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A Bioengineered In Vitro Model to Assess AAV-Based Gene Therapies for Cyclic GMP-Related Disorders. Int J Mol Sci 2022; 23:ijms23094538. [PMID: 35562929 PMCID: PMC9101586 DOI: 10.3390/ijms23094538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 02/01/2023] Open
Abstract
The emergence of efficient viral vectors derived from adeno-associated viruses (AAV) has led many groups to develop gene therapies for inherited monogenic diseases, such as retinal dystrophies. To evaluate the potency of new gene therapy vectors in a preclinical context, it is common to use animal models, such as gene-deficient or mutant animal models of a given human disease, and then assess vision restoration with functional or behavioral assays. While such animal models are invaluable to the preclinical testing process, they cannot be readily used as batch release tests during manufacturing or to validate biological activity at later stages of development. There is therefore a need for rapid and reliable in vitro models that can determine whether therapeutic vectors have delivered their cargo gene, and more importantly, whether this has resulted in the intended biological activity. Given our previous experience, we chose CNGA3-linked achromatopsia to develop a cell-based system to verify biological activity of AAV vectors designed to deliver a healthy CNGA3 gene copy into human cone photoreceptors. Our system is based on an immortalized cell line with high susceptibility to AAV transduction, i.e., HeLa cells, which we engineered to express a fungal rhodopsin guanylyl cyclase (RhGC) from Blastocladiella emersonii and a sensitive genetically encoded calcium indicator (GECI) under the control of a tetracycline operator. Using this system, we were able to confirm and quantify the function of the ion channel encoded by AAV/CNGA3 and differentiate between AAV vector potencies with a simple fluorometric assay. Finally, we show that this approach can be readily adapted for the assessment of phosphodiesterase function.
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Photoreceptor Phosphodiesterase (PDE6): Structure, Regulatory Mechanisms, and Implications for Treatment of Retinal Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1371:33-59. [PMID: 34170501 DOI: 10.1007/5584_2021_649] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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] [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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Leinonen H, Cheng C, Pitkänen M, Sander CL, Zhang J, Saeid S, Turunen T, Shmara A, Weiss L, Ta L, Ton T, Koskelainen A, Vargas JD, Kimonis V, Palczewski K. A p97/Valosin-Containing Protein Inhibitor Drug CB-5083 Has a Potent but Reversible Off-Target Effect on Phosphodiesterase-6. J Pharmacol Exp Ther 2021; 378:31-41. [PMID: 33931547 DOI: 10.1124/jpet.120.000486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 04/29/2021] [Indexed: 12/16/2022] Open
Abstract
CB-5083 is an inhibitor of p97/valosin-containing protein (VCP), for which phase I trials for cancer were terminated because of adverse effects on vision, such as photophobia and dyschromatopsia. Lower dose CB-5083 could combat inclusion body myopathy with early-onset Paget disease and frontotemporal dementia or multisystem proteinopathy caused by gain-of-function mutations in VCP. We hypothesized that the visual impairment in the cancer trial was due to CB-5083's inhibition of phosphodiesterase (PDE)-6, which mediates signal transduction in photoreceptors. To test our hypothesis, we used in vivo and ex vivo electroretinography (ERG) in mice and a PDE6 activity assay of bovine rod outer segment (ROS) extracts. Additionally, histology and optical coherence tomography were used to assess CB-5083's long-term ocular toxicity. A single administration of CB-5083 led to robust ERG signal deterioration, specifically in photoresponse kinetics. Similar recordings with known PDE inhibitors sildenafil, tadalafil, vardenafil, and zaprinast showed that only vardenafil had as strong an effect on the ERG signal in vivo as did CB-5083. In the biochemical assay, CB-5083 inhibited PDE6 activity with a potency higher than sildenafil but lower than that of vardenafil. Ex vivo ERG revealed a PDE6 inhibition constant of 80 nM for CB-5083, which is 7-fold smaller than that for sildenafil. Finally, we showed that the inhibitory effect of CB-5083 on visual function is reversible, and its chronic administration does not cause permanent retinal anomalies in aged VCP-disease model mice. Our results warrant re-evaluation of CB-5083 as a clinical therapeutic agent. We recommend preclinical ERG recordings as a routine drug safety screen. SIGNIFICANCE STATEMENT: This report supports the use of a valosin-containing protein (VCP) inhibitor drug, CB-5083, for the treatment of neuromuscular VCP disease despite CB-5083's initial clinical failure for cancer treatment due to side effects on vision. The data show that CB-5083 displays a dose-dependent but reversible inhibitory action on phosphodiesterase-6, an essential enzyme in retinal photoreceptor function, but no long-term consequences on retinal function or structure.
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Affiliation(s)
- Henri Leinonen
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Cheng Cheng
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Marja Pitkänen
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Christopher L Sander
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Jianye Zhang
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Sama Saeid
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Teemu Turunen
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Alyaa Shmara
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Lan Weiss
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Lac Ta
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Timothy Ton
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Ari Koskelainen
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Jesse D Vargas
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Virginia Kimonis
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Department of Ophthalmology (H.L., C.L.S., J.Z., K.P.), Department of Physiology & Biophysics (K.P.), Department of Chemistry (K.P.), and Division of Genetics and Genomic Medicine, Department of Pediatrics (C.C., A.S., L.W., L.T., T.T., V.K.), University of California Irvine, Irvine, California; Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio (C.L.S.); Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland (M.P., S.S., T.T., A.K.); and Cleave Therapeutics, Inc., San Francisco, California (J.D.V.)
