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Lefevre TJ, Wei W, Mukhaleva E, Meda Venkata SP, Chandan NR, Abraham S, Li Y, Dessauer CW, Vaidehi N, Smrcka AV. Stabilization of interdomain interactions in G protein α subunits as a determinant of Gα i subtype signaling specificity. J Biol Chem 2024; 300:107211. [PMID: 38522511 PMCID: PMC11066577 DOI: 10.1016/j.jbc.2024.107211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 03/26/2024] Open
Abstract
Highly homologous members of the Gαi family, Gαi1-3, have distinct tissue distributions and physiological functions, yet their biochemical and functional properties are very similar. We recently identified PDZ-RhoGEF (PRG) as a novel Gαi1 effector that is poorly activated by Gαi2. In a proteomic proximity labeling screen we observed a strong preference for Gαi1 relative to Gαi2 with respect to engagement of a broad range of potential targets. We investigated the mechanistic basis for this selectivity using PRG as a representative target. Substitution of either the helical domain (HD) from Gαi1 into Gαi2 or substitution of a single amino acid, A230 in Gαi2 with the corresponding D in Gαi1, largely rescues PRG activation and interactions with other potential Gαi targets. Molecular dynamics simulations combined with Bayesian network models revealed that in the GTP bound state, separation at the HD-Ras-like domain (RLD) interface is more pronounced in Gαi2 than Gαi1. Mutation of A230 to D in Gαi2 stabilizes HD-RLD interactions via ionic interactions with R145 in the HD which in turn modify the conformation of Switch III. These data support a model where D229 in Gαi1 interacts with R144 and stabilizes a network of interactions between HD and RLD to promote protein target recognition. The corresponding A230 in Gαi2 is unable to stabilize this network leading to an overall lower efficacy with respect to target interactions. This study reveals distinct mechanistic properties that could underly differential biological and physiological consequences of activation of Gαi1 or Gαi2 by G protein-coupled receptors.
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Affiliation(s)
- Tyler J Lefevre
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Wenyuan Wei
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Elizaveta Mukhaleva
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | | | - Naincy R Chandan
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Genentech, South San Francisco, California, USA
| | - Saji Abraham
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Yong Li
- Department of Integrative Biology and Pharmacology McGovern Medical School, UTHealth, Houston, Texas, USA
| | - Carmen W Dessauer
- Department of Integrative Biology and Pharmacology McGovern Medical School, UTHealth, Houston, Texas, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Alan V Smrcka
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA.
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2
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Klindt DA, Hyvärinen A, Levy A, Miolane N, Poitevin F. Towards Interpretable Cryo-EM: Disentangling Latent Spaces of Molecular Conformations. bioRxiv 2024:2024.03.18.585544. [PMID: 38562740 PMCID: PMC10983934 DOI: 10.1101/2024.03.18.585544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy (cryo-EM) allows for acquisition of large image datasets of individual molecules. Recent advances in computational cryo-EM have made it possible to learn latent variable models of conformation landscapes. However, interpreting these latent spaces remains a challenge as their individual dimensions are often arbitrary. The key message of our work is that this interpretation challenge can be viewed as an Independent Component Analysis (ICA) problem where we seek models that have the property of identifiability. That means, they have an essentially unique solution, representing a conformational latent space that separates the different degrees of freedom a molecule is equipped with in nature. Thus, we aim to advance the computational field of cryo-EM beyond visualizations as we connect it with the theoretical framework of (nonlinear) ICA and discuss the need for identifiable models, improved metrics, and benchmarks. Moving forward, we propose future directions for enhancing the disentanglement of latent spaces in cryo-EM, refining evaluation metrics and exploring techniques that leverage physics-based decoders of biomolecular systems. Moreover, we discuss how future technological developments in time-resolved single particle imaging may enable the application of nonlinear ICA models that can discover the true conformation changes of molecules in nature. The pursuit of interpretable conformational latent spaces will empower researchers to unravel complex biological processes and facilitate targeted interventions. This has significant implications for drug discovery and structural biology more broadly. More generally, latent variable models are deployed widely across many scientific disciplines. Thus, the argument we present in this work has much broader applications in AI for science if we want to move from impressive nonlinear neural network models to mathematically grounded methods that can help us learn something new about nature.
