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Gyawali R, Dhakal A, Wang L, Cheng J. Accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and specialized U-Net. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.02.560572. [PMID: 37873264 PMCID: PMC10592924 DOI: 10.1101/2023.10.02.560572] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Picking protein particles in cryo-electron microscopy (cryo-EM) micrographs is a crucial step in the cryo-EM-based structure determination. However, existing methods trained on a limited amount of cryo-EM data still cannot accurately pick protein particles from noisy cryo-EM images. The general foundational artificial intelligence (AI)-based image segmentation model such as Meta's Segment Anything Model (SAM) cannot segment protein particles well because their training data do not include cryo-EM images. Here, we present a novel approach (CryoSegNet) of integrating an attention-gated U-shape network (U-Net) specially designed and trained for cryo-EM particle picking and the SAM. The U-Net is first trained on a large cryo-EM image dataset and then used to generate input from original cryo-EM images for SAM to make particle pickings. CryoSegNet shows both high precision and recall in segmenting protein particles from cryo-EM micrographs, irrespective of protein type, shape, and size. On several independent datasets of various protein types, CryoSegNet outperforms two top machine learning particle pickers crYOLO and Topaz as well as SAM itself. The average resolution of density maps reconstructed from the particles picked by CryoSegNet is 3.32 Å, 7% better than 3.57 Å of Topaz and 14% better than 3.85 Å of crYOLO.
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2
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Choi SW, Kwon JW, Kang TM, Park KS, Kim SJ. Calcium homeostasis modulator 2 (Calhm2) as slowly activating membrane current channel in mouse B cells. Biochem Biophys Res Commun 2024; 699:149561. [PMID: 38280307 DOI: 10.1016/j.bbrc.2024.149561] [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: 12/13/2023] [Revised: 12/18/2023] [Accepted: 01/20/2024] [Indexed: 01/29/2024]
Abstract
In mouse B lymphocytes, an unidentified slow-activating voltage-dependent current resembling the characteristics of the Calhm family ion channel (ICalhm-L) was investigated. RT-PCR analysis revealed the presence of Calhm2 and 6 transcripts, with subsequent whole-cell patch-clamp studies indicating that the ICalhm-L is augmented by heat, alkaline pH, and low extracellular [Ca2+]. Overexpression of Calhm2, but not Calhm6, in N2A cells recapitulated ICalhm-L. Moreover, Calhm2 knockdown in Bal-17 cells abolished ICalhm-L. We firstly identify the voltage-dependent ion channel function of the Calhm2 in the mouse immune cells. ATP release assays in primary mouse B cells suggested a significant contribution of Calhm2 for purinergic signaling at physiological temperature.
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Affiliation(s)
- Si Won Choi
- Department of Physiology, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea; Wide River Institute of Immunology, Seoul National University College of Medicine, Hongcheon, Republic of Korea
| | - Jae-Won Kwon
- Department of Physiology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Tong Mook Kang
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyoung Sun Park
- Wide River Institute of Immunology, Seoul National University College of Medicine, Hongcheon, Republic of Korea.
| | - Sung Joon Kim
- Department of Physiology, Seoul National University College of Medicine, Seoul, Republic of Korea; Wide River Institute of Immunology, Seoul National University College of Medicine, Hongcheon, Republic of Korea.
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3
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Lázaro SF, Tonhati H, Oliveira HR, Silva AA, Scalez DCB, Nascimento AV, Santos DJA, Stefani G, Carvalho IS, Sandoval AF, Brito LF. Genetic parameters and genome-wide association studies for mozzarella and milk production traits, lactation length, and lactation persistency in Murrah buffaloes. J Dairy Sci 2024; 107:992-1021. [PMID: 37730179 DOI: 10.3168/jds.2023-23284] [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: 01/18/2023] [Accepted: 08/30/2023] [Indexed: 09/22/2023]
Abstract
Genetic and genomic analyses of longitudinal traits related to milk production efficiency are paramount for optimizing water buffaloes breeding schemes. Therefore, this study aimed to (1) compare single-trait random regression models under a single-step genomic BLUP setting based on alternative covariance functions (i.e., Wood, Wilmink, and Ali and Schaeffer) to describe milk (MY), fat (FY), protein (PY), and mozzarella (MZY) yields, fat-to-protein ratio (FPR), somatic cell score (SCS), lactation length (LL), and lactation persistency (LP) in Murrah dairy buffaloes (Bubalus bubalis); (2) combine the best functions for each trait under a multiple-trait framework; (3) estimate time-dependent SNP effects for all the studied longitudinal traits; and (4) identify the most likely candidate genes associated with the traits. A total of 323,140 test-day records from the first lactation of 4,588 Murrah buffaloes were made available for the study. The model included the average curve of the population nested within herd-year-season of calving, systematic effects of number of milkings per day, and age at first calving as linear and quadratic covariates, and additive genetic, permanent environment, and residual as random effects. The Wood model had the best goodness of fit based on the deviance information criterion and posterior model probabilities for all traits. Moderate heritabilities were estimated over time for most traits (0.30 ± 0.02 for MY; 0.26 ± 0.03 for FY; 0.45 ± 0.04 for PY; 0.28 ± 0.05 for MZY; 0.13 ± 0.02 for FPR; and 0.15 ± 0.03 for SCS). The heritability estimates for LP ranged from 0.38 ± 0.02 to 0.65 ± 0.03 depending on the trait definition used. Similarly, heritabilities estimated for LL ranged from 0.10 ± 0.01 to 0.14 ± 0.03. The genetic correlation estimates across days in milk (DIM) for all traits ranged from -0.06 (186-215 DIM for MY-SCS) to 0.78 (66-95 DIM for PY-MZY). The SNP effects calculated for the random regression model coefficients were used to estimate the SNP effects throughout the lactation curve (from 5 to 305 d). Numerous relevant genomic regions and candidate genes were identified for all traits, confirming their polygenic nature. The candidate genes identified contribute to a better understanding of the genetic background of milk-related traits in Murrah buffaloes and reinforce the value of incorporating genomic information in their breeding programs.
