobility of the biomolecule with its label is the same as that of the unlabeled molecule. However, this assumption is rarely tested due to a lack of suitable methods. In this work, a new technique to perform label-free diffusivity measurements is developed and used to measure the effect of the label for two common protein-lipid systems: 1) streptavidin (SA) coupled to a supported lipid bilayer (SLB) through biotinylated lipids and 2) the extracellular part of the T-cell adhesion protein CD2, coupled to an SLB through histidine tags to nickel-chelating lipids. A measurable (≈12%) decrease in diffusivity is found for both labeled proteins, even though the molecular mass of the label is almost 100 times smaller than those of the proteins (≈50 kDa). The results illustrate the importance of being able to study different biophysical properties of cell membranes and their mimics without relying on fluorescent labels, especially if fluorescent labeling is difficult or is expected to affect the nature of the intermolecular interactions being studied.
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Affiliation(s)
- Björn Johansson
- Department of Applied Physics, Chalmers University of Technology, 41296 Gothenburg (Sweden)
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Dell'Orco D. A physiological role for the supramolecular organization of rhodopsin and transducin in rod photoreceptors. FEBS Lett 2013; 587:2060-6. [PMID: 23684654 DOI: 10.1016/j.febslet.2013.05.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 05/06/2013] [Indexed: 10/26/2022]
Abstract
Vertebrate vision in rod photoreceptors begins when a photon hits the visual pigment rhodopsin (Rh) and triggers the phototransduction cascade. Although the fine biochemical and biophysical details of this paradigmatic signalling pathway have been studied for decades, phototransduction still presents unclear mechanistic aspects. Increasing lines of evidence suggest that the visual pigment rhodopsin (Rh) is natively organized in dimers on the surface of disc membranes, and may form higher order "paracrystalline" assemblies, which are not easy to reconcile with the classical collision-coupling mechanistic scenario evoked to explain the extremely fast molecular processes required in phototransduction. The questioned and criticized existence of paracrystalline Rh rafts can be fully accepted only if it can be explained in functional terms by a solid mechanistic picture. Here we discuss how recent data suggest a physiological role for supramolecular assemblies of Rh and its cognate G protein transducin (Gt), which by forming transient complexes in the dark may ensure rapid activation of the cascade even in a crowded environment that, according to the classical picture, would otherwise stop the cascade.
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Affiliation(s)
- Daniele Dell'Orco
- Department of Life Sciences and Reproduction, Section of Biological Chemistry, and Centre for Biomedical Computing, University of Verona, Strada le Grazie 8, 37134 Verona, Italy.
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Najafi M, Haeri M, Knox BE, Schiesser WE, Calvert PD. Impact of signaling microcompartment geometry on GPCR dynamics in live retinal photoreceptors. ACTA ACUST UNITED AC 2012; 140:249-66. [PMID: 22891277 PMCID: PMC3434098 DOI: 10.1085/jgp.201210818] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
G protein–coupled receptor (GPCR) cascades rely on membrane protein diffusion for signaling and are generally found in spatially constrained subcellular microcompartments. How the geometry of these microcompartments impacts cascade activities, however, is not understood, primarily because of the inability of current live cell–imaging technologies to resolve these small structures. Here, we examine the dynamics of the GPCR rhodopsin within discrete signaling microcompartments of live photoreceptors using a novel high resolution approach. Rhodopsin fused to green fluorescent protein variants, either enhanced green fluorescent protein (EGFP) or the photoactivatable PAGFP (Rho-E/PAGFP), was expressed transgenically in Xenopus laevis rod photoreceptors, and the geometries of light signaling microcompartments formed by lamellar disc membranes and their incisure clefts were resolved by confocal imaging. Multiphoton fluorescence relaxation after photoconversion experiments were then performed with a Ti–sapphire laser focused to the diffraction limit, which produced small sub–cubic micrometer volumes of photoconverted molecules within the discrete microcompartments. A model of molecular diffusion was developed that allows the geometry of the particular compartment being examined to be specified. This was used to interpret the experimental results. Using this unique approach, we showed that rhodopsin mobility across the disc surface was highly heterogeneous. The overall relaxation of Rho-PAGFP fluorescence photoactivated within a microcompartment was biphasic, with a fast phase lasting several seconds and a slow phase of variable duration that required up to several minutes to reach equilibrium. Local Rho-EGFP diffusion within defined compartments was monotonic, however, with an effective lateral diffusion coefficient Dlat = 0.130 ± 0.012 µm2s−1. Comparison of rhodopsin-PAGFP relaxation time courses with model predictions revealed that microcompartment geometry alone may explain both fast local rhodopsin diffusion and its slow equilibration across the greater disc membrane. Our approach has for the first time allowed direct examination of GPCR dynamics within a live cell signaling microcompartment and a quantitative assessment of the impact of compartment geometry on GPCR activity.
