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Zheng G, Li J, Zhou Y, Gao H, Wan N, Wu C, Chen F, Zhou R, Shen M, Lu F, Wang Y. Outer retina and choroid as potential imaging markers for evaluation of neural impairment in early type 2 diabetic patients. Eur J Ophthalmol 2024:11206721241258637. [PMID: 38862403 DOI: 10.1177/11206721241258637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
PURPOSE To quantify the presence of early structural alterations in the outer retinal layer and choroid among healthy subjects and diabetic patients with no or mild diabetic retinopathy, and to establish the correlation between the measured structural parameters and retinal sensitivity. METHODS In total, 31 eyes from subjects with type 2 diabetes and 29 eyes from healthy subjects were enrolled. Optical coherence tomography was used to measure outer retina layers and choroid, while microperimetry was used to characterize the changes of visual function in a 6-mm diameter area at macula. Quantitative analysis of structural and functional changes was performed between groups and the structure-function correlations were determined. RESULTS The thickness of myoid and ellipsoid zone, choroid and the mean retinal sensitivity were significantly smaller in diabetic group than that in controls (all P values < 0.05). Besides, thinner choroid and outer retina was associated with the decreased retinal sensitivity,especially in diabetic patients (r = 0.377, P = 0.048; r = 0.401, P = 0.034; respectively). Final multiple regression models showed the outer retinal thickness (ORT) (P = 0.033), choroidal thickness (P = 0.003) and the interaction between ORT and choroidal thickness (P = 0.001) were significant predictors to retinal sensitivity. CONCLUSIONS Thinning of choroid and outer retina were significantly correlated with reduced retinal sensitivity, which indicate outer retina and choroid might be potential imaging markers for evaluation of visual function related to neural impairment in type 2 diabetic patients without or in the early stage of diabetic retinopathy.
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Affiliation(s)
- Gu Zheng
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Disease, Wenzhou, Zhejiang, China
| | - Jin Li
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Disease, Wenzhou, Zhejiang, China
| | - Yue Zhou
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Disease, Wenzhou, Zhejiang, China
| | - Hongjian Gao
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Disease, Wenzhou, Zhejiang, China
| | - Ni Wan
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Disease, Wenzhou, Zhejiang, China
| | - Chaoming Wu
- The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Feng Chen
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Disease, Wenzhou, Zhejiang, China
| | - Rong Zhou
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Disease, Wenzhou, Zhejiang, China
| | - Meixiao Shen
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Disease, Wenzhou, Zhejiang, China
| | - Fan Lu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Disease, Wenzhou, Zhejiang, China
| | - Yuanyuan Wang
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Wenzhou University of Technology, 1 Jingguan Road, Wenzhou University Town, Wenzhou, Zhejiang, China
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Sarimov RM, Serov DA, Gudkov SV. Hypomagnetic Conditions and Their Biological Action (Review). BIOLOGY 2023; 12:1513. [PMID: 38132339 PMCID: PMC10740674 DOI: 10.3390/biology12121513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
The geomagnetic field plays an important role in the existence of life on Earth. The study of the biological effects of (hypomagnetic conditions) HMC is an important task in magnetobiology. The fundamental importance is expanding and clarifying knowledge about the mechanisms of magnetic field interaction with living systems. The applied significance is improving the training of astronauts for long-term space expeditions. This review describes the effects of HMC on animals and plants, manifested at the cellular and organismal levels. General information is given about the probable mechanisms of HMC and geomagnetic field action on living systems. The main experimental approaches are described. We attempted to systematize quantitative data from various studies and identify general dependencies of the magnetobiology effects' value on HMC characteristics (induction, exposure duration) and the biological parameter under study. The most pronounced effects were found at the cellular level compared to the organismal level. Gene expression and protein activity appeared to be the most sensitive to HMC among the molecular cellular processes. The nervous system was found to be the most sensitive in the case of the organism level. The review may be of interest to biologists, physicians, physicists, and specialists in interdisciplinary fields.
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Affiliation(s)
| | | | - Sergey V. Gudkov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilove St. 38, 119991 Moscow, Russia; (R.M.S.); (D.A.S.)
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3
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Senapati S, Park PSH. Understanding the Rhodopsin Worldview Through Atomic Force Microscopy (AFM): Structure, Stability, and Activity Studies. CHEM REC 2023; 23:e202300113. [PMID: 37265335 PMCID: PMC10908267 DOI: 10.1002/tcr.202300113] [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: 03/28/2023] [Revised: 05/12/2023] [Indexed: 06/03/2023]
Abstract
Rhodopsin is a G protein-coupled receptor (GPCR) present in the rod outer segment (ROS) of photoreceptor cells that initiates the phototransduction cascade required for scotopic vision. Due to the remarkable advancements in technological tools, the chemistry of rhodopsin has begun to unravel especially over the past few decades, but mostly at the ensemble scale. Atomic force microscopy (AFM) is a tool capable of providing critical information from a single-molecule point of view. In this regard, to bolster our understanding of rhodopsin at the nanoscale level, AFM-based imaging, force spectroscopy, and nano-indentation techniques were employed on ROS disc membranes containing rhodopsin, isolated from vertebrate species both in normal and diseased states. These AFM studies on samples from native retinal tissue have provided fundamental insights into the structure and function of rhodopsin under normal and dysfunctional states. We review here the findings from these AFM studies that provide important insights on the supramolecular organization of rhodopsin within the membrane and factors that contribute to this organization, the molecular interactions stabilizing the structure of the receptor and factors that can modify those interactions, and the mechanism underlying constitutive activity in the receptor that can cause disease.
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Affiliation(s)
- Subhadip Senapati
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
- Prayoga Institute of Education Research, Bengaluru, KA 560116, India
| | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
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4
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Radzin S, Wiśniewska-Becker A, Markiewicz M, Bętkowski S, Furso J, Waresiak J, Grolik J, Sarna T, Pawlak AM. Structural Impact of Selected Retinoids on Model Photoreceptor Membranes. MEMBRANES 2023; 13:575. [PMID: 37367779 DOI: 10.3390/membranes13060575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/07/2023] [Accepted: 05/27/2023] [Indexed: 06/28/2023]
Abstract
Photoreceptor membranes have a unique lipid composition. They contain a high level of polyunsaturated fatty acids including the most unsaturated fatty acid in nature, docosahexaenoic acid (22:6), and are enriched in phosphatidylethanolamines. The phospholipid composition and cholesterol content of the subcellular components of photoreceptor outer segments enables to divide photoreceptor membranes into three types: plasma membranes, young disc membranes, and old disc membranes. A high degree of lipid unsaturation, extended exposure to intensive irradiation, and high respiratory demands make these membranes sensitive to oxidative stress and lipid peroxidation. Moreover, all-trans retinal (AtRAL), which is a photoreactive product of visual pigment bleaching, accumulates transiently inside these membranes, where its concentration may reach a phototoxic level. An elevated concentration of AtRAL leads to accelerated formation and accumulation of bisretinoid condensation products such as A2E or AtRAL dimers. However, a possible structural impact of these retinoids on the photoreceptor-membrane properties has not yet been studied. In this work we focused just on this aspect. The changes induced by retinoids, although noticeable, seem not to be significant enough to be physiologically relevant. This is, however, an positive conclusion because it can be assumed that accumulation of AtRAL in photoreceptor membranes will not affect the transduction of visual signals and will not disturb the interaction of proteins engaged in this process.
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Affiliation(s)
- Szymon Radzin
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Anna Wiśniewska-Becker
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Michał Markiewicz
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics, Jagiellonian University, 30-387 Krakow, Poland
| | - Sebastian Bętkowski
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics, Jagiellonian University, 30-387 Krakow, Poland
| | - Justyna Furso
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Joanna Waresiak
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jarosław Grolik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-387 Krakow, Poland
| | - Tadeusz Sarna
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Anna M Pawlak
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
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Zhen F, Zou T, Wang T, Zhou Y, Dong S, Zhang H. Rhodopsin-associated retinal dystrophy: Disease mechanisms and therapeutic strategies. Front Neurosci 2023; 17:1132179. [PMID: 37077319 PMCID: PMC10106759 DOI: 10.3389/fnins.2023.1132179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/13/2023] [Indexed: 04/05/2023] Open
Abstract
Rhodopsin is a light-sensitive G protein-coupled receptor that initiates the phototransduction cascade in rod photoreceptors. Mutations in the rhodopsin-encoding gene RHO are the leading cause of autosomal dominant retinitis pigmentosa (ADRP). To date, more than 200 mutations have been identified in RHO. The high allelic heterogeneity of RHO mutations suggests complicated pathogenic mechanisms. Here, we discuss representative RHO mutations as examples to briefly summarize the mechanisms underlying rhodopsin-related retinal dystrophy, which include but are not limited to endoplasmic reticulum stress and calcium ion dysregulation resulting from protein misfolding, mistrafficking, and malfunction. Based on recent advances in our understanding of disease mechanisms, various treatment methods, including adaptation, whole-eye electrical stimulation, and small molecular compounds, have been developed. Additionally, innovative therapeutic treatment strategies, such as antisense oligonucleotide therapy, gene therapy, optogenetic therapy, and stem cell therapy, have achieved promising outcomes in preclinical disease models of rhodopsin mutations. Successful translation of these treatment strategies may effectively ameliorate, prevent or rescue vision loss related to rhodopsin mutations.
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Affiliation(s)
- Fangyuan Zhen
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Provincial Ophthalmic Hospital, Zhengzhou, China
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Tongdan Zou
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Ting Wang
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yongwei Zhou
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Provincial Ophthalmic Hospital, Zhengzhou, China
| | - Shuqian Dong
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Provincial Ophthalmic Hospital, Zhengzhou, China
- *Correspondence: Shuqian Dong, ; Houbin Zhang,
| | - Houbin Zhang
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, Sichuan, China
- *Correspondence: Shuqian Dong, ; Houbin Zhang,
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6
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Wolf A, Volz-Rakebrand P, Balke J, Alexiev U. Diffusion Analysis of NAnoscopic Ensembles: A Tracking-Free Diffusivity Analysis for NAnoscopic Ensembles in Biological Samples and Nanotechnology. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206722. [PMID: 36670094 DOI: 10.1002/smll.202206722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/16/2022] [Indexed: 06/17/2023]
Abstract
The rapid development of microscopic techniques over the past decades enables the establishment of single molecule fluorescence imaging as a powerful tool in biological and biomedical sciences. Single molecule fluorescence imaging allows to study the chemical, physicochemical, and biological properties of target molecules or particles by tracking their molecular position in the biological environment and determining their dynamic behavior. However, the precise determination of particle distribution and diffusivities is often challenging due to high molecule/particle densities, fast diffusion, and photobleaching/blinking of the fluorophore. A novel, accurate, and fast statistical analysis tool, Diffusion Analysis of NAnoscopic Ensembles (DANAE), that solves all these obstacles is introduced. DANAE requires no approximations or any a priori input regarding unknown system-inherent parameters, such as background distributions; a requirement that is vitally important when studying the behavior of molecules/particles in living cells. The superiority of DANAE with various data from simulations is demonstrated. As experimental applications of DANAE, membrane receptor diffusion in its natural membrane environment, and cargo mobility/distribution within nanostructured lipid nanoparticles are presented. Finally, the method is extended to two-color channel fluorescence microscopy.