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Affiliation(s)
- Sirlene F Lázaro
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Humberto Tonhati
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Alessandra A Silva
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Daiane C B Scalez
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - André V Nascimento
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | | | - Gabriela Stefani
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Isabella S Carvalho
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Amanda F Sandoval
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
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Liao Y, Wang Y, Tao QQ, Yang C, Wang J, Cheng J, Ma J, Wu ZY, Pan RY, Yuan Z. CALHM2 V136G polymorphism reduces astrocytic ATP release and is associated with depressive symptoms and Alzheimer's disease risk. Alzheimers Dement 2023; 19:4407-4420. [PMID: 37493186 DOI: 10.1002/alz.13366] [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: 12/01/2022] [Revised: 05/19/2023] [Accepted: 06/04/2023] [Indexed: 07/27/2023]
Abstract
INTRODUCTION Depression is considered a prodromal state of Alzheimer's disease (AD), yet the underlying mechanism(s) by which depression increases the risk of AD are not known. METHODS Single-nucleotide polymorphism (SNP) analysis was used to determine the CALHM2 variants in AD patients. Cellular and molecular experiments were conducted to investigate the function of CALHM2 V136G mutation. We generated a new genetically engineered Calhm2 V136G mouse model and performed behavioral tests with these mice. RESULTS CALHM2 V136G mutation (rs232660) is significantly associated with AD. V136G mutation resulted in loss of the CALHM2 ATP-release function in astrocytes and impaired synaptic plasticity. Mice homozygous for the Calhm2 V136G allele displayed depressive-like behaviors that were rescued by administration of exogenous ATP. Moreover, Calhm2 V136G mutation predisposed mice to cognitive decline in old age. DISCUSSION CALHM2 dysfunction is a biologically relevant mechanism that may contribute to the observed clinical correlation between depression and AD.
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Affiliation(s)
- Yang Liao
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Yingyi Wang
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Qing-Qing Tao
- Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Chaoguang Yang
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jinlei Wang
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jinbo Cheng
- Center on Translational Neuroscience, College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Jun Ma
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Zhi-Ying Wu
- Department of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Rui-Yuan Pan
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zengqiang Yuan
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, China
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Chen GL, Li J, Zhang J, Zeng B. To Be or Not to Be an Ion Channel: Cryo-EM Structures Have a Say. Cells 2023; 12:1870. [PMID: 37508534 PMCID: PMC10378246 DOI: 10.3390/cells12141870] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
Ion channels are the second largest class of drug targets after G protein-coupled receptors. In addition to well-recognized ones like voltage-gated Na/K/Ca channels in the heart and neurons, novel ion channels are continuously discovered in both excitable and non-excitable cells and demonstrated to play important roles in many physiological processes and diseases such as developmental disorders, neurodegenerative diseases, and cancer. However, in the field of ion channel discovery, there are an unignorable number of published studies that are unsolid and misleading. Despite being the gold standard of a functional assay for ion channels, electrophysiological recordings are often accompanied by electrical noise, leak conductance, and background currents of the membrane system. These unwanted signals, if not treated properly, lead to the mischaracterization of proteins with seemingly unusual ion-conducting properties. In the recent ten years, the technical revolution of cryo-electron microscopy (cryo-EM) has greatly advanced our understanding of the structures and gating mechanisms of various ion channels and also raised concerns about the pore-forming ability of some previously identified channel proteins. In this review, we summarize cryo-EM findings on ion channels with molecular identities recognized or disputed in recent ten years and discuss current knowledge of proposed channel proteins awaiting cryo-EM analyses. We also present a classification of ion channels according to their architectures and evolutionary relationships and discuss the possibility and strategy of identifying more ion channels by analyzing structures of transmembrane proteins of unknown function. We propose that cross-validation by electrophysiological and structural analyses should be essentially required for determining molecular identities of novel ion channels.
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Affiliation(s)
- Gui-Lan Chen
- Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China
| | - Bo Zeng
- Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
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6
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Syrjänen JL, Epstein M, Gómez R, Furukawa H. Structure of human CALHM1 reveals key locations for channel regulation and blockade by ruthenium red. Nat Commun 2023; 14:3821. [PMID: 37380652 PMCID: PMC10307800 DOI: 10.1038/s41467-023-39388-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/08/2023] [Indexed: 06/30/2023] Open
Abstract
Calcium homeostasis modulator 1 (CALHM1) is a voltage-dependent channel involved in neuromodulation and gustatory signaling. Despite recent progress in the structural biology of CALHM1, insights into functional regulation, pore architecture, and channel blockade remain limited. Here we present the cryo-EM structure of human CALHM1, revealing an octameric assembly pattern similar to the non-mammalian CALHM1s and the lipid-binding pocket conserved across species. We demonstrate by MD simulations that this pocket preferentially binds a phospholipid over cholesterol to stabilize its structure and regulate the channel activities. Finally, we show that residues in the amino-terminal helix form the channel pore that ruthenium red binds and blocks.
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Affiliation(s)
- Johanna L Syrjänen
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Max Epstein
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Ricardo Gómez
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Hiro Furukawa
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA.
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7
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Dhakal A, Gyawali R, Wang L, Cheng J. A large expert-curated cryo-EM image dataset for machine learning protein particle picking. Sci Data 2023; 10:392. [PMID: 37349345 PMCID: PMC10287764 DOI: 10.1038/s41597-023-02280-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.
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Affiliation(s)
- Ashwin Dhakal
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA
| | - Rajan Gyawali
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA
| | - Liguo Wang
- Laboratory for BioMolecular Structure (LBMS), Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, NextGen Precision Health, University of Missouri, Columbia, MO, 65211, USA.
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8
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Danielli S, Ma Z, Pantazi E, Kumar A, Demarco B, Fischer FA, Paudel U, Weissenrieder J, Lee RJ, Joyce S, Foskett JK, Bezbradica JS. The ion channel CALHM6 controls bacterial infection-induced cellular cross-talk at the immunological synapse. EMBO J 2023; 42:e111450. [PMID: 36861806 PMCID: PMC10068325 DOI: 10.15252/embj.2022111450] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 03/03/2023] Open
Abstract
Membrane ion channels of the calcium homeostasis modulator (CALHM) family promote cell-cell crosstalk at neuronal synapses via ATP release, where ATP acts as a neurotransmitter. CALHM6, the only CALHM highly expressed in immune cells, has been linked to the induction of natural killer (NK) cell anti-tumour activity. However, its mechanism of action and broader functions in the immune system remain unclear. Here, we generated Calhm6-/- mice and report that CALHM6 is important for the regulation of the early innate control of Listeria monocytogenes infection in vivo. We find that CALHM6 is upregulated in macrophages by pathogen-derived signals and that it relocates from the intracellular compartment to the macrophage-NK cell synapse, facilitating ATP release and controlling the kinetics of NK cell activation. Anti-inflammatory cytokines terminate CALHM6 expression. CALHM6 forms an ion channel when expressed in the plasma membrane of Xenopus oocytes, where channel opening is controlled by a conserved acidic residue, E119. In mammalian cells, CALHM6 is localised to intracellular compartments. Our results contribute to the understanding of neurotransmitter-like signal exchange between immune cells that fine-tunes the timing of innate immune responses.