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Affiliation(s)
- Mehdi Najafi
- Department of Ophthalmology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA
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Periole X, Knepp AM, Sakmar TP, Marrink SJ, Huber T. Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers. J Am Chem Soc 2012; 134:10959-65. [PMID: 22679925 PMCID: PMC3406292 DOI: 10.1021/ja303286e] [Citation(s) in RCA: 177] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The G protein-coupled receptor (GPCR) rhodopsin self-assembles into supramolecular structures in native bilayers, but the structural determinants of receptor oligomerization are not known. We carried out multiple self-assembly coarse-grained molecular dynamics (CGMD) simulations of model membranes containing up to 64 molecules of the visual receptor rhodopsin over time scales reaching 100 μs. The simulations show strong preferential interaction modes between receptors. Two primary modes of receptor-receptor interactions are consistent with umbrella sampling/potential of mean force (PMF) calculations as a function of the distance between a pair of receptors. The preferential interfaces, involving helices (H) 1/8, 4/5 and 5, present no energy barrier to forming a very stable receptor dimer. Most notably, the PMFs show that the preferred rhodopsin dimer exists in a tail-to-tail conformation, with the interface comprising transmembrane H1/H2 and amphipathic H8 at the extracellular and cytoplasmic surfaces, respectively. This dimer orientation is in line with earlier electron microscopy, X-ray, and cross-linking experiments of rhodopsin and other GPCRs. Less stable interfaces, involving H4 and H6, have a free energy barrier for desolvation (delipidation) of the interfaces and appear to be designed to stabilize "lubricated" (i.e., lipid-coated) dimers. The overall CGMD strategy used here is general and can be applied to study the homo- and heterodimerization of GPCRs and other transmembrane proteins. Systematic extension of the work will deepen our understanding of the forces involved in the membrane organization of integral membrane proteins.
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Affiliation(s)
- Xavier Periole
- Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Adam M. Knepp
- Laboratory of Molecular Biology & Biochemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Thomas P. Sakmar
- Laboratory of Molecular Biology & Biochemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Siewert J. Marrink
- Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Thomas Huber
- Laboratory of Molecular Biology & Biochemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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Cordomí A, Perez JJ. Structural Rearrangements of Rhodopsin Subunits in a Dimer Complex: a Molecular Dynamics Simulation Study. J Biomol Struct Dyn 2012; 27:127-47. [DOI: 10.1080/07391102.2009.10507303] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Arnau Cordomí
- a Dept d'Enginyeria Química , Technical University of Catalonia (UPC), ETS d'Enginyeria Industrial , Av. Diagonal 647, 08028 , Barcelona , Spain
| | - Juan J. Perez
- a Dept d'Enginyeria Química , Technical University of Catalonia (UPC), ETS d'Enginyeria Industrial , Av. Diagonal 647, 08028 , Barcelona , Spain
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Ishikawa-Ankerhold HC, Ankerhold R, Drummen GPC. Advanced fluorescence microscopy techniques--FRAP, FLIP, FLAP, FRET and FLIM. Molecules 2012; 17:4047-132. [PMID: 22469598 PMCID: PMC6268795 DOI: 10.3390/molecules17044047] [Citation(s) in RCA: 273] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 03/21/2012] [Accepted: 03/21/2012] [Indexed: 12/19/2022] Open
Abstract
Fluorescence microscopy provides an efficient and unique approach to study fixed and living cells because of its versatility, specificity, and high sensitivity. Fluorescence microscopes can both detect the fluorescence emitted from labeled molecules in biological samples as images or photometric data from which intensities and emission spectra can be deduced. By exploiting the characteristics of fluorescence, various techniques have been developed that enable the visualization and analysis of complex dynamic events in cells, organelles, and sub-organelle components within the biological specimen. The techniques described here are fluorescence recovery after photobleaching (FRAP), the related fluorescence loss in photobleaching (FLIP), fluorescence localization after photobleaching (FLAP), Förster or fluorescence resonance energy transfer (FRET) and the different ways how to measure FRET, such as acceptor bleaching, sensitized emission, polarization anisotropy, and fluorescence lifetime imaging microscopy (FLIM). First, a brief introduction into the mechanisms underlying fluorescence as a physical phenomenon and fluorescence, confocal, and multiphoton microscopy is given. Subsequently, these advanced microscopy techniques are introduced in more detail, with a description of how these techniques are performed, what needs to be considered, and what practical advantages they can bring to cell biological research.