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Affiliation(s)
- Alexander Wolf
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Pierre Volz-Rakebrand
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Jens Balke
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Ulrike Alexiev
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
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7
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Starr CR, Gorbatyuk MS. Posttranslational modifications of proteins in diseased retina. Front Cell Neurosci 2023; 17:1150220. [PMID: 37066080 PMCID: PMC10097899 DOI: 10.3389/fncel.2023.1150220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Posttranslational modifications (PTMs) are known to constitute a key step in protein biosynthesis and in the regulation of protein functions. Recent breakthroughs in protein purification strategies and current proteome technologies make it possible to identify the proteomics of healthy and diseased retinas. Despite these advantages, the research field identifying sets of posttranslationally modified proteins (PTMomes) related to diseased retinas is significantly lagging, despite knowledge of the major retina PTMome being critical to drug development. In this review, we highlight current updates regarding the PTMomes in three retinal degenerative diseases-namely, diabetic retinopathy (DR), glaucoma, and retinitis pigmentosa (RP). A literature search reveals the necessity to expedite investigations into essential PTMomes in the diseased retina and validate their physiological roles. This knowledge would accelerate the development of treatments for retinal degenerative disorders and the prevention of blindness in affected populations.
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Affiliation(s)
| | - Marina S. Gorbatyuk
- Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, AL, United States
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8
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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: 21] [Impact Index Per Article: 21.0] [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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Yee C, Görtemaker K, Wellpott R, Koch KW. Kinetics of cone specific G-protein signaling in avian photoreceptor cells. Front Mol Neurosci 2023; 16:1107025. [PMID: 36733826 PMCID: PMC9887155 DOI: 10.3389/fnmol.2023.1107025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Cone photoreceptor cells of night-migratory songbirds seem to process the primary steps of two different senses, vision and magnetoreception. The molecular basis of phototransduction is a prototypical G protein-coupled receptor pathway starting with the photoexcitation of rhodopsin or cone opsin thereby activating a heterotrimeric G protein named transducin. This interaction is well understood in vertebrate rod cells, but parameter describing protein-protein interactions of cone specific proteins are rare and not available for migratory birds. European robin is a model organism for studying the orientation of birds in the earth magnetic field. Recent findings showed a link between the putative magnetoreceptor cryptochrome 4a and the cone specific G-protein of European robin. In the present work, we investigated the interaction of European robin cone specific G protein and cytoplasmic regions of long wavelength opsin. We identified the second loop in opsin connecting transmembrane regions three and four as a critical binding interface. Surface plasmon resonance studies using a synthetic peptide representing the second cytoplasmic loop and purified G protein α-subunit showed a high affinity interaction with a K D value of 21 nM. Truncation of the G protein α-subunit at the C-terminus by six amino acids slightly decreased the affinity. Our results suggest that binding of the G protein to cryptochrome can compete with the interaction of G protein and non-photoexcited long wavelength opsin. Thus, the parallel presence of two different sensory pathways in bird cone photoreceptors is reasonable under dark-adapted conditions or during illumination with short wavelengths.
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Affiliation(s)
- Chad Yee
- Division of Biochemistry, Department of Neuroscience, University of Oldenburg, Oldenburg, Germany
| | - Katharina Görtemaker
- Division of Biochemistry, Department of Neuroscience, University of Oldenburg, Oldenburg, Germany
| | - Rieke Wellpott
- Division of Biochemistry, Department of Neuroscience, University of Oldenburg, Oldenburg, Germany
| | - Karl-Wilhelm Koch
- Division of Biochemistry, Department of Neuroscience, University of Oldenburg, Oldenburg, Germany,Research Center Neurosensory Sciences, University of Oldenburg, Oldenburg, Germany,*Correspondence: Karl-Wilhelm Koch, ✉
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Pasquaré SJ, Chamorro-Aguirre E, Gaveglio VL. The endocannabinoid system in the visual process. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2022. [DOI: 10.1016/j.jpap.2022.100159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Ortega JT, Jastrzebska B. Rhodopsin as a Molecular Target to Mitigate Retinitis Pigmentosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1371:61-77. [PMID: 34962636 DOI: 10.1007/5584_2021_682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Retinitis pigmentosa (RP) is a group of hereditary degenerative diseases affecting 1 of 4000 people worldwide and being the most prevalent cause of visual handicap among working populations in developed countries. These disorders are mainly related to the abnormalities in the rod G protein-coupled receptor (GPCR), rhodopsin reflected in the dysregulated membrane trafficking, stability and phototransduction processes that lead to progressive loss of retina function and eventually blindness. Currently, there is no cure for RP, and the therapeutic options are limited. Targeting rhodopsin with small molecule chaperones to improve the folding and stability of the mutant receptor is one of the most promising pharmacological approaches to alleviate the pathology of RP. This review provides an update on the current knowledge regarding small molecule compounds that have been evaluated as rhodopsin modulators to be considered as leads for the development of novel therapies for RP.
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Affiliation(s)
- Joseph T Ortega
- Department of Pharmacology, School of Medicine, Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Beata Jastrzebska
- Department of Pharmacology, School of Medicine, Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH, USA.
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Liu X, Jia R, Meng X, Li Y, Yang L. Retinal degeneration in humanized mice expressing mutant rhodopsin under the control of the endogenous murine promoter. Exp Eye Res 2021; 215:108893. [PMID: 34919893 DOI: 10.1016/j.exer.2021.108893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/31/2021] [Accepted: 12/08/2021] [Indexed: 11/04/2022]
Abstract
RHO is one of the most common genetic causes of autosomal dominant retinitis Pigmentosa (adRP) and there is no effective therapy for this disease. While rapidly developed CRISPR/Cas9 gene editing technology presents a promising therapeutic strategy to treat adRP. A large number of studies for treating adRP using CRISPR/Cas9 have been performed based on transgenic mouse models which are affected with adRP caused by mutant mouse rhodopsin allele, the counterpart of human rhodopsin. Recently, some RHO humanized mouse models like T17M, P23H are generated, which permit testing of the therapeutic effect of CRISPR/Cas9 in preclinical in vivo systems, without putting humans at risk. While available humanized mouse models are few compared to the number of known RHO mutations, but it is time-consuming and costly to build humanized mice for each mutation. We wonder whether a humanized mouse model having several mutations simultaneously can be developed, although which rarely occurs in patients, to investigate the therapeutic effect of CRISPR/Cas9 for RHO-mediated adRP in preclinical in vivo systems. Homology directed repair strategy combing with CRISPR/Cas9 was employed to introduce human RHO genomic fragment containing the replacement of mouse exon1(mE1) after the start codon to mE5 before the stop codon and all introns by the human counterparts. The human rhodopsin could express under the control of the endogenous murine promoter both transcriptionally and translationally in vivo. Human rhodopsin in humanized mouse lines (without mutation) could replace murine rhodopsin morphologically and functionally. While human rhodopsin containing T17M, G51D, G114R, R135W and P171R mutations simultaneously in mutant humanized (Mut-Rhowt/hum and Mut-Rhohum/hum) mouse lines caused retinal degeneration. Mut-Rhohum/hum mice suffered from severe retinal degeneration with defective formation of rod outer segment, leaving nonrecordable electroretinogram (ERG) at 3 months. Mut- Rhowt/hum mice had a slower rate of photoreceptors loss. In 7-month-old Mut- Rhowt/hum mice, statistically reduced scotopic ERG responses were visible compared with age-matched WT mice, but the shortened outer segment and thinner outer nuclear layer could be observed from 3 months. From 7 months to 9 months, significantly abnormal scotopic ERG responses were visible and photoreceptors loss were also obvious in 9-month-old Mut-Rhowt/hum mice. In 12-month-old Mut- Rhowt/hum mice, statistically reduced scotopic and photopic ERG responses and retinal degeneration throughout the retina were visible. Because scotopic responses were more affected than photopic responses in mutant humanized mice, demonstrating that rods dysfunction was more severe than cones dysfunction and deteriorated earlier, the pattern of retinal degeneration caused by mutant human rhodopsin was a typical rod-cone decay. Immunocytochemistry in cells indicated human rhodopsin proteins with 5 mutations aggregated in the cytoplasm and were also retained in the endoplasmic reticulum. The mutant human rhodopsin also accumulated in rod inner segments and cellular bodies in vivo. In conclusion, our humanized models provide excellent opportunities to study the human rhodopsin expression patterns. Our mutant humanized heterozygotes can provide opportunities to explore gene editing therapies via CRISPR/Cas9 for these five mutations in preclinical studies, it is time-saving and cost-effective.
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Affiliation(s)
- Xiaozhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Ruixuan Jia
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Xiang Meng
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Ying Li
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China.
