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Hu Y, Li G, Zhao S, Dai J, Peng X, Zhao Q. Charge transfer characteristics in rhodopsin mimics during photoexcitation. Phys Chem Chem Phys 2024; 26:26004-26011. [PMID: 39370953 DOI: 10.1039/d4cp02970d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
To gain insights into the light-harvesting capabilities of the chromophores, it is essential to understand their molecular and electronic structures within their natural chemical or biological contexts. Rhodopsins display varied absorption characteristics due to the interaction between the chromophore retinal and its surrounding protein environments. In this study, we employed a quantum mechanics/molecular mechanics approach to examine a series of artificially designed rhodopsin mimics based on human cellular retinol acid binding protein 2 (hCRABP II). We elucidated the electron transfer within the all-trans protonated Schiff base upon light excitation, and our calculated absorption spectra show well consistency with the experimental result. Furthermore, the interaction mechanisms between the chromophore and the protein were investigated, and the relationship between the blueshifts and redshifts in the absorption spectra was analyzed. Our calculation demonstrates that the blueshifts and redshifts in the rhodopsin mimics correlate well with attractive (such as the hydrogen bonds or electrostatic interactions) and repulsive interactions (such as the steric effects) between the chromophore and the protein environment, respectively. These findings could provide hints for designing rhodopsin with absorption spectra at different wavelengths.
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Affiliation(s)
- Yongnan Hu
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Gaoshang Li
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Siteng Zhao
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Jin Dai
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Xubiao Peng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
- Beijing Academy of Quantum Information Sciences, Beijing 100193, China.
| | - Qing Zhao
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
- Beijing Academy of Quantum Information Sciences, Beijing 100193, China.
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2
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Brooks C, Kolson D, Sechrest E, Chuah J, Schupp J, Billington N, Deng WT, Smith D, Sokolov M. Therapeutic potential of archaeal unfoldase PANet and the gateless T20S proteasome in P23H rhodopsin retinitis pigmentosa mice. PLoS One 2024; 19:e0308058. [PMID: 39361629 PMCID: PMC11449290 DOI: 10.1371/journal.pone.0308058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 09/19/2024] [Indexed: 10/05/2024] Open
Abstract
Neurodegenerative diseases are characterized by the presence of misfolded and aggregated proteins which are thought to contribute to the development of the disease. In one form of inherited blinding disease, retinitis pigmentosa, a P23H mutation in the light-sensing receptor, rhodopsin causes rhodopsin misfolding resulting in complete vision loss. We investigated whether a xenogeneic protein-unfolding ATPase (unfoldase) from thermophilic Archaea, termed PANet, could counteract the proteotoxicity of P23H rhodopsin. We found that PANet increased the number of surviving photoreceptors in P23H rhodopsin mice and recognized rhodopsin as a substate in vitro. This data supports the feasibility and efficacy of using a xenogeneic unfoldase as a therapeutic approach in mouse models of human neurodegenerative diseases. We also showed that an archaeal proteasome, called the T20S can degrade rhodopsin in vitro and demonstrated that it is feasible and safe to express gateless T20S proteasomes in vivo in mouse rod photoreceptors. Expression of archaeal proteasomes may be an effective therapeutic approach to stimulate protein degradation in retinopathies and neurodegenerative diseases with protein-misfolding etiology.
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Affiliation(s)
- Celine Brooks
- Department of Ophthalmology, West Virginia University, Morgantown, West Virginia, United States of America
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - Douglas Kolson
- Department of Ophthalmology, West Virginia University, Morgantown, West Virginia, United States of America
| | - Emily Sechrest
- Department of Ophthalmology, West Virginia University, Morgantown, West Virginia, United States of America
| | - Janelle Chuah
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - Jane Schupp
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - Neil Billington
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - Wen-Tao Deng
- Department of Ophthalmology, West Virginia University, Morgantown, West Virginia, United States of America
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - David Smith
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, United States of America
- Department of Neuroscience, West Virginia University, Morgantown, West Virginia, United States of America
| | - Maxim Sokolov
- Department of Ophthalmology, West Virginia University, Morgantown, West Virginia, United States of America
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, United States of America
- Department of Neuroscience, West Virginia University, Morgantown, West Virginia, United States of America
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3
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Carrero L, Antequera D, Municio C, Carro E. Circadian rhythm disruption and retinal dysfunction: a bidirectional link in Alzheimer's disease? Neural Regen Res 2024; 19:1967-1972. [PMID: 38227523 DOI: 10.4103/1673-5374.390962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/07/2023] [Indexed: 01/17/2024] Open
Abstract
Dysfunction in circadian rhythms is a common occurrence in patients with Alzheimer's disease. A predominant function of the retina is circadian synchronization, carrying information to the brain through the retinohypothalamic tract, which projects to the suprachiasmatic nucleus. Notably, Alzheimer's disease hallmarks, including amyloid-β, are present in the retinas of Alzheimer's disease patients, followed/associated by structural and functional disturbances. However, the mechanistic link between circadian dysfunction and the pathological changes affecting the retina in Alzheimer's disease is not fully understood, although some studies point to the possibility that retinal dysfunction could be considered an early pathological process that directly modulates the circadian rhythm.
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Affiliation(s)
- Laura Carrero
- Group of Neurodegenerative Diseases, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain; Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
- PhD Program in Neuroscience, Autonoma de Madrid University, Madrid, Spain
| | - Desireé Antequera
- Neurobiology of Alzheimer's Disease Unit, Functional Unit for Research into Chronic Diseases, Instituto de Salud Carlos III, Madrid, Spain; Network Centre for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
| | - Cristina Municio
- Group of Neurodegenerative Diseases, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain; Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
| | - Eva Carro
- Neurobiology of Alzheimer's Disease Unit, Functional Unit for Research into Chronic Diseases, Instituto de Salud Carlos III, Madrid, Spain; Network Centre for Biomedical Research in Neurodegenerative Diseases (CIBERNED), ISCIII, Madrid, Spain
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4
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Cvekl A, Vijg J. Aging of the eye: Lessons from cataracts and age-related macular degeneration. Ageing Res Rev 2024; 99:102407. [PMID: 38977082 DOI: 10.1016/j.arr.2024.102407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/18/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024]
Abstract
Aging is the greatest risk factor for chronic human diseases, including many eye diseases. Geroscience aims to understand the effects of the aging process on these diseases, including the genetic, molecular, and cellular mechanisms that underlie the increased risk of disease over the lifetime. Understanding of the aging eye increases general knowledge of the cellular physiology impacted by aging processes at various biological extremes. Two major diseases, age-related cataract and age-related macular degeneration (AMD) are caused by dysfunction of the lens and retina, respectively. Lens transparency and light refraction are mediated by lens fiber cells lacking nuclei and other organelles, which provides a unique opportunity to study a single aging hallmark, i.e., loss of proteostasis, within an environment of limited metabolism. In AMD, local dysfunction of the photoreceptors/retinal pigmented epithelium/Bruch's membrane/choriocapillaris complex in the macula leads to the loss of photoreceptors and eventually loss of central vision, and is driven by nearly all the hallmarks of aging and shares features with Alzheimer's disease, Parkinson's disease, cardiovascular disease, and diabetes. The aging eye can function as a model for studying basic mechanisms of aging and, vice versa, well-defined hallmarks of aging can be used as tools to understand age-related eye disease.
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Affiliation(s)
- Ales Cvekl
- Departments of Genetics and Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Jan Vijg
- Departments of Genetics and Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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5
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Quan J, Yan H, Periyasami G, Li H. A Visible-Light Regulated ATP Transport in Retinal-Modified Pillar[6]arene Layer-by-Layer Self-Assembled Sub-Nanochannel. Chemistry 2024; 30:e202401045. [PMID: 38693094 DOI: 10.1002/chem.202401045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/16/2024] [Accepted: 04/29/2024] [Indexed: 05/03/2024]
Abstract
Natural light-responsive rhodopsins play a critical role in visual conversion, signal transduction, energy transmission, etc., which has aroused extensive interest in the past decade. Inspired by these gorgeous works of living beings, scientists have constructed various biomimetic light-responsive nanochannels to mimic the behaviors of rhodopsins. However, it is still challenging to build stimuli-responsive sub-nanochannels only regulated by visible light as the rhodopsins are always at the sub-nanometer level and regulated by visible light. Pillar[6]arenes have an open cavity of 6.7 Å, which can selectively recognize small organic molecules. They can be connected to ions of ammonium or carboxylate groups on the rims. Therefore, we designed and synthesized the amino and carboxyl-derived side chains of pillar[6]arenes with opposite charges. The sub-nanochannels were constructed through the electrostatic interaction of layer-by-layer self-assembled amino and carboxyl-derived pillar[6]arenes. Then, the natural chromophore of the retinal with visible light-responsive performance was modified on the upper edge of the sub-nanochannel to realize the visible light switched on and off. Finally, we successfully constructed a visible light-responsive sub-nanochannel, providing a novel method for regulating the selective transport of energy-donating molecules of ATP.
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Affiliation(s)
- Jiaxin Quan
- Department of Chemistry and Environmental Engineering, Hanjiang Normal University, Shiyan, 442000, China
| | - Hewei Yan
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, 330063, P.R. China
| | - Govindasami Periyasami
- Department of Chemistry, College of Science, King Saud University, P.O.Box 2455, Riyadh, 11451, Saudi Arabia
| | - Haibing Li
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, 430079, P.R. China
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6
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Lucock MD. Vitomics: A novel paradigm for examining the role of vitamins in human biology. Bioessays 2023; 45:e2300127. [PMID: 37727095 DOI: 10.1002/bies.202300127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
The conventional view of vitamins reflects a diverse group of small molecules that facilitate critical aspects of metabolism and prevent potentially fatal deficiency syndromes. However, vitamins also contribute to the shaping and maintenance of the human phenome over lifecycle and evolutionary timescales, enabling a degree of phenotypic plasticity that operates to allow adaptive responses that are appropriate to key periods of sensitivity (i.e., epigenetic response during prenatal development within the lifecycle or as an evolved response to environmental challenge over a great many lifecycles). Individually, vitamins are important, but their effect is often based on nutrient-nutrient (vitamin-vitamin), nutrient-gene (vitamin-gene), and gene-gene interactions, and the environmental influence of shifting geophysical cycles, as well as evolving cultural practices. These ideas will be explored within what I refer to as the "adaptive vitome (vitomics)" paradigm.