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Affiliation(s)
- Hellen C. Ishikawa-Ankerhold
- Ludwig Maximilian University of Munich, Institute of Anatomy and Cell Biology, Schillerstr. 42, 80336 München, Germany
| | - Richard Ankerhold
- Carl Zeiss Microimaging GmbH, Kistlerhofstr. 75, 81379 München, Germany
| | - Gregor P. C. Drummen
- Bionanoscience and Bio-Imaging Program, Cellular Stress and Ageing Program, Bio&Nano-Solutions, Helmutstr. 3A, 40472 Düsseldorf, Germany
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A dynamic scaffolding mechanism for rhodopsin and transducin interaction in vertebrate vision. Biochem J 2012; 440:263-71. [PMID: 21843151 DOI: 10.1042/bj20110871] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The early steps in vertebrate vision require fast interactions between Rh (rhodopsin) and Gt (transducin), which are classically described by a collisional coupling mechanism driven by the free diffusion of monomeric proteins on the disc membranes of rod and cone cells. Recent findings, however, point to a very low mobility for Rh and support a substantially different supramolecular organization. Moreover, Rh-G(t) interactions seem to possibly occur even prior to light stimuli, which is also difficult to reconcile with the classical scenario. We investigated the kinetics of interaction between native Rh and G(t) in different conditions by surface plasmon resonance and analysed the results in the general physiological context by employing a holistic systems modelling approach. The results from the present study point to a mechanism that is intermediate between pure collisional coupling and physical scaffolding. Such a 'dynamic scaffolding', in which prevalently dimeric Rh and G(t) interact in the dark by forming transient complexes (~25% of G(t) is precoupled to Rh), does not slow down the phototransduction cascade, but is compatible with the observed photoresponses on a broad scale of light stimuli. We conclude that Rh molecules and Rh-G(t) complexes can both absorb photons and trigger the visual cascade.
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38
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Berta ÁI, Boesze-Battaglia K, Genini S, Goldstein O, O'Brien PJ, Szél Á, Acland GM, Beltran WA, Aguirre GD. Photoreceptor cell death, proliferation and formation of hybrid rod/S-cone photoreceptors in the degenerating STK38L mutant retina. PLoS One 2011; 6:e24074. [PMID: 21980341 PMCID: PMC3184085 DOI: 10.1371/journal.pone.0024074] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 08/02/2011] [Indexed: 11/19/2022] Open
Abstract
A homozygous mutation in STK38L in dogs impairs the late phase of photoreceptor development, and is followed by photoreceptor cell death (TUNEL) and proliferation (PCNA, PHH3) events that occur independently in different cells between 7-14 weeks of age. During this period, the outer nuclear layer (ONL) cell number is unchanged. The dividing cells are of photoreceptor origin, have rod opsin labeling, and do not label with markers specific for macrophages/microglia (CD18) or Müller cells (glutamine synthetase, PAX6). Nestin labeling is absent from the ONL although it labels the peripheral retina and ciliary marginal zone equally in normals and mutants. Cell proliferation is associated with increased cyclin A1 and LATS1 mRNA expression, but CRX protein expression is unchanged. Coincident with photoreceptor proliferation is a change in the photoreceptor population. Prior to cell death the photoreceptor mosaic is composed of L/M- and S-cones, and rods. After proliferation, both cone types remain, but the majority of rods are now hybrid photoreceptors that express rod opsin and, to a lesser extent, cone S-opsin, and lack NR2E3 expression. The hybrid photoreceptors renew their outer segments diffusely, a characteristic of cones. The results indicate the capacity for terminally differentiated, albeit mutant, photoreceptors to divide with mutations in this novel retinal degeneration gene.