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Photoreceptor phosphodiesterase (PDE6): activation and inactivation mechanisms during visual transduction in rods and cones. Pflugers Arch 2021; 473:1377-1391. [PMID: 33860373 DOI: 10.1007/s00424-021-02562-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [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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Maryam A, Vedithi SC, Khalid RR, Alsulami AF, Torres PHM, Siddiqi AR, Blundell TL. The Molecular Organization of Human cGMP Specific Phosphodiesterase 6 (PDE6): Structural Implications of Somatic Mutations in Cancer and Retinitis Pigmentosa. Comput Struct Biotechnol J 2019; 17:378-389. [PMID: 30962868 PMCID: PMC6434069 DOI: 10.1016/j.csbj.2019.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/24/2019] [Accepted: 03/03/2019] [Indexed: 01/12/2023] Open
Abstract
In the cyclic guanosine monophosphate (cGMP) signaling pathway, phosphodiesterase 6 (PDE6) maintains a critical balance of the intracellular concentration of cGMP by catalyzing it to 5′ guanosine monophosphate (5′-GMP). To gain insight into the mechanistic impacts of the PDE6 somatic mutations that are implicated in cancer and retinitis pigmentosa, we first defined the structure and organization of the human PDE6 heterodimer using computational comparative modelling. Each subunit of PDE6αβ possesses three domains connected through long α-helices. The heterodimer model indicates that the two chains are likely related by a pseudo two-fold axis. The N-terminal region of each subunit is comprised of two allosteric cGMP-binding domains (Gaf-A & Gaf-B), oriented in the same way and interacting with the catalytic domain present at the C-terminal in a way that would allow the allosteric cGMP-binding domains to influence catalytic activity. Subsequently, we applied an integrated knowledge-driven in silico mutation analysis approach to understand the structural and functional implications of experimentally identified mutations that cause various cancers and retinitis pigmentosa, as well as computational saturation mutagenesis of the dimer interface and cGMP-binding residues of both Gaf-A, and the catalytic domains. We studied the impact of mutations on the stability of PDE6αβ structure, subunit-interfaces and Gaf-cGMP interactions. Further, we discussed the changes in interatomic interactions of mutations that are destabilizing in Gaf-A (R93L, V141 M, F162 L), catalytic domain (D600N, F742 L, F776 L) and at the dimer interface (F426A, F248G, F424 N). This study establishes a possible link of change in PDE6αβ structural stability to the experimentally observed disease phenotypes.
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Affiliation(s)
- Arooma Maryam
- Department of Biosciences, COMSATS University Islamabad (CUI), Park Road, Islamabad, Pakistan.,Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | | | - Rana Rehan Khalid
- Department of Biosciences, COMSATS University Islamabad (CUI), Park Road, Islamabad, Pakistan
| | - Ali F Alsulami
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | | | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University Islamabad (CUI), Park Road, Islamabad, Pakistan
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
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Gulati S, Palczewski K, Engel A, Stahlberg H, Kovacik L. Cryo-EM structure of phosphodiesterase 6 reveals insights into the allosteric regulation of type I phosphodiesterases. SCIENCE ADVANCES 2019; 5:eaav4322. [PMID: 30820458 PMCID: PMC6392808 DOI: 10.1126/sciadv.aav4322] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/14/2019] [Indexed: 05/27/2023]
Abstract
Cyclic nucleotide phosphodiesterases (PDEs) work in conjunction with adenylate/guanylate cyclases to regulate the key second messengers of G protein-coupled receptor signaling. Previous attempts to determine the full-length structure of PDE family members at high-resolution have been hindered by structural flexibility, especially in their linker regions and N- and C-terminal ends. Therefore, most structure-activity relationship studies have so far focused on truncated and conserved catalytic domains rather than the regulatory domains that allosterically govern the activity of most PDEs. Here, we used single-particle cryo-electron microscopy to determine the structure of the full-length PDE6αβ2γ complex. The final density map resolved at 3.4 Å reveals several previously unseen structural features, including a coiled N-terminal domain and the interface of PDE6γ subunits with the PDE6αβ heterodimer. Comparison of the PDE6αβ2γ complex with the closed state of PDE2A sheds light on the conformational changes associated with the allosteric activation of type I PDEs.