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Affiliation(s)
- Mark D Lucock
- School of Environmental & Life Sciences, University of Newcastle, Ourimbah, NSW, Australia
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7
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Bohn T, de Lera AR, Landrier JF, Rühl R. Carotenoid metabolites, their tissue and blood concentrations in humans and further bioactivity via retinoid receptor-mediated signalling. Nutr Res Rev 2023; 36:498-511. [PMID: 36380523 DOI: 10.1017/s095442242200021x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Many epidemiological studies have emphasised the relation between carotenoid dietary intake and their circulating concentrations and beneficial health effects, such as lower risk of cardiometabolic diseases and cancer. However, there is dispute as to whether the attributed health benefits are due to native carotenoids or whether they are instead induced by their metabolites. Several categories of metabolites have been reported, most notably involving (a) modifications at the cyclohexenyl ring or the polyene chain, such as epoxides and geometric isomers, (b) excentric cleavage metabolites with alcohol-, aldehyde- or carboxylic acid-functional groups or (c) centric cleaved metabolites with additional hydroxyl, aldehyde or carboxyl functionalities, not counting their potential phase-II glucuronidated / sulphated derivatives. Of special interest are the apo-carotenoids, which originate in the intestine and other tissues from carotenoid cleavage by β-carotene oxygenases 1/2 in a symmetrical / non-symmetrical fashion. These are more water soluble and more electrophilic and, therefore, putative candidates for interactions with transcription factors such as NF-kB and Nrf2, as well as ligands for RAR-RXR nuclear receptor interactions. In this review, we discuss in vivo detected apo-carotenoids, their reported tissue concentrations, and potential associated health effects, focusing exclusively on the human situation and based on quantified / semi-quantified carotenoid metabolites proven to be present in humans.
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Affiliation(s)
- Torsten Bohn
- Nutrition and Health Research Group, Precision Health Department, Luxembourg Institute of Health, 1 A-B, rue Thomas Edison, L-1445, Strassen, Luxembourg
| | - Angel R de Lera
- Departmento de Química Orgánica, Facultade de Química, CINBIO and IBIV, Universidade de Vigo, 36310 Vigo, Spain
| | | | - Ralph Rühl
- CISCAREX UG, Berlin, Germany
- Paprika Bioanalytics BT, Debrecen, Hungary
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8
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Prajapati B, Ambhore MD, Dang DK, Chmielewski PJ, Lis T, Gómez-García CJ, Zimmerman PM, Stępień M. Tetrafluorenofulvalene as a sterically frustrated open-shell alkene. Nat Chem 2023; 15:1541-1548. [PMID: 37783726 PMCID: PMC10624625 DOI: 10.1038/s41557-023-01341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023]
Abstract
Electronic and steric effects are known to greatly influence the structure, characteristics and reactivity of organic compounds. A typical π bond is weakened by oxidation (corresponding to the removal of electrons from bonding orbitals), by reduction (through addition of electrons to antibonding orbitals) and by unpairing of the bonding electrons, such as in the triplet state. Here we describe tetrafluorenofulvalene (TFF), a twisted, open-shell alkene for which these general rules do not hold. Through the synthesis, experimental characterization and computational analysis of its charged species spanning seven redox states, the central alkene bond in TFF is shown to become substantially stronger in the tri- and tetraanion, generated by chemical reduction. Furthermore, although its triplet state contains a weaker alkene bond than the singlet, in the quintet state its bond order increases substantially, yielding a flatter structure. This behaviour originates from the doubly bifurcated topology of the underlying spin system and can be rationalized by the balancing effects of benzenoid aromaticity and spin pairing.
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Affiliation(s)
| | | | - Duy-Khoi Dang
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Tadeusz Lis
- Wydział Chemii, Uniwersytet Wrocławski, Wrocław, Poland
| | - Carlos J Gómez-García
- Departamento de Química Inorgánica and Instituto de Ciencia Molecular, Universidad de Valencia, Paterna, Spain
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Marcin Stępień
- Wydział Chemii, Uniwersytet Wrocławski, Wrocław, Poland.
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9
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Bouhraoua A, Khamaysa O, Selatnia I, Lgaz H, Sid A, Zeghache H, Ebenso EE, Lee HS. Experimental and computational studies on the corrosion mitigation properties of a newly synthesized imine derivative for carbon steel in HCl medium. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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10
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Wu KY, Kulbay M, Toameh D, Xu AQ, Kalevar A, Tran SD. Retinitis Pigmentosa: Novel Therapeutic Targets and Drug Development. Pharmaceutics 2023; 15:685. [PMID: 36840007 PMCID: PMC9963330 DOI: 10.3390/pharmaceutics15020685] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/12/2023] [Accepted: 02/16/2023] [Indexed: 02/19/2023] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of hereditary diseases characterized by progressive degeneration of retinal photoreceptors leading to progressive visual decline. It is the most common type of inherited retinal dystrophy and has a high burden on both patients and society. This condition causes gradual loss of vision, with its typical manifestations including nyctalopia, concentric visual field loss, and ultimately bilateral central vision loss. It is one of the leading causes of visual disability and blindness in people under 60 years old and affects over 1.5 million people worldwide. There is currently no curative treatment for people with RP, and only a small group of patients with confirmed RPE65 mutations are eligible to receive the only gene therapy on the market: voretigene neparvovec. The current therapeutic armamentarium is limited to retinoids, vitamin A supplements, protection from sunlight, visual aids, and medical and surgical interventions to treat ophthalmic comorbidities, which only aim to slow down the progression of the disease. Considering such a limited therapeutic landscape, there is an urgent need for developing new and individualized therapeutic modalities targeting retinal degeneration. Although the heterogeneity of gene mutations involved in RP makes its target treatment development difficult, recent fundamental studies showed promising progress in elucidation of the photoreceptor degeneration mechanism. The discovery of novel molecule therapeutics that can selectively target specific receptors or specific pathways will serve as a solid foundation for advanced drug development. This article is a review of recent progress in novel treatment of RP focusing on preclinical stage fundamental research on molecular targets, which will serve as a starting point for advanced drug development. We will review the alterations in the molecular pathways involved in the development of RP, mainly those regarding endoplasmic reticulum (ER) stress and apoptotic pathways, maintenance of the redox balance, and genomic stability. We will then discuss the therapeutic approaches under development, such as gene and cell therapy, as well as the recent literature identifying novel potential drug targets for RP.
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Affiliation(s)
- Kevin Y. Wu
- Division of Ophthalmology, Department of Surgery, University of Sherbrooke, Sherbrooke, QC J1G 2E8, Canada
| | - Merve Kulbay
- Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Dana Toameh
- Faculty of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
| | - An Qi Xu
- Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Ananda Kalevar
- Division of Ophthalmology, Department of Surgery, University of Sherbrooke, Sherbrooke, QC J1G 2E8, Canada
| | - Simon D. Tran
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC H3A 1G1, Canada
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Willeford K. The Luminescence Hypothesis of Olfaction. SENSORS (BASEL, SWITZERLAND) 2023; 23:1333. [PMID: 36772376 PMCID: PMC9919928 DOI: 10.3390/s23031333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
A new hypothesis for the mechanism of olfaction is presented. It begins with an odorant molecule binding to an olfactory receptor. This is followed by the quantum biology event of inelastic electron tunneling as has been suggested with both the vibration and swipe card theories. It is novel in that it is not concerned with the possible effects of the tunneled electrons as has been discussed with the previous theories. Instead, the high energy state of the odorant molecule in the receptor following inelastic electron tunneling is considered. The hypothesis is that, as the high energy state decays, there is fluorescence luminescence with radiative emission of multiple photons. These photons pass through the supporting sustentacular cells and activate a set of olfactory neurons in near-simultaneous timing, which provides the temporal basis for the brain to interpret the required complex combinatorial coding as an odor. The Luminescence Hypothesis of Olfaction is the first to present the necessity of or mechanism for a 1:3 correspondence of odorant molecule to olfactory nerve activations. The mechanism provides for a consistent and reproducible time-based activation of sets of olfactory nerves correlated to an odor. The hypothesis has a biological precedent: an energy feasibility assessment is included, explaining the anosmia seen with COVID-19, and can be confirmed with existing laboratory techniques.
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Affiliation(s)
- Kenneth Willeford
- Coastal Carolinas Integrated Medicine, 10 Doctors Circle, STE 2, Supply, NC 28462, USA
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12
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Chen C, Yang K, He D, Yang B, Tao L, Chen J, Wu Y. Induction of ferroptosis by HO-1 contributes to retinal degeneration in mice with defective clearance of all-trans-retinal. Free Radic Biol Med 2023; 194:245-254. [PMID: 36509314 DOI: 10.1016/j.freeradbiomed.2022.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
The accumulation of all-trans-retinal (atRAL) in photoreceptors and the retinal pigment epithelium (RPE), which is induced by chaos in visual (retinoid) cycle, is closely associated with the pathogenesis of dry age-related macular degeneration (AMD) and autosomal recessive Stargardt's disease (STGD1). Although we have reported that the induction of ferroptosis by atRAL is an important cause of photoreceptor loss, but its mechanisms still remain unclear. In this study, we identified heme oxygenase-1 (HO-1) as an inducer of photoreceptor ferroptosis elicited by atRAL. In atRAL-loaded photoreceptor cells, inhibition of Kelch-like ECH-associated protein 1 (KEAP1) at least in part by reactive oxygen species (ROS) production evoked the release of nuclear factor-erythroid 2-related factor-2 (NRF2) from KEAP1, followed by the translocation of active NRF2 into the nucleus where it promoted the transcription of the Ho-1 gene, thereby leading to HO-1 overexpression in the cytosol. A significant elevation of Fe2+ levels in photoreceptor cells resulted from activation of HO-1 by atRAL, and it facilitated ROS overproduction and then triggered ferroptotic cell death through ROS-mediated lipid peroxidation. Both treatment with HO-1 repressor Zinc protoporphyrin IX (ZnPP) and knockout of Ho-1 gene clearly rescued photoreceptor cells against ferroptosis arising from atRAL overload. Light-exposed Abca4-/-Rdh8-/- mice rapidly display severe defects in atRAL clearance, and serve as an acute model of dry AMD and STGD1. HO-1 activation was distinctly observed in neural retina of Abca4-/-Rdh8-/- mice after exposure to light, and it was visibly relieved by intraperitoneally injected ferroptosis inhibitor ferrostatin-1. More notably, intraperitoneal administration of ZnPP effectively alleviated both photoreceptor degeneration and RPE atrophy in Abca4-/-Rdh8-/- mice in response to light exposure by repressing HO-1-mediated ferroptosis. Our study suggests that HO-1 is a key factor that regulates atRAL-induced ferroptosis in photoreceptors and the RPE, and its inhibition may hold promises for the therapy of dry AMD and STGD1.