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3
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Aplin C, Cerione RA. Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6. J Biol Chem 2024; 300:105608. [PMID: 38159849 PMCID: PMC10838916 DOI: 10.1016/j.jbc.2023.105608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/23/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Phototransduction in retinal rods occurs when the G protein-coupled photoreceptor rhodopsin triggers the activation of phosphodiesterase 6 (PDE6) by GTP-bound alpha subunits of the G protein transducin (GαT). Recently, we presented a cryo-EM structure for a complex between two GTP-bound recombinant GαT subunits and native PDE6, that included a bivalent antibody bound to the C-terminal ends of GαT and the inhibitor vardenafil occupying the active sites on the PDEα and PDEβ subunits. We proposed GαT-activated PDE6 by inducing a striking reorientation of the PDEγ subunits away from the catalytic sites. However, questions remained including whether in the absence of the antibody GαT binds to PDE6 in a similar manner as observed when the antibody is present, does GαT activate PDE6 by enabling the substrate cGMP to access the catalytic sites, and how does the lipid membrane enhance PDE6 activation? Here, we demonstrate that 2:1 GαT-PDE6 complexes form with either recombinant or retinal GαT in the absence of the GαT antibody. We show that GαT binding is not necessary for cGMP nor competitive inhibitors to access the active sites; instead, occupancy of the substrate binding sites enables GαT to bind and reposition the PDE6γ subunits to promote catalytic activity. Moreover, we demonstrate by reconstituting GαT-stimulated PDE6 activity in lipid bilayer nanodiscs that the membrane-induced enhancement results from an increase in the apparent binding affinity of GαT for PDE6. These findings provide new insights into how the retinal G protein stimulates rapid catalytic turnover by PDE6 required for dim light vision.
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Affiliation(s)
- Cody Aplin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Richard A Cerione
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA; Department of Molecular Medicine, Cornell University, Ithaca, New York, USA.
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4
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Moakedi F, Aljammal R, Poria D, Saravanan T, Rhodes SB, Reid C, Guan T, Kefalov VJ, Ramamurthy V. Prenylation is essential for the enrichment of cone phosphodiesterase-6 (PDE6) in outer segments and efficient cone phototransduction. Hum Mol Genet 2023; 32:2735-2750. [PMID: 37384398 PMCID: PMC10460490 DOI: 10.1093/hmg/ddad108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/01/2023] Open
Abstract
Phosphodiesterase-6 (PDE6) is the key phototransduction effector enzyme residing in the outer segment (OS) of photoreceptors. Cone PDE6 is a tetrameric protein consisting of two inhibitory subunits (γ') and two catalytic subunits (α'). The catalytic subunit of cone PDE6 contains a C-terminus prenylation motif. Deletion of PDE6α' C-terminal prenylation motif is linked to achromatopsia (ACHM), a type of color blindness in humans. However, mechanisms behind the disease and roles for lipidation of cone PDE6 in vision are unknown. In this study, we generated two knock-in mouse models expressing mutant variants of cone PDE6α' lacking the prenylation motif (PDE6α'∆C). We find that the C-terminal prenylation motif is the primary determinant for the association of cone PDE6 protein with membranes. Cones from PDE6α'∆C homozygous mice are less sensitive to light, and their response to light is delayed, whereas cone function in heterozygous PDE6α'∆C/+ mice is unaffected. Surprisingly, the expression level and assembly of cone PDE6 protein were unaltered in the absence of prenylation. Unprenylated assembled cone PDE6 in PDE6α'∆C homozygous animals is mislocalized and enriched in the cone inner segment and synaptic terminal. Interestingly, the disk density and the overall length of cone OS in PDE6α'∆C homozygous mutants are altered, highlighting a novel structural role for PDE6 in maintaining cone OS length and morphology. The survival of cones in the ACHM model generated in this study bodes well for gene therapy as a treatment option for restoring vision in patients with similar mutations in the PDE6C gene.