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Affiliation(s)
- Sahil Gulati
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, 829 Health Sciences Road, Irvine, CA 92617, USA
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, 1819 East 101st Street, Cleveland, OH 44106, USA
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, 829 Health Sciences Road, Irvine, CA 92617, USA
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, 1819 East 101st Street, Cleveland, OH 44106, USA
| | - Andreas Engel
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Lubomir Kovacik
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
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Pattis JG, Kamal S, Li B, May ER. Catalytic Domains of Phosphodiesterase 5, 6, and 5/6 Chimera Display Differential Dynamics and Ligand Dissociation Energy Barriers. J Phys Chem B 2019; 123:825-835. [PMID: 30616346 PMCID: PMC6502234 DOI: 10.1021/acs.jpcb.8b11370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The enzyme phosphodiesterase 6 (PDE6) is a critical component of the visual signaling pathway and functions to convert cGMP to GMP. The ability of PDE6 to affect cellular cGMP levels leads to deactivation of cGMP-gated ion channels in both rod and cone cells. PDE6 has been difficult to structurally characterize experimentally, though the structures of the closely related PDE5 and a PDE5/6 chimera have been determined by X-ray crystallography. In this work, we employ a computational approach to study the dynamics of the catalytic domains of PDE6, PDE5, and the PDE5/6 chimera. Through equilibrium molecular dynamics (MD) simulations, we identify a region of PDE6 (α12) to be correlated to distal regions of the enzyme (H- and M-loops), which surround the catalytic center. These correlations are not observed for PDE5, and we speculate that these unique motions in PDE6 may relate to the high catalytic efficiency of PDE6 and the requirement for an endogenous inhibitory subunit (Pγ). We further investigate the ligand binding pathways and energetics by enhanced sampling simulations (metadynamics) using the inhibitor sildenafil and GMP. The energetics and pathways of ligand binding are consistent with the high efficiency of PDE6 and further implicate the α12 region as an important regulatory element for PDE6 functional dynamics.
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Affiliation(s)
| | | | - Boyang Li
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Eric R. May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
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Wang T, Reingruber J, Woodruff ML, Majumder A, Camarena A, Artemyev NO, Fain GL, Chen J. The PDE6 mutation in the rd10 retinal degeneration mouse model causes protein mislocalization and instability and promotes cell death through increased ion influx. J Biol Chem 2018; 293:15332-15346. [PMID: 30126843 DOI: 10.1074/jbc.ra118.004459] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/13/2018] [Indexed: 12/20/2022] Open
Abstract
The retinal degeneration model rd10 contains a missense mutation of the catalytic PDE6 β subunit, which hydrolyzes cGMP in response to light. This model produces cell death more slowly than others caused by PDE6 loss of function, making it of particular interest for studying potential therapeutics. We used morphology, biochemistry, and single-cell physiology to examine the mechanism of rd10 degeneration. Our results show that the mutation produces no alteration of Pde6b RNA but does dramatically decrease maximal and basal PDE6 activity, apparently caused by a decrease in protein stability and transport. The enzymatic properties of the remaining mutant PDE6 appear to be nearly normal. We demonstrate that an increase in free cGMP, which would result from decreased PDE6 activity and serve to increase opening of the cGMP-gated channels and calcium influx, is an underlying cause of cell death: degeneration of rd10/Cngb1 -/- double mutants is slower than the parent rd10 line. Paradoxically, degeneration in rd10/Cngb1 -/- is also slower than in Cngb1 -/- This rescue is correlated with a lowering of cGMP content in Cngb1 -/- retinas and suggests that it may be caused by mislocalization of active PDE6. Single-cell recordings from rd10 rods show that the rates of rise and decay of the response are significantly slower; simulations indicate that these changes are primarily the result of the decrease in PDE6 concentration and rod collecting area. Together, these results provide insights into the complex mechanisms that underlie rd10-mediated retinal degeneration and a cautionary note for analysis of therapeutic interventions.
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Affiliation(s)
- Tian Wang
- From the Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California 90089-2821
| | - Jürgen Reingruber
- the Institut de Biologie, Group of Computational Biology and Applied Mathematics, École Normale Supérieure, 75005 Paris, France
| | - Michael L Woodruff
- the Department of Integrative Biology and Physiology, UCLA, Los Angeles, California 90095-1606
| | - Anurima Majumder
- the Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, and
| | - Andres Camarena
- From the Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California 90089-2821
| | - Nikolai O Artemyev
- the Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, and
| | - Gordon L Fain
- the Department of Integrative Biology and Physiology, UCLA, Los Angeles, California 90095-1606.,the Department of Ophthalmology, Jules Stein Eye Institute, David Geffen School of Medicine at UCLA, Los Angeles, California 90095-7000
| | - Jeannie Chen
- From the Zilkha Neurogenetic Institute and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, California 90089-2821,
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10
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Qureshi BM, Behrmann E, Schöneberg J, Loerke J, Bürger J, Mielke T, Giesebrecht J, Noé F, Lamb TD, Hofmann KP, Spahn CMT, Heck M. It takes two transducins to activate the cGMP-phosphodiesterase 6 in retinal rods. Open Biol 2018; 8:180075. [PMID: 30068566 PMCID: PMC6119865 DOI: 10.1098/rsob.180075] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/06/2018] [Indexed: 12/21/2022] Open
Abstract
Among cyclic nucleotide phosphodiesterases (PDEs), PDE6 is unique in serving as an effector enzyme in G protein-coupled signal transduction. In retinal rods and cones, PDE6 is membrane-bound and activated to hydrolyse its substrate, cGMP, by binding of two active G protein α-subunits (Gα*). To investigate the activation mechanism of mammalian rod PDE6, we have collected functional and structural data, and analysed them by reaction-diffusion simulations. Gα* titration of membrane-bound PDE6 reveals a strong functional asymmetry of the enzyme with respect to the affinity of Gα* for its two binding sites on membrane-bound PDE6 and the enzymatic activity of the intermediary 1 : 1 Gα* · PDE6 complex. Employing cGMP and its 8-bromo analogue as substrates, we find that Gα* · PDE6 forms with high affinity but has virtually no cGMP hydrolytic activity. To fully activate PDE6, it takes a second copy of Gα* which binds with lower affinity, forming Gα* · PDE6 · Gα*. Reaction-diffusion simulations show that the functional asymmetry of membrane-bound PDE6 constitutes a coincidence switch and explains the lack of G protein-related noise in visual signal transduction. The high local concentration of Gα* generated by a light-activated rhodopsin molecule efficiently activates PDE6, whereas the low density of spontaneously activated Gα* fails to activate the effector enzyme.