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Affiliation(s)
- Chao Chen
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Fujian Engineering and Research Center of Eye Regenerative Medicine, Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Eye Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Kunhuan Yang
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Fujian Engineering and Research Center of Eye Regenerative Medicine, Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Eye Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Danxue He
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Fujian Engineering and Research Center of Eye Regenerative Medicine, Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Eye Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Bo Yang
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Fujian Engineering and Research Center of Eye Regenerative Medicine, Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Eye Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Lei Tao
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Fujian Engineering and Research Center of Eye Regenerative Medicine, Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Eye Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jingmeng Chen
- School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yalin Wu
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Fujian Engineering and Research Center of Eye Regenerative Medicine, Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Eye Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, China; Shenzhen Research Institute of Xiamen University, Shenzhen, 518063, Guangdong, China; Xiamen Eye Center of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361001, Fujian, China.
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13
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The Role of G Protein-Coupled Receptor Kinase 6 Regulation in Inflammation and Pain. Int J Mol Sci 2022; 23:ijms232415880. [PMID: 36555521 PMCID: PMC9784940 DOI: 10.3390/ijms232415880] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
The G protein-coupled receptor kinase 6 is associated with inflammation and pathological pain. Impairment of GRK6 expression was described in chronic inflammatory diseases such as rheumatoid arthritis and this was shown to be accompanied by an imbalance of downstream signaling pathways. Here, we discuss novel aspects of GRK6 interaction and its impact upon hyperalgesia and inflammatory processes. In this review, we compile important findings concerning GRK6 regulation for a better pathophysiological understanding of the intracellular interaction in the context of inflammation and show clinical implications-for example, the identification of possible therapy goals in the treatment of chronic inflammatory hyperalgesia.
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14
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Guo X, Wang H, Xu J, Hua H. Impacts of vitamin A deficiency on biological rhythms: Insights from the literature. Front Nutr 2022; 9:886244. [PMID: 36466383 PMCID: PMC9718491 DOI: 10.3389/fnut.2022.886244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 11/02/2022] [Indexed: 03/21/2024] Open
Abstract
Vitamin A is essential for brain function, in addition to its important roles in vision, immunity, and reproduction. Previous studies have shown that retinoic acid (RA), the bioactive form of vitamin A, is involved in the regulation of various intracellular responses related to biological rhythms. RA is reported to affect the circadian rhythm by binding to RA receptors, such as receptors in the circadian feedback loops in the mammalian suprachiasmatic nucleus. However, evidence of the impacts of vitamin A deficiency (VAD) on biological rhythms is limited, and most of the related studies were conducted on animals. In this review, we described the physiological functions of biological rhythms and physiological pathways/molecular mechanisms regulating the biological rhythms. We then discussed the current understanding of the associations of VAD with biological rhythm disorders/diseases (sleep disorders, impairments in learning/memory, emotional disorders, and other immune or metabolism diseases) and summarized the currently proposed mechanisms (mainly by retinoid nuclear receptors and related proteins) for the associations. This review may help recognize the role of VAD in biological rhythm disorders and stimulate clinical or epidemiological studies to confirm the findings of related animal studies.
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Affiliation(s)
- Xiangrong Guo
- Shanghai Key Laboratory of Embryo Original Diseases, The International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Wang
- MOE-Shanghai Key Lab of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Xu
- Shanghai Key Laboratory of Embryo Original Diseases, The International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Hua
- Shanghai Key Laboratory of Embryo Original Diseases, The International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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15
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Sudarkova SM, Ioffe IN. E/ Z photoisomerization pathway in pristine and fluorinated di(3-furyl)ethenes. Phys Chem Chem Phys 2022; 24:23749-23757. [PMID: 36156663 DOI: 10.1039/d2cp02563a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report an XMCQDPT2 study of the E/Z photoisomerization in a series of fluorinated di(3-furyl)ethenes (3DFEs). Upon excitation, pristine and low-fluorinated 3DFE show conventional behavior of many diarylethenes: unhindered twisting motion toward the pyramidalized zwitterionic state where relaxation to the ground state occurs. However, deep fluorination of 3DFEs can hamper E-to-Z isomerization by giving rise to an alternative excited-state relaxation pathway: an out-of-plane motion of a ring fluorine atom. Importantly, the case of fluorinated 3DFEs reveals serious deficiencies of the popular TDDFT approach. With some commonly used exchange-correlation functionals, the alternative relaxation pathway is not reproduced and, moreover, an irrelevant ring rotation coordinate is predicted instead. Nevertheless, TDDFT remains qualitatively adequate for the E-to-Z twisting coordinate taken alone.
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Affiliation(s)
- Svetlana M Sudarkova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Ilya N Ioffe
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia.
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16
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Majumdar S, Roy AK. Recent Advances in Cartesian-Grid DFT in Atoms and Molecules. Front Chem 2022; 10:926916. [PMID: 35936092 PMCID: PMC9354079 DOI: 10.3389/fchem.2022.926916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022] Open
Abstract
In the past several decades, density functional theory (DFT) has evolved as a leading player across a dazzling variety of fields, from organic chemistry to condensed matter physics. The simple conceptual framework and computational elegance are the underlying driver for this. This article reviews some of the recent developments that have taken place in our laboratory in the past 5 years. Efforts are made to validate a viable alternative for DFT calculations for small to medium systems through a Cartesian coordinate grid- (CCG-) based pseudopotential Kohn-Sham (KS) DFT framework using LCAO-MO ansatz. In order to legitimize its suitability and efficacy, at first, electric response properties, such as dipole moment ( μ ), static dipole polarizability ( α ), and first hyperpolarizability ( β ), are calculated. Next, we present a purely numerical approach in CCG for proficient computation of exact exchange density contribution in certain types of orbital-dependent density functionals. A Fourier convolution theorem combined with a range-separated Coulomb interaction kernel is invoked. This takes motivation from a semi-numerical algorithm, where the rate-deciding factor is the evaluation of electrostatic potential. Its success further leads to a systematic self-consistent approach from first principles, which is desirable in the development of optimally tuned range-separated hybrid and hyper functionals. Next, we discuss a simple, alternative time-independent DFT procedure, for computation of single-particle excitation energies, by means of "adiabatic connection theorem" and virial theorem. Optical gaps in organic chromophores, dyes, linear/non-linear PAHs, and charge transfer complexes are faithfully reproduced. In short, CCG-DFT is shown to be a successful route for various practical applications in electronic systems.
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Affiliation(s)
| | - Amlan K. Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
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17
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Lewandowski D, Sander CL, Tworak A, Gao F, Xu Q, Skowronska-Krawczyk D. Dynamic lipid turnover in photoreceptors and retinal pigment epithelium throughout life. Prog Retin Eye Res 2022; 89:101037. [PMID: 34971765 PMCID: PMC10361839 DOI: 10.1016/j.preteyeres.2021.101037] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022]
Abstract
The retinal pigment epithelium-photoreceptor interphase is renewed each day in a stunning display of cellular interdependence. While photoreceptors use photosensitive pigments to convert light into electrical signals, the RPE supports photoreceptors in their function by phagocytizing shed photoreceptor tips, regulating the blood retina barrier, and modulating inflammatory responses, as well as regenerating the 11-cis-retinal chromophore via the classical visual cycle. These processes involve multiple protein complexes, tightly regulated ligand-receptors interactions, and a plethora of lipids and protein-lipids interactions. The role of lipids in maintaining a healthy interplay between the RPE and photoreceptors has not been fully delineated. In recent years, novel technologies have resulted in major advancements in understanding several facets of this interplay, including the involvement of lipids in phagocytosis and phagolysosome function, nutrient recycling, and the metabolic dependence between the two cell types. In this review, we aim to integrate the complex role of lipids in photoreceptor and RPE function, emphasizing the dynamic exchange between the cells as well as discuss how these processes are affected in aging and retinal diseases.
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Affiliation(s)
- Dominik Lewandowski
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA
| | - Christopher L Sander
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA; Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Aleksander Tworak
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA
| | - Fangyuan Gao
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA
| | - Qianlan Xu
- Department of Physiology and Biophysics, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA
| | - Dorota Skowronska-Krawczyk
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA; Department of Physiology and Biophysics, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA.