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Affiliation(s)
- Ágnes I. Berta
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvanis, United States of America
- Department of Human Morphology and Developmental Biology, Semmelweis University of Medicine, Budapest, Hungary
| | - Kathleen Boesze-Battaglia
- School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sem Genini
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvanis, United States of America
| | - Orly Goldstein
- J.A. Baker Institute, College of Veterinary Medicine, Cornell University, Ithaca New York, United States of America
| | - Paul J. O'Brien
- Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ágoston Szél
- Department of Human Morphology and Developmental Biology, Semmelweis University of Medicine, Budapest, Hungary
| | - Gregory M. Acland
- J.A. Baker Institute, College of Veterinary Medicine, Cornell University, Ithaca New York, United States of America
| | - William A. Beltran
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvanis, United States of America
| | - Gustavo D. Aguirre
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvanis, United States of America
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39
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A simplified mass-transfer model for visual pigments in amphibian retinal-cone outer segments. Biophys J 2011; 100:525-534. [PMID: 21281566 DOI: 10.1016/j.bpj.2010.11.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 11/10/2010] [Accepted: 11/15/2010] [Indexed: 11/22/2022] Open
Abstract
When radiolabeled precursors and autoradiography are used to investigate turnover of protein components in photoreceptive cone outer segments (COSs), the labeled components--primarily visual pigment molecules (opsins)--are diffusely distributed along the COS. To further assess this COS labeling pattern, we derive a simplified mass-transfer model for quantifying the contributions of advective and diffusive mechanisms to the distribution of opsins within COSs of the frog retina. Two opsin-containing regions of the COS are evaluated: the core axial array of disks and the plasmalemma. Numerical solutions of the mass-transfer model indicate three distinct stages of system evolution. In the first stage, plasmalemma diffusion is dominant. In the second stage, the plasmalemma density reaches a metastable state and transfer between the plasmalemma and disk region occurs, which is followed by an increase in density that is qualitatively similar for both regions. The final stage consists of both regions slowly evolving to the steady-state solution. Our results indicate that autoradiographic and cognate approaches for tracking labeled opsins in the COS cannot be effective methodologies for assessing new disk formation at the base of the COS.
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40
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Goehring NW, Hoege C, Grill SW, Hyman AA. PAR proteins diffuse freely across the anterior-posterior boundary in polarized C. elegans embryos. ACTA ACUST UNITED AC 2011; 193:583-94. [PMID: 21518794 PMCID: PMC3087016 DOI: 10.1083/jcb.201011094] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
FRAP reveals that a stable PAR boundary requires balancing diffusive flux of PAR proteins between domains with spatial differences in PAR protein membrane affinities. Polarization of cells by PAR proteins requires the segregation of antagonistic sets of proteins into two mutually exclusive membrane-associated domains. Understanding how nanometer scale interactions between individual PAR proteins allow spatial organization across cellular length scales requires determining the kinetic properties of PAR proteins and how they are modified in space. We find that PAR-2 and PAR-6, which localize to opposing PAR domains, undergo exchange between well mixed cytoplasmic populations and laterally diffusing membrane-associated states. Domain maintenance does not involve diffusion barriers, lateral sorting, or active transport. Rather, both PAR proteins are free to diffuse between domains, giving rise to a continuous boundary flux because of lateral diffusion of molecules down the concentration gradients that exist across the embryo. Our results suggest that the equalizing effects of lateral diffusion are countered by actin-independent differences in the effective membrane affinities of PAR proteins between the two domains, which likely depend on the ability of each PAR species to locally modulate the membrane affinity of opposing PAR species within its domain. We propose that the stably polarized embryo reflects a dynamic steady state in which molecules undergo continuous diffusion between regions of net association and dissociation.