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Zhang J, Gao F, Ma Y, Xue T, Shen Y. Identification of early-onset photoreceptor degeneration in transgenic mouse models of Alzheimer's disease. iScience 2021; 24:103327. [PMID: 34805789 PMCID: PMC8581578 DOI: 10.1016/j.isci.2021.103327] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/23/2021] [Accepted: 10/19/2021] [Indexed: 12/20/2022] Open
Abstract
Light sensitivity of the vertebrate retina relies on the integrity of photoreceptors, including rods and cones. Research in patients with Alzheimer's disease (AD) and in AD transgenic mice reports that accumulated amyloid-β (Aβ) plaques in the retina are toxic to retinal neurons. Moreover, Aβ plaques are deposited around the rods and cones, yet photoreceptor anomalies remain unclear in AD. Here, we identify the progressive degeneration of rods and cones characterized by impaired expression of phototransduction proteins, morphological alterations, functional deficits, and even cell loss. Furthermore, we demonstrate that cell senescence and necroptosis were involved in rod degeneration. Importantly, using in vivo scotopic electroretinogram, we detected rod degeneration in early-stage AD transgenic mice before Aβ plaques were observed in the brain. Moreover, we demonstrate that rod degeneration was among the earliest AD retinal manifestations compared with other types of retinal neurons. Overall, our study is the first to identify and detect in vivo, early-onset photoreceptor degeneration in AD. Progressive rod degeneration has been identified in AD transgenic mice Cell senescence and necroptosis were involved in rod degeneration Rod degeneration can be detected by in vivo scotopic electroretinogram Rod degeneration has earlier onset than amyloid-β plaques in the brain
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Affiliation(s)
- Jie Zhang
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Science, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230026, China
- Neurodegenerative Disorder Research Center, CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei 230026, China
| | - Feng Gao
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Science, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230026, China
- Neurodegenerative Disorder Research Center, CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei 230026, China
| | - Yuqian Ma
- Neurodegenerative Disorder Research Center, CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei 230026, China
- Eye Center at The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Tian Xue
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Science, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230026, China
- Neurodegenerative Disorder Research Center, CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei 230026, China
- Eye Center at The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230026, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Shen
- Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Science, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230026, China
- Neurodegenerative Disorder Research Center, CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei 230026, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- Corresponding author
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14
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Sadeghi M, Noé F. Hydrodynamic coupling for particle-based solvent-free membrane models. J Chem Phys 2021; 155:114108. [PMID: 34551532 DOI: 10.1063/5.0061623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The great challenge with biological membrane systems is the wide range of scales involved, from nanometers and picoseconds for individual lipids to the micrometers and beyond millisecond for cellular signaling processes. While solvent-free coarse-grained membrane models are convenient for large-scale simulations and promising to provide insight into slow processes involving membranes, these models usually have unrealistic kinetics. One major obstacle is the lack of an equally convenient way of introducing hydrodynamic coupling without significantly increasing the computational cost of the model. To address this, we introduce a framework based on anisotropic Langevin dynamics, for which major in-plane and out-of-plane hydrodynamic effects are modeled via friction and diffusion tensors from analytical or semi-analytical solutions to Stokes hydrodynamic equations. Using this framework, in conjunction with our recently developed membrane model, we obtain accurate dispersion relations for planar membrane patches, both free-standing and in the vicinity of a wall. We briefly discuss how non-equilibrium dynamics is affected by hydrodynamic interactions. We also measure the surface viscosity of the model membrane and discuss the affecting dissipative mechanisms.
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Affiliation(s)
- Mohsen Sadeghi
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
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15
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A hybrid stochastic/deterministic model of single photon response and light adaptation in mouse rods. Comput Struct Biotechnol J 2021; 19:3720-3734. [PMID: 34285774 PMCID: PMC8258797 DOI: 10.1016/j.csbj.2021.06.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 12/02/2022] Open
Abstract
A hybrid stochastic/deterministic model of mouse rod phototransduction is presented. Rod photocurrent to photovoltage conversion in darkness is accurately characterized. Photoresponses to dim and bright stimuli and in various mutants are well reproduced. Recently debated molecular mechanisms of the phototransduction cascade are examined.
The phototransduction cascade is paradigmatic for signaling pathways initiated by G protein-coupled receptors and is characterized by a fine regulation of photoreceptor sensitivity and electrical response to a broad range of light stimuli. Here, we present a biochemically comprehensive model of phototransduction in mouse rods based on a hybrid stochastic and deterministic mathematical framework, and a quantitatively accurate description of the rod impedance in the dark. The latter, combined with novel patch clamp recordings from rod outer segments, enables the interconversion of dim flash responses between photovoltage and photocurrent and thus direct comparison with the simulations. The model reproduces the salient features of the experimental photoresponses at very dim and bright stimuli, for both normal photoreceptors and those with genetically modified cascade components. Our modelling approach recapitulates a number of recent findings in vertebrate phototransduction. First, our results are in line with the recently established requirement of dimeric activation of PDE6 by transducin and further show that such conditions can be fulfilled at the expense of a significant excess of G protein activated by rhodopsin. Secondly, simulations suggest a crucial role of the recoverin-mediated Ca2+-feedback on rhodopsin kinase in accelerating the shutoff, when light flashes are delivered in the presence of a light background. Finally, stochastic simulations suggest that transient complexes between dark rhodopsin and transducin formed prior to light stimulation increase the reproducibility of single photon responses. Current limitations of the model are likely associated with the yet unknown mechanisms governing the shutoff of the cascade.
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Key Words
- ADP, adenosine diphosphate
- ATP, adenosine-5′-triphosphate
- Arr, arrestin
- BG, background illumination
- CNG, cyclic nucleotide-gated (channel)
- CSM, completely substituted mutant of rhodopsin
- CV, coefficient of variation
- DM, deterministic model
- Dynamic modeling
- E, effector of the phototransduction cascade, activated PDE
- FFT, fast Fourier-transform
- GC, guanylate cyclase
- GCAPs, guanylate cyclase-activating proteins
- GDP, guanosine-5′-diphosphate
- GPCR, G protein-coupled receptor
- GTP, guanosine-5′-triphosphate
- Gt, G protein/transducin
- Gα, α-subunit of the G protein
- Gβγ, β- and γ-subunit of the G protein
- HSDM, hybrid stochastic/deterministic model
- Light adaptation
- MPR, multiple photon response
- PDE, phosphodiesterase 6
- Ph, photons
- Phototransduction
- R, rhodopsin
- RGS, regulator of G protein signaling
- RK, rhodopsin kinase
- ROS, rod outer segment
- Rec, recoverin
- Rn, activated rhodopsin that has been phosphorylated n times
- SD, standard deviation
- SPR, single photon response
- Stochastic simulation
- Systems biology
- TTP, time to peak
- cGMP, cyclic guanosine monophosphate
- ΔJ, photocurrent
- ΔU, photovoltage
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16
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Fernandez-Gonzalez P, Mas-Sanchez A, Garriga P. Polyphenols and Visual Health: Potential Effects on Degenerative Retinal Diseases. Molecules 2021; 26:3407. [PMID: 34199888 PMCID: PMC8200069 DOI: 10.3390/molecules26113407] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/26/2022] Open
Abstract
Dietary polyphenols are a group of natural compounds that have been proposed to have beneficial effects on human health. They were first known for their antioxidant properties, but several studies over the years have shown that these compounds can exert protective effects against chronic diseases. Nonetheless, the mechanisms underlying these potential benefits are still uncertain and contradictory effects have been reported. In this review, we analyze the potential effects of polyphenol compounds on some visual diseases, with a special focus on retinal degenerative diseases. Current effective therapies for the treatment of such retinal diseases are lacking and new strategies need to be developed. For this reason, there is currently a renewed interest in finding novel ligands (or known ligands with previously unexpected features) that could bind to retinal photoreceptors and modulate their molecular properties. Some polyphenols, especially flavonoids (e.g., quercetin and tannic acid), could attenuate light-induced receptor damage and promote visual health benefits. Recent evidence suggests that certain flavonoids could help stabilize the correctly folded conformation of the visual photoreceptor protein rhodopsin and offset the deleterious effect of retinitis pigmentosa mutations. In this regard, certain polyphenols, like the flavonoids mentioned before, have been shown to improve the stability, expression, regeneration and folding of rhodopsin mutants in experimental in vitro studies. Moreover, these compounds appear to improve the integration of the receptor into the cell membrane while acting against oxidative stress at the same time. We anticipate that polyphenol compounds can be used to target visual photoreceptor proteins, such as rhodopsin, in a way that has only been recently proposed and that these can be used in novel approaches for the treatment of retinal degenerative diseases like retinitis pigmentosa; however, studies in this field are limited and further research is needed in order to properly characterize the effects of these compounds on retinal degenerative diseases through the proposed mechanisms.
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Affiliation(s)
| | | | - Pere Garriga
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d’Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, 08222 Terrassa, Spain; (P.F.-G.); (A.M.-S.)
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17
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Pilecky M, Závorka L, Arts MT, Kainz MJ. Omega-3 PUFA profoundly affect neural, physiological, and behavioural competences - implications for systemic changes in trophic interactions. Biol Rev Camb Philos Soc 2021; 96:2127-2145. [PMID: 34018324 DOI: 10.1111/brv.12747] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
In recent decades, much conceptual thinking in trophic ecology has been guided by theories of nutrient limitation and the flow of elements, such as carbon and nitrogen, within and among ecosystems. More recently, ecologists have also turned their attention to examining the value of specific dietary nutrients, in particular polyunsaturated fatty acids (PUFA), among which the omega-3 PUFA, especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) play a central role as essential components of neuronal cell membranes in many organisms. This review focuses on a new neuro-ecological approach stemming from the biochemical (mechanistic) and physiological (functional) role of DHA in neuronal cell membranes, in particular in conjunction with G-protein coupled receptors (GPCRs). We link the co-evolution of these neurological functions to metabolic dependency on dietary omega-3 PUFA. We outline ways in which deficiencies in dietary DHA supply may affect, cognition, vision, and behaviour, and ultimately, the biological fitness of consumers. We then review emerging evidence that changes in access to dietary omega-3 PUFA may ultimately have profound impacts on trophic interactions leading to potential changes in community structure and ecosystem functioning that, in turn, may affect the supply of DHA within and across ecosystems, including the supply for human consumption.
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Affiliation(s)
- Matthias Pilecky
- WasserCluster Lunz - Biologische Station, Inter-University Center for Aquatic Ecosystem Research, Dr. Carl-Kupelwieser Promenade 5, Lunz am See, 3293, Austria.,Department of Biomedical Research, Donau-Universität Krems, Dr. Karl Dorrek-Straße 30, Krems, 3500, Austria
| | - Libor Závorka
- WasserCluster Lunz - Biologische Station, Inter-University Center for Aquatic Ecosystem Research, Dr. Carl-Kupelwieser Promenade 5, Lunz am See, 3293, Austria
| | - Michael T Arts
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St, Toronto, ON, M5B 2K3, Canada
| | - Martin J Kainz
- WasserCluster Lunz - Biologische Station, Inter-University Center for Aquatic Ecosystem Research, Dr. Carl-Kupelwieser Promenade 5, Lunz am See, 3293, Austria.,Department of Biomedical Research, Donau-Universität Krems, Dr. Karl Dorrek-Straße 30, Krems, 3500, Austria
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18
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Khelashvili G, Pillai AN, Lee J, Pandey K, Payne AM, Siegel Z, Cuendet MA, Lewis TR, Arshavsky VY, Broichhagen J, Levitz J, Menon AK. Unusual mode of dimerization of retinitis pigmentosa-associated F220C rhodopsin. Sci Rep 2021; 11:10536. [PMID: 34006992 PMCID: PMC8131606 DOI: 10.1038/s41598-021-90039-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/29/2021] [Indexed: 12/30/2022] Open
Abstract
Mutations in the G protein-coupled receptor (GPCR) rhodopsin are a common cause of autosomal dominant retinitis pigmentosa, a blinding disease. Rhodopsin self-associates in the membrane, and the purified monomeric apo-protein opsin dimerizes in vitro as it transitions from detergent micelles to reconstitute into a lipid bilayer. We previously reported that the retinitis pigmentosa-linked F220C opsin mutant fails to dimerize in vitro, reconstituting as a monomer. Using fluorescence-based assays and molecular dynamics simulations we now report that whereas wild-type and F220C opsin display distinct dimerization propensities in vitro as previously shown, they both dimerize in the plasma membrane of HEK293 cells. Unexpectedly, molecular dynamics simulations show that F220C opsin forms an energetically favored dimer in the membrane when compared with the wild-type protein. The conformation of the F220C dimer is unique, with transmembrane helices 5 and 6 splayed apart, promoting widening of the intracellular vestibule of each protomer and influx of water into the protein interior. FRET experiments with SNAP-tagged wild-type and F220C opsin expressed in HEK293 cells are consistent with this conformational difference. We speculate that the unusual mode of dimerization of F220C opsin in the membrane may have physiological consequences.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA.