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Affiliation(s)
- Faezeh Moakedi
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
- Department of Ophthalmology and Visual Sciences, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Rawaa Aljammal
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
- Department of Ophthalmology and Visual Sciences, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Deepak Poria
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA
| | - Thamaraiselvi Saravanan
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
- Department of Ophthalmology and Visual Sciences, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Scott B Rhodes
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
- Department of Ophthalmology and Visual Sciences, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Chyanne Reid
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
- Department of Ophthalmology and Visual Sciences, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Tongju Guan
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
- Department of Ophthalmology and Visual Sciences, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Vladimir J Kefalov
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697, USA
| | - Visvanathan Ramamurthy
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
- Department of Ophthalmology and Visual Sciences, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
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5
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Barret D, Schuster D, Rodrigues M, Leitner A, Picotti P, Schertler G, Kaupp U, Korkhov V, Marino J. Structural basis of calmodulin modulation of the rod cyclic nucleotide-gated channel. Proc Natl Acad Sci U S A 2023; 120:e2300309120. [PMID: 37011209 PMCID: PMC10104587 DOI: 10.1073/pnas.2300309120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/06/2023] [Indexed: 04/05/2023] Open
Abstract
Calmodulin (CaM) regulates many ion channels to control calcium entry into cells, and mutations that alter this interaction are linked to fatal diseases. The structural basis of CaM regulation remains largely unexplored. In retinal photoreceptors, CaM binds to the CNGB subunit of cyclic nucleotide-gated (CNG) channels and, thereby, adjusts the channel's Cyclic guanosine monophosphate (cGMP) sensitivity in response to changes in ambient light conditions. Here, we provide the structural characterization for CaM regulation of a CNG channel by using a combination of single-particle cryo-electron microscopy and structural proteomics. CaM connects the CNGA and CNGB subunits, resulting in structural changes both in the cytosolic and transmembrane regions of the channel. Cross-linking and limited proteolysis-coupled mass spectrometry mapped the conformational changes induced by CaM in vitro and in the native membrane. We propose that CaM is a constitutive subunit of the rod channel to ensure high sensitivity in dim light. Our mass spectrometry-based approach is generally relevant for studying the effect of CaM on ion channels in tissues of medical interest, where only minute quantities are available.
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Affiliation(s)
- Diane C. A. Barret
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232Villigen, Switzerland
| | - Dina Schuster
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232Villigen, Switzerland
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8049Zürich, Switzerland
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8049Zurich, Switzerland
| | - Matthew J. Rodrigues
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232Villigen, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8049Zürich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8049Zürich, Switzerland
| | | | - U. Benjamin Kaupp
- Life and Medical Sciences Institute, University of Bonn, 53115Bonn, Germany
- Max Planck Institute for Multidisciplinary Sciences, 37077Göttingen, Germany
| | - Volodymyr M. Korkhov
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232Villigen, Switzerland
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8049Zurich, Switzerland
| | - Jacopo Marino
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232Villigen, Switzerland
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6
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Gerhardt MJ, Petersen-Jones SM, Michalakis S. CNG channel-related retinitis pigmentosa. Vision Res 2023; 208:108232. [PMID: 37054604 PMCID: PMC10373105 DOI: 10.1016/j.visres.2023.108232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/15/2023]
Abstract
The genes CNGA1 and CNGB1 encode the alpha and beta subunits of the rod CNG channel, a ligand-gated cation channel whose activity is controlled by cyclic guanosine monophosphate (cGMP). Autosomal inherited mutations in either of the genes lead to a progressive rod-cone retinopathy known as retinitis pigmentosa (RP). The rod CNG channel is expressed in the plasma membrane of the outer segment and functions as a molecular switch that converts light-mediated changes in cGMP into a voltage and Ca2+ signal. Here, we will first review the molecular properties and physiological role of the rod CNG channel and then discuss the characteristics of CNG-related RP. Finally, we will summarize recent activities in the field of gene therapy aimed at developing therapies for CNG-related RP.