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18
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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19
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Poddar H, Heyes DJ, Zhang S, Hardman SJ, Sakuma M, Scrutton NS. An unusual light-sensing function for coenzyme B 12 in bacterial transcription regulator CarH. Methods Enzymol 2022; 668:349-372. [PMID: 35589201 DOI: 10.1016/bs.mie.2021.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Coenzyme B12 is one of the most complex cofactors found in nature and synthesized de novo by certain groups of bacteria. Although its use in various enzymatic reactions is well characterized, only recently an unusual light-sensing function has been ascribed to coenzyme B12. It has been reported that the coenzyme B12 binding protein CarH, found in the carotenoid biosynthesis pathway of several thermostable bacteria, binds to the promoter region of DNA and suppresses transcription. To overcome the harmful effects of light-induced damage in the cells, CarH releases DNA in the presence of light and promotes transcription and synthesis of carotenoids, thereby working as a photoreceptor. CarH is able to achieve this by exploiting the photosensitive nature of the CoC bond between the adenosyl moiety and the cobalt atom in the coenzyme B12 molecule. Extensive structural and spectroscopy studies provided a mechanistic understanding of the molecular basis of this unique light-sensitive reaction. Most studies on CarH have used the ortholog from the thermostable bacterium Thermus thermophilus, due to the ease with which it can be expressed and purified in high quantities. In this chapter we give an overview of this intriguing class of photoreceptors and report a step-by-step protocol for expression, purification and spectroscopy experiments (both static and time-resolved techniques) employed in our laboratory to study CarH from T. thermophilus. We hope the contents of this chapter will be of interest to the wider coenzyme B12 community and apprise them of the potential and possibilities of using coenzyme B12 as a light-sensing probe in a protein scaffold.
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Affiliation(s)
- Harshwardhan Poddar
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Shaowei Zhang
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Samantha J Hardman
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Michiyo Sakuma
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom.
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20
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Saha A, Capowski E, Fernandez Zepeda MA, Nelson EC, Gamm DM, Sinha R. Cone photoreceptors in human stem cell-derived retinal organoids demonstrate intrinsic light responses that mimic those of primate fovea. Cell Stem Cell 2022; 29:460-471.e3. [PMID: 35104442 PMCID: PMC9093561 DOI: 10.1016/j.stem.2022.01.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 11/11/2021] [Accepted: 01/04/2022] [Indexed: 02/06/2023]
Abstract
High-definition vision in humans and nonhuman primates is initiated by cone photoreceptors located within a specialized region of the retina called the fovea. Foveal cone death is the ultimate cause of central blindness in numerous retinal dystrophies, including macular degenerative diseases. 3D retinal organoids (ROs) derived from human pluripotent stem cells (hPSCs) hold tremendous promise to model and treat such diseases. To achieve this goal, RO cones should elicit robust and intrinsic light-evoked electrical responses (i.e., phototransduction) akin to adult foveal cones, which has not yet been demonstrated. Here, we show strong, graded, repetitive, and wavelength-specific light-evoked responses from RO cones. The photoresponses and membrane physiology of a significant fraction of these lab-generated cones are comparable with those of intact ex vivo primate fovea. These results greatly increase confidence in ROs as potential sources of functional human cones for cell replacement therapies, drug testing, and in vitro models of retinal dystrophies.
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Affiliation(s)
- Aindrila Saha
- Department of Neuroscience, University of Wisconsin, Madison, WI, USA; McPherson Eye Research Institute, University of Wisconsin, Madison, WI, USA; Cellular and Molecular Biology Training Program, University of Wisconsin, Madison, WI, USA
| | | | | | - Emma C Nelson
- Waisman Center, University of Wisconsin, Madison, WI, USA
| | - David M Gamm
- McPherson Eye Research Institute, University of Wisconsin, Madison, WI, USA; Cellular and Molecular Biology Training Program, University of Wisconsin, Madison, WI, USA; Waisman Center, University of Wisconsin, Madison, WI, USA; Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI, USA
| | - Raunak Sinha
- Department of Neuroscience, University of Wisconsin, Madison, WI, USA; McPherson Eye Research Institute, University of Wisconsin, Madison, WI, USA; Cellular and Molecular Biology Training Program, University of Wisconsin, Madison, WI, USA; Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI, USA.
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21
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Trifonov L, Rothstein A, Korshin EE, Viskind O, Afri M, Leitus G, Palczewski K, Gruzman A. Straightforward Access to Terminally Disubstituted Electron‐Deficient Alkylidene Cyclopent‐2‐en‐4‐ones through Olefination with α‐Carbonyl and α‐Cyano Secondary Alkyl Sulfones. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lena Trifonov
- Department of Chemistry, Bar-Ilan University Max and Anna Webb St. Ramat-Gan 5290002 Israel
| | - Ayelet Rothstein
- Department of Chemistry, Bar-Ilan University Max and Anna Webb St. Ramat-Gan 5290002 Israel
| | - Edward E. Korshin
- Department of Chemistry, Bar-Ilan University Max and Anna Webb St. Ramat-Gan 5290002 Israel
| | - Olga Viskind
- Department of Chemistry, Bar-Ilan University Max and Anna Webb St. Ramat-Gan 5290002 Israel
| | - Michal Afri
- Department of Chemistry, Bar-Ilan University Max and Anna Webb St. Ramat-Gan 5290002 Israel
| | - Gregory Leitus
- Department of Chemical Research Support the Weizmann Institute of Science Rehovot 76100 Israel
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute Department of Ophthalmology and Departments of Physiology and Biophysics and Chemistry and Molecular Biology and Biochemistry, University of California Irvine CA 92697 USA
| | - Arie Gruzman
- Department of Chemistry, Bar-Ilan University Max and Anna Webb St. Ramat-Gan 5290002 Israel
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22
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Phototransduction in Anuran Green Rods: Origins of Extra-Sensitivity. Int J Mol Sci 2021; 22:ijms222413400. [PMID: 34948198 PMCID: PMC8707487 DOI: 10.3390/ijms222413400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 01/13/2023] Open
Abstract
Green rods (GRs) represent a unique type of photoreceptor to be found in the retinas of anuran amphibians. These cells harbor a cone-specific blue-sensitive visual pigment but exhibit morphology of the outer segment typical for classic red rods (RRs), which makes them a perspective model object for studying cone–rod transmutation. In the present study, we performed detailed electrophysiological examination of the light sensitivity, response kinetics and parameters of discrete and continuous dark noise in GRs of the two anuran species: cane toad and marsh frog. Our results confirm that anuran GRs are highly specialized nocturnal vision receptors. Moreover, their rate of phototransduction quenching appeared to be about two-times slower than in RRs, which makes them even more efficient single photon detectors. The operating intensity ranges for two rod types widely overlap supposedly allowing amphibians to discriminate colors in the scotopic region. Unexpectedly for typical cone pigments but in line with some previous reports, the spontaneous isomerization rate of the GR visual pigment was found to be the same as for rhodopsin of RRs. Thus, our results expand the knowledge on anuran GRs and show that these are even more specialized single photon catchers than RRs, which allows us to assign them a status of “super-rods”.
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23
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Demoulin B, Maiuri M, Berbasova T, Geiger JH, Borhan B, Garavelli M, Cerullo G, Rivalta I. Control of Protonated Schiff Base Excited State Decay within Visual Protein Mimics: A Unified Model for Retinal Chromophores. Chemistry 2021; 27:16389-16400. [PMID: 34653286 DOI: 10.1002/chem.202102383] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 11/07/2022]
Abstract
Artificial biomimetic chromophore-protein complexes inspired by natural visual pigments can feature color tunability across the full visible spectrum. However, control of excited state dynamics of the retinal chromophore, which is of paramount importance for technological applications, is lacking due to its complex and subtle photophysics/photochemistry. Here, ultrafast transient absorption spectroscopy and quantum mechanics/molecular mechanics simulations are combined for the study of highly tunable rhodopsin mimics, as compared to retinal chromophores in solution. Conical intersections and transient fluorescent intermediates are identified with atomistic resolution, providing unambiguous assignment of their ultrafast excited state absorption features. The results point out that the electrostatic environment of the chromophore, modified by protein point mutations, affects its excited state properties allowing control of its photophysics with same power of chemical modifications of the chromophore. The complex nature of such fine control is a fundamental knowledge for the design of bio-mimetic opto-electronic and photonic devices.
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Affiliation(s)
- Baptiste Demoulin
- Laboratoire de Chimie, Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, 69342, Lyon, France
| | - Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133, Milano, Italy
| | - Tetyana Berbasova
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - James H Geiger
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Babak Borhan
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133, Milano, Italy
| | - Ivan Rivalta
- Laboratoire de Chimie, Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, 69342, Lyon, France.,Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
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24
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Sajjan M, Sureshbabu SH, Kais S. Quantum Machine-Learning for Eigenstate Filtration in Two-Dimensional Materials. J Am Chem Soc 2021; 143:18426-18445. [PMID: 34705449 DOI: 10.1021/jacs.1c06246] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantum machine-learning algorithms have emerged to be a promising alternative to their classical counterparts as they leverage the power of quantum computers. Such algorithms have been developed to solve problems like electronic structure calculations of molecular systems and spin models in magnetic systems. However, the discussion in all these recipes focuses specifically on targeting the ground state. Herein we demonstrate a quantum algorithm that can filter any energy eigenstate of the system based on either symmetry properties or a predefined choice of the user. The workhorse of our technique is a shallow neural network encoding the desired state of the system with the amplitude computed by sampling the Gibbs-Boltzmann distribution using a quantum circuit and the phase information obtained classically from the nonlinear activation of a separate set of neurons. We show that the resource requirements of our algorithm are strictly quadratic. To demonstrate its efficacy, we use state filtration in monolayer transition metal dichalcogenides which are hitherto unexplored in any flavor of quantum simulations. We implement our algorithm not only on quantum simulators but also on actual IBM-Q quantum devices and show good agreement with the results procured from conventional electronic structure calculations. We thus expect our protocol to provide a new alternative in exploring the band structures of exquisite materials to usual electronic structure methods or machine-learning techniques that are implementable solely on a classical computer.