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Affiliation(s)
- Sara Danielli
- The Kennedy Institute of RheumatologyUniversity of OxfordOxfordUK
| | - Zhongming Ma
- Department of Physiology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Eirini Pantazi
- The Kennedy Institute of RheumatologyUniversity of OxfordOxfordUK
| | - Amrendra Kumar
- Department of Veterans AffairsTennessee Valley Healthcare SystemNashvilleTNUSA
- Department of Pathology, Microbiology, & ImmunologyVanderbilt University Medical CenterNashvilleTNUSA
| | - Benjamin Demarco
- The Kennedy Institute of RheumatologyUniversity of OxfordOxfordUK
| | - Fabian A Fischer
- The Kennedy Institute of RheumatologyUniversity of OxfordOxfordUK
| | - Usha Paudel
- Department of Physiology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Jillian Weissenrieder
- Department of Physiology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Robert J Lee
- Department of Physiology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Department of Otorhinolaryngology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Sebastian Joyce
- Department of Veterans AffairsTennessee Valley Healthcare SystemNashvilleTNUSA
- Department of Pathology, Microbiology, & ImmunologyVanderbilt University Medical CenterNashvilleTNUSA
| | - J Kevin Foskett
- Department of Physiology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Department of Cell and Developmental Biology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
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Dale N, Butler J, Dospinescu VM, Nijjar S. Channel-mediated ATP release in the nervous system. Neuropharmacology 2023; 227:109435. [PMID: 36690324 DOI: 10.1016/j.neuropharm.2023.109435] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023]
Abstract
ATP is well established as a transmitter and modulator in the peripheral and central nervous system. While conventional exocytotic release of ATP at synapses occurs, this transmitter is unusual in also being released into the extracellular space via large-pored plasma membrane channels. This review considers the channels that are known to be permeable to ATP and some of the functions of channel-mediated ATP release. While the possibility of ATP release via channels mediating volume transmission has been known for some time, localised ATP release via channels at specialised synapses made by taste cells to the afferent nerve has recently been documented in taste buds. This raises the prospect that "channel synapses" may occur in other contexts. However, volume transmission and channel synapses are not necessarily mutually exclusive. We suggest that certain glial cells in the brain stem and hypothalamus, which possess long processes and are known to release ATP, may be candidates for both modes of ATP release -channel-mediated volume transmission in the region of their somata and more localised transmission possibly via either conventional or channel synapses from their processes at distal targets. Finally, we consider the different characteristics of vesicular and channel synapses and suggest that channel synapses may be advantageous in requiring less energy than their conventional vesicular counterparts. This article is part of the Special Issue on "Purinergic Signaling: 50 years".
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Affiliation(s)
- Nicholas Dale
- School of Life Sciences, University of Warwick, Coventry, CV4, AL, UK.
| | - Jack Butler
- School of Life Sciences, University of Warwick, Coventry, CV4, AL, UK
| | | | - Sarbjit Nijjar
- School of Life Sciences, University of Warwick, Coventry, CV4, AL, UK
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10
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Taruno A, Gordon MD. Molecular and Cellular Mechanisms of Salt Taste. Annu Rev Physiol 2023; 85:25-45. [PMID: 36332657 DOI: 10.1146/annurev-physiol-031522-075853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Salt taste, the taste of sodium chloride (NaCl), is mechanistically one of the most complex and puzzling among basic tastes. Sodium has essential functions in the body but causes harm in excess. Thus, animals use salt taste to ingest the right amount of salt, which fluctuates by physiological needs: typically, attraction to low salt concentrations and rejection of high salt. This concentration-valence relationship is universally observed in terrestrial animals, and research has revealed complex peripheral codes for NaCl involving multiple taste pathways of opposing valence. Sodium-dependent and -independent pathways mediate attraction and aversion to NaCl, respectively. Gustatory sensors and cells that transduce NaCl have been uncovered, along with downstream signal transduction and neurotransmission mechanisms. However, much remains unknown. This article reviews classical and recent advances in our understanding of the molecular and cellular mechanisms underlying salt taste in mammals and insects and discusses perspectives on human salt taste.
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Affiliation(s)
- Akiyuki Taruno
- Department of Molecular Cell Physiology, Kyoto Prefectural University of Medicine, Kyoto, Japan; .,Japan Science and Technology Agency, CREST, Saitama, Japan
| | - Michael D Gordon
- Department of Zoology and Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
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11
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Vega JL, Gutiérrez C, Rojas M, Güiza J, Sáez JC. Contribution of large-pore channels to inflammation induced by microorganisms. Front Cell Dev Biol 2023; 10:1094362. [PMID: 36699007 PMCID: PMC9868820 DOI: 10.3389/fcell.2022.1094362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/22/2022] [Indexed: 01/12/2023] Open
Abstract
Plasma membrane ionic channels selectively permeate potassium, sodium, calcium, and chloride ions. However, large-pore channels are permeable to ions and small molecules such as ATP and glutamate, among others. Large-pore channels are structures formed by several protein families with little or no evolutionary linkages including connexins (Cxs), pannexins (Panxs), innexin (Inxs), unnexins (Unxs), calcium homeostasis modulator (CALHMs), and Leucine-rich repeat-containing 8 (LRRC8) proteins. Large-pore channels are key players in inflammatory cell response, guiding the activation of inflammasomes, the release of pro-inflammatory cytokines such as interleukin-1 beta (IL-1ß), and the release of adenosine-5'-triphosphate (ATP), which is considered a danger signal. This review summarizes our current understanding of large-pore channels and their contribution to inflammation induced by microorganisms, virulence factors or their toxins.