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Affiliation(s)
- Nathan W Goehring
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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41
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Sommer ME, Hofmann KP, Heck M. Arrestin-rhodopsin binding stoichiometry in isolated rod outer segment membranes depends on the percentage of activated receptors. J Biol Chem 2010; 286:7359-69. [PMID: 21169358 DOI: 10.1074/jbc.m110.204941] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In the rod cell of the retina, arrestin is responsible for blocking signaling of the G-protein-coupled receptor rhodopsin. The general visual signal transduction model implies that arrestin must be able to interact with a single light-activated, phosphorylated rhodopsin molecule (Rho*P), as would be generated at physiologically relevant low light levels. However, the elongated bi-lobed structure of arrestin suggests that it might be able to accommodate two rhodopsin molecules. In this study, we directly addressed the question of binding stoichiometry by quantifying arrestin binding to Rho*P in isolated rod outer segment membranes. We manipulated the "photoactivation density," i.e. the percentage of active receptors in the membrane, with the use of a light flash or by partially regenerating membranes containing phosphorylated opsin with 11-cis-retinal. Curiously, we found that the apparent arrestin-Rho*P binding stoichiometry was linearly dependent on the photoactivation density, with one-to-one binding at low photoactivation density and one-to-two binding at high photoactivation density. We also observed that, irrespective of the photoactivation density, a single arrestin molecule was able to stabilize the active metarhodopsin II conformation of only a single Rho*P. We hypothesize that, although arrestin requires at least a single Rho*P to bind the membrane, a single arrestin can actually interact with a pair of receptors. The ability of arrestin to interact with heterogeneous receptor pairs composed of two different photo-intermediate states would be well suited to the rod cell, which functions at low light intensity but is routinely exposed to several orders of magnitude more light.
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Affiliation(s)
- Martha E Sommer
- Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany
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42
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Onaizi SA, He L, Middelberg AP. The construction, fouling and enzymatic cleaning of a textile dye surface. J Colloid Interface Sci 2010; 351:203-9. [DOI: 10.1016/j.jcis.2010.07.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/13/2010] [Accepted: 07/13/2010] [Indexed: 11/26/2022]
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43
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Goehring NW, Chowdhury D, Hyman AA, Grill SW. FRAP analysis of membrane-associated proteins: lateral diffusion and membrane-cytoplasmic exchange. Biophys J 2010; 99:2443-52. [PMID: 20959084 PMCID: PMC2956213 DOI: 10.1016/j.bpj.2010.08.033] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 08/13/2010] [Accepted: 08/13/2010] [Indexed: 10/18/2022] Open
Abstract
Obtaining quantitative kinetic parameters from fluorescence recovery after photobleaching (FRAP) experiments generally requires a theoretical analysis of protein mobility and appropriate solutions for FRAP recovery derived for a given geometry. Here we provide a treatment of FRAP recovery for a molecule undergoing a combined process of reversible membrane association and lateral diffusion on the plasma membrane for two commonly used bleach geometries: stripes, and boxes. Such analysis is complicated by the fact that diffusion of a molecule during photobleaching can lead to broadening of the bleach area, resulting in significant deviations of the actual bleach shape from the desired bleach geometry, which creates difficulty in accurately measuring kinetic parameters. Here we overcome the problem of deviations between actual and idealized bleach geometries by parameterizing, more accurately, the initial postbleach state. This allows for reconstruction of an accurate and analytically tractable approximation of the actual fluorescence distribution. Through simulated FRAP experiments, we demonstrate that this method can be used to accurately measure a broad range of combinations of diffusion constants and exchange rates. Use of this method to analyze the plextrin homology domain of PLC-δ1 in Caenorhabditis elegans results in quantitative agreement with prior analysis of this domain in other cells using other methods. Because of the flexibility, relative ease of implementation, and its use of standard, easily obtainable bleach geometries, this method should be broadly applicable to investigation of protein dynamics at the plasma membrane.