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Affiliation(s)
- Manas Sajjan
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Shree Hari Sureshbabu
- Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sabre Kais
- Department of Chemistry, Department of Physics and Astronomy, and Purdue Quantum Science and Engineering Institute, Purdue University, West Lafayette, Indiana 47907, United States
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25
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Young BD, Varney KM, Wilder PT, Costabile BK, Pozharski E, Cook ME, Godoy-Ruiz R, Clarke OB, Mancia F, Weber DJ. Physiologically Relevant Free Ca 2+ Ion Concentrations Regulate STRA6-Calmodulin Complex Formation via the BP2 Region of STRA6. J Mol Biol 2021; 433:167272. [PMID: 34592217 PMCID: PMC8568335 DOI: 10.1016/j.jmb.2021.167272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/13/2021] [Accepted: 09/21/2021] [Indexed: 11/28/2022]
Abstract
The interaction of calmodulin (CaM) with the receptor for retinol uptake, STRA6, involves an α-helix termed BP2 that is located on the intracellular side of this homodimeric transporter (Chen et al., 2016 [1]). In the absence of Ca2+, NMR data showed that a peptide derived from BP2 bound to the C-terminal lobe (C-lobe) of Mg2+-bound CaM (MgCaM). Upon titration of Ca2+ into MgCaM-BP2, NMR chemical shift perturbations (CSPs) were observed for residues in the C-lobe, including those in the EF-hand Ca2+-binding domains, EF3 and EF4 (CaKD = 60 ± 7 nM). As higher concentrations of free Ca2+ were achieved, CSPs occurred for residues in the N-terminal lobe (N-lobe) including those in EF1 and EF2 (CaKD = 1000 ± 160 nM). Thermodynamic and kinetic Ca2+ binding studies showed that BP2 addition increased the Ca2+-binding affinity of CaM and slowed its Ca2+ dissociation rates (koff) in both the C- and N-lobe EF-hand domains, respectively. These data are consistent with BP2 binding to the C-lobe of CaM at low free Ca2+ concentrations (<100 nM) like those found at resting intracellular levels. As free Ca2+ levels approach 1000 nM, which is typical inside a cell upon an intracellular Ca2+-signaling event, BP2 is shown here to interact with both the N- and C-lobes of Ca2+-loaded CaM (CaCaM-BP2). Because this structural rearrangement observed for the CaCaM-BP2 complex occurs as intracellular free Ca2+ concentrations approach those typical of a Ca2+-signaling event (CaKD = 1000 ± 160 nM), this conformational change could be relevant to vitamin A transport by full-length CaCaM-STRA6.
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Affiliation(s)
- Brianna D Young
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA
| | - Kristen M Varney
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA
| | - Paul T Wilder
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA
| | - Brianna K Costabile
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Edwin Pozharski
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA
| | - Mary E Cook
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA
| | - Raquel Godoy-Ruiz
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - David J Weber
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA.
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26
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Brady RP, Zhang C, DeFrancisco JR, Barrett BJ, Cheng L, Bragg AE. Multiphoton Control of 6π Photocyclization via State-Dependent Reactant-Product Correlations. J Phys Chem Lett 2021; 12:9493-9500. [PMID: 34559534 DOI: 10.1021/acs.jpclett.1c02353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Multiphoton excitation promises opportunities for opening new photochemical reaction pathways and controlling photoproduct distributions. We demonstrate photonic control of the 6π photocyclization of ortho-terphenyl to make 4a,4b-dihydrotriphenylene (DHT). Using pump-repump-probe spectroscopy we show that 1 + 1' excitation to a high-lying reactant electronic state generates a metastable species characterized by a red absorption feature that accompanies a repump-induced depletion in the one-photon trans-dihydro product (trans-DHT); signatures of the new photoproduct are clearer for a structural analogue of the reactant that is sterically inhibited against one-photon cyclization. Quantum-chemical computations support assignment of this species to cis-DHT, which is accessible photochemically along a disrotatory coordinate from high-lying electronic states reached by 1 + 1' excitation. We use time-resolved spectroscopy to track photochemical dynamics producing cis-DHT. In total, we demonstrate that selective multiphoton excitation opens a new photoreaction channel in these photocyclizing reactants by taking advantage of state-dependent correlations between reactant and product electronic states.
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Affiliation(s)
- Ryan P Brady
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Chaoqun Zhang
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Justin R DeFrancisco
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Brandon J Barrett
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Lan Cheng
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Arthur E Bragg
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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27
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Hidalgo-Alvarez V, Dhowre HS, Kingston OA, Sheridan CM, Levis HJ. Biofabrication of Artificial Stem Cell Niches in the Anterior Ocular Segment. Bioengineering (Basel) 2021; 8:135. [PMID: 34677208 PMCID: PMC8533470 DOI: 10.3390/bioengineering8100135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022] Open
Abstract
The anterior segment of the eye is a complex set of structures that collectively act to maintain the integrity of the globe and direct light towards the posteriorly located retina. The eye is exposed to numerous physical and environmental insults such as infection, UV radiation, physical or chemical injuries. Loss of transparency to the cornea or lens (cataract) and dysfunctional regulation of intra ocular pressure (glaucoma) are leading causes of worldwide blindness. Whilst traditional therapeutic approaches can improve vision, their effect often fails to control the multiple pathological events that lead to long-term vision loss. Regenerative medicine approaches in the eye have already had success with ocular stem cell therapy and ex vivo production of cornea and conjunctival tissue for transplant recovering patients' vision. However, advancements are required to increase the efficacy of these as well as develop other ocular cell therapies. One of the most important challenges that determines the success of regenerative approaches is the preservation of the stem cell properties during expansion culture in vitro. To achieve this, the environment must provide the physical, chemical and biological factors that ensure the maintenance of their undifferentiated state, as well as their proliferative capacity. This is likely to be accomplished by replicating the natural stem cell niche in vitro. Due to the complex nature of the cell microenvironment, the creation of such artificial niches requires the use of bioengineering techniques which can replicate the physico-chemical properties and the dynamic cell-extracellular matrix interactions that maintain the stem cell phenotype. This review discusses the progress made in the replication of stem cell niches from the anterior ocular segment by using bioengineering approaches and their therapeutic implications.
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Affiliation(s)
- Veronica Hidalgo-Alvarez
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Hala S. Dhowre
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK; (H.S.D.); (O.A.K.)
| | - Olivia A. Kingston
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK; (H.S.D.); (O.A.K.)
| | - Carl M. Sheridan
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK; (H.S.D.); (O.A.K.)
| | - Hannah J. Levis
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK; (H.S.D.); (O.A.K.)
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28
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Roy R, Ghosal A, Roy AK. A Simple Effective Δ SCF Method for Computing Optical Gaps in Organic Chromophores. Chem Asian J 2021; 16:2729-2739. [PMID: 34331415 DOI: 10.1002/asia.202100692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/28/2021] [Indexed: 11/09/2022]
Abstract
Photoluminescence effects in organic chromophores are of significant importance and requires precise description of low lying excited states. In this communication, we put forward an alternative time-independent DFT scheme for computing lowest single-particle excitation energy, especially for singlet excited state. This adopts a recently developed "virial"-theorem based model of singlet-triplet splitting which requires a DFT calculation on closed shell ground state and a restricted open-shell triplet excited state, followed by a simple 2 e - integral evaluation. This produces vertical excitation energies in small molecules, linear and non-linear polycyclic aromatic hydrocarbon and organic dyes in comparable accuracy to the TDDFT. We also explore the functional dependency of present method with three different functionals (B3LYP, wB97X and CAM-B3LYP) for polyenes and linear acenes. A systematic comparison with literature value illustrates the validity and usefulness of the present scheme in determining optical gap with fair computational cost.
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Affiliation(s)
- Raj Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata Nadia, Mohanpur, 741246, WB, India
| | - Abhisek Ghosal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata Nadia, Mohanpur, 741246, WB, India.,Present Address : Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), Mumbai, 400005, Maharastra, India
| | - Amlan K Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata Nadia, Mohanpur, 741246, WB, India
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29
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Ebke LA, Sinha S, Pauer GJT, Hagstrom SA. Photoreceptor Compartment-Specific TULP1 Interactomes. Int J Mol Sci 2021; 22:ijms22158066. [PMID: 34360830 PMCID: PMC8348715 DOI: 10.3390/ijms22158066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 12/16/2022] Open
Abstract
Photoreceptors are highly compartmentalized cells with large amounts of proteins synthesized in the inner segment (IS) and transported to the outer segment (OS) and synaptic terminal. Tulp1 is a photoreceptor-specific protein localized to the IS and synapse. In the absence of Tulp1, several OS-specific proteins are mislocalized and synaptic vesicle recycling is impaired. To better understand the involvement of Tulp1 in protein trafficking, our approach in the current study was to physically isolate Tulp1-containing photoreceptor compartments by serial tangential sectioning of retinas and to identify compartment-specific Tulp1 binding partners by immunoprecipitation followed by liquid chromatography tandem mass spectrometry. Our results indicate that Tulp1 has two distinct interactomes. We report the identification of: (1) an IS-specific interaction between Tulp1 and the motor protein Kinesin family member 3a (Kif3a), (2) a synaptic-specific interaction between Tulp1 and the scaffold protein Ribeye, and (3) an interaction between Tulp1 and the cytoskeletal protein microtubule-associated protein 1B (MAP1B) in both compartments. Immunolocalization studies in the wild-type retina indicate that Tulp1 and its binding partners co-localize to their respective compartments. Our observations are compatible with Tulp1 functioning in protein trafficking in multiple photoreceptor compartments, likely as an adapter molecule linking vesicles to molecular motors and the cytoskeletal scaffold.
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Affiliation(s)
- Lindsey A. Ebke
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (L.A.E.); (S.S.); (G.J.T.P.)
| | - Satyabrata Sinha
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (L.A.E.); (S.S.); (G.J.T.P.)
| | - Gayle J. T. Pauer
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (L.A.E.); (S.S.); (G.J.T.P.)
| | - Stephanie A. Hagstrom
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (L.A.E.); (S.S.); (G.J.T.P.)