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Affiliation(s)
- Maximilian J Gerhardt
- Department of Ophthalmology, University Hospital, LMU Munich, Mathildenstraße 8, 80336 München, Germany
| | - Simon M Petersen-Jones
- College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, United States
| | - Stylianos Michalakis
- Department of Ophthalmology, University Hospital, LMU Munich, Mathildenstraße 8, 80336 München, Germany.
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7
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Lefevre TJ, Wei W, Mukhaleva E, Venkata SPM, Chandan NR, Abraham S, Li Y, Dessauer CW, Vaidehi N, Smrcka AV. Stabilization of Interdomain Interactions in G protein α i Subunits Determines Gα i Subtype Signaling Specificity. bioRxiv 2023:2023.03.10.532072. [PMID: 37066214 PMCID: PMC10103935 DOI: 10.1101/2023.03.10.532072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Highly homologous members of the Gαi family, Gαi1-3, have distinct tissue distributions and physiological functions, yet the functional properties of these proteins with respect to GDP/GTP binding and regulation of adenylate cyclase are very similar. We recently identified PDZ-RhoGEF (PRG) as a novel Gαi1 effector, however, it is poorly activated by Gαi2. Here, in a proteomic proximity labeling screen we observed a strong preference for Gαi1 relative to Gαi2 with respect to engagement of a broad range of potential targets. We investigated the mechanistic basis for this selectivity using PRG as a representative target. Substitution of either the helical domain (HD) from Gαi1 into Gαi2 or substitution of a single amino acid, A230 in Gαi2 to the corresponding D in Gαi1, largely rescues PRG activation and interactions with other Gαi targets. Molecular dynamics simulations combined with Bayesian network models revealed that in the GTP bound state, dynamic separation at the HD-Ras-like domain (RLD) interface is prevalent in Gαi2 relative to Gαi1 and that mutation of A230s4h3.3 to D in Gαi2 stabilizes HD-RLD interactions through formation of an ionic interaction with R145HD.11 in the HD. These interactions in turn modify the conformation of Switch III. These data support a model where D229s4h3.3 in Gαi1 interacts with R144HD.11 stabilizes a network of interactions between HD and RLD to promote protein target recognition. The corresponding A230 in Gαi2 is unable to form the "ionic lock" to stabilize this network leading to an overall lower efficacy with respect to target interactions. This study reveals distinct mechanistic properties that could underly differential biological and physiological consequences of activation of Gαi1 or Gαi2 by GPCRs.
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Affiliation(s)
- Tyler J. Lefevre
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI
| | - Wenyuan Wei
- Department of Integrative Biology and Pharmacology McGovern Medical School, UTHealth, Houston, TX
| | - Elizaveta Mukhaleva
- Department of Integrative Biology and Pharmacology McGovern Medical School, UTHealth, Houston, TX
| | | | - Naincy R. Chandan
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI
- Genentech, South San Francisco, CA
| | - Saji Abraham
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI
| | - Yong Li
- Department of Integrative Biology and Pharmacology McGovern Medical School, UTHealth, Houston, TX
| | - Carmen W. Dessauer
- Department of Integrative Biology and Pharmacology McGovern Medical School, UTHealth, Houston, TX
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA
| | - Alan V. Smrcka
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI
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8
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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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9
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Gerhardt MJ, Priglinger SG, Biel M, Michalakis S. Biology, Pathobiology and Gene Therapy of CNG Channel-Related Retinopathies. Biomedicines 2023; 11. [PMID: 36830806 DOI: 10.3390/biomedicines11020269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
The visual process begins with the absorption of photons by photopigments of cone and rod photoreceptors in the retina. In this process, the signal is first amplified by a cyclic guanosine monophosphate (cGMP)-based signaling cascade and then converted into an electrical signal by cyclic nucleotide-gated (CNG) channels. CNG channels are purely ligand-gated channels whose activity can be controlled by cGMP, which induces a depolarizing Na+/Ca2+ current upon binding to the channel. Structurally, CNG channels belong to the superfamily of pore-loop cation channels and share structural similarities with hyperpolarization-activated cyclic nucleotide (HCN) and voltage-gated potassium (KCN) channels. Cone and rod photoreceptors express distinct CNG channels encoded by homologous genes. Mutations in the genes encoding the rod CNG channel (CNGA1 and CNGB1) result in retinitis-pigmentosa-type blindness. Mutations in the genes encoding the cone CNG channel (CNGA3 and CNGB3) lead to achromatopsia. Here, we review the molecular properties of CNG channels and describe their physiological and pathophysiological roles in the retina. Moreover, we summarize recent activities in the field of gene therapy aimed at developing the first gene therapies for CNG channelopathies.