- Institute of Computational Biomedicine, Weill Cornell Medical College, New York, NY, 10065, USA.
| | | | - Joon Lee
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kalpana Pandey
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Alexander M Payne
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Zarek Siegel
- Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michel A Cuendet
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, University Hospital of Lausanne, 1009, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Tylor R Lewis
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut Für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA.
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, 10065, USA.
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19
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Lamprakis C, Andreadelis I, Manchester J, Velez-Vega C, Duca JS, Cournia Z. Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments. J Chem Theory Comput 2021; 17:3088-3102. [PMID: 33913726 DOI: 10.1021/acs.jctc.0c00507] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein-protein complex assembly is one of the major drivers of biological response. Understanding the mechanisms of protein oligomerization/dimerization would allow one to elucidate how these complexes participate in biological activities and could ultimately lead to new approaches in designing novel therapeutic agents. However, determining the exact association pathways and structures of such complexes remains a challenge. Here, we use parallel tempering metadynamics simulations in the well-tempered ensemble to evaluate the performance of Martini 2.2P and Martini open-beta 3 (Martini 3) force fields in reproducing the structure and energetics of the dimerization process of membrane proteins and proteins in an aqueous solution in reasonable accuracy and throughput. We find that Martini 2.2P systematically overestimates the free energy of association by estimating large barriers in distinct areas, which likely leads to overaggregation when multiple monomers are present. In comparison, the less viscous Martini 3 results in a systematic underestimation of the free energy of association for proteins in solution, while it performs well in describing the association of membrane proteins. In all cases, the near-native dimer complexes are identified as minima in the free energy surface albeit not always as the lowest minima. In the case of Martini 3, we find that the spurious supramolecular protein aggregation present in Martini 2.2P multimer simulations is alleviated and thus this force field may be more suitable for the study of protein oligomerization. We propose that the use of enhanced sampling simulations with a refined coarse-grained force field and appropriately defined collective variables is a robust approach for studying the protein dimerization process, although one should be cautious of the ranking of energy minima.
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Affiliation(s)
- Christos Lamprakis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Ioannis Andreadelis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - John Manchester
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Camilo Velez-Vega
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - José S Duca
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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20
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Functional compartmentalization of photoreceptor neurons. Pflugers Arch 2021; 473:1493-1516. [PMID: 33880652 DOI: 10.1007/s00424-021-02558-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022]
Abstract
Retinal photoreceptors are neurons that convert dynamically changing patterns of light into electrical signals that are processed by retinal interneurons and ultimately transmitted to vision centers in the brain. They represent the essential first step in seeing without which the remainder of the visual system is rendered moot. To support this role, the major functions of photoreceptors are segregated into three main specialized compartments-the outer segment, the inner segment, and the pre-synaptic terminal. This compartmentalization is crucial for photoreceptor function-disruption leads to devastating blinding diseases for which therapies remain elusive. In this review, we examine the current understanding of the molecular and physical mechanisms underlying photoreceptor functional compartmentalization and highlight areas where significant knowledge gaps remain.
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21
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Bolte P, Einwich A, Seth PK, Chetverikova R, Heyers D, Wojahn I, Janssen-Bienhold U, Feederle R, Hore P, Dedek K, Mouritsen H. Cryptochrome 1a localisation in light- and dark-adapted retinae of several migratory and non-migratory bird species: no signs of light-dependent activation. ETHOL ECOL EVOL 2021. [DOI: 10.1080/03949370.2020.1870571] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Petra Bolte
- Institute for Biology and Environmental Sciences, Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Angelika Einwich
- Institute for Biology and Environmental Sciences, Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Pranav K. Seth
- Institute for Biology and Environmental Sciences, Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Raisa Chetverikova
- Institute for Biology and Environmental Sciences, Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Dominik Heyers
- Institute for Biology and Environmental Sciences, Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
- Research Centre for Neurosensory Sciences, Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Irina Wojahn
- Institute for Biology and Environmental Sciences, Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Ulrike Janssen-Bienhold
- Research Centre for Neurosensory Sciences, Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
- Department of Neuroscience, Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Regina Feederle
- Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Peter Hore
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Karin Dedek
- Institute for Biology and Environmental Sciences, Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
- Research Centre for Neurosensory Sciences, Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Henrik Mouritsen
- Institute for Biology and Environmental Sciences, Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
- Research Centre for Neurosensory Sciences, Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
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22
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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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23
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Cross-linking of bovine rhodopsin with sulfosuccinimidyl 4-(N maleimidomethyl)cyclohexane-1-carboxylate affects its functionality. Biochem J 2020; 477:2295-2312. [PMID: 32497171 DOI: 10.1042/bcj20200376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 02/08/2023]
Abstract
Rhodopsin is the photoreceptor protein involved in visual excitation in retinal rods. The functionality of bovine rhodopsin was determined following treatment with sulfosuccinimidyl 4-(N maleimidomethyl)cyclohexane-1-carboxylate (sulfo-SMCC), a bifunctional reagent capable of forming covalent cross-links between suitable placed lysines and cysteines. Denaturing polyacrylamide gel electrophoresis showed that rhodopsin incubated with sulfo-SMCC generated intermolecular dimers, trimers, and higher oligomers, although most of the sulfo-SMCC-treated protein remained as a monomer. Minor alterations on the absorption spectrum of light-activated sulfo-SMCC-treated rhodopsin were observed. However, only ∼2% stimulation of the guanine nucleotide binding activity of transducin was measured in the presence of sulfo-SMCC-cross-linked photolyzed rhodopsin. Moreover, rhodopsin kinase was not able of phosphorylating sulfo-SMCC-cross-linked rhodopsin after illumination. Rhodopsin was purified in the presence of either 0.1% or 1% n-dodecyl β-d-maltoside, to obtain dimeric and monomeric forms of the protein, respectively. Interestingly, no generation of the regular F1 and F2 thermolytic fragments was perceived with sulfo-SMCC-cross-linked rhodopsin either in the dimeric or monomeric state, implying the formation of intramolecular connections in the protein that might thwart the light-induced conformational changes required for interaction with transducin and rhodopsin kinase. Structural analysis of the rhodopsin three-dimensional structure suggested that the following lysine and cysteine pairs: Lys66/Lys67 and Cys316, Cys140 and Lys141, Cys140 and Lys248, Lys311 and Cys316, and/or Cys316 and Lys325 are potential candidates to generate intramolecular cross-links in the protein. Yet, the lack of fragmentation of sulfo-SMCC-treated Rho with thermolysin is consistent with the formation of cross-linking bridges between Lys66/Lys67 and Cys316, and/or Cys140 and Lys248.
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24
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Vasudevan S, Park PSH. Differential Aggregation Properties of Mutant Human and Bovine Rhodopsin. Biochemistry 2020; 60:6-18. [PMID: 33356167 DOI: 10.1021/acs.biochem.0c00733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rhodopsin is the light receptor required for the function and health of photoreceptor cells. Mutations in rhodopsin can cause misfolding and aggregation of the receptor, which leads to retinal degeneration. Bovine rhodopsin is often used as a model to understand the effect of pathogenic mutations in rhodopsin due to the abundance of structural information on the bovine form of the receptor. It is unclear whether or not the bovine rhodopsin template is adequate in predicting the effect of these mutations occurring in human retinal disease or in predicting the efficacy of therapeutic strategies. To better understand the extent to which bovine rhodopsin can serve as a model, human and bovine P23H rhodopsin mutants expressed heterologously in cells were examined. The aggregation properties and cellular localization of the mutant receptors were determined by Förster resonance energy transfer and confocal microscopy. The potential therapeutic effects of the pharmacological compounds 9-cis retinal and metformin were also examined. Human and bovine P23H rhodopsin mutants exhibited different aggregation properties and responses to the pharmacological compounds tested. These observations would lead to different predictions on the severity of the phenotype and divergent predictions on the benefit of the therapeutic compounds tested. The bovine rhodopsin template does not appear to adequately model the effects of the P23H mutation in the human form of the receptor.
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Affiliation(s)
- Sreelakshmi Vasudevan
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, Ohio 44106, United States
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Sechrest ER, Murphy J, Senapati S, Goldberg AFX, Park PSH, Kolandaivelu S. Loss of PRCD alters number and packaging density of rhodopsin in rod photoreceptor disc membranes. Sci Rep 2020; 10:17885. [PMID: 33087780 PMCID: PMC7577997 DOI: 10.1038/s41598-020-74628-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023] Open
Abstract
Progressive rod-cone degeneration (PRCD) is a small protein localized to photoreceptor outer segment (OS) disc membranes. Several mutations in PRCD are linked to retinitis pigmentosa (RP) in canines and humans, and while recent studies have established that PRCD is required for high fidelity disc morphogenesis, its precise role in this process remains a mystery. To better understand the part which PRCD plays in disease progression as well as its contribution to photoreceptor OS disc morphogenesis, we generated a Prcd-KO animal model using CRISPR/Cas9. Loss of PRCD from the retina results in reduced visual function accompanied by slow rod photoreceptor degeneration. We observed a significant decrease in rhodopsin levels in Prcd-KO retina prior to photoreceptor degeneration. Furthermore, ultrastructural analysis demonstrates that rod photoreceptors lacking PRCD display disoriented and dysmorphic OS disc membranes. Strikingly, atomic force microscopy reveals that many disc membranes in Prcd-KO rod photoreceptor neurons are irregular, containing fewer rhodopsin molecules and decreased rhodopsin packing density compared to wild-type discs. This study strongly suggests an important role for PRCD in regulation of rhodopsin incorporation and packaging density into disc membranes, a process which, when dysregulated, likely gives rise to the visual defects observed in patients with PRCD-associated RP.