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Correspondence:
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30
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Kolesov DV, Sokolinskaya EL, Lukyanov KA, Bogdanov AM. Molecular Tools for Targeted Control of Nerve Cell Electrical Activity. Part I. Acta Naturae 2021; 13:52-64. [PMID: 34707897 PMCID: PMC8526180 DOI: 10.32607/actanaturae.11414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/14/2021] [Indexed: 12/18/2022] Open
Abstract
In modern life sciences, the issue of a specific, exogenously directed manipulation of a cell's biochemistry is a highly topical one. In the case of electrically excitable cells, the aim of the manipulation is to control the cells' electrical activity, with the result being either excitation with subsequent generation of an action potential or inhibition and suppression of the excitatory currents. The techniques of electrical activity stimulation are of particular significance in tackling the most challenging basic problem: figuring out how the nervous system of higher multicellular organisms functions. At this juncture, when neuroscience is gradually abandoning the reductionist approach in favor of the direct investigation of complex neuronal systems, minimally invasive methods for brain tissue stimulation are becoming the basic element in the toolbox of those involved in the field. In this review, we describe three approaches that are based on the delivery of exogenous, genetically encoded molecules sensitive to external stimuli into the nervous tissue. These approaches include optogenetics (Part I) as well as chemogenetics and thermogenetics (Part II), which are significantly different not only in the nature of the stimuli and structure of the appropriate effector proteins, but also in the details of experimental applications. The latter circumstance is an indication that these are rather complementary than competing techniques.
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Affiliation(s)
- D. V. Kolesov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - E. L. Sokolinskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - K. A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - A. M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
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31
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Khan S, Beavers S, Rice C, Atan D. Why can't I see in the dark? BMJ 2021; 373:n1573. [PMID: 34193459 DOI: 10.1136/bmj.n1573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
| | | | - Claire Rice
- Bristol Medical School, University of Bristol, UK
| | - Denize Atan
- Bristol Medical School, University of Bristol, UK
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32
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Zhao CY, Ji DW, Zheng H, He GC, Liu H, Hu YC, Chen QA. Pd-Catalyzed Redox Divergent Coupling of Ketones with Terpenols. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Chao-Yang Zhao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Ding-Wei Ji
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Hao Zheng
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Gu-Cheng He
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Heng Liu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Yan-Cheng Hu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Qing-An Chen
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
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33
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Poddar H, Heyes DJ, Schirò G, Weik M, Leys D, Scrutton NS. A guide to time-resolved structural analysis of light-activated proteins. FEBS J 2021; 289:576-595. [PMID: 33864718 DOI: 10.1111/febs.15880] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/03/2021] [Accepted: 04/13/2021] [Indexed: 01/08/2023]
Abstract
Dynamical changes in protein structures are essential for protein function and occur over femtoseconds to seconds timescales. X-ray free electron lasers have facilitated investigations of structural dynamics in proteins with unprecedented temporal and spatial resolution. Light-activated proteins are attractive targets for time-resolved structural studies, as the reaction chemistry and associated protein structural changes can be triggered by short laser pulses. Proteins with different light-absorbing centres have evolved to detect light and harness photon energy to bring about downstream chemical and biological output responses. Following light absorption, rapid chemical/small-scale structural changes are typically localised around the chromophore. These localised changes are followed by larger structural changes propagated throughout the photoreceptor/photocatalyst that enables the desired chemical and/or biological output response. Time-resolved serial femtosecond crystallography (SFX) and solution scattering techniques enable direct visualisation of early chemical change in light-activated proteins on timescales previously inaccessible, whereas scattering gives access to slower timescales associated with more global structural change. Here, we review how advances in time-resolved SFX and solution scattering techniques have uncovered mechanisms of photochemistry and its coupling to output responses. We also provide a prospective on how these time-resolved structural approaches might impact on other photoreceptors/photoenzymes that have not yet been studied by these methods.
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Affiliation(s)
- Harshwardhan Poddar
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Giorgio Schirò
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Martin Weik
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - David Leys
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
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34
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Sugimoto T, Katayama K, Kandori H. Role of Thr82 for the unique photochemistry of TAT rhodopsin. Biophys Physicobiol 2021; 18:108-115. [PMID: 34026400 PMCID: PMC8116198 DOI: 10.2142/biophysico.bppb-v18.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/14/2021] [Indexed: 12/01/2022] Open
Abstract
Marine bacterial TAT rhodopsin possesses the pKa of the retinal Schiff base, the chromophore, at neutral pH, and photoexcitation of the visible protonated state forms the isomerized 13-cis state, but reverts to the original state within 10–5 sec. To understand the origin of these unique molecular properties of TAT rhodopsin, we mutated Thr82 into Asp, because many microbial rhodopsins contain Asp at the corresponding position as the Schiff base counterion. A pH titration study revealed that the pKa of the Schiff base increased considerably in T82D (>10.5), and that the pKa of the counterion, which is likely to be D82, is 8.1. It was thus concluded that T82 is the origin of the neutral pKa of the Schiff base in TAT rhodopsin. The photocycle of T82D TAT rhodopsin exhibited strong pH dependence. When pH is lower than the pKa of the counterion (pH <8.1), formation of the primary K intermediate was observed by low-temperature UV-visible spectroscopy, but flash photolysis failed to monitor photointermdiates at >10–5 sec. The results were identical for the wild-type TAT rhodopsin. In contrast, when pH was higher than the pKa of the counterion, we observed the formation of the M intermediate, which decayed with the time constants of 3.75 ms and 12.2 sec. It is likely that the protonation state of D82 dramatically switches the photoreaction dynamics of T82D, whose duration lies between <10–5 sec and >10 sec. It was thus concluded that T82 is one of the determinants of the unique photochemistry of TAT rhodopsin.
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Affiliation(s)
- Teppei Sugimoto
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
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35
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Kataoka C, Sugimoto T, Shigemura S, Katayama K, Tsunoda SP, Inoue K, Béjà O, Kandori H. TAT Rhodopsin Is an Ultraviolet-Dependent Environmental pH Sensor. Biochemistry 2021; 60:899-907. [PMID: 33721993 DOI: 10.1021/acs.biochem.0c00951] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In many rhodopsins, the retinal Schiff base pKa remains very high, ensuring Schiff base protonation captures visible light. Nevertheless, recently we found that TAT rhodopsin contains protonated and unprotonated forms at physiological pH. The protonated form displays a unique photochemical behavior in which the primary K intermediate returns to the original state within 10-5 s, and the lack of photocycle completion poses questions about the functional role of TAT rhodopsin. Here we studied the molecular properties of the protonated and unprotonated forms of the Schiff base in TAT rhodopsin. We confirmed no photointermediate formation at >10-5 s for the protonated form of TAT rhodopsin in microenvironments such as detergents, nanodiscs, and liposomes. In contrast, the unprotonated form features a very long photocycle with a time constant of 15 s. A low-temperature study revealed that the primary reaction of the unprotonated form is all-trans to 13-cis photoisomerization, which is usual, but with a proton transfer reaction occurring at 77 K, which is unusual. The active intermediate contains the unprotonated Schiff base as well as the resting state. Electrophysiological measurements excluded ion-transport activity for TAT rhodopsin, while transient outward proton movement only at an alkaline extracellular pH indicates that TAT rhodopsin senses the extracellular pH. On the basis of the findings presented here, we propose that TAT rhodopsin is an ultraviolet (UV)-dependent environmental pH sensor in marine bacteria. At acidic pH, absorbed visible light energy is quickly dissipated into heat without any function. In contrast, when the environmental pH becomes high, absorption of UV/blue light yields formation of the long-lived intermediates, possibly driving the signal transduction cascade in marine bacteria.
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Affiliation(s)
- Chihiro Kataoka
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Teppei Sugimoto
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shunta Shigemura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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36
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Ramkumar S, Moon J, Golczak M, von Lintig J. LRAT coordinates the negative-feedback regulation of intestinal retinoid biosynthesis from β-carotene. J Lipid Res 2021; 62:100055. [PMID: 33631212 PMCID: PMC8010212 DOI: 10.1016/j.jlr.2021.100055] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/02/2021] [Accepted: 02/17/2021] [Indexed: 11/23/2022] Open
Abstract
There is increasing recognition that dietary lipids can affect the expression of genes encoding their metabolizing enzymes, transporters, and binding proteins. This mechanism plays a pivotal role in controlling tissue homeostasis of these compounds and avoiding diseases. The regulation of retinoid biosynthesis from β-carotene (BC) is a classic example for such an interaction. The intestine-specific homeodomain transcription factor (ISX) controls the activity of the vitamin A-forming enzyme β-carotene oxygenase-1 in intestinal enterocytes in response to increasing concentration of the vitamin A metabolite retinoic acid. However, it is unclear how cells control the concentration of the signaling molecule in this negative-feedback loop. We demonstrate in mice that the sequestration of retinyl esters by the enzyme lecithin:retinol acyltransferase (LRAT) is central for this process. Using genetic and pharmacological approaches in mice, we observed that in LRAT deficiency, the transcription factor ISX became hypersensitive to dietary vitamin A and suppressed retinoid biosynthesis. The dysregulation of the pathway resulted in BC accumulation and vitamin A deficiency of extrahepatic tissues. Pharmacological inhibition of retinoid signaling and genetic depletion of the Isx gene restored retinoid biosynthesis in enterocytes. We provide evidence that the catalytic activity of LRAT coordinates the negative-feedback regulation of intestinal retinoid biosynthesis and maintains optimal retinoid levels in the body.