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Affiliation(s)
- Bilal M Qureshi
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Elmar Behrmann
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Johannes Schöneberg
- Department of Mathematics, Computer Science and Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Thorsten Mielke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Microscopy and Cryo Electron Microscopy Group, Max-Planck Institut für Molekulare Genetik, Berlin, Germany
| | - Jan Giesebrecht
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Frank Noé
- Department of Mathematics, Computer Science and Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2600, Australia
| | - Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Zentrum für Biophysik und Bioinformatik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Martin Heck
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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11
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Deng WT, Kolandaivelu S, Dinculescu A, Li J, Zhu P, Chiodo VA, Ramamurthy V, Hauswirth WW. Cone Phosphodiesterase-6γ' Subunit Augments Cone PDE6 Holoenzyme Assembly and Stability in a Mouse Model Lacking Both Rod and Cone PDE6 Catalytic Subunits. Front Mol Neurosci 2018; 11:233. [PMID: 30038560 PMCID: PMC6046437 DOI: 10.3389/fnmol.2018.00233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/13/2018] [Indexed: 11/13/2022] Open
Abstract
Rod and cone phosphodiesterase 6 (PDE6) are key effector enzymes of the vertebrate phototransduction pathway. Rod PDE6 consists of two catalytic subunits PDE6α and PDE6β and two identical inhibitory PDE6γ subunits, while cone PDE6 is composed of two identical PDE6α’ catalytic subunits and two identical cone-specific PDE6γ’ inhibitory subunits. Despite their prominent function in regulating cGMP levels and therefore rod and cone light response properties, it is not known how each subunit contributes to the functional differences between rods and cones. In this study, we generated an rd10/cpfl1 mouse model lacking rod PDE6β and cone PDE6α’ subunits. Both rod and cone photoreceptor cells are degenerated with age and all PDE6 subunits degrade in rd10/cpfl1 mice. We expressed cone PDE6α’ in both rods and cones of rd10/cpfl1 mice by adeno-associated virus (AAV)-mediated delivery driven by the ubiquitous, constitutive small chicken β-actin promoter. We show that expression of PDE6α’ rescues rod function in rd10/cpfl1 mice, and the restoration of rod light sensitivity is attained through restoration of endogenous rod PDE6γ and formation of a functional PDE6α’γ complex. However, improved photopic cone responses were achieved only after supplementation of both cone PDE6α’ and PDE6γ’ subunits but not by PDE6α’ treatment alone. We observed a two fold increase of PDE6α’ levels in the eyes injected with both PDE6α’ plus PDE6γ’ relative to eyes receiving PDE6α’ alone. Despite the presence of both PDE6γ’ and PDE6γ, the majority of PDE6α’ formed functional complexes with PDE6γ’, suggesting that PDE6α’ has a higher association affinity for PDE6γ’ than for PDE6γ. These results suggest that the presence of PDE6γ’ augments cone PDE6 assembly and enhances its stability. Our finding has important implication for gene therapy of PDE6α’-associated achromatopsia.
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Affiliation(s)
- Wen-Tao Deng
- Department of Ophthalmology, University of Florida, Gainesville, FL, United States
| | - Saravanan Kolandaivelu
- Departments of Ophthalmology and Biochemistry, Center for Neuroscience, West Virginia University, Morgantown, WV, United States
| | - Astra Dinculescu
- Department of Ophthalmology, University of Florida, Gainesville, FL, United States
| | - Jie Li
- Department of Ophthalmology, University of Florida, Gainesville, FL, United States
| | - Ping Zhu
- Department of Ophthalmology, University of Florida, Gainesville, FL, United States
| | - Vince A Chiodo
- Department of Ophthalmology, University of Florida, Gainesville, FL, United States
| | - Visvanathan Ramamurthy
- Departments of Ophthalmology and Biochemistry, Center for Neuroscience, West Virginia University, Morgantown, WV, United States
| | - William W Hauswirth
- Department of Ophthalmology, University of Florida, Gainesville, FL, United States
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12
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Qureshi BM, Schmidt A, Behrmann E, Bürger J, Mielke T, Spahn CMT, Heck M, Scheerer P. Mechanistic insights into the role of prenyl-binding protein PrBP/δ in membrane dissociation of phosphodiesterase 6. Nat Commun 2018; 9:90. [PMID: 29311697 PMCID: PMC5758567 DOI: 10.1038/s41467-017-02569-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/11/2017] [Indexed: 01/01/2023] Open
Abstract
Isoprenylated proteins are associated with membranes and their inter-compartmental distribution is regulated by solubilization factors, which incorporate lipid moieties in hydrophobic cavities and thereby facilitate free diffusion during trafficking. Here we report the crystal structure of a solubilization factor, the prenyl-binding protein (PrBP/δ), at 1.81 Å resolution in its ligand-free apo-form. Apo-PrBP/δ harbors a preshaped, deep hydrophobic cavity, capacitating apo-PrBP/δ to readily bind its prenylated cargo. To investigate the molecular mechanism of cargo solubilization we analyzed the PrBP/δ-induced membrane dissociation of rod photoreceptor phosphodiesterase (PDE6). The results suggest that PrBP/δ exclusively interacts with the soluble fraction of PDE6. Depletion of soluble species in turn leads to dissociation of membrane-bound PDE6, as both are in equilibrium. This “solubilization by depletion” mechanism of PrBP/δ differs from the extraction of prenylated proteins by the similar folded solubilization factor RhoGDI, which interacts with membrane bound cargo via an N-terminal structural element lacking in PrBP/δ. The prenyl-binding protein PrBP/δ is a solubilization factor involved in trafficking of prenylated proteins. Here the authors present the ligand-free apo-PrBP/δ structure and propose a "solubilization by depletion" mechanism, where PrBP/δ sequesters only soluble rod photoreceptor phosphodiesterase (PDE6), leading to a dissociation of membrane-bound PDE6.