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Affiliation(s)
- Emily R Sechrest
- Department of Pharmaceutical Sciences, One Medical Center Drive, West Virginia University, Morgantown, WV, 26506-9193, USA.,Department of Ophthalmology and Visual Sciences, Eye Institute, One Medical Center Drive, West Virginia University, Morgantown, WV, 26506-9193, USA
| | - Joseph Murphy
- Department of Ophthalmology and Visual Sciences, Eye Institute, One Medical Center Drive, West Virginia University, Morgantown, WV, 26506-9193, USA.,Department of Biochemistry, One Medical Center Drive, West Virginia University, Morgantown, WV, 26506-9193, USA
| | - Subhadip Senapati
- 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
| | - Saravanan Kolandaivelu
- Department of Ophthalmology and Visual Sciences, Eye Institute, One Medical Center Drive, West Virginia University, Morgantown, WV, 26506-9193, USA. .,Department of Biochemistry, One Medical Center Drive, West Virginia University, Morgantown, WV, 26506-9193, USA.
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de Assis LVM, Mendes D, Silva MM, Kinker GS, Pereira-Lima I, Moraes MN, Menck CFM, Castrucci AMDL. Melanopsin mediates UVA-dependent modulation of proliferation, pigmentation, apoptosis, and molecular clock in normal and malignant melanocytes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2020; 1867:118789. [PMID: 32645331 DOI: 10.1016/j.bbamcr.2020.118789] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/04/2020] [Accepted: 06/26/2020] [Indexed: 12/19/2022]
Abstract
Cutaneous melanocytes and melanoma cells express several opsins, of which melanopsin (OPN4) detects temperature and UVA radiation. To evaluate the interaction between OPN4 and UVA radiation, normal and malignant Opn4WT and Opn4KO melanocytes were exposed to three daily low doses (total 13.2 kJ/m2) of UVA radiation. UVA radiation led to a reduction of proliferation in both Opn4WT cell lines; however, only in melanoma cells this effect was associated with increased cell death by apoptosis. Daily UVA stimuli induced persistent pigment darkening (PPD) in both Opn4WT cell lines. Upon Opn4 knockout, all UVA-induced effects were lost in three independent clones of Opn4KO melanocytes and melanoma cells. Per1 bioluminescence was reduced after 1st and 2nd UVA radiations in Opn4WT cells. In Opn4KO melanocytes and melanoma cells, an acute increase of Per1 expression was seen immediately after each stimulus. We also found that OPN4 expression is downregulated in human melanoma compared to normal skin, and it decreases with disease progression. Interestingly, metastatic melanomas with low expression of OPN4 present increased expression of BMAL1 and longer overall survival. Collectively, our findings reinforce the functionality of the photosensitive system of melanocytes that may subsidize advancements in the understanding of skin related diseases, including cancer.
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Affiliation(s)
- Leonardo Vinícius Monteiro de Assis
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Davi Mendes
- DNA Repair Lab, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Matheus Molina Silva
- DNA Repair Lab, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Gabriela Sarti Kinker
- Laboratory of Neuroimmunoendocrinology, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Isabella Pereira-Lima
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Maria Nathália Moraes
- Laboratory of Neurobiology, Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Carlos Frederico Martins Menck
- DNA Repair Lab, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Ana Maria de Lauro Castrucci
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil; Department of Biology, University of Virginia, Charlottesville, VA, USA.
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Senapati S, Park PSH. Differential adaptations in rod outer segment disc membranes in different models of congenital stationary night blindness. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183396. [PMID: 32533975 DOI: 10.1016/j.bbamem.2020.183396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/01/2020] [Accepted: 06/08/2020] [Indexed: 01/20/2023]
Abstract
Rod photoreceptor cells initiate scotopic vision when the light receptor rhodopsin absorbs a photon of light to initiate phototransduction. These photoreceptor cells are exquisitely sensitive and have adaptive mechanisms in place to maintain optimal function and to overcome dysfunctional states. One adaptation rod photoreceptor cells exhibit is in the packing properties of rhodopsin within the membrane. The mechanism underlying these adaptations is unclear. Mouse models of congenital stationary night blindness with different molecular causes were investigated to determine which signals are important for adaptations in rod photoreceptor cells. Night blindness in these mice is caused by dysfunction in either rod photoreceptor cell signaling or bipolar cell signaling. Changes in the packing of rhodopsin within photoreceptor cell membranes were examined by atomic force microscopy. Mice expressing constitutively active rhodopsin did not exhibit any adaptations, even under constant dark conditions. Mice with disrupted bipolar cell signaling exhibited adaptations, however, they were distinct from those in mice with disrupted phototransduction. These differential adaptations demonstrate that although multiple molecular defects can lead to a similar primary defect causing disease (i.e., night blindness), they can cause different secondary effects (i.e., adaptations). The lighting environment or signaling defects present from birth and during early rearing can condition mice and affect the adaptations occurring in more mature animals. A comparison of effects in wild-type mice, mice with defective phototransduction, and mice with defective bipolar cell signaling, indicated that bipolar cell signaling plays a role in this conditioning but is not required for adaptations in more mature animals.
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Affiliation(s)
- Subhadip Senapati
- 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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Lewis TR, Shores CR, Cady MA, Hao Y, Arshavsky VY, Burns ME. The F220C and F45L rhodopsin mutations identified in retinitis pigmentosa patients do not cause pathology in mice. Sci Rep 2020; 10:7538. [PMID: 32371886 PMCID: PMC7200662 DOI: 10.1038/s41598-020-64437-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/18/2020] [Indexed: 11/12/2022] Open
Abstract
Retinitis pigmentosa is a retinal degenerative disease that leads to blindness through photoreceptor loss. Rhodopsin is the most frequently mutated protein in this disease. While many rhodopsin mutations have well-understood consequences that lead to cell death, the disease association of several rhodopsin mutations identified in retinitis pigmentosa patients, including F220C and F45L, has been disputed. In this study, we generated two knockin mouse lines bearing each of these mutations. We did not observe any photoreceptor degeneration in either heterozygous or homozygous animals of either line. F220C mice exhibited minor disruptions of photoreceptor outer segment dimensions without any mislocalization of outer segment proteins, whereas photoreceptors of F45L mice were normal. Suction electrode recordings from individual photoreceptors of both mutant lines showed normal flash sensitivity and photoresponse kinetics. Taken together, these data suggest that neither the F220C nor F45L mutation has pathological consequences in mice and, therefore, may not be causative of retinitis pigmentosa in humans.
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Affiliation(s)
- Tylor R Lewis
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, 27710, United States
| | - Camilla R Shores
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, 95616, United States
| | - Martha A Cady
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, 27710, United States
| | - Ying Hao
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, 27710, United States
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, 27710, United States.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, United States
| | - Marie E Burns
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA, 95616, United States. .,Center for Neuroscience and Department of Ophthalmology & Vision Science, University of California, Davis, CA, 95616, United States.
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Christie S, Shi X, Smith AW. Resolving Membrane Protein-Protein Interactions in Live Cells with Pulsed Interleaved Excitation Fluorescence Cross-Correlation Spectroscopy. Acc Chem Res 2020; 53:792-799. [PMID: 32227891 DOI: 10.1021/acs.accounts.9b00625] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The cell plasma membrane (PM) contains thousands of proteins that sense and respond to the outside environment. These proteins have evolved sensitivity to a wide variety of physical and chemical signals and act as a delivery system across the PM. Membrane proteins are critical for information flow and decision making in the cell and thus are important targets in drug development. A critical aspect of membrane protein function is the way they interact with other proteins, often through the formation of dimers or small oligomers that regulate function at the protein, cell, and organism levels. Resolving membrane protein interactions in a live cell environment is challenging because of the chemical diversity and spatial heterogeneity of the PM. In this Account, we describe a fluorescence technique called pulsed interleaved excitation fluorescence cross-correlation spectroscopy (PIE-FCCS) that is ideally suited to quantify membrane associations in live cells. PIE-FCCS is a two-color fluorescence fluctuation method that can simultaneously measure the concentration, mobility, proximity, and oligomerization state of membrane proteins in situ. It has several advantages over two related approaches, single-molecule tracking (SMT) and Förster resonance energy transfer (FRET), including that it measures all of the properties listed above in a single measurement. Another advantage is that PIE-FCCS is most sensitive at the physiological expression levels for many membrane proteins rather than the very low or high levels typical in other techniques. Here, we review the history of FCCS as it has been applied to study membrane protein interactions in cells. We also describe PIE-FCCS and the advantages it has over biochemical approaches like coimmunoprecipitation (co-IP) and proximity ligation assays (PLA). Finally, we review two classes of membrane proteins that have been studied with FCCS and PIE-FCCS: receptor tyrosine kinases (RTKs) and G protein-coupled receptors (GPCRs). For RTKs, ligand induced dimerization directly regulates the catalytic activity of the kinase, but higher order oligomerization and ligand-independent dimerization can complicate this historically simple paradigm. PIE-FCCS data have resolved a low population of EGFR dimers under basal conditions and assembly into multimers when stimulated with ligand. While GPCRs function primarily as monomers, dimerization has been hypothesized to regulate function for some receptors. PIE-FCCS data have established the dimerization potential of rhodopsin at low densities and were critical for the discovery of a novel dimerization interface in human cone opsins. This Account describes the how FCCS and PIE-FCCS can reveal the details of quaternary interactions in each of these receptor systems.
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Affiliation(s)
- Shaun Christie
- Department of Chemistry, University of Akron, Akron, Ohio 44325, United States
| | - Xiaojun Shi
- Department of Chemistry, University of Akron, Akron, Ohio 44325, United States
| | - Adam W. Smith
- Department of Chemistry, University of Akron, Akron, Ohio 44325, United States
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Kaneshige Y, Hayashi F, Morigaki K, Tanimoto Y, Yamashita H, Fujii M, Awazu A. Affinity of rhodopsin to raft enables the aligned oligomer formation from dimers: Coarse-grained molecular dynamics simulation of disk membranes. PLoS One 2020; 15:e0226123. [PMID: 32032370 PMCID: PMC7006936 DOI: 10.1371/journal.pone.0226123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/13/2020] [Indexed: 12/16/2022] Open
Abstract
The visual photopigment protein rhodopsin (Rh) is a typical G protein-coupled receptor (GPCR) that initiates the phototransduction cascade in retinal disk membrane of rod-photoreceptor cells. Rh molecule has a tendency to form dimer, and the dimer tends to form rows, which is suggested to heighten phototransduction efficiency in single-photon regime. In addition, the dimerization confers Rh an affinity for lipid raft, i.e. raftophilicity. However, the mechanism by which Rh-dimer raftophilicity contributes to the organization of the higher order structure remains unknown. In this study, we performed coarse-grained molecular dynamics simulations of a disk membrane model containing unsaturated lipids, saturated lipids with cholesterol, and Rh-dimers. We described the Rh-dimers by two-dimensional particle populations where the palmitoyl moieties of each Rh exhibits raftophilicity. We simulated the structuring of Rh in a disk for two types of Rh-dimer, i.e., the most and second most stable Rh dimers, which exposes the raftophilic regions at the dimerization-interface (H1/H8 dimer) and two edges away from the interface (H4/H5 dimer), respectively. Our simulations revealed that only the H1/H8 dimer could form a row structure. A small number of raftophilic lipids recruited to and intercalated in a narrow space between H1/H8 dimers stabilize the side-by-side interaction between dimers in a row. Our results implicate that the nano-sized lipid raft domains act as a “glue” to organize the long row structures of Rh-dimers.