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Affiliation(s)
- Srinivasagan Ramkumar
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jean Moon
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Marcin Golczak
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Johannes von Lintig
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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37
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Staheli CF, Barney J, Clark TR, Bowles M, Jeppesen B, Oblinsky DG, Steffensen MB, Dean JC. Spectroscopic and Photophysical Investigation of Model Dipyrroles Common to Bilins: Exploring Natural Design for Steering Torsion to Divergent Functions. Front Chem 2021; 9:628852. [PMID: 33681146 PMCID: PMC7925881 DOI: 10.3389/fchem.2021.628852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/05/2021] [Indexed: 11/13/2022] Open
Abstract
Biliproteins are a unique class of photosynthetic proteins in their diverse, and at times, divergent biophysical function. The two contexts of photosynthetic light harvesting and photoreception demonstrate characteristically opposite criteria for success, with light harvesting demanding structurally-rigid chromophores which minimize excitation quenching, and photoreception requiring structural flexibility to enable conformational isomerization. The functional plasticity borne out in these two biological contexts is a consequence of the structural plasticity of the pigments utilized by biliproteins―linear tetrapyrroles, or bilins. In this work, the intrinsic flexibility of the bilin framework is investigated in a bottom-up fashion by reducing the active nuclear degrees of freedom through model dipyrrole subunits of the bilin core and terminus free of external protein interactions. Steady-state spectroscopy was carried out on the dipyrrole (DPY) and dipyrrinone (DPN) subunits free in solution to characterize their intrinsic spectroscopic properties including absorption strengths and nonradiative activity. Transient absorption (TA) spectroscopy was utilized to determine the mechanism and kinetics of nonradiative decay of the dipyrrole subunits, revealing dynamics dominated by rapid internal conversion with some Z→E isomerization observable in DPY. Computational analysis of the ground state conformational landscapes indicates enhanced complexity in the asymmetric terminal subunit, and the prediction was confirmed by heterogeneity of species and kinetics observed in TA. Taken together, the large oscillator strengths (f ∼ 0.6) of the dipyrrolic derivatives and chemically-efficient spectral tunability seen through the ∼100 nm difference in absorption spectra, validate Nature's "selection" of multi-pyrrole pigments for light capture applications. However, the rapid deactivation of the excited state via their natural torsional activity when free in solution would limit their effective biological function. Comparison with phytochrome and phycocyanin 645 crystal structures reveals binding motifs within the in vivo bilin environment that help to facilitate or inhibit specific inter-pyrrole twisting vital for protein operation.
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Affiliation(s)
- Clayton F Staheli
- Department of Physical Science, Southern Utah University, Cedar City, UT, United States
| | - Jaxon Barney
- Department of Physical Science, Southern Utah University, Cedar City, UT, United States.,Department of Chemistry, The Pennsylvania State University, State College, PA, United States
| | - Taime R Clark
- Department of Physical Science, Southern Utah University, Cedar City, UT, United States
| | - Maxwell Bowles
- Department of Physical Science, Southern Utah University, Cedar City, UT, United States.,Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Bridger Jeppesen
- Department of Physical Science, Southern Utah University, Cedar City, UT, United States
| | - Daniel G Oblinsky
- Department of Chemistry, Princeton University, Princeton, NJ, United States
| | - Mackay B Steffensen
- Department of Physical Science, Southern Utah University, Cedar City, UT, United States
| | - Jacob C Dean
- Department of Physical Science, Southern Utah University, Cedar City, UT, United States
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"Shedding Light on Light": A Review on the Effects on Mental Health of Exposure to Optical Radiation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18041670. [PMID: 33572423 PMCID: PMC7916252 DOI: 10.3390/ijerph18041670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/11/2021] [Accepted: 02/03/2021] [Indexed: 01/10/2023]
Abstract
In relation to human health and functioning, light, or more specifically optical radiation, plays many roles, beyond allowing vision. These may be summarized as: regulation of circadian rhythms; consequences of direct exposure to the skin; and more indirect effects on well-being and functioning, also related to lifestyle and contact with natural and urban environments. Impact on mental health is relevant for any of these specifications and supports a clinical use of this knowledge for the treatment of psychiatric conditions, such as depression or anxiety, somatic symptom disorder, and others, with reference to light therapy in particular. The scope of this narrative review is to provide a summary of recent findings and evidence on the regulating functions of light on human beings’ biology, with a specific focus on mental health, its prevention and care.
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Quan J, Zhu F, Dhinakaran MK, Yang Y, Johnson RP, Li H. A Visible-Light-Regulated Chloride Transport Channel Inspired by Rhodopsin. Angew Chem Int Ed Engl 2021; 60:2892-2897. [PMID: 33145896 DOI: 10.1002/anie.202012984] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/30/2020] [Indexed: 01/16/2023]
Abstract
Inspired by the light-regulating capabilities of naturally occurring rhodopsin, we have constructed a visible-light-regulated Cl- -transport membrane channel based on a supramolecular host-guest interaction. A natural retinal chromophore, capable of a visible-light response, is used as the guest and grafted into the artificial channel. Upon introduction of an ethyl-urea-derived pillar[6]arene (Urea-P6) host, threading or de-threading of the retinal and selective bonding of Cl- can be utilized to regulate ion transport. Based on the visible-light responsiveness of the host-guest interaction, Cl- transport can be regulated by visible light between ON and OFF states. Visible-light-regulated Cl- transport as a chemical model permits to understand comparable biological ion-selective transport behaviors. Furthermore, this result also supplies a smart visible-light-responsive Cl- transporter, which may have applications in natural photoelectric conversion and photo-controlled delivery systems.
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Affiliation(s)
- Jiaxin Quan
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Fei Zhu
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Manivannan Kalavathi Dhinakaran
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Yingying Yang
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Robert P Johnson
- School of Chemistry, University College Dublin, Dublin, 4, Ireland
| | - Haibing Li
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
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Quan J, Zhu F, Dhinakaran MK, Yang Y, Johnson RP, Li H. A Visible‐Light‐Regulated Chloride Transport Channel Inspired by Rhodopsin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jiaxin Quan
- Key Laboratory of Pesticide and Chemical Biology (CCNU) Ministry of Education College of Chemistry Central China Normal University Wuhan 430079 P. R. China
| | - Fei Zhu
- Key Laboratory of Pesticide and Chemical Biology (CCNU) Ministry of Education College of Chemistry Central China Normal University Wuhan 430079 P. R. China
| | - Manivannan Kalavathi Dhinakaran
- Key Laboratory of Pesticide and Chemical Biology (CCNU) Ministry of Education College of Chemistry Central China Normal University Wuhan 430079 P. R. China
| | - Yingying Yang
- Key Laboratory of Pesticide and Chemical Biology (CCNU) Ministry of Education College of Chemistry Central China Normal University Wuhan 430079 P. R. China
| | | | - Haibing Li
- Key Laboratory of Pesticide and Chemical Biology (CCNU) Ministry of Education College of Chemistry Central China Normal University Wuhan 430079 P. R. China
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Kiser PD, Palczewski K. Pathways and disease-causing alterations in visual chromophore production for vertebrate vision. J Biol Chem 2021; 296:100072. [PMID: 33187985 PMCID: PMC7948990 DOI: 10.1074/jbc.rev120.014405] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/14/2022] Open
Abstract
All that we view of the world begins with an ultrafast cis to trans photoisomerization of the retinylidene chromophore associated with the visual pigments of rod and cone photoreceptors. The continual responsiveness of these photoreceptors is then sustained by regeneration processes that convert the trans-retinoid back to an 11-cis configuration. Recent biochemical and electrophysiological analyses of the retinal G-protein-coupled receptor (RGR) suggest that it could sustain the responsiveness of photoreceptor cells, particularly cones, even under bright light conditions. Thus, two mechanisms have evolved to accomplish the reisomerization: one involving the well-studied retinoid isomerase (RPE65) and a second photoisomerase reaction mediated by the RGR. Impairments to the pathways that transform all-trans-retinal back to 11-cis-retinal are associated with mild to severe forms of retinal dystrophy. Moreover, with age there also is a decline in the rate of chromophore regeneration. Both pharmacological and genetic approaches are being used to bypass visual cycle defects and consequently mitigate blinding diseases. Rapid progress in the use of genome editing also is paving the way for the treatment of disparate retinal diseases. In this review, we provide an update on visual cycle biochemistry and then discuss visual-cycle-related diseases and emerging therapeutics for these disorders. There is hope that these advances will be helpful in treating more complex diseases of the eye, including age-related macular degeneration (AMD).
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Affiliation(s)
- Philip D Kiser
- The Department of Physiology & Biophysics, University of California, Irvine, California, USA; Research Service, The VA Long Beach Health Care System, Long Beach, California, USA; The Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California, USA.
| | - Krzysztof Palczewski
- The Department of Physiology & Biophysics, University of California, Irvine, California, USA; The Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California, USA; The Department of Chemistry, University of California, Irvine, California, USA.
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Deretic D, Lorentzen E, Fresquez T. The ins and outs of the Arf4-based ciliary membrane-targeting complex. Small GTPases 2021; 12:1-12. [PMID: 31068062 PMCID: PMC7781591 DOI: 10.1080/21541248.2019.1616355] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/09/2019] [Accepted: 05/02/2019] [Indexed: 10/26/2022] Open
Abstract
The small GTPase Arf4-based ciliary membrane-targeting complex recognizes specific targeting signals within sensory receptors and regulates their directed movement to primary cilia. Activated Arf4 directly binds the VxPx ciliary-targeting signal (CTS) of the light-sensing receptor rhodopsin. Recent findings revealed that at the trans-Golgi, marked by the small GTPase Rab6, activated Arf4 forms a functional complex with rhodopsin and the Arf guanine nucleotide exchange factor (GEF) GBF1, providing positive feedback that drives further Arf4 activation in ciliary trafficking. Arf4 function is conserved across diverse cell types; however, it appears that not all its aspects are conserved across species, as mouse Arf4 is a natural mutant in the conserved α3 helix, which is essential for its interaction with rhodopsin. Generally, activated Arf4 regulates the assembly of the targeting nexus containing the Arf GAP ASAP1 and the Rab11a-FIP3-Rabin8 dual effector complex, which controls the assembly of the highly conserved Rab11a-Rabin8-Rab8 ciliary-targeting module. It was recently found that this module interacts with the R-SNARE VAMP7, likely in its activated, c-Src-phosphorylated form. Rab11 and Rab8 bind VAMP7 regulatory longin domain (LD), whereas Rabin8 interacts with the SNARE domain, capturing VAMP7 for delivery to the ciliary base and subsequent pairing with the cognate SNAREs syntaxin 3 and SNAP-25. This review will focus on the implications of these novel findings that further illuminate the role of well-ordered Arf and Rab interaction networks in targeting of sensory receptors to primary cilia. Abbreviations: CTS: Ciliary-Targeting Signal; GAP: GTPase Activating Protein; GEF: Guanine Nucleotide Exchange Factor; RTC(s), Rhodopsin Transport Carrier(s); SNARE: Soluble N-ethylmaleimide-sensitive Factor Attachment Protein Receptor; TGN: Trans-Golgi Network.