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Affiliation(s)
- Nathan W. Goehring
- Max Planck Institute of Molecular Cell Biology & Genetics, Dresden, Germany
| | - Debanjan Chowdhury
- Max Planck Institute for Physics of Complex Systems, Dresden, Germany
- Department of Physics, Indian Institute of Technology, Kanpur, India
| | - Anthony A. Hyman
- Max Planck Institute of Molecular Cell Biology & Genetics, Dresden, Germany
| | - Stephan W. Grill
- Max Planck Institute of Molecular Cell Biology & Genetics, Dresden, Germany
- Max Planck Institute for Physics of Complex Systems, Dresden, Germany
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44
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Sadegh Zadeh K, Montas HJ. A class of exact solutions for biomacromolecule diffusion–reaction in live cells. J Theor Biol 2010; 264:914-33. [DOI: 10.1016/j.jtbi.2010.03.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 03/15/2010] [Accepted: 03/16/2010] [Indexed: 11/30/2022]
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45
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46
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Wang Q, Zhang X, Zhang L, He F, Zhang G, Jamrich M, Wensel TG. Activation-dependent hindrance of photoreceptor G protein diffusion by lipid microdomains. J Biol Chem 2008; 283:30015-24. [PMID: 18713731 DOI: 10.1074/jbc.m803953200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The dynamics of G protein-mediated signal transduction depend on the two-dimensional diffusion of membrane-bound G proteins and receptors, which has been suggested to be rate-limiting for vertebrate phototransduction, a highly amplified G protein-coupled signaling pathway. Using fluorescence recovery after photobleaching (FRAP), we measured the diffusion of the G protein transducin alpha-subunit (Galpha(t)) and the G protein-coupled receptor rhodopsin on disk membranes of living rod photoreceptors from transgenic Xenopus laevis. Treatment with either methyl-beta-cyclodextrin or filipin III to disrupt cholesterol-containing lipid microdomains dramatically accelerated diffusion of Galpha(t) in its GTP-bound state and of the rhodopsin-Galphabetagamma(t) complex but not of rhodopsin or inactive GDP-bound Galphabetagamma. These results imply an activity-dependent sequestration of G proteins into cholesterol-dependent lipid microdomains, which limits diffusion and exclude the majority of free rhodopsin and the free G protein heterotrimer. Our data offer a novel demonstration of lipid microdomains in the internal membranes of living sensory neurons.
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Affiliation(s)
- Qiong Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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47
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Dell'Orco D, Schmidt H. Mesoscopic Monte Carlo simulations of stochastic encounters between photoactivated rhodopsin and transducin in disc membranes. J Phys Chem B 2008; 112:4419-26. [PMID: 18345658 DOI: 10.1021/jp709963f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The issue of how the molecular organization of rod outer segments (ROS) discs affects the initial timing of the photoresponse in vertebrates has been recently raised by novel structural findings that raise doubts about the classical scenario of monomeric rhodopsin (R) and heterotrimeric transducin (G) freely diffusing in the membrane milieu. In this study, we investigate this issue by means of mesoscopic Monte Carlo (MMC) simulations of the stochastic encounters between one photoactivated R and one G, explicitly taking into account the molecular size and the diffusion coefficient of each species as well as crowding effects. Three different scenarios were compared with respect to their effects on timing, namely, (a) the classical framework, where both G and monomeric R are allowed to freely diffuse in the ROS disc membrane, (b) the ideal paracrystalline organization of R dimers considered as a structural unit, where ordered rows completely cover the disc membrane patch, and (c) the scenario suggested by recent AFM data, where R dimers organize in differently sized rafts with varying local concentrations. Our simulations suggest that a similar kinetic response could arise from very different microscopic scenarios, thus opening new interpretations to the controversial recent findings. Moreover, we show that if high-density R packing on ROS discs is characterized by a highly ordered structural organization rather than unspecific aggregation, an unexpected favorable effect on the temporal response of early phototransduction reactions can occur.
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Affiliation(s)
- Daniele Dell'Orco
- Department of Chemistry, University of Modena and Reggio Emilia and Dulbecco Telethon Institute, via Campi 183 41100 Modena, Italy.
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48
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Abstract
Fluorescence recovery after photobleaching (FRAP) reveals the dynamics of fluorescently tagged molecules within live cells. These molecular dynamics are governed by diffusion of the molecule and its in vivo binding interactions. As a result, quantitative estimates of the association and dissociation rates of binding can be extracted from the FRAP. This chapter describes a systematic procedure to acquire the FRAP data, and then fit it with appropriate mathematical models to estimate in vivo association and dissociation rates of binding. Also discussed are the applicability and limitations of the models, the utility of the estimated parameters, and the prospects for increased accuracy and confidence in the estimates.