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Affiliation(s)
- José L. Vega
- Laboratory of Gap Junctions Proteins and Parasitic Diseases (GaPaL), Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile,Centro de Investigación en Inmunología y Biotecnología Biomédica de Antofagasta (CIIBBA), Universidad de Antofagasta, Antofagasta, Chile,Centro de Fisiología y Medicina de Altura (FIMEDALT), Universidad de Antofagasta, Antofagasta, Chile,*Correspondence: José L. Vega,
| | - Camila Gutiérrez
- Laboratory of Gap Junctions Proteins and Parasitic Diseases (GaPaL), Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Mauro Rojas
- Laboratory of Gap Junctions Proteins and Parasitic Diseases (GaPaL), Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Juan Güiza
- Laboratory of Gap Junctions Proteins and Parasitic Diseases (GaPaL), Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Juan C. Sáez
- Centro Interdisciplinario de Neurociencias de Valparaíso (CINV), Instituto de Neurociencias, Universidad de Valparaíso, Valparaíso, Chile
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12
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Kwon JW, Jeon YK, Kim SJ. Bidirectional sensitivity of CALHM1 channel to protons from both sides of plasma membrane. Am J Physiol Cell Physiol 2023; 324:C98-C112. [PMID: 36409172 DOI: 10.1152/ajpcell.00250.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Calcium homeostasis modulator 1 (CALHM1), a newly discovered voltage-dependent nonselective ion channel, has drawn attention for its role in neuronal activity and taste sensation. Its sluggish voltage-dependent activation is facilitated by lowering extracellular Ca2+ concentration ([Ca2+]e). Here, we investigated the effects of extracellular and intracellular pH (pHe and pHi) on human CALHM1. When normalized to the amplitude of the CALHM1 current (ICALHM1) under whole cell patch clamp at symmetrical pH 7.4, ICALHM1 decreased at acidic pHe or pHi, whereas it sharply increased at alkaline pHe or pHi. The effects of pH were preserved in the inside-out configuration. The voltage dependence of ICALHM1 showed leftward and rightward shifts at alkaline and acidic pHe and pHi, respectively. Site-directed mutagenesis of the water-accessible charged residues of the pore and nearby domains revealed that E17, K229, E233, D257, and E259 are nonadditively responsible for facilitation at alkaline pHi. Identification of the pHe-sensing residue was not possible because mutation of putative residues impaired membrane expression, resulting in undetectable ICALHM1. Alkaline pHe-dependent facilitation appeared gradually with depolarization, suggesting that the sensitivity to pHe might be due to H+ diffusion through the open-state CALHM1. At pHe 6.2, decreased [Ca2+]e could not recover the inhibited ICALHM1 but further augmented the increased ICALHM1 at pHe 8.6, suggesting that unidentified common residues might contribute to the [Ca2+]e and acidic pHe. This study is the first, to our knowledge, to demonstrate the remarkable pH sensitivity of CALHM1, which might contribute to the pH-dependent modulation of neuronal excitability or taste sensation.
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Affiliation(s)
- Jae Won Kwon
- Department of Physiology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Keul Jeon
- Department of Physiology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Joon Kim
- Department of Physiology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.,Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
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13
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Alhadyan SK, Sivaraman V, Onyenwoke RU. E-cigarette Flavors, Sensory Perception, and Evoked Responses. Chem Res Toxicol 2022; 35:2194-2209. [PMID: 36480683 DOI: 10.1021/acs.chemrestox.2c00268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The chemosensory experiences evoked by flavors encompass a number of unique sensations that include olfactory stimuli (smell), gustatory stimuli (taste, i.e., salty, sweet, sour, bitter, and umami (also known as "savoriness")), and chemesthesis (touch). As such, the responses evoked by flavors are complex and, as briefly stated above, involve multiple perceptive mechanisms. The practice of adding flavorings to tobacco products dates back to the 17th century but is likely much older. More recently, the electronic cigarette or "e-cigarette" and its accompanying flavored e-liquids emerged on to the global market. These new products contain no combustible tobacco but often contain large concentrations (reported from 0 to more than 50 mg/mL) of nicotine as well as numerous flavorings and/or flavor chemicals. At present, there are more than 400 e-cigarette brands available along with potentially >15,000 different/unique flavored products. However, surprisingly little is known about the flavors/flavor chemicals added to these products, which can account for >1% by weight of some e-liquids, and their resultant chemosensory experiences, and the US FDA has done relatively little, until recently, to regulate these products. This article will discuss e-cigarette flavors and flavor chemicals, their elicited responses, and their sensory effects in some detail.
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Affiliation(s)
- Shatha K Alhadyan
- Department of Pharmaceutical Sciences, North Carolina Central University, Durham, North Carolina 27707, United States
| | - Vijay Sivaraman
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, North Carolina 27707, United States
| | - Rob U Onyenwoke
- Department of Pharmaceutical Sciences, North Carolina Central University, Durham, North Carolina 27707, United States.,Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University, Durham, North Carolina 27707, United States
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14
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Suppression of Selective Voltage-Gated Calcium Channels Alleviates Neuronal Degeneration and Dysfunction through Glutathione S-Transferase-Mediated Oxidative Stress Resistance in a Caenorhabditis elegans Model of Alzheimer's Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8287633. [PMID: 36600949 PMCID: PMC9806690 DOI: 10.1155/2022/8287633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/18/2022] [Accepted: 10/31/2022] [Indexed: 12/05/2022]
Abstract
Calcium homeostasis plays a vital role in protecting against Alzheimer's disease (AD). In this study, amyloid-β (Aβ)-induced C. elegans models of AD were used to elucidate the mechanisms underlying calcium homeostasis in AD. Calcium acetate increased the intracellular calcium content, exacerbated Aβ 1-42 aggregation, which is closely associated with oxidative stress, aggravated neuronal degeneration and dysfunction, and shortened the lifespan of the C. elegans models. Ethylene glycol tetraacetic acid (EGTA) and nimodipine were used to decrease the intracellular calcium content. Both EGTA and nimodipine showed remarkable inhibitory effects on Aβ 1-42 aggregations by increasing oxidative stress resistance. Moreover, both compounds significantly delayed the onset of Aβ-induced paralysis, rescued memory deficits, ameliorated behavioral dysfunction, decreased the vulnerability of two major (GABAergic and dopaminergic) neurons and synapses, and extended the lifespan of the C. elegans AD models. Furthermore, RNA sequencing of nimodipine-treated worms revealed numerous downstream differentially expressed genes related to calcium signaling. Nimodipine-induced inhibition of selective voltage-gated calcium channels was shown to activate other calcium channels of the plasma membrane (clhm-1) and endoplasmic reticulum (unc-68), in addition to sodium-calcium exchanger channels (ncx-1). These channels collaborated to activate downstream events to resist oxidative stress through glutathione S-transferase activity mediated by HPGD and skn-1, as verified by RNA interference. These results may be applied for the treatment of Alzheimer's disease.