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Affiliation(s)
- Bilal M Qureshi
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Cryo Electron Microscopy, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Enzyme Kinetics, Charitéplatz 1, D-10117, Berlin, Germany.,Division of Biological & Environmental Sciences & Engineering, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Andrea Schmidt
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117, Berlin, Germany
| | - Elmar Behrmann
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Cryo Electron Microscopy, Charitéplatz 1, D-10117, Berlin, Germany.,Research Group Structural Dynamics of Proteins, Center of Advanced European Studies and Research (Caesar), Ludwig-Erhard-Allee 2, D-53175, Bonn, Germany.,Institute of Biochemistry-Structural Biochemistry, University of Cologne, Zuelpicher Straße 47, D-50674, Cologne, Germany
| | - Jörg Bürger
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Cryo Electron Microscopy, Charitéplatz 1, D-10117, Berlin, Germany.,UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195, Berlin, Germany
| | - Thorsten Mielke
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195, Berlin, Germany
| | - Christian M T Spahn
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Cryo Electron Microscopy, Charitéplatz 1, D-10117, Berlin, Germany
| | - Martin Heck
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Enzyme Kinetics, Charitéplatz 1, D-10117, Berlin, Germany
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany. .,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117, Berlin, Germany.
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13
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Zhang Z, He F, Constantine R, Baker ML, Baehr W, Schmid MF, Wensel TG, Agosto MA. Domain organization and conformational plasticity of the G protein effector, PDE6. J Biol Chem 2015; 290:12833-43. [PMID: 25809480 DOI: 10.1074/jbc.m115.647636] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Indexed: 11/06/2022] Open
Abstract
The cGMP phosphodiesterase of rod photoreceptor cells, PDE6, is the key effector enzyme in phototransduction. Two large catalytic subunits, PDE6α and -β, each contain one catalytic domain and two non-catalytic GAF domains, whereas two small inhibitory PDE6γ subunits allow tight regulation by the G protein transducin. The structure of holo-PDE6 in complex with the ROS-1 antibody Fab fragment was determined by cryo-electron microscopy. The ∼11 Å map revealed previously unseen features of PDE6, and each domain was readily fit with high resolution structures. A structure of PDE6 in complex with prenyl-binding protein (PrBP/δ) indicated the location of the PDE6 C-terminal prenylations. Reconstructions of complexes with Fab fragments bound to N or C termini of PDE6γ revealed that PDE6γ stretches from the catalytic domain at one end of the holoenzyme to the GAF-A domain at the other. Removal of PDE6γ caused dramatic structural rearrangements, which were reversed upon its restoration.
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Affiliation(s)
- Zhixian Zhang
- From the Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 and
| | - Feng He
- From the Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 and
| | - Ryan Constantine
- Department of Ophthalmology, Moran Eye Center, University of Utah, Salt Lake City, Utah 84132
| | - Matthew L Baker
- From the Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 and
| | - Wolfgang Baehr
- Department of Ophthalmology, Moran Eye Center, University of Utah, Salt Lake City, Utah 84132
| | - Michael F Schmid
- From the Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 and
| | - Theodore G Wensel
- From the Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 and
| | - Melina A Agosto
- From the Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 and
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14
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Baehr W. Membrane protein transport in photoreceptors: the function of PDEδ: the Proctor lecture. Invest Ophthalmol Vis Sci 2014; 55:8653-66. [PMID: 25550383 DOI: 10.1167/iovs.14-16066] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
This lecture details the elucidation of cGMP phosphodiesterase (PDEδ), discovered 25 years ago by Joe Beavo at the University of Washington. PDEδ, once identified as a fourth PDE6 subunit, is now regarded as a promiscuous prenyl-binding protein and important chaperone of prenylated small G proteins of the Ras superfamily and prenylated proteins of phototransduction. Alfred Wittinghofer's group in Germany showed that PDEδ forms an immunoglobulin-like β-sandwich fold that is closely related in structure to other lipid-binding proteins, for example, Uncoordinated 119 (UNC119) and RhoGDI. His group cocrystallized PDEδ with ARL (Arf-like) 2(GTP), and later with farnesylated Rheb (ras homolog expressed in brain). PDEδ specifically accommodates farnesyl and geranylgeranyl moieties in the absence of bound protein. Germline deletion of the Pde6d gene encoding PDEδ impeded transport of rhodopsin kinase (GRK1) and PDE6 to outer segments, causing slowly progressing, recessive retinitis pigmentosa. A rare PDE6D null allele in human patients, discovered by Tania Attié-Bitach in France, specifically impeded trafficking of farnesylated phosphatidylinositol 3,4,5-trisphosphate (PIP3) 5-phosphatase (INPP5E) to cilia, causing severe syndromic ciliopathy (Joubert syndrome). Binding of cargo to PDEδ is controlled by Arf-like proteins, ARL2 and ARL3, charged with guanosine-5'-triphosphate (GTP). Arf-like proteins 2 and 3 are unprenylated small GTPases that serve as cargo displacement factors. The lifetime of ARL3(GTP) is controlled by its GTPase-activating protein, retinitis pigmentosa protein 2 (RP2), which accelerates GTPase activity up to 90,000-fold. RP2 null alleles in human patients are associated with severe X-linked retinitis pigmentosa (XLRP). Germline deletion of RP2 in mouse, however, causes only a mild form of XLRP. Absence of RP2 prolongs the activity of ARL3(GTP) that, in turn, impedes PDE6δ-cargo interactions and trafficking of prenylated protein to the outer segments. Hyperactive ARL3(GTP), acting as a hyperactive cargo displacement factor, is predicted to be key in the pathobiology of RP2-XLRP.