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10
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Terashi G, Wang X, Kihara D. Protein model refinement for cryo-EM maps using AlphaFold2 and the DAQ score. Acta Crystallogr D Struct Biol 2023; 79:10-21. [PMID: 36601803 PMCID: PMC9815095 DOI: 10.1107/s2059798322011676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
As more protein structure models have been determined from cryogenic electron microscopy (cryo-EM) density maps, establishing how to evaluate the model accuracy and how to correct models in cases where they contain errors is becoming crucial to ensure the quality of the structural models deposited in the public database, the PDB. Here, a new protocol is presented for evaluating a protein model built from a cryo-EM map and applying local structure refinement in the case where the model has potential errors. Firstly, model evaluation is performed using a deep-learning-based model-local map assessment score, DAQ, that has recently been developed. The subsequent local refinement is performed by a modified AlphaFold2 procedure, in which a trimmed template model and a trimmed multiple sequence alignment are provided as input to control which structure regions to refine while leaving other more confident regions of the model intact. A benchmark study showed that this protocol, DAQ-refine, consistently improves low-quality regions of the initial models. Among 18 refined models generated for an initial structure, DAQ shows a high correlation with model quality and can identify the best accurate model for most of the tested cases. The improvements obtained by DAQ-refine were on average larger than other existing methods.
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Affiliation(s)
- Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Xiao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA,Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA,Correspondence e-mail:
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11
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Terashi G, Wang X, Maddhuri Venkata Subramaniya SR, Tesmer JJG, Kihara D. Residue-wise local quality estimation for protein models from cryo-EM maps. Nat Methods 2022; 19:1116-25. [PMID: 35953671 DOI: 10.1038/s41592-022-01574-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 07/11/2022] [Indexed: 01/31/2023]
Abstract
An increasing number of protein structures are being determined by cryogenic electron microscopy (cryo-EM). Although the resolution of determined cryo-EM density maps is improving in general, there are still many cases where amino acids of a protein are assigned with different levels of confidence. Here we developed a method that identifies potential misassignment of residues in the map, including residue shifts along an otherwise correct main-chain trace. The score, named DAQ, computes the likelihood that the local density corresponds to different amino acids, atoms, and secondary structures, estimated via deep learning, and assesses the consistency of the amino acid assignment in the protein structure model with that likelihood. When DAQ was applied to different versions of model structures in the Protein Data Bank that were derived from the same density maps, a clear improvement in the DAQ score was observed in the newer versions of the models. DAQ also found potential misassignment errors in a substantial number of deposited protein structure models built into cryo-EM maps.
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12
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Barret DC, Kaupp UB, Marino J. The structure of cyclic nucleotide-gated channels in rod and cone photoreceptors. Trends Neurosci 2022; 45:763-776. [DOI: 10.1016/j.tins.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 10/16/2022]
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13
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Fina ME, Wang J, Vedula P, Tang HY, Kashina A, Dong DW. Arginylation Regulates G-protein Signaling in the Retina. Front Cell Dev Biol 2022; 9:807345. [PMID: 35127722 PMCID: PMC8815403 DOI: 10.3389/fcell.2021.807345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/17/2021] [Indexed: 12/03/2022] Open
Abstract
Arginylation is a post-translational modification mediated by the arginyltransferase (Ate1). We recently showed that conditional deletion of Ate1 in the nervous system leads to increased light-evoked response sensitivities of ON-bipolar cells in the retina, indicating that arginylation regulates the G-protein signaling complexes of those neurons and/or photoreceptors. However, none of the key players in the signaling pathway were previously shown to be arginylated. Here we show that Gαt1, Gβ1, RGS6, and RGS7 are arginylated in the retina and RGS6 and RGS7 protein levels are elevated in Ate1 knockout, suggesting that arginylation plays a direct role in regulating their protein level and the G-protein-mediated responses in the retina.