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15
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Clupper M, Gill R, Elsayyid M, Touroutine D, Caplan JL, Tanis JE. Kinesin-2 motors differentially impact biogenesis of extracellular vesicle subpopulations shed from sensory cilia. iScience 2022; 25:105262. [PMID: 36304122 PMCID: PMC9593189 DOI: 10.1016/j.isci.2022.105262] [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: 01/12/2022] [Revised: 07/13/2022] [Accepted: 09/26/2022] [Indexed: 01/21/2023] Open
Abstract
Extracellular vesicles (EVs) are bioactive lipid-bilayer enclosed particles released from nearly all cells. One specialized site for EV shedding is the primary cilium. Here, we discover the conserved ion channel CLHM-1 as a ciliary EV cargo. Imaging of EVs released from sensory neuron cilia of Caenorhabditis elegans expressing fluorescently tagged CLHM-1 and TRP polycystin-2 channel PKD-2 shows enrichment of these cargoes in distinct EV subpopulations that are differentially shed in response to mating partner availability. PKD-2 alone is present in EVs shed from the cilium distal tip, whereas CLHM-1 EVs bud from a secondary site(s), including the ciliary base. Heterotrimeric and homodimeric kinesin-2 motors have discrete impacts on PKD-2 and CLHM-1 colocalization in both cilia and EVs. Total loss of kinesin-2 activity decreases shedding of PKD-2 but not CLHM-1 EVs. Our data demonstrate that anterograde intraflagellar transport is required for selective enrichment of protein cargoes into heterogeneous EVs with different signaling potentials.
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Affiliation(s)
- Michael Clupper
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Rachael Gill
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Malek Elsayyid
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Denis Touroutine
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Jeffrey L. Caplan
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Jessica E. Tanis
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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16
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Zhou Y, Moscovich A, Bartesaghi A. Data-driven determination of number of discrete conformations in single-particle cryo-EM. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 221:106892. [PMID: 35597206 PMCID: PMC10131080 DOI: 10.1016/j.cmpb.2022.106892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND OBJECTIVE One of the strengths of single-particle cryo-EM compared to other structural determination techniques is its ability to image heterogeneous samples containing multiple molecular species, different oligomeric states or distinct conformations. This is achieved using routines for in-silico 3D classification that are now well established in the field and have successfully been used to characterize the structural heterogeneity of important biomolecules. These techniques, however, rely on expert-user knowledge and trial-and-error experimentation to determine the correct number of conformations, making it a labor intensive, subjective, and difficult to reproduce procedure. METHODS We propose an approach to address the problem of automatically determining the number of discrete conformations present in heterogeneous single-particle cryo-EM datasets. We do this by systematically evaluating all possible partitions of the data and selecting the result that maximizes the average variance of similarities measured between particle images and the corresponding 3D reconstructions. RESULTS Using this strategy, we successfully analyzed datasets of heterogeneous protein complexes, including: 1) in-silico mixtures obtained by combining closely related antibody-bound HIV-1 Env trimers and other important membrane channels, and 2) naturally occurring mixtures from diverse and dynamic protein complexes representing varying degrees of structural heterogeneity and conformational plasticity. CONCLUSIONS The availability of unsupervised strategies for 3D classification combined with existing approaches for fully automatic pre-processing and 3D refinement, represents an important step towards converting single-particle cryo-EM into a high-throughput technique.
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Affiliation(s)
- Ye Zhou
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Amit Moscovich
- Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv, Israel
| | - Alberto Bartesaghi
- Department of Computer Science, Duke University, Durham, NC 27708, USA; Department of Biochemistry, Duke University School of Medicine, Durham, NC 27708, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA.
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17
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Ren Y, Li Y, Wang Y, Wen T, Lu X, Chang S, Zhang X, Shen Y, Yang X. Cryo-EM structure of the heptameric calcium homeostasis modulator 1 channel. J Biol Chem 2022; 298:101838. [PMID: 35339491 PMCID: PMC9035704 DOI: 10.1016/j.jbc.2022.101838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 12/01/2022] Open
Abstract
Calcium homeostasis modulator 1 (CALHM1) is a voltage- and Ca2+-gated ATP channel that plays an important role in neuronal signaling. However, as the previously reported CALHM structures are all in the ATP-conducting state, the gating mechanism of ATP permeation is still elusive. Here, we report cryo-EM reconstructions of two Danio rerio CALHM1 heptamers with ordered or flexible long C-terminal helices at resolutions of 3.2 Å and 2.9 Å, respectively, and one D. rerio CALHM1 octamer with flexible long C-terminal helices at a resolution of 3.5 Å. Structural analysis shows that the heptameric CALHM1s are in an ATP-nonconducting state with a central pore diameter of approximately 6.6 Å. Compared with those inside the octameric CALHM1, the N-helix inside the heptameric CALHM1 is in the “down” position to avoid steric clashing with the adjacent TM1 helix. Molecular dynamics simulations show that as the N-helix moves from the “down” position to the “up” position, the pore size of ATP molecule permeation increases significantly. Our results provide important information for elucidating the mechanism of ATP molecule permeation in the CALHM1 channel.
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Affiliation(s)
- Yue Ren
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Yang Li
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Yaojie Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Tianlei Wen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Xuhang Lu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Shenghai Chang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, China
| | - Xing Zhang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuequan Shen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; Synergetic Innovation Center of Chemical Science and Engineering, 94 Weijin Road, Tianjin 300071, China.
| | - Xue Yang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.