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Affiliation(s)
- Yukito Kaneshige
- Department of Mathematical and Life Sciences, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
| | - Fumio Hayashi
- Graduate School of Science, Kobe University, Rokkodaicho, Nada, Kobe, Japan
| | - Kenichi Morigaki
- Biosignal Research Center, Kobe University, Rokkodaicho, Nada, Kobe, Japan
| | - Yasushi Tanimoto
- Graduate School of Science, Kobe University, Rokkodaicho, Nada, Kobe, Japan
| | - Hayato Yamashita
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Masashi Fujii
- Department of Mathematical and Life Sciences, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
| | - Akinori Awazu
- Department of Mathematical and Life Sciences, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
- * E-mail:
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Ng CT, Gan L. Investigating eukaryotic cells with cryo-ET. Mol Biol Cell 2020; 31:87-100. [PMID: 31935172 PMCID: PMC6960407 DOI: 10.1091/mbc.e18-05-0329] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 01/06/2023] Open
Abstract
The interior of eukaryotic cells is mysterious. How do the large communities of macromolecular machines interact with each other? How do the structures and positions of these nanoscopic entities respond to new stimuli? Questions like these can now be answered with the help of a method called electron cryotomography (cryo-ET). Cryo-ET will ultimately reveal the inner workings of a cell at the protein, secondary structure, and perhaps even side-chain levels. Combined with genetic or pharmacological perturbation, cryo-ET will allow us to answer previously unimaginable questions, such as how structure, biochemistry, and forces are related in situ. Because it bridges structural biology and cell biology, cryo-ET is indispensable for structural cell biology-the study of the 3-D macromolecular structure of cells. Here we discuss some of the key ideas, strategies, auxiliary techniques, and innovations that an aspiring structural cell biologist will consider when planning to ask bold questions.
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Affiliation(s)
- Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
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Wang Y, Ye J, Shen M, Yao A, Xue A, Fan Y, Huang S, Wang J, Lu F, Shao Y. Photoreceptor Degeneration is Correlated With the Deterioration of Macular Retinal Sensitivity in High Myopia. Invest Ophthalmol Vis Sci 2019; 60:2800-2810. [PMID: 31266057 DOI: 10.1167/iovs.18-26085] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To investigate structural changes in the retinal outer layers and choroid using adaptive optics (AO) and optical coherence tomography (OCT) in eyes with myopia, and to correlate the changes with decreased macular light sensitivity (MLS). Methods This prospective study included 27 subjects with emmetropia and low myopia (EM/LM), 25 with moderate myopia (MM), and 25 with high myopia (HM). Microperimetry was used to quantify MLS in each subject, while AO and OCT images of fundus were analyzed to quantify cone density and regularity and thickness of outer retinal sublayers and choroid. Differences of MLS, cone distribution, and chorioretinal thicknesses were compared among the three groups, and the associations among photoreceptor morphological alterations, MLS, and other parameters were analyzed. Results In HM, the MLS, cone density and regularity, and thicknesses of the myoid and ellipsoid zone (MEZ), Henle fiber layer and outer nuclear layer, interdigitation zone and RPE/Bruch complex, and choroid were lower than in EM/LM. Decreased MLS was correlated with lower cone density and regularity, and thinner MEZ and choroid in the inner region, and with lower cone density, thinner MEZ and choroid, and longer axial length in the outer region. Multivariate regression showed that better MLS was correlated with thicker MEZ in the inner region and with higher cone density in the outer region. Conclusions Altered cone distribution and outer retinal thickness, especially cone density and MEZ thickness, were significantly correlated with decline of MLS in HM, which may help to evaluate and monitor visual impairment in HM.
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Affiliation(s)
- Yuanyuan Wang
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jie Ye
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Meixiao Shen
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Aixia Yao
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Anquan Xue
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yuchen Fan
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shenghai Huang
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jianhua Wang
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
| | - Fan Lu
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yilei Shao
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
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33
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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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34
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Zhao DY, Pöge M, Morizumi T, Gulati S, Van Eps N, Zhang J, Miszta P, Filipek S, Mahamid J, Plitzko JM, Baumeister W, Ernst OP, Palczewski K. Cryo-EM structure of the native rhodopsin dimer in nanodiscs. J Biol Chem 2019; 294:14215-14230. [PMID: 31399513 PMCID: PMC6768649 DOI: 10.1074/jbc.ra119.010089] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/02/2019] [Indexed: 02/03/2023] Open
Abstract
Imaging of rod photoreceptor outer-segment disc membranes by atomic force microscopy and cryo-electron tomography has revealed that the visual pigment rhodopsin, a prototypical class A G protein-coupled receptor (GPCR), can organize as rows of dimers. GPCR dimerization and oligomerization offer possibilities for allosteric regulation of GPCR activity, but the detailed structures and mechanism remain elusive. In this investigation, we made use of the high rhodopsin density in the native disc membranes and of a bifunctional cross-linker that preserves the native rhodopsin arrangement by covalently tethering rhodopsins via Lys residue side chains. We purified cross-linked rhodopsin dimers and reconstituted them into nanodiscs for cryo-EM analysis. We present cryo-EM structures of the cross-linked rhodopsin dimer as well as a rhodopsin dimer reconstituted into nanodiscs from purified monomers. We demonstrate the presence of a preferential 2-fold symmetrical dimerization interface mediated by transmembrane helix 1 and the cytoplasmic helix 8 of rhodopsin. We confirmed this dimer interface by double electron-electron resonance measurements of spin-labeled rhodopsin. We propose that this interface and the arrangement of two protomers is a prerequisite for the formation of the observed rows of dimers. We anticipate that the approach outlined here could be extended to other GPCRs or membrane receptors to better understand specific receptor dimerization mechanisms.
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Affiliation(s)
- Dorothy Yanling Zhao
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Matthias Pöge
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sahil Gulati
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jianye Zhang
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Przemyslaw Miszta
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw 02-093, Poland
| | - Slawomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw 02-093, Poland
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
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35
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Ye J, Shen M, Huang S, Fan Y, Yao A, Pan C, Shi X, Lu F, Shao Y. Visual Acuity in Pathological Myopia Is Correlated With the Photoreceptor Myoid and Ellipsoid Zone Thickness and Affected by Choroid Thickness. Invest Ophthalmol Vis Sci 2019; 60:1714-1723. [PMID: 31013344 DOI: 10.1167/iovs.18-26086] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To quantify the thickness of the outer retinal sublayers and choroid in pathological myopia and examine associations between these factors and best-corrected visual acuity (BCVA). Methods The cohort was composed of 21 eyes with emmetropia and 70 eyes with high myopia (49 simple high myopia; 21 pathological myopia). Optical coherence tomography images were segmented to determine macular thicknesses of the choroid and the following outer retinal sublayers: outer plexiform layer (OPL), Henle fiber layer and outer nuclear layer (HFL + ONL), myoid and ellipsoid zone (MEZ), outer segment of photoreceptors (OS), and interdigitation zone and RPE/Bruch complex (IZ + RPE). Correlations between BCVA and thickness of the outer retinal sublayers and choroid were determined. Results In pathological myopia, the choroid, HFL + ONL, MEZ, and IZ + RPE were thinner than in emmetropia and simple high myopia (P < 0.05). Simple and multiple regression models showed that MEZ thickness was correlated with BCVA (both P < 0.001). The relationship between MEZ thickness and BCVA varied with choroidal thickness (P = 0.006). For a constant MEZ thickness, thinner choroids were associated with worse vision. In the final multiple regression predictive model, MEZ thickness, choroidal thickness, and interaction between MEZ and choroidal thickness (all P < 0.001) were predictors of BCVA. Conclusions Outer retinal alterations, especially thinning of the MEZ, occurred in pathological myopia. The MEZ thickness was associated with BCVA, and this relationship was affected by choroidal thickness.
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Affiliation(s)
- Jie Ye
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Meixiao Shen
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shenghai Huang
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yuchen Fan
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Aixia Yao
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chen Pan
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiutong Shi
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Fan Lu
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yilei Shao
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
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Single Proteoliposome High-Content Analysis Reveals Differences in the Homo-Oligomerization of GPCRs. Biophys J 2019; 115:300-312. [PMID: 30021106 DOI: 10.1016/j.bpj.2018.05.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/28/2018] [Accepted: 05/31/2018] [Indexed: 11/23/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) control vital cellular signaling pathways. GPCR oligomerization is proposed to increase signaling diversity. However, many reports have arrived at disparate conclusions regarding the existence, stability, and stoichiometry of GPCR oligomers, partly because of cellular complexity and ensemble averaging of intrareconstitution heterogeneities that complicate the interpretation of oligomerization data. To overcome these limitations, we exploited fluorescence-microscopy-based high-content analysis of single proteoliposomes. This allowed multidimensional quantification of intrinsic monomer-monomer interactions of three class A GPCRs (β2-adrenergic receptor, cannabinoid receptor type 1, and opsin). Using a billion-fold less protein than conventional assays, we quantified oligomer stoichiometries, association constants, and the influence of two ligands and membrane curvature on oligomerization, revealing key similarities and differences for three GPCRs with decidedly different physiological functions. The assays introduced here will assist with the quantitative experimental observation of oligomerization for transmembrane proteins in general.