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Affiliation(s)
- Marie E. Fina
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, United States
| | - Junling Wang
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, United States
| | - Pavan Vedula
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, United States
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, United States
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Anna Kashina, ; Dawei W. Dong,
| | - Dawei W. Dong
- Department of Biomedical Sciences, School of Veterinary Medicines, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Anna Kashina, ; Dawei W. Dong,
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Cote RH, Gupta R, Irwin MJ, Wang X. Photoreceptor Phosphodiesterase (PDE6): Structure, Regulatory Mechanisms, and Implications for Treatment of Retinal Diseases. Adv Exp Med Biol 2021. [PMID: 34170501 DOI: 10.1007/5584_2021_649] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The photoreceptor phosphodiesterase (PDE6) is a member of large family of Class I phosphodiesterases responsible for hydrolyzing the second messengers cAMP and cGMP. PDE6 consists of two catalytic subunits and two inhibitory subunits that form a tetrameric protein. PDE6 is a peripheral membrane protein that is localized to the signal-transducing compartment of rod and cone photoreceptors. As the central effector enzyme of the G-protein coupled visual transduction pathway, activation of PDE6 catalysis causes a rapid decrease in cGMP levels that results in closure of cGMP-gated ion channels in the photoreceptor plasma membrane. Because of its importance in the phototransduction pathway, mutations in PDE6 genes result in various retinal diseases that currently lack therapeutic treatment strategies due to inadequate knowledge of the structure, function, and regulation of this enzyme. This review focuses on recent progress in understanding the structure of the regulatory and catalytic domains of the PDE6 holoenzyme, the central role of the multi-functional inhibitory γ-subunit, the mechanism of activation by the heterotrimeric G protein, transducin, and future directions for pharmacological interventions to treat retinal degenerative diseases arising from mutations in the PDE6 genes.
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Gulati S, Palczewski K. New focus on regulation of the rod photoreceptor phosphodiesterase. Curr Opin Struct Biol 2021; 69:99-107. [PMID: 33945959 DOI: 10.1016/j.sbi.2021.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/18/2021] [Accepted: 03/25/2021] [Indexed: 02/03/2023]
Abstract
Rod photoreceptor phosphodiesterase (PDE6) is the key catalytic enzyme of visual phototransduction. PDE6 is the only member of the phosphodiesterase family that consists of a heterodimeric catalytic core composed of PDE6α and PDE6β subunits and two inhibitory PDE6γ subunits. Both PDE6α and PDE6β contain two regulatory GAF domains and one catalytic domain. GAF domains and the tightly bound PDE6γ subunits allosterically regulate the activity of the catalytic domain in association with the GTP-bound transducin alpha subunit (Gtα-GTP). Recent cryo-electron microscopy structures of the PDE6αγβγ and PDE6αγβγ-(Gtα-GTP)2 complexes have provided valuable knowledge shedding additional light on the allosteric activation of PDE6 by Gtα-GTP. Here we discuss recent developments in our understanding of the mechanism of PDE6 activation.
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Affiliation(s)
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, Center for Translational Vision Research, University of California, 829 Health Sciences Road, Irvine, CA 92617, USA; The Department of Physiology & Biophysics, University of California, Irvine, CA 92697, USA; The Department of Chemistry, University of California, Irvine, CA 92697, USA.