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Affiliation(s)
- Dusanka Deretic
- Departments of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM, USA
- Cell Biology and Physiology, University of New Mexico, Albuquerque, NM, USA
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Theresa Fresquez
- Departments of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM, USA
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Kandori H. History and Perspectives of Ion-Transporting Rhodopsins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:3-19. [PMID: 33398804 DOI: 10.1007/978-981-15-8763-4_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The first light-sensing proteins used in optogenetics were rhodopsins. The word "rhodopsin" originates from the Greek words "rhodo" and "opsis," indicating rose and sight, respectively. Although the classical meaning of rhodopsin is the red-colored pigment in our eyes, the modern meaning of rhodopsin encompasses photoactive proteins containing a retinal chromophore in animals and microbes. Animal and microbial rhodopsins possess 11-cis and all-trans retinal, respectively, to capture light in seven transmembrane α-helices, and photoisomerizations into all-trans and 13-cis forms, respectively, initiate each function. We are able to find ion-transporting proteins in microbial rhodopsins, such as light-gated channels and light-driven pumps, which are the main tools in optogenetics. In this chapter, historical aspects and molecular properties of rhodopsins are introduced. In the first part, "what is rhodopsin?", general introduction of rhodopsin is presented. Then, molecular mechanism of bacteriorodopsin, a light-driven proton pump and the best-studied microbial rhodopsin, is described. In the section of channelrhodopsin, the light-gated ion channel, molecular properties, and several variants are introduced. As the history has proven, understanding the molecular mechanism of microbial rhodopsins is a prerequisite for useful functional design of optogenetics tools in future.
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Affiliation(s)
- Hideki Kandori
- Department of Life Science and Applied Chemistry & OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan.
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Schafer CT, Shumate A, Farrens DL. Novel fluorescent GPCR biosensor detects retinal equilibrium binding to opsin and active G protein and arrestin signaling conformations. J Biol Chem 2020; 295:17486-17496. [PMID: 33453993 DOI: 10.1074/jbc.ra120.014631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/25/2020] [Indexed: 01/14/2023] Open
Abstract
Rhodopsin is a canonical class A photosensitive G protein-coupled receptor (GPCR), yet relatively few pharmaceutical agents targeting this visual receptor have been identified, in part due to the unique characteristics of its light-sensitive, covalently bound retinal ligands. Rhodopsin becomes activated when light isomerizes 11-cis-retinal into an agonist, all-trans-retinal (ATR), which enables the receptor to activate its G protein. We have previously demonstrated that, despite being covalently bound, ATR can display properties of equilibrium binding, yet how this is accomplished is unknown. Here, we describe a new approach for both identifying compounds that can activate and attenuate rhodopsin and testing the hypothesis that opsin binds retinal in equilibrium. Our method uses opsin-based fluorescent sensors, which directly report the formation of active receptor conformations by detecting the binding of G protein or arrestin fragments that have been fused onto the receptor's C terminus. We show that these biosensors can be used to monitor equilibrium binding of the agonist, ATR, as well as the noncovalent binding of β-ionone, an antagonist for G protein activation. Finally, we use these novel biosensors to observe ATR release from an activated, unlabeled receptor and its subsequent transfer to the sensor in real time. Taken together, these data support the retinal equilibrium binding hypothesis. The approach we describe should prove directly translatable to other GPCRs, providing a new tool for ligand discovery and mutant characterization.
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Affiliation(s)
- Christopher T Schafer
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Anthony Shumate
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA
| | - David L Farrens
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA.
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El‐Tahawy MMT, Conti I, Bonfanti M, Nenov A, Garavelli M. Tailoring Spectral and Photochemical Properties of Bioinspired Retinal Mimics by in Silico Engineering. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mohsen M. T. El‐Tahawy
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
- Chemistry Department Faculty of Science Damanhour University Damanhour 22511 Egypt
| | - Irene Conti
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
| | - Matteo Bonfanti
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
| | - Artur Nenov
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
| | - Marco Garavelli
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
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Parmar T, Ortega JT, Jastrzebska B. Retinoid analogs and polyphenols as potential therapeutics for age-related macular degeneration. Exp Biol Med (Maywood) 2020; 245:1615-1625. [PMID: 32438835 PMCID: PMC7787542 DOI: 10.1177/1535370220926938] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
IMPACT STATEMENT Age-related macular degeneration (AMD) is a devastating retinal degenerative disease. Epidemiological reports showed an expected increasing prevalence of AMD in the near future. The only one existing FDA-approved pharmacological treatment involves an anti-vascular endothelial growth factor (VEGF) therapy with serious disadvantages. This limitation emphasizes an alarming need to develop new therapeutic approaches to prevent and treat AMD. In this review, we summarize scientific data unraveling the therapeutic potential of the specific retinoid and natural compounds. The experimental results reported by us and other research groups demonstrated that retinoid analogs and compounds with natural product scaffolds could serve as lead compounds for the development of new therapeutic agents with potential to prevent or slow down the pathogenesis of AMD.
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Affiliation(s)
- Tanu Parmar
- Department of Pharmacology, and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Joseph T Ortega
- Department of Pharmacology, and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Beata Jastrzebska
- Department of Pharmacology, and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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Sechrest ER, Murphy J, Senapati S, Goldberg AFX, Park PSH, Kolandaivelu S. Loss of PRCD alters number and packaging density of rhodopsin in rod photoreceptor disc membranes. Sci Rep 2020; 10:17885. [PMID: 33087780 PMCID: PMC7577997 DOI: 10.1038/s41598-020-74628-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023] Open
Abstract
Progressive rod-cone degeneration (PRCD) is a small protein localized to photoreceptor outer segment (OS) disc membranes. Several mutations in PRCD are linked to retinitis pigmentosa (RP) in canines and humans, and while recent studies have established that PRCD is required for high fidelity disc morphogenesis, its precise role in this process remains a mystery. To better understand the part which PRCD plays in disease progression as well as its contribution to photoreceptor OS disc morphogenesis, we generated a Prcd-KO animal model using CRISPR/Cas9. Loss of PRCD from the retina results in reduced visual function accompanied by slow rod photoreceptor degeneration. We observed a significant decrease in rhodopsin levels in Prcd-KO retina prior to photoreceptor degeneration. Furthermore, ultrastructural analysis demonstrates that rod photoreceptors lacking PRCD display disoriented and dysmorphic OS disc membranes. Strikingly, atomic force microscopy reveals that many disc membranes in Prcd-KO rod photoreceptor neurons are irregular, containing fewer rhodopsin molecules and decreased rhodopsin packing density compared to wild-type discs. This study strongly suggests an important role for PRCD in regulation of rhodopsin incorporation and packaging density into disc membranes, a process which, when dysregulated, likely gives rise to the visual defects observed in patients with PRCD-associated RP.
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Affiliation(s)
- Emily R Sechrest
- Department of Pharmaceutical Sciences, One Medical Center Drive, West Virginia University, Morgantown, WV, 26506-9193, USA.,Department of Ophthalmology and Visual Sciences, Eye Institute, One Medical Center Drive, West Virginia University, Morgantown, WV, 26506-9193, USA
| | - Joseph Murphy
- Department of Ophthalmology and Visual Sciences, Eye Institute, One Medical Center Drive, West Virginia University, Morgantown, WV, 26506-9193, USA.,Department of Biochemistry, One Medical Center Drive, West Virginia University, Morgantown, WV, 26506-9193, USA
| | - Subhadip Senapati
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | | | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Saravanan Kolandaivelu
- Department of Ophthalmology and Visual Sciences, Eye Institute, One Medical Center Drive, West Virginia University, Morgantown, WV, 26506-9193, USA. .,Department of Biochemistry, One Medical Center Drive, West Virginia University, Morgantown, WV, 26506-9193, USA.
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Tian Y, Yang S, Gao S. Advances, Perspectives and Potential Engineering Strategies of Light-Gated Phosphodiesterases for Optogenetic Applications. Int J Mol Sci 2020; 21:E7544. [PMID: 33066112 PMCID: PMC7590022 DOI: 10.3390/ijms21207544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/24/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
The second messengers, cyclic adenosine 3'-5'-monophosphate (cAMP) and cyclic guanosine 3'-5'-monophosphate (cGMP), play important roles in many animal cells by regulating intracellular signaling pathways and modulating cell physiology. Environmental cues like temperature, light, and chemical compounds can stimulate cell surface receptors and trigger the generation of second messengers and the following regulations. The spread of cAMP and cGMP is further shaped by cyclic nucleotide phosphodiesterases (PDEs) for orchestration of intracellular microdomain signaling. However, localized intracellular cAMP and cGMP signaling requires further investigation. Optogenetic manipulation of cAMP and cGMP offers new opportunities for spatio-temporally precise study of their signaling mechanism. Light-gated nucleotide cyclases are well developed and applied for cAMP/cGMP manipulation. Recently discovered rhodopsin phosphodiesterase genes from protists established a new and direct biological connection between light and PDEs. Light-regulated PDEs are under development, and of demand to complete the toolkit for cAMP/cGMP manipulation. In this review, we summarize the state of the art, pros and cons of artificial and natural light-regulated PDEs, and discuss potential new strategies of developing light-gated PDEs for optogenetic manipulation.
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Affiliation(s)
| | | | - Shiqiang Gao
- Department of Neurophysiology, Physiological Institute, University of Wuerzburg, 97070 Wuerzburg, Germany; (Y.T.); (S.Y.)
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El‐Tahawy MMT, Conti I, Bonfanti M, Nenov A, Garavelli M. Tailoring Spectral and Photochemical Properties of Bioinspired Retinal Mimics by in Silico Engineering. Angew Chem Int Ed Engl 2020; 59:20619-20627. [DOI: 10.1002/anie.202008644] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Mohsen M. T. El‐Tahawy
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
- Chemistry Department Faculty of Science Damanhour University Damanhour 22511 Egypt
| | - Irene Conti
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
| | - Matteo Bonfanti
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
| | - Artur Nenov
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
| | - Marco Garavelli
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
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