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Affiliation(s)
- James G McNally
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, Maryland 20892, USA
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Periole X, Huber T, Marrink SJ, Sakmar TP. G Protein-Coupled Receptors Self-Assemble in Dynamics Simulations of Model Bilayers. J Am Chem Soc 2007; 129:10126-32. [PMID: 17658882 DOI: 10.1021/ja0706246] [Citation(s) in RCA: 243] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many integral membrane proteins assemble to form oligomeric structures in biological membranes. In particular, seven-transmembrane helical G protein-coupled receptors (GPCRs) appear to self-assemble constitutively in membranes, but the mechanism and physiological role of this assembly are unknown. We developed and employed coarse-grain molecular dynamics (CGMD) models to investigate the molecular basis of how the physicochemical properties of the phospholipid bilayer membrane affect self-assembly of visual rhodopsin, a prototypical GPCR. The CGMD method is a mesoscopic simulation technique in which groups of atoms are mapped to particles on the basis of a four-to-one rule. This systematic reduction of the degrees of freedom allows for computationally efficient calculation of the structure and dynamics of molecular assemblies for larger time and length scales than accessible to atomistic models, providing here an unprecedented view of spontaneous protein assembly in biomembranes. Systems with up to 16 rhodopsin molecules at a protein-to-lipid ratio of 1:100 were simulated for time scales of up to 8 micros. The results obtained for four different phospholipid environments showed that localized adaptation of the membrane bilayer to the presence of receptors is reproducibly most pronounced near transmembrane helices 2, 4, and 7. This local membrane deformation appears to be a key factor defining the rate, extent, and orientational preference of protein-protein association. The implications of our findings are discussed within a framework of a generalized mechanism of membrane protein self-assembly.
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Affiliation(s)
- Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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Sadegh Zadeh K, Elman HC, Montas HJ, Shirmohammadi A. A finite element model for protein transport in vivo. Biomed Eng Online 2007; 6:24. [PMID: 17598901 PMCID: PMC1940256 DOI: 10.1186/1475-925x-6-24] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Accepted: 06/28/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biological mass transport processes determine the behavior and function of cells, regulate interactions between synthetic agents and recipient targets, and are key elements in the design and use of biosensors. Accurately predicting the outcomes of such processes is crucial to both enhancing our understanding of how these systems function, enabling the design of effective strategies to control their function, and verifying that engineered solutions perform according to plan. METHODS A Galerkin-based finite element model was developed and implemented to solve a system of two coupled partial differential equations governing biomolecule transport and reaction in live cells. The simulator was coupled, in the framework of an inverse modeling strategy, with an optimization algorithm and an experimental time series, obtained by the Fluorescence Recovery after Photobleaching (FRAP) technique, to estimate biomolecule mass transport and reaction rate parameters. In the inverse algorithm, an adaptive method was implemented to calculate sensitivity matrix. A multi-criteria termination rule was developed to stop the inverse code at the solution. The applicability of the model was illustrated by simulating the mobility and binding of GFP-tagged glucocorticoid receptor in the nucleoplasm of mouse adenocarcinoma. RESULTS The numerical simulator shows excellent agreement with the analytic solutions and experimental FRAP data. Detailed residual analysis indicates that residuals have zero mean and constant variance and are normally distributed and uncorrelated. Therefore, the necessary and sufficient criteria for least square parameter optimization, which was used in this study, were met. CONCLUSION The developed strategy is an efficient approach to extract as much physiochemical information from the FRAP protocol as possible. Well-posedness analysis of the inverse problem, however, indicates that the FRAP protocol provides insufficient information for unique simultaneous estimation of diffusion coefficient and binding rate parameters. Care should be exercised in drawing inferences, from FRAP data, regarding concentrations of free and bound proteins, average binding and diffusion times, and protein mobility unless they are confirmed by long-range Markov Chain-Monte Carlo (MCMC) methods and experimental observations.
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Affiliation(s)
- Kouroush Sadegh Zadeh
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Howard C Elman
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Hubert J Montas
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Adel Shirmohammadi
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
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