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18
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Kuzuya M, Hirano H, Hayashida K, Watanabe M, Kobayashi K, Terada T, Mahmood MI, Tama F, Tani K, Fujiyoshi Y, Oshima A. Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids. Sci Signal 2022; 15:eabg6941. [PMID: 35133866 DOI: 10.1126/scisignal.abg6941] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pannexin (PANX) family proteins form large-pore channels that mediate purinergic signaling. We analyzed the cryo-EM structures of human PANX1 in lipid nanodiscs to elucidate the gating mechanism and its regulation by the amino terminus in phospholipids. The wild-type channel has an amino-terminal funnel in the pore, but in the presence of the inhibitor probenecid, a cytoplasmically oriented amino terminus and phospholipids obstruct the pore. Functional analysis using whole-cell patch-clamp and oocyte voltage clamp showed that PANX1 lacking the amino terminus did not open and had a dominant negative effect on channel activity, thus confirming that the amino-terminal domain played an essential role in channel opening. These observations suggest that dynamic conformational changes in the amino terminus of human PANX1 are associated with lipid movement in and out of the pore. Moreover, the data provide insight into the gating mechanism of PANX1 and, more broadly, other large-pore channels.
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Affiliation(s)
- Maki Kuzuya
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hidemi Hirano
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kenichi Hayashida
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Masakatsu Watanabe
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | | | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyō-ku, Tokyo 113-8657, Japan
| | - Md Iqbal Mahmood
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Florence Tama
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Kazutoshi Tani
- Graduate School of Medicine, Mie University, 2-174 Edobashi Tsu, Mie 514-8507, Japan
| | - Yoshinori Fujiyoshi
- Advanced Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyō-ku, Tokyo 113-8510, Japan.,CeSPIA Inc., Otemachi, Chiyoda, Tokyo 100-0004, Japan
| | - Atsunori Oshima
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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19
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Kwon JW, Jeon YK, Kim J, Kim SJ, Kim SJ. Intramolecular Disulfide Bonds for Biogenesis of CALHM1 Ion Channel Are Dispensable for Voltage-Dependent Activation. Mol Cells 2021; 44:758-769. [PMID: 34711692 PMCID: PMC8560582 DOI: 10.14348/molcells.2021.0131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/19/2021] [Accepted: 09/06/2021] [Indexed: 11/27/2022] Open
Abstract
Calcium homeostasis modulator 1 (CALHM1) is a membrane protein with four transmembrane helices that form an octameric ion channel with voltage-dependent activation. There are four conserved cysteine (Cys) residues in the extracellular domain that form two intramolecular disulfide bonds. We investigated the roles of C42-C127 and C44-C161 in human CALHM1 channel biogenesis and the ionic current (ICALHM1). Replacing Cys with Ser or Ala abolished the membrane trafficking as well as ICALHM1. Immunoblotting analysis revealed dithiothreitol-sensitive multimeric CALHM1, which was markedly reduced in C44S and C161S, but preserved in C42S and C127S. The mixed expression of C42S and wild-type did not show a dominant-negative effect. While the heteromeric assembly of CALHM1 and CALHM3 formed active ion channels, the co-expression of C42S and CALHM3 did not produce functional channels. Despite the critical structural role of the extracellular cysteine residues, a treatment with the membrane-impermeable reducing agent tris(2-carboxyethyl) phosphine (TCEP, 2 mM) did not affect ICALHM1 for up to 30 min. Interestingly, incubation with TCEP (2 mM) for 2-6 h reduced both ICALHM1 and the surface expression of CALHM1 in a time-dependent manner. We propose that the intramolecular disulfide bonds are essential for folding, oligomerization, trafficking and maintenance of CALHM1 in the plasma membrane, but dispensable for the voltage-dependent activation once expressed on the plasma membrane.
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Affiliation(s)
- Jae Won Kwon
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Young Keul Jeon
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jinsung Kim
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Sang Jeong Kim
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Sung Joon Kim
- Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Korea
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20
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Yamashita K, Palmer CM, Burnley T, Murshudov GN. Cryo-EM single-particle structure refinement and map calculation using Servalcat. Acta Crystallogr D Struct Biol 2021; 77:1282-1291. [PMID: 34605431 PMCID: PMC8489229 DOI: 10.1107/s2059798321009475] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/11/2021] [Indexed: 11/10/2022] Open
Abstract
In 2020, cryo-EM single-particle analysis achieved true atomic resolution thanks to technological developments in hardware and software. The number of high-resolution reconstructions continues to grow, increasing the importance of the accurate determination of atomic coordinates. Here, a new Python package and program called Servalcat is presented that is designed to facilitate atomic model refinement. Servalcat implements a refinement pipeline using the program REFMAC5 from the CCP4 package. After the refinement, Servalcat calculates a weighted Fo - Fc difference map, which is derived from Bayesian statistics. This map helps manual and automatic model building in real space, as is common practice in crystallography. The Fo - Fc map helps in the visualization of weak features including hydrogen densities. Although hydrogen densities are weak, they are stronger than in the electron-density maps produced by X-ray crystallography, and some H atoms are even visible at ∼1.8 Å resolution. Servalcat also facilitates atomic model refinement under symmetry constraints. If point-group symmetry has been applied to the map during reconstruction, the asymmetric unit model is refined with the appropriate symmetry constraints.
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Affiliation(s)
- Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Colin M. Palmer
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0FA, United Kingdom
| | - Tom Burnley
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0FA, United Kingdom
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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21
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Gaete PS, Lillo MA, López W, Liu Y, Jiang W, Luo Y, Harris AL, Contreras JE. A novel voltage-clamp/dye uptake assay reveals saturable transport of molecules through CALHM1 and connexin channels. J Gen Physiol 2021; 152:211474. [PMID: 33074302 PMCID: PMC7579738 DOI: 10.1085/jgp.202012607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022] Open
Abstract
Large-pore channels permeable to small molecules such as ATP, in addition to atomic ions, are emerging as important regulators in health and disease. Nonetheless, their mechanisms of molecular permeation and selectivity remain mostly unexplored. Combining fluorescence microscopy and electrophysiology, we developed a novel technique that allows kinetic analysis of molecular permeation through connexin and CALHM1 channels in Xenopus oocytes rendered translucent. Using this methodology, we found that (1) molecular flux through these channels saturates at low micromolar concentrations, (2) kinetic parameters of molecular transport are sensitive to modulators of channel gating, (3) molecular transport and ionic currents can be differentially affected by mutation and gating, and (4) N-terminal regions of these channels control transport kinetics and permselectivity. Our methodology allows analysis of how human disease-causing mutations affect kinetic properties and permselectivity of molecular signaling and enables the study of molecular mechanisms, including selectivity and saturability, of molecular transport in other large-pore channels.