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16
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Cote RH. Photoreceptor phosphodiesterase (PDE6): activation and inactivation mechanisms during visual transduction in rods and cones. Pflugers Arch 2021; 473:1377-91. [PMID: 33860373 DOI: 10.1007/s00424-021-02562-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/27/2021] [Accepted: 03/30/2021] [Indexed: 01/16/2023]
Abstract
Rod and cone photoreceptors of the vertebrate retina utilize cGMP as the primary intracellular messenger for the visual signaling pathway that converts a light stimulus into an electrical response. cGMP metabolism in the signal-transducing photoreceptor outer segment reflects the balance of cGMP synthesis (catalyzed by guanylyl cyclase) and degradation (catalyzed by the photoreceptor phosphodiesterase, PDE6). Upon light stimulation, rapid activation of PDE6 by the heterotrimeric G-protein (transducin) triggers a dramatic drop in cGMP levels that lead to cell hyperpolarization. Following cessation of the light stimulus, the lifetime of activated PDE6 is also precisely regulated by additional processes. This review summarizes recent advances in the structural characterization of the rod and cone PDE6 catalytic and regulatory subunits in the context of previous biochemical studies of the enzymological properties and allosteric regulation of PDE6. Emphasis is given to recent advances in understanding the structural and conformational changes underlying the mechanism by which the activated transducin α-subunit binds to-and relieves inhibition of-PDE6 catalysis that is controlled by its intrinsically disordered, inhibitory γ-subunit. The role of the regulator of G-protein signaling 9-1 (RGS9-1) in regulating the lifetime of the transducin-PDE6 is also briefly covered. The therapeutic potential of pharmacological compounds acting as inhibitors or activators targeting PDE6 is discussed in the context of inherited retinal diseases resulting from mutations in rod and cone PDE6 genes as well as other inherited defects that arise from excessive cGMP accumulation in retinal photoreceptor cells.
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Sargazi S, Shahraki S, Shahraki O, Zargari F, Sheervalilou R, Maghsoudi S, Soltani Rad MN, Saravani R. 8-Alkylmercaptocaffeine derivatives: antioxidant, molecular docking, and in-vitro cytotoxicity studies. Bioorg Chem 2021; 111:104900. [PMID: 33894429 DOI: 10.1016/j.bioorg.2021.104900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022]
Abstract
Due to their unique pharmacological characteristics, methylxanthines are known as therapeutic agents in a fascinating range of medicinal scopes. In this report, we aimed to examine some biological effects of previously synthesized 8-alkylmercaptocaffeine derivatives. Cytotoxic and antioxidative activity of 8-alkylmercaptocaffeine derivatives were measured in malignant A549, MCF7, and C152 cell lines. Assessment of cGMP levels and caspase-3 activity were carried out using a colorimetric competitive ELISA kit. Computational approaches were employed to discover the inhibitory mechanism of synthesized compounds. Among the twelve synthesized derivatives, three compounds (C1, C5, and C7) bearing propyl, heptyl, and 3-methyl-butyl moieties showed higher and more desirable cytotoxic activity against all the studied cell lines (IC50 < 100 µM). Furthermore, C5 synergistically enhanced cisplatin-induced cytotoxicity in MCF-7 cells (CI < 1). Both C5 and C7 significantly increased caspase-3 activity and intracellular cGMP levels at specific time intervals in all studied cell lines (P < 0.05). However, these derivatives did not elevate LDH leakage (P > 0.05) and exhibited no marked ameliorating effects on oxidative damage (P > 0.05). Computational studies showed that H-bond formation between the nitrogen atom in pyrazolo[4,3-D] pyrimidine moiety with Gln817 and creating a hydrophobic cavity result in the stability of the alkyl group in the PDE5A active site. We found that synthesized 8-alkylmercaptocaffeine derivatives induced cell death in different cancer cells through the cGMP pathway. These findings will help us to get a deeper insight into the role of methylxanthines as useful alternatives to conventional cancer therapeutics.