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Affiliation(s)
- Wolfgang Baehr
- Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, University of Utah, Salt Lake City, Utah, United StatesDepartment of Neurobiology and Anatomy, University of Utah Health Science Center, University of Utah, Salt Lake City, Utah, United StatesDepartment of Biology, University of Utah, Salt Lake City, Utah, United States
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15
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Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F. Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling. J Mol Biol 2014; 426:3713-3728. [PMID: 25149264 DOI: 10.1016/j.jmb.2014.07.033] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/01/2014] [Accepted: 07/28/2014] [Indexed: 11/20/2022]
Abstract
Photoreceptor phosphodiesterase (PDE6) is the central effector enzyme in visual excitation pathway in rod and cone photoreceptors. Its tight regulation is essential for the speed, sensitivity, recovery and adaptation of visual detection. Although major steps in the PDE6 activation/deactivation pathway have been identified, mechanistic understanding of PDE6 regulation is limited by the lack of knowledge about the molecular organization of the PDE6 holoenzyme (αβγγ). Here, we characterize the PDE6 holoenzyme by integrative structural determination of the PDE6 catalytic dimer (αβ), based primarily on chemical cross-linking and mass spectrometric analysis. Our models built from high-density cross-linking data elucidate a parallel organization of the two catalytic subunits, with juxtaposed α-helical segments within the tandem regulatory GAF domains to provide multiple sites for dimerization. The two catalytic domains exist in an open configuration when compared to the structure of PDE2 in the apo state. Detailed structural elements for differential binding of the γ-subunit to the GAFa domains of the α- and β-subunits are revealed, providing insight into the regulation of the PDE6 activation/deactivation cycle.
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Affiliation(s)
- Xiaohui Zeng-Elmore
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA
| | - Xiong-Zhuo Gao
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Xiu-Jun Zhang
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Katie A Kozacka
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Yang Tang
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA
| | - Robert J Chalkley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Rick H Cote
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Feixia Chu
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA.
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16
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Orban T, Jastrzebska B, Palczewski K. Structural approaches to understanding retinal proteins needed for vision. Curr Opin Cell Biol 2013; 27:32-43. [PMID: 24680428 DOI: 10.1016/j.ceb.2013.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 12/21/2022]
Abstract
The past decade has witnessed an impressive expansion of our knowledge of retinal photoreceptor signal transduction and the regulation of the visual cycle required for normal eyesight. Progress in human genetics and next generation sequencing technologies have revealed the complexity behind many inherited retinal diseases. Structural studies have markedly increased our understanding of the visual process. Moreover, technical innovations and improved methodologies in proteomics, macromolecular crystallization and high resolution imaging at different levels set the scene for even greater advances. Pharmacology combined with structural biology of membrane proteins holds great promise for developing innovative accessible therapies for millions robbed of their sight or progressing toward blindness.
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Affiliation(s)
- Tivadar Orban
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Beata Jastrzebska
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Krzysztof Palczewski
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA.
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17
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Zhang H, Constantine R, Frederick JM, Baehr W. The prenyl-binding protein PrBP/δ: a chaperone participating in intracellular trafficking. Vision Res 2012; 75:19-25. [PMID: 22960045 PMCID: PMC3514561 DOI: 10.1016/j.visres.2012.08.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/17/2012] [Accepted: 08/20/2012] [Indexed: 01/21/2023]
Abstract
Expressed ubiquitously, PrBP/δ functions as chaperone/co-factor in the transport of a subset of prenylated proteins. PrBP/δ features an immunoglobulin-like β-sandwich fold for lipid binding, and interacts with diverse partners. PrBP/δ binds both C-terminal C15 and C20 prenyl side chains of phototransduction polypeptides and small GTP-binding (G) proteins of the Ras superfamily. PrBP/δ also interacts with the small GTPases, ARL2 and ARL3, which act as release factors (GDFs) for prenylated cargo. Targeted deletion of the mouse Pde6d gene encoding PrBP/δ resulted in impeded trafficking to the outer segments of GRK1 and cone PDE6 which are predicted to be farnesylated and geranylgeranylated, respectively. Rod and cone transducin trafficking was largely unaffected. These trafficking defects produce progressive cone-rod dystrophy in the Pde6d(-/-) mouse.