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Affiliation(s)
- Pablo S Gaete
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - Mauricio A Lillo
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - William López
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - Yu Liu
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - Wenjuan Jiang
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA
| | - Yun Luo
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA
| | - Andrew L Harris
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
| | - Jorge E Contreras
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ
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22
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Rodriguez M, Chen J, Jain PP, Babicheva A, Xiong M, Li J, Lai N, Zhao T, Hernandez M, Balistrieri A, Parmisano S, Simonson T, Breen E, Valdez-Jasso D, Thistlethwaite PA, Shyy JYJ, Wang J, Garcia JGN, Makino A, Yuan JXJ. Upregulation of Calcium Homeostasis Modulators in Contractile-To-Proliferative Phenotypical Transition of Pulmonary Arterial Smooth Muscle Cells. Front Physiol 2021; 12:714785. [PMID: 34408668 PMCID: PMC8364962 DOI: 10.3389/fphys.2021.714785] [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: 05/25/2021] [Accepted: 07/13/2021] [Indexed: 12/14/2022] Open
Abstract
Excessive pulmonary artery (PA) smooth muscle cell (PASMC) proliferation and migration are implicated in the development of pathogenic pulmonary vascular remodeling characterized by concentric arterial wall thickening and arteriole muscularization in patients with pulmonary arterial hypertension (PAH). Pulmonary artery smooth muscle cell contractile-to-proliferative phenotypical transition is a process that promotes pulmonary vascular remodeling. A rise in cytosolic Ca2+ concentration [(Ca2+)cyt] in PASMCs is a trigger for pulmonary vasoconstriction and a stimulus for pulmonary vascular remodeling. Here, we report that the calcium homeostasis modulator (CALHM), a Ca2+ (and ATP) channel that is allosterically regulated by voltage and extracellular Ca2+, is upregulated during the PASMC contractile-to-proliferative phenotypical transition. Protein expression of CALHM1/2 in primary cultured PASMCs in media containing serum and growth factors (proliferative PASMC) was significantly greater than in freshly isolated PA (contractile PASMC) from the same rat. Upregulated CALHM1/2 in proliferative PASMCs were associated with an increased ratio of pAKT/AKT and pmTOR/mTOR and an increased expression of the cell proliferation marker PCNA, whereas serum starvation and rapamycin significantly downregulated CALHM1/2. Furthermore, CALHM1/2 were upregulated in freshly isolated PA from rats with monocrotaline (MCT)-induced PH and in primary cultured PASMC from patients with PAH in comparison to normal controls. Intraperitoneal injection of CGP 37157 (0.6 mg/kg, q8H), a non-selective blocker of CALHM channels, partially reversed established experimental PH. These data suggest that CALHM upregulation is involved in PASMC contractile-to-proliferative phenotypical transition. Ca2+ influx through upregulated CALHM1/2 may play an important role in the transition of sustained vasoconstriction to excessive vascular remodeling in PAH or precapillary PH. Calcium homeostasis modulator could potentially be a target to develop novel therapies for PAH.
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Affiliation(s)
- Marisela Rodriguez
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States.,Department of Pediatrics, Tucson, AZ, United States
| | - Jiyuan Chen
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States.,State Key Laboratory of Respiratory Diseases, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Pritesh P Jain
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States
| | - Aleksandra Babicheva
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States
| | - Mingmei Xiong
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States.,State Key Laboratory of Respiratory Diseases, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jifeng Li
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States.,Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Ning Lai
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States.,State Key Laboratory of Respiratory Diseases, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Tengteng Zhao
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States
| | - Moises Hernandez
- Division of Cardiothoracic Surgery, Department of Surgery, La Jolla, CA, United States
| | - Angela Balistrieri
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States
| | - Sophia Parmisano
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States
| | - Tatum Simonson
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States
| | - Ellen Breen
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States
| | - Daniela Valdez-Jasso
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | | | - John Y-J Shyy
- Division of Cardiovascular Medicine, Department of Medicine, La Jolla, CA, United States
| | - Jian Wang
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States.,State Key Laboratory of Respiratory Diseases, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Joe G N Garcia
- Department of Medicine, The University of Arizona, Tucson, AZ, United States
| | - Ayako Makino
- Division of Endocrinology and Metabolism, La Jolla, CA, United States
| | - Jason X-J Yuan
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, La Jolla, CA, United States
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23
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Syrjanen J, Michalski K, Kawate T, Furukawa H. On the molecular nature of large-pore channels. J Mol Biol 2021; 433:166994. [PMID: 33865869 PMCID: PMC8409005 DOI: 10.1016/j.jmb.2021.166994] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 12/25/2022]
Abstract
Membrane transport is a fundamental means to control basic cellular processes such as apoptosis, inflammation, and neurodegeneration and is mediated by a number of transporters, pumps, and channels. Accumulating evidence over the last half century has shown that a type of so-called "large-pore channel" exists in various tissues and organs in gap-junctional and non-gap-junctional forms in order to flow not only ions but also metabolites such as ATP. They are formed by a number of protein families with little or no evolutionary linkages including connexin, innexin, pannexin, leucine-rich repeat-containing 8 (LRRC8), and calcium homeostasis modulator (CALHM). This review summarizes the history and concept of large-pore channels starting from connexin gap junction channels to the more recent developments in innexin, pannexin, LRRC8, and CALHM. We describe structural and functional features of large-pore channels that are crucial for their diverse functions on the basis of available structures.