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Getter T, Gulati S, Zimmerman R, Chen Y, Vinberg F, Palczewski K. Stereospecific modulation of dimeric rhodopsin. FASEB J 2019; 33:9526-9539. [PMID: 31121099 PMCID: PMC6662988 DOI: 10.1096/fj.201900443rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/23/2019] [Indexed: 11/11/2022]
Abstract
The classic concept that GPCRs function as monomers has been challenged by the emerging evidence of GPCR dimerization and oligomerization. Rhodopsin (Rh) is the only GPCR whose native oligomeric arrangement was revealed by atomic force microscopy demonstrating that Rh exists as a dimer. However, the role of Rh dimerization in retinal physiology is currently unknown. In this study, we identified econazole and sulconazole, two small molecules that disrupt Rh dimer contacts, by implementing a cell-based high-throughput screening assay. Racemic mixtures of identified lead compounds were separated and tested for their stereospecific binding to Rh using UV-visible spectroscopy and intrinsic fluorescence of tryptophan (Trp) 265 after illumination. By following the changes in UV-visible spectra and Trp265 fluorescence in vitro, we found that binding of R-econazole modulates the formation of Meta III and quenches the intrinsic fluorescence of Trp265. In addition, electrophysiological ex vivo recording revealed that R-econazole slows photoresponse kinetics, whereas S-econazole decreased the sensitivity of rods without effecting the kinetics. Thus, this study contributes new methodology to identify compounds that disrupt the dimerization of GPCRs in general and validates the first active compounds that disrupt the Rh dimer specifically.-Getter, T., Gulati, S., Zimmerman, R., Chen, Y., Vinberg, F., Palczewski, K. Stereospecific modulation of dimeric rhodopsin.
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Affiliation(s)
- Tamar Getter
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Sahil Gulati
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Physiology and Biophysics, University of California–Irvine, Irvine, California, USA
| | - Remy Zimmerman
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
| | - Yuanyuan Chen
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Frans Vinberg
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Physiology and Biophysics, University of California–Irvine, Irvine, California, USA
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38
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Van Nynatten A, Janzen FH, Brochu K, Maldonado-Ocampo JA, Crampton WGR, Chang BSW, Lovejoy NR. To see or not to see: molecular evolution of the rhodopsin visual pigment in neotropical electric fishes. Proc Biol Sci 2019; 286:20191182. [PMID: 31288710 DOI: 10.1098/rspb.2019.1182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Functional variation in rhodopsin, the dim-light-specialized visual pigment, frequently occurs in species inhabiting light-limited environments. Variation in visual function can arise through two processes: relaxation of selection or adaptive evolution improving photon detection in a given environment. Here, we investigate the molecular evolution of rhodopsin in Gymnotiformes, an order of mostly nocturnal South American fishes that evolved sophisticated electrosensory capabilities. Our initial sequencing revealed a mutation associated with visual disease in humans. As these fishes are thought to have poor vision, this would be consistent with a possible sensory trade-off between the visual system and a novel electrosensory system. To investigate this, we surveyed rhodopsin from 147 gymnotiform species, spanning the order, and analysed patterns of molecular evolution. In contrast with our expectation, we detected strong selective constraint in gymnotiform rhodopsin, with rates of non-synonymous to synonymous substitutions lower in gymnotiforms than in other vertebrate lineages. In addition, we found evidence for positive selection on the branch leading to gymnotiforms and on a branch leading to a clade of deep-channel specialized gymnotiform species. We also found evidence that deleterious effects of a human disease-associated substitution are likely to be masked by epistatic substitutions at nearby sites. Our results suggest that rhodopsin remains an important component of the gymnotiform sensory system alongside electrolocation, and that photosensitivity of rhodopsin is well adapted for vision in dim-light environments.
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Affiliation(s)
- Alexander Van Nynatten
- 1 Department of Cell and Systems Biology, University of Toronto , Toronto, Ontario , Canada M5S 3G5.,2 Department of Biological Sciences, University of Toronto Scarborough , Toronto, Ontario , Canada M1C 1A4
| | - Francesco H Janzen
- 3 Department of Biology, University of Ottawa , Ottawa, Ontario , Canada K1N 6N5.,4 Canadian Museum of Nature , Ottawa, Ontario , Canada K1P 6P4
| | - Kristen Brochu
- 5 Department of Entomology, Penn State University , University Park, Pennsylvania 16802 USA
| | - Javier A Maldonado-Ocampo
- 6 Laboratorio de Ictiología, Unidad de Ecología y Sistemática-UNESIS, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana , Bogotá , Colombia
| | - William G R Crampton
- 7 Department of Biology, University of Central Florida , Orlando, FL 32816 , USA
| | - Belinda S W Chang
- 1 Department of Cell and Systems Biology, University of Toronto , Toronto, Ontario , Canada M5S 3G5.,8 Department of Ecology and Evolutionary Biology, University of Toronto , Toronto, Ontario , Canada M5S 3B2.,9 Centre for the Analysis of Genome Evolution and Function, University of Toronto , Toronto, Ontario , Canada M5S 3B2
| | - Nathan R Lovejoy
- 1 Department of Cell and Systems Biology, University of Toronto , Toronto, Ontario , Canada M5S 3G5.,2 Department of Biological Sciences, University of Toronto Scarborough , Toronto, Ontario , Canada M1C 1A4.,8 Department of Ecology and Evolutionary Biology, University of Toronto , Toronto, Ontario , Canada M5S 3B2
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Park PSH. Rhodopsin Oligomerization and Aggregation. J Membr Biol 2019; 252:413-423. [PMID: 31286171 DOI: 10.1007/s00232-019-00078-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/25/2019] [Indexed: 12/18/2022]
Abstract
Rhodopsin is the light receptor in photoreceptor cells of the retina and a prototypical G protein-coupled receptor. Two types of quaternary structures can be adopted by rhodopsin. If rhodopsin folds and attains a proper tertiary structure, it can then form oligomers and nanodomains within the photoreceptor cell membrane. In contrast, if rhodopsin misfolds, it cannot progress through the biosynthetic pathway and instead will form aggregates that can cause retinal degenerative disease. In this review, emerging views are highlighted on the supramolecular organization of rhodopsin within the membrane of photoreceptor cells and the aggregation of rhodopsin that can lead to retinal degeneration.
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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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40
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Xue L, Sun Q, Zhao H, Rovira X, Gai S, He Q, Pin JP, Liu J, Rondard P. Rearrangement of the transmembrane domain interfaces associated with the activation of a GPCR hetero-oligomer. Nat Commun 2019; 10:2765. [PMID: 31235691 PMCID: PMC6591306 DOI: 10.1038/s41467-019-10834-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 06/04/2019] [Indexed: 02/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs) can integrate extracellular signals via allosteric interactions within dimers and higher-order oligomers. However, the structural bases of these interactions remain unclear. Here, we use the GABAB receptor heterodimer as a model as it forms large complexes in the brain. It is subjected to genetic mutations mainly affecting transmembrane 6 (TM6) and involved in human diseases. By cross-linking, we identify the transmembrane interfaces involved in GABAB1-GABAB2, as well as GABAB1-GABAB1 interactions. Our data are consistent with an oligomer made of a row of GABAB1. We bring evidence that agonist activation induces a concerted rearrangement of the various interfaces. While the GB1-GB2 interface is proposed to involve TM5 in the inactive state, cross-linking of TM6s lead to constitutive activity. These data bring insight for our understanding of the allosteric interaction between GPCRs within oligomers. G protein-coupled receptors (GPCRs), such as GABAB, can integrate extracellular signals via allosteric interactions within dimers and oligomers. Here authors use crosslinking and identify two transmembrane interfaces in GABAB which undergo a concerted rearrangement upon agonist activation.
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Affiliation(s)
- Li Xue
- Cellular Signaling laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qian Sun
- Cellular Signaling laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Han Zhao
- Cellular Signaling laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Xavier Rovira
- Institut de Génomique Fonctionnelle (IGF), CNRS, INSERM, Université de Montpellier, Montpellier, 34094 Montpellier cedex 05, France.,Molecular Photopharmacology Research Group, The Tissue Repair and Regeneration Laboratory, University of Vic - Central University of Catalonia, C. de la Laura, 13, Vic, 08500, Spain
| | - Siyu Gai
- Cellular Signaling laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qianwen He
- Cellular Signaling laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle (IGF), CNRS, INSERM, Université de Montpellier, Montpellier, 34094 Montpellier cedex 05, France.
| | - Jianfeng Liu
- Cellular Signaling laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
| | - Philippe Rondard
- Institut de Génomique Fonctionnelle (IGF), CNRS, INSERM, Université de Montpellier, Montpellier, 34094 Montpellier cedex 05, France
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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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42
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Sapra KT, Spoerri PM, Engel A, Alsteens D, Müller DJ. Seeing and sensing single G protein-coupled receptors by atomic force microscopy. Curr Opin Cell Biol 2019; 57:25-32. [PMID: 30412846 PMCID: PMC6472649 DOI: 10.1016/j.ceb.2018.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 12/21/2022]
Abstract
G protein-coupled receptors (GPCRs) relay extracellular information across cell membranes through a continuum of conformations that are not always captured in structures. Hence, complementary approaches are required to quantify the physical and chemical properties of the dynamic conformations linking to GPCR function. Atomic force microscopy (AFM)-based high-resolution imaging and force spectroscopy are unique methods to scrutinize GPCRs and to sense their interactions. Here, we exemplify recent AFM-based applications to directly observe the supramolecular assembly of GPCRs in native membranes, to measure the ligand-binding free-energy landscape, and how interactions modulate the structural properties of GPCRs. Common trends in GPCR function are beginning to emerge. We envision that technical developments in combining AFM with superresolution fluorescence imaging will provide insights into how cellular states modulate GPCRs and vice versa.
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Affiliation(s)
- K Tanuj Sapra
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Patrizia M Spoerri
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Andreas Engel
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.07., B-1348 Louvain-la-Neuve, Belgium
| | - Daniel J Müller
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland.
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Hamzeh H, Alvarez L, Strünker T, Kierzek M, Brenker C, Deal PE, Miller EW, Seifert R, Kaupp UB. Kinetic and photonic techniques to study chemotactic signaling in sea urchin sperm. Methods Cell Biol 2019; 151:487-517. [PMID: 30948028 DOI: 10.1016/bs.mcb.2018.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Sperm from sea urchins are attracted by chemical cues released by the egg-a mechanism called chemotaxis. We describe here the signaling pathway and molecular components endowing sperm with single-molecule sensitivity. Chemotactic signaling and behavioral responses occur on a timescale of a few milliseconds to seconds. We describe the techniques and chemical tools used to resolve the signaling events in time. The techniques include rapid-mixing devices, rapid stroboscopic microscopy, and photolysis of caged second messengers and chemoattractants.
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Affiliation(s)
- Hussein Hamzeh
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Bonn, Germany
| | - Luis Alvarez
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Bonn, Germany
| | - Timo Strünker
- Center of Reproductive Medicine and Andrology, University Hospital Münster, University of Münster, Münster, Germany
| | - Michelina Kierzek
- Center of Reproductive Medicine and Andrology, University Hospital Münster, University of Münster, Münster, Germany
| | - Christoph Brenker
- Center of Reproductive Medicine and Andrology, University Hospital Münster, University of Münster, Münster, Germany
| | - Parker E Deal
- Department of Chemistry, University of California, Berkeley, CA, United States
| | - Evan W Miller
- Department of Chemistry, University of California, Berkeley, CA, United States; Department of Molecular & Cell Biology, University of California, Berkeley, CA, United States; Helen Wills Neuroscience Institute, University of California, Berkeley, CA, United States
| | - Reinhard Seifert
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Bonn, Germany
| | - U Benjamin Kaupp
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Bonn, Germany.