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Affiliation(s)
- Houbin Zhang
- Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, 65 Mario Capecchi Dr., Salt Lake City UT 84132, USA
| | - Ryan Constantine
- Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, 65 Mario Capecchi Dr., Salt Lake City UT 84132, USA
- Graduate Program in Neuroscience, University of Utah Health Science Center, Salt Lake City UT 84132, USA
| | - Jeanne M. Frederick
- Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, 65 Mario Capecchi Dr., Salt Lake City UT 84132, USA
| | - Wolfgang Baehr
- Department of Ophthalmology, John A. Moran Eye Center, University of Utah Health Science Center, 65 Mario Capecchi Dr., Salt Lake City UT 84132, USA
- Department of Neurobiology and Anatomy, University of Utah Health Science Center, Salt Lake City UT 84132, USA
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, Utah 84112, USA
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18
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Maisel T, Joseph S, Mielke T, Bürger J, Schwarzinger S, Meyer O. The CoxD protein, a novel AAA+ ATPase involved in metal cluster assembly: hydrolysis of nucleotide-triphosphates and oligomerization. PLoS One 2012; 7:e47424. [PMID: 23077613 PMCID: PMC3471820 DOI: 10.1371/journal.pone.0047424] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 09/17/2012] [Indexed: 11/18/2022] Open
Abstract
CoxD of the α-proteobacterium Oligotropha carboxidovorans is a membrane protein which is involved in the posttranslational biosynthesis of the [CuSMoO₂] cluster in the active site of the enzyme CO dehydrogenase. The bacteria synthesize CoxD only in the presence of CO. Recombinant CoxD produced in E. coli K38 pGP1-2/pETMW2 appeared in inclusion bodies from where it was solubilized by urea and refolded by stepwise dilution. Circular dichroism spectroscopy revealed the presence of secondary structural elements in refolded CoxD. CoxD is a P-loop ATPase of the AAA-protein family. Refolded CoxD catalyzed the hydrolysis of MgATP yielding MgADP and inorganic phosphate at a 1∶1∶1 molar ratio. The reaction was inhibited by the slow hydrolysable MgATP-γ-S. GTPase activity of CoxD did not exceed 2% of the ATPase activity. Employing different methods (non linear regression, Hanes and Woolf, Lineweaver-Burk), preparations of CoxD revealed a mean K(M) value of 0.69±0.14 mM ATP and an apparent V(max) value of 19.3±2.3 nmol ATP hydrolyzed min⁻¹ mg⁻¹. Sucrose density gradient centrifugation and gel filtration showed that refolded CoxD can exist in various multimeric states (2-mer, 4-mer or 6-mer), preferentially as hexamer or dimer. Within weeks the hexamer dissociates into the dimer, a process which can be reversed by MgATP or MgATP-γ-S within hours. Only the hexamers and the dimers exhibited MgATPase activity. Transmission electron microscopy of negatively stained CoxD preparations revealed distinct particles within a size range of 10-16 nm, which further corroborates the oligomeric organization. The 3D structure of CoxD was modeled with the 3D structure of BchI from Rhodobacter capsulatus as template. It has the key elements of an AAA+ domain in the same arrangement and at same positions as in BchI and displays the characteristic inserts of the PS-II-insert clade. Possible functions of CoxD in [CuSMoO₂] cluster assembly are discussed.
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Affiliation(s)
- Tobias Maisel
- Chair of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Stephanie Joseph
- Chair of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Thorsten Mielke
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Jörg Bürger
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Stephan Schwarzinger
- Chair of Biopolymers, University of Bayreuth, Bayreuth, Germany
- The Bayreuth Research Center for Bio-Macromolecules, Bayreuth, Germany
| | - Ortwin Meyer
- Chair of Microbiology, University of Bayreuth, Bayreuth, Germany
- The Bayreuth Research Center for Bio-Macromolecules, Bayreuth, Germany
- * E-mail:
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19
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Cahill KB, Quade JH, Carleton KL, Cote RH. Identification of amino acid residues responsible for the selectivity of tadalafil binding to two closely related phosphodiesterases, PDE5 and PDE6. J Biol Chem 2012; 287:41406-16. [PMID: 23033484 DOI: 10.1074/jbc.m112.389189] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 11 families of the Class I cyclic nucleotide phosphodiesterases (PDEs) are critical for regulation of cyclic nucleotide signaling. PDE5 (important in regulating vascular smooth muscle contraction) and PDE6 (responsible for regulating visual transduction in vertebrate photoreceptors) are structurally similar but have several functional differences whose structural basis is poorly understood. Using evolutionary trace analysis and structural homology modeling in conjunction with site-directed mutagenesis, we have tested the hypothesis that class-specific differences between PDE5 and PDE6 account for the biochemical and pharmacological differences in the two enzyme families. Replacing human PDE5 residues in the M-loop region of the binding site for the PDE5-selective inhibitor tadalafil (Cialis®) with the corresponding class-specific cone PDE6 residues (P773E, I778V, E780L, F787W, E796V, D803P, L804M, N806D, I813L, S815K) reduces tadalafil binding affinity to levels characteristic of PDE6. These mutations fail to alter vardenafil (Levitra®) affinity for the active site. Class-specific differences in PDE5 versus cone PDE6 that contribute to the accelerated catalytic efficiency of PDE6 were identified but required heterologous expression of full-length PDE5 constructs. Introduction of PDE6 residues into the background of the PDE5 protein sequence often led to loss of catalytic activity and reduced protein solubility, supporting the idea that multiple structural elements of PDE6 are highly susceptible to misfolding during heterologous expression. This work validates the use of PDE5 as a template to identify functional differences between PDE5 and PDE6 that will accelerate efforts to develop the next generation of PDE5-selective inhibitors with fewer adverse side effects resulting from PDE6 inhibition.