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Affiliation(s)
- Saman Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Sheida Shahraki
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Omolbanin Shahraki
- Pharmacology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Farshid Zargari
- Pharmacology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran; Department of Chemistry, Faculty of Science, University of Sistan and balouchestan, Zahedan, Iran
| | | | - Saeid Maghsoudi
- Medicinal Chemistry Research Laboratory, Department of Chemistry, Shiraz University of Technology, Shiraz, Iran
| | - Mohammad Navid Soltani Rad
- Medicinal Chemistry Research Laboratory, Department of Chemistry, Shiraz University of Technology, Shiraz, Iran
| | - Ramin Saravani
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran; Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
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18
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Le Bon C, Michon B, Popot JL, Zoonens M. Amphipathic environments for determining the structure of membrane proteins by single-particle electron cryo-microscopy. Q Rev Biophys 2021; 54:e6. [PMID: 33785082 DOI: 10.1017/S0033583521000044] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, the structural biology of membrane proteins (MPs) has taken a new turn thanks to epoch-making technical progress in single-particle electron cryo-microscopy (cryo-EM) as well as to improvements in sample preparation. The present analysis provides an overview of the extent and modes of usage of the various types of surfactants for cryo-EM studies. Digitonin, dodecylmaltoside, protein-based nanodiscs, lauryl maltoside-neopentyl glycol, glyco-diosgenin, and amphipols (APols) are the most popular surfactants at the vitrification step. Surfactant exchange is frequently used between MP purification and grid preparation, requiring extensive optimization each time the study of a new MP is undertaken. The variety of both the surfactants and experimental approaches used over the past few years bears witness to the need to continue developing innovative surfactants and optimizing conditions for sample preparation. The possibilities offered by novel APols for EM applications are discussed.
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Srivastava D, Yadav RP, Inamdar SM, Huang Z, Sokolov M, Boyd K, Artemyev NO. Transducin Partners Outside the Phototransduction Pathway. Front Cell Neurosci 2020; 14:589494. [PMID: 33173469 PMCID: PMC7591391 DOI: 10.3389/fncel.2020.589494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/10/2020] [Indexed: 11/13/2022] Open
Abstract
Transducin mediates signal transduction in a classical G protein-coupled receptor (GPCR) phototransduction cascade. Interactions of transducin with the receptor and the effector molecules had been extensively investigated and are currently defined at the atomic level. However, partners and functions of rod transducin α (Gαt 1) and βγ (Gβ1γ1) outside the visual pathway are not well-understood. In particular, light-induced redistribution of rod transducin from the outer segment to the inner segment and synaptic terminal (IS/ST) allows Gαt1 and/or Gβ1γ1 to modulate synaptic transmission from rods to rod bipolar cells (RBCs). Protein-protein interactions underlying this modulation are largely unknown. We discuss known interactors of transducin in the rod IS/ST compartment and potential pathways leading to the synaptic effects of light-dispersed Gαt1 and Gβ1γ1. Furthermore, we show that a prominent non-GPCR guanine nucleotide exchange factor (GEF) and a chaperone of Gα subunits, resistance to inhibitors of cholinesterase 8A (Ric-8A) protein, is expressed throughout the retina including photoreceptor cells. Recent structures of Ric-8A alone and in complexes with Gα subunits have illuminated the structural underpinnings of the Ric-8A activities. We generated a mouse model with conditional knockout of Ric-8A in rods in order to begin defining the functional roles of the protein in rod photoreceptors and the retina. Our analysis suggests that Ric-8A is not an obligate chaperone of Gαt1. Further research is needed to investigate probable roles of Ric-8A as a GEF, trafficking chaperone, or a mediator of the synaptic effects of Gαt1.
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Affiliation(s)
- Dhiraj Srivastava
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Ravi P Yadav
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Shivangi M Inamdar
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Zhen Huang
- Department of Neurology and Neuroscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Maxim Sokolov
- Department of Ophthalmology, Biochemistry and Neuroscience, West Virginia University, Morgantown, WV, United States
| | - Kimberly Boyd
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Nikolai O Artemyev
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA, United States.,Department of Ophthalmology and Visual Sciences, Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, United States
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