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44
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Bocchero U, Tam BM, Chiu CN, Torre V, Moritz OL. Electrophysiological Changes During Early Steps of Retinitis Pigmentosa. Invest Ophthalmol Vis Sci 2019; 60:933-943. [PMID: 30840038 DOI: 10.1167/iovs.18-25347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose The rhodopsin mutation P23H is responsible for a significant portion of autosomal-dominant retinitis pigmentosa, a disorder characterized by rod photoreceptor death. The mechanisms of toxicity remain unclear; previous studies implicate destabilization of P23H rhodopsin during light exposure, causing decreased endoplasmic reticulum (ER) exit and ER stress responses. Here, we probed phototransduction in Xenopus laevis rods expressing bovine P23H rhodopsin, in which retinal degeneration is inducible by light exposure, in order to examine early physiological changes that occur during retinal degeneration. Methods We recorded single-cell and whole-retina responses to light stimuli using electrophysiology. Moreover, we monitored morphologic changes in rods after different periods of light exposure. Results Initially, P23H rods had almost normal photoresponses, but following a brief light exposure varying from 4 to 32 photoisomerizations per disc, photoresponses became irreversibly prolonged. In intact retinas, rods began to shed OS fragments after a rod-saturating exposure of 12 minutes, corresponding to approximately 10 to 100 times more photoisomerizations. Conclusions Our results indicate that in P23H rods light-induced degeneration occurs in at least two stages, the first involving impairment of phototransduction and the second involving initiation of morphologic changes.
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Affiliation(s)
- Ulisse Bocchero
- Neuroscience Department, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Beatrice M Tam
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Colette N Chiu
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vincent Torre
- Neuroscience Department, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Orson L Moritz
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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Hoffmann M, Fröhner C, Noé F. ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics. PLoS Comput Biol 2019; 15:e1006830. [PMID: 30818351 PMCID: PMC6413953 DOI: 10.1371/journal.pcbi.1006830] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 03/12/2019] [Accepted: 01/16/2019] [Indexed: 12/30/2022] Open
Abstract
Interacting-particle reaction dynamics (iPRD) combines the simulation of dynamical trajectories of interacting particles as in molecular dynamics (MD) simulations with reaction kinetics, in which particles appear, disappear, or change their type and interactions based on a set of reaction rules. This combination facilitates the simulation of reaction kinetics in crowded environments, involving complex molecular geometries such as polymers, and employing complex reaction mechanisms such as breaking and fusion of polymers. iPRD simulations are ideal to simulate the detailed spatiotemporal reaction mechanism in complex and dense environments, such as in signalling processes at cellular membranes, or in nano- to microscale chemical reactors. Here we introduce the iPRD software ReaDDy 2, which provides a Python interface in which the simulation environment, particle interactions and reaction rules can be conveniently defined and the simulation can be run, stored and analyzed. A C++ interface is available to enable deeper and more flexible interactions with the framework. The main computational work of ReaDDy 2 is done in hardware-specific simulation kernels. While the version introduced here provides single- and multi-threading CPU kernels, the architecture is ready to implement GPU and multi-node kernels. We demonstrate the efficiency and validity of ReaDDy 2 using several benchmark examples. ReaDDy 2 is available at the https://readdy.github.io/ website.
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Affiliation(s)
- Moritz Hoffmann
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Christoph Fröhner
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
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Senapati S, Park PSH. Investigating the Nanodomain Organization of Rhodopsin in Native Membranes by Atomic Force Microscopy. Methods Mol Biol 2019; 1886:61-74. [PMID: 30374862 DOI: 10.1007/978-1-4939-8894-5_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Membrane proteins play an integral role in cellular communication. They are often organized within the crowded cell membrane into nanoscale domains (i.e., nanodomains), which facilitates their function in cell signaling processes. The visualization of membrane proteins and nanodomains within biological membranes under physiological conditions presents a challenge and is not possible using conventional microscopy methods. Atomic force microscopy (AFM) provides an opportunity to study the organization of membrane proteins within biological membranes with sub-nanometer resolution. An example of a membrane protein organized into nanodomains is rhodopsin. Rhodopsin is expressed in photoreceptor cells of the retina and upon photoactivation initiates a series of biochemical reactions called phototransduction, which represents the first steps of vision. AFM has provided an opportunity to directly visualize the packing of rhodopsin in native retinal membranes and the quantitative analysis of AFM images is beginning to reveal insights about the nanodomain organization of rhodopsin in the membrane. In this report, we outline procedures for imaging rhodopsin nanodomains by AFM and the quantitative analysis of those AFM images.
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Affiliation(s)
- Subhadip Senapati
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, USA.
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47
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Pfeffer S, Mahamid J. Unravelling molecular complexity in structural cell biology. Curr Opin Struct Biol 2018; 52:111-118. [PMID: 30339965 DOI: 10.1016/j.sbi.2018.08.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/18/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022]
Abstract
Structural and cell biology have traditionally been separate disciplines and employed techniques that were well defined within the realm of either one or the other. Recent technological breakthroughs propelled electron microscopy of frozen hydrated specimens (cryo-EM) followed by single-particle analysis (SPA) to become a widely applied approach for obtaining near-atomic resolution structures of purified macromolecules. In parallel, ongoing developments on sample preparation are increasingly successful in bringing molecular views into cell biology. Cryo-electron tomography (cryo-ET) has so far served as the main imaging modality employed in these efforts towards obtaining three-dimensional (3D) volumes of heterogeneous molecular assemblies. We review the state-of-the-art in cryo-ET and computational processing and describe the current opportunities and frontiers for in-cell applications.
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Affiliation(s)
- Stefan Pfeffer
- Centre for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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48
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Ramirez SA, Leidy C. Effect of the Organization of Rhodopsin on the Association between Transducin and a Photoactivated Receptor. J Phys Chem B 2018; 122:8872-8879. [PMID: 30156842 DOI: 10.1021/acs.jpcb.8b07401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
After photoactivation, rhodopsin (R), a G-protein-coupled receptor, rapidly activates multiple transducin G-proteins (G) in an initial amplification step of phototransduction. G-protein activation requires diffusion-mediated association with an active rhodopsin (R*) at the rod disk membrane. Different organizations of R within the membrane have been revealded by several microscopy studies, including static and freely diffusing situations. However, it is unclear how such different scenarios influence the activation rate of G proteins. Through Monte Carlo simulations, we study the association reaction between a photoactivated rhodopsin and transducin under different reported receptor organizations including (a) R monomers diffusing freely, (b) R forming static dispersed crystalline domains made of rows of dimers, and (c) R arranged in static tracks formed by two adjacent rows of dimers. A key parameter in our simulations is the probability of binding following a collision ( p). For high p, the association rate between R* and G is higher in the freely diffusive system than in the static organizations, but for low collision efficiencies, the static organizations can result in faster association rates than the mobile system. We also observe that with low p, increasing the concentration of R increases the association rate significantly in the dispersed crystals configuration and just slightly in the free diffusive system. In summary, the lateral organization of rhodopsin influences the association rate between R* and G in a manner strongly dependent on the collision efficiency.
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Affiliation(s)
- Samuel A Ramirez
- Department of Pharmacology , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 ; United States
| | - Chad Leidy
- Department of Physics , Universidad de los Andes , Bogotá 111711 , Colombia
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49
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Abstract
Interacting-particle reaction dynamics (iPRD) simulates the spatiotemporal evolution of particles that experience interaction forces and can react with one another. The combination of interaction forces and reactions enables a wide range of complex reactive systems in biology and chemistry to be simulated, but gives rise to new questions such as how to evolve the dynamical equations in a computationally efficient and statistically correct manner. Here we consider reversible reactions such as A + B ⇄ C with interacting particles and derive expressions for the microscopic iPRD simulation parameters such that desired values for the equilibrium constant and the dissociation rate are obtained in the dilute limit. We then introduce a Monte Carlo algorithm that ensures detailed balance in the iPRD time-evolution (iPRD-DB). iPRD-DB guarantees the correct thermodynamics at all concentrations and maintains the desired kinetics in the dilute limit, where chemical rates are well-defined and kinetic measurement experiments usually operate. We show that in dense particle systems, the incorporation of detailed balance is essential to obtain physically realistic solutions. iPRD-DB is implemented in ReaDDy 2.
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Affiliation(s)
- Christoph Fröhner
- Fachbereich Mathematik und Informatik , Freie Universität Berlin , Arnimallee 6 , 14195 Berlin , Germany
| | - Frank Noé
- Fachbereich Mathematik und Informatik , Freie Universität Berlin , Arnimallee 6 , 14195 Berlin , Germany
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50
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Sadeghi M, Weikl TR, Noé F. Particle-based membrane model for mesoscopic simulation of cellular dynamics. J Chem Phys 2018; 148:044901. [PMID: 29390800 DOI: 10.1063/1.5009107] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on interacting and reacting particles, each representing a coarse patch of a lipid monolayer. Particle interactions include nearest-neighbor bond-stretching and angle-bending and are parameterized so as to reproduce the local membrane mechanics given by the Helfrich energy density over a range of relevant curvatures. In-plane fluidity is implemented with Monte Carlo bond-flipping moves. The physical accuracy of the model is verified by five tests: (i) Power spectrum analysis of equilibrium thermal undulations is used to verify that the particle-based representation correctly captures the dynamics predicted by the continuum model of fluid membranes. (ii) It is verified that the input bending stiffness, against which the potential parameters are optimized, is accurately recovered. (iii) Isothermal area compressibility modulus of the membrane is calculated and is shown to be tunable to reproduce available values for different lipid bilayers, independent of the bending rigidity. (iv) Simulation of two-dimensional shear flow under a gravity force is employed to measure the effective in-plane viscosity of the membrane model and show the possibility of modeling membranes with specified viscosities. (v) Interaction of the bilayer membrane with a spherical nanoparticle is modeled as a test case for large membrane deformations and budding involved in cellular processes such as endocytosis. The results are shown to coincide well with the predicted behavior of continuum models, and the membrane model successfully mimics the expected budding behavior. We expect our model to be of high practical usability for ultra coarse-grained molecular dynamics or particle-based reaction-diffusion simulations of biological systems.
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Affiliation(s)
- Mohsen Sadeghi
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Thomas R Weikl
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
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