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Affiliation(s)
- Karyn B Cahill
- Department of Molecular, Cellular and Biomedical Sciences University of New Hampshire, Durham, New Hampshire 03824, USA
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20
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Matte SL, Laue TM, Cote RH. Characterization of conformational changes and protein-protein interactions of rod photoreceptor phosphodiesterase (PDE6). J Biol Chem 2012; 287:20111-21. [PMID: 22514270 DOI: 10.1074/jbc.m112.354647] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
As the central effector of visual transduction, the regulation of photoreceptor phosphodiesterase (PDE6) is controlled by both allosteric mechanisms and extrinsic binding partners. However, the conformational changes and interactions of PDE6 with known interacting proteins are poorly understood. Using a fluorescence detection system for the analytical ultracentrifuge, we examined allosteric changes in PDE6 structure and protein-protein interactions with its inhibitory γ-subunit, the prenyl-binding protein (PrBP/δ), and activated transducin. In solution, the PDE6 catalytic dimer (Pαβ) exhibits a more asymmetric shape (axial ratio of 6.6) than reported previously. The inhibitory Pγ subunit behaves as an intrinsically disordered protein in solution but binds with high affinity to the catalytic dimer to reconstitute the holoenzyme without a detectable change in shape. Whereas the closely related PDE5 homodimer undergoes a significant change in its sedimentation properties upon cGMP binding to its regulatory cGMP binding site, no such change was detected upon ligand binding to the PDE6 catalytic dimer. However, when Pαβ was reconstituted with Pγ truncation mutants lacking the C-terminal inhibitory region, cGMP-dependent allosteric changes were observed. PrBP/δ bound to the PDE6 holoenzyme with high affinity (K(D) = 6.2 nm) and induced elongation of the protein complex. Binding of activated transducin to PDE6 holoenzyme resulted in a concentration-dependent increase in the sedimentation coefficient, reflecting a dynamic equilibrium between transducin and PDE6. We conclude that allosteric regulation of PDE6 is more complex than for PDE5 and is dependent on interactions of regions of Pγ with the catalytic dimer.
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Affiliation(s)
- Suzanne L Matte
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, USA
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21
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Abstract
Visual perception in humans occurs through absorption of electromagnetic radiation from 400 to 780 nm by photoreceptors in the retina. A photon of visible light carries a sufficient amount of energy to cause, when absorbed, a cis,trans-geometric isomerization of the 11-cis-retinal chromophore, a vitamin A derivative bound to rhodopsin and cone opsins of retinal photoreceptors. The unique biochemistry of these complexes allows us to reliably and reproducibly collect continuous visual information about our environment. Moreover, other nonconventional retinal opsins such as the circadian rhythm regulator melanopsin also initiate light-activated signaling based on similar photochemistry.
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Affiliation(s)
- Krzysztof Palczewski
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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22
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Baker BY, Palczewski K. Detergents stabilize the conformation of phosphodiesterase 6. Biochemistry 2011; 50:9520-31. [PMID: 21978030 DOI: 10.1021/bi2014695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Membrane-bound phosphodiesterase 6 (PDE6) plays an important role in visual signal transduction by regulating cGMP levels in rod photoreceptor cells. Our understanding of PDE6 catalysis and structure suffers from inadequate characterization of the α and β subunit catalytic core, interactions of the core with two intrinsically disordered, proteolysis-prone inhibitory PDEγ (Pγ) subunits, and binding of two types of isoprenyl-binding protein δ, called PrBP/δ, to the isoprenylated C-termini of the catalytic core. Structural studies of native PDE6 have been also been hampered by the lack of a heterologous expression system for the holoenzyme. In this work, we purified PDE6 in the presence of PrBP/δ and screened for additives and detergents that selectively suppress PDE6 basal activity while sparing that of the trypsin-activated enzyme. Some detergents removed PrBP/δ from the PDE complex, separating it from the holoenzyme after PDE6 purification. Additionally, selected detergents also significantly reduced the level of dissociation of PDE6 subunits, increasing their homogeneity and stabilizing the holoenzyme by substituting for its native membrane environment.
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Affiliation(s)
- Bo Y Baker
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
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23
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Abstract
Network Map States Transitions Functions Protein Classes Sequence Interactions Pathways Domains & Motifs Protein Structure Orthologs Sequence Interactions Pathways Domains & Motifs Protein Structure Orthologs Blast Data.
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Affiliation(s)
- Hannah J Gitschier
- Molecular, Cellular & Biomedical Sciences, University of New Hampshire, NH 03824, US
| | - Rick H Cote
- Molecular, Cellular & Biomedical Sciences, University of New Hampshire, NH 03824, US
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