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Affiliation(s)
- Johanna Syrjanen
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kevin Michalski
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Toshimitsu Kawate
- Department of Molecular Medicine, Fields of Biochemistry, Molecular, and Cell Biology (BMCB), and Biophysics, Cornell University, Ithaca, NY 14853, USA
| | - Hiro Furukawa
- W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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24
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Okui M, Murakami T, Sun H, Ikeshita C, Kanamura N, Taruno A. Posttranslational regulation of CALHM1/3 channel: N-linked glycosylation and S-palmitoylation. FASEB J 2021; 35:e21527. [PMID: 33788965 DOI: 10.1096/fj.202002632r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/08/2021] [Accepted: 03/01/2021] [Indexed: 11/11/2022]
Abstract
Among calcium homeostasis modulator (CALHM) family members, CALHM1 and 3 together form a voltage-gated large-pore ion channel called CALHM1/3. CALHM1/3 plays an essential role in taste perception by mediating neurotransmitter release at channel synapses of taste bud cells. However, it is poorly understood how CALHM1/3 is regulated. Biochemical analyses of the two subunits following site-directed mutagenesis and pharmacological treatments established that both CALHM1 and 3 were N-glycosylated at single Asn residues in their second extracellular loops. Biochemical and electrophysiological studies revealed that N-glycan acquisition on CALHM1 and 3, respectively, controls the biosynthesis and gating kinetics of the CALHM1/3 channel. Furthermore, failure in subsequent remodeling of N-glycans decelerated the gating kinetics. Thus, the acquisition of N-glycans on both subunits and their remodeling differentially contribute to the functional expression of CALHM1/3. Meanwhile, metabolic labeling and acyl-biotin exchange assays combined with genetic modification demonstrated that CALHM3 was reversibly palmitoylated at three intracellular Cys residues. Screening of the DHHC protein acyltransferases identified DHHC3 and 15 as CALHM3 palmitoylating enzymes. The palmitoylation-deficient mutant CALHM3 showed a normal degradation rate and interaction with CALHM1. However, the same mutation markedly attenuated the channel activity but not surface localization of CALHM1/3, suggesting that CALHM3 palmitoylation is a critical determinant of CALHM1/3 activity but not its formation or forward trafficking. Overall, this study characterized N-glycosylation and S-palmitoylation of CALHM1/3 subunits and clarified their differential contributions to its functional expression, providing insights into the fine control of the CALHM1/3 channel and associated physiological processes.
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Affiliation(s)
- Motoki Okui
- Department of Molecular Cell Physiology, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Dental Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tatsuro Murakami
- Department of Molecular Cell Physiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hongxin Sun
- Department of Molecular Cell Physiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Chiaki Ikeshita
- Department of Molecular Cell Physiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Narisato Kanamura
- Department of Dental Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Akiyuki Taruno
- Department of Molecular Cell Physiology, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Japan Science and Technology Agency, PRESTO, Kawaguchi, Japan
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25
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Bhat EA, Sajjad N, Banawas S, Khan J. Human CALHM5: Insight in large pore lipid gating ATP channel and associated neurological pathologies. Mol Cell Biochem 2021; 476:3711-3718. [PMID: 34089472 DOI: 10.1007/s11010-021-04198-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Recently calcium homeostasis modulators (CALHMs) are identified as ATP release channels play crucial role in functioning of neurons including gustatory signaling and neuronal excitability. Pathologies of Alzheimer's disease and depression have been associated with the dysfunction of CALHMs. Recently, CALHMs has been emerged as an important therapeutic research particularly in neurobiological studies. CALHM1 is most extensively studied among CALHMs and is an ATP and ion channel that is activated by membrane depolarization or removal of extracellular Ca2+. Despite the emerged role of CALHM5 shown by an recently assembled data; however, the neuronal function remains obscure until the first Cryo-EM structure of CALHM5 was recently solved by various research group which acts as a template to study the hidden functional properties of the CALHM5 protein based on structure function mechanism. It provides insight in some of the different pathophysiological roles. CALHM5 structure showed an abnormally large pore channel structure assembled as an undecamer with four transmembrane helices (TM1-TM4), an N-terminal helix (NTH), an extracellular loop region and an intracellular C-terminal domain (CTD) that consists of three α-helices CH1-3. The TM1 and NTH were always poorly defined among all CALHMs; however, these regions were well defined in CALHM5 channel structure. In this context, this review will provide insight in structure, function and mechanism to understand its significant role in pathological diseases particularly in Alzheimer's disease. Moreover, it focuses on CALHM5 structure and recent associated properties based on Cryo-EM research.
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Affiliation(s)
- Eijaz Ahmed Bhat
- Life Science Institute, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China. .,Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India.
| | - Nasreena Sajjad
- Department of Biochemistry, University of Kashmir, Hazratbal, Jammu and Kashmir, India
| | - Saeed Banawas
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, 11952, Kingdom of Saudi Arabia. .,Health and Basic Sciences Research Center, Majmaah University, Majmaah, 11952, Saudi Arabia. .,Departments of Biomedical Sciences, Oregon State University, Corvallis, OR, 97331, USA.
| | - Johra Khan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, 11952, Kingdom of Saudi Arabia.,Health and Basic Sciences Research Center, Majmaah University, Majmaah, 11952, Saudi Arabia
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26
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Cryo-EM structures of human calcium homeostasis modulator 5. Cell Discov 2020; 6:81. [PMID: 33298887 PMCID: PMC7652935 DOI: 10.1038/s41421-020-00228-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 10/09/2020] [Indexed: 01/03/2023] Open
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27
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Taruno A, Nomura K, Kusakizako T, Ma Z, Nureki O, Foskett JK. Taste transduction and channel synapses in taste buds. Pflugers Arch 2020; 473:3-13. [PMID: 32936320 DOI: 10.1007/s00424-020-02464-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 07/29/2020] [Accepted: 09/07/2020] [Indexed: 12/31/2022]
Abstract
The variety of taste sensations, including sweet, umami, bitter, sour, and salty, arises from diverse taste cells, each of which expresses specific taste sensor molecules and associated components for downstream signal transduction cascades. Recent years have witnessed major advances in our understanding of the molecular mechanisms underlying transduction of basic tastes in taste buds, including the identification of the bona fide sour sensor H+ channel OTOP1, and elucidation of transduction of the amiloride-sensitive component of salty taste (the taste of sodium) and the TAS1R-independent component of sweet taste (the taste of sugar). Studies have also discovered an unconventional chemical synapse termed "channel synapse" which employs an action potential-activated CALHM1/3 ion channel instead of exocytosis of synaptic vesicles as the conduit for neurotransmitter release that links taste cells to afferent neurons. New images of the channel synapse and determinations of the structures of CALHM channels have provided structural and functional insights into this unique synapse. In this review, we discuss the current view of taste transduction and neurotransmission with emphasis on recent advances in the field.
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Affiliation(s)
- Akiyuki Taruno
- Department of Molecular Cell Physiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan. .,Japan Science and Technology Agency, PRESTO, Kawaguchi, Saitama, Japan.
| | - Kengo Nomura
- Department of Molecular Cell Physiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Zhongming Ma
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - J Kevin Foskett
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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