1
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Gao J, Li H, Lv H, Cheng X. Mutation of TRPML1 Channel and Pathogenesis of Neurodegeneration in Haimeria. Mol Neurobiol 2024; 61:4992-5001. [PMID: 38157120 DOI: 10.1007/s12035-023-03874-y] [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: 10/13/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Neurodegenerative diseases, a group of debilitating disorders, have garnered increasing attention due to their escalating prevalence, particularly among aging populations. Alzheimer's disease (AD) reigns as a prominent exemplar within this category, distinguished by its relentless progression of cognitive impairment and the accumulation of aberrant protein aggregates within the intricate landscape of the brain. While the intricate pathogenesis of neurodegenerative diseases has been the subject of extensive investigation, recent scientific inquiry has unveiled a novel player in this complex scenario-transient receptor potential mucolipin 1 (TRPML1) channels. This comprehensive review embarks on an exploration of the intricate interplay between TRPML1 channels and neurodegenerative diseases, with an explicit spotlight on Alzheimer's disease. It immerses itself in the intricate molecular mechanisms governing TRPML1 channel functionality and elucidates their profound implications for the well-being of neurons. Furthermore, the review ventures into the realm of therapeutic potential, pondering the possibilities and challenges associated with targeting TRPML1 channels as a promising avenue for the amelioration of neurodegenerative disorders. As we traverse this multifaceted terrain of neurodegeneration and the enigmatic role of TRPML1 channels, we embark on a journey that not only broadens our understanding of the intricate machinery governing neuronal health but also holds promise for the development of innovative therapeutic interventions in the relentless battle against neurodegenerative diseases.
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Affiliation(s)
- Junqing Gao
- Department of Neurology, Shaanxi Provincial People's Hospital, Shaanxi, Xi'an, 710068, China
| | - Huanhuan Li
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Shaanxi, Xi'an, 710038, China
| | - Hua Lv
- Department of Neurology, Shaanxi Provincial People's Hospital, Shaanxi, Xi'an, 710068, China
| | - Xiansong Cheng
- Department of Neurology, Shaanxi Provincial People's Hospital, Shaanxi, Xi'an, 710068, China.
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2
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Wang X, Zhu H, Terashi G, Taluja M, Kihara D. DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576370. [PMID: 38328203 PMCID: PMC10849514 DOI: 10.1101/2024.01.20.576370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Cryogenic electron microscopy (cryo-EM) has now been widely used for determining multi-chain protein complexes. However, modeling a complex structure is challenging particularly when the map resolution is low, typically in the intermediate resolution range of 5 to 10 Å. Within this resolution range, even accurate structure fitting is difficult, let alone de novo modeling. To address this challenge, here we present DiffModeler, a fully automated method for modeling protein complex structures. DiffModeler employs a diffusion model for backbone tracing and integrates AlphaFold2-predicted single-chain structures for structure fitting. Extensive testing on cryo-EM maps at intermediate resolutions demonstrates the exceptional accuracy of DiffModeler in structure modeling, achieving an average TM-Score of 0.92, surpassing existing methodologies significantly. Notably, DiffModeler successfully modeled a protein complex composed of 47 chains and 13,462 residues, achieving a high TM-Score of 0.94. Further benchmarking at low resolutions (10-20 Å confirms its versatility, demonstrating plausible performance. Moreover, when coupled with CryoREAD, DiffModeler excels in constructing protein-DNA/RNA complex structures for near-atomic resolution maps (0-5 Å), showcasing state-of-the-art performance with average TM-Scores of 0.88 and 0.91 across two datasets.
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Affiliation(s)
- Xiao Wang
- Department of Computer Science, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Han Zhu
- Department of Computer Science, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Manav Taluja
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
- School of Computer Science and Engineering, Vellore Institute of Technology, Tamil Nadu 642014, India
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, Indiana, 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
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3
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Abstract
This chapter explores the existing structural and functional studies on the endo-lysosomal channel TRPML1 and its analogs TRPML2, TRPML3. These channels represent the mucolipin subfamily of the TRP channel superfamily comprising important roles in sensory physiology, ion homeostasis, and signal transduction. Since 2016, numerous structures have been determined for all three members using either cryo-EM or X-ray crystallography. These studies along with recent functional analysis have considerably strengthened our knowledge on TRPML channels and its related endo-lysosomal function. This chapter, together with relevant reports in other chapters from this handbook, provides an informative and detailed tool to study the endo-lysosomal cation channels.
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Affiliation(s)
- Michael Fine
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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4
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Gaudioso Á, Silva TP, Ledesma MD. Models to study basic and applied aspects of lysosomal storage disorders. Adv Drug Deliv Rev 2022; 190:114532. [PMID: 36122863 DOI: 10.1016/j.addr.2022.114532] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 08/05/2022] [Accepted: 09/04/2022] [Indexed: 01/24/2023]
Abstract
The lack of available treatments and fatal outcome in most lysosomal storage disorders (LSDs) have spurred research on pathological mechanisms and novel therapies in recent years. In this effort, experimental methodology in cellular and animal models have been developed, with aims to address major challenges in many LSDs such as patient-to-patient variability and brain condition. These techniques and models have advanced knowledge not only of LSDs but also for other lysosomal disorders and have provided fundamental insights into the biological roles of lysosomes. They can also serve to assess the efficacy of classical therapies and modern drug delivery systems. Here, we summarize the techniques and models used in LSD research, which include both established and recently developed in vitro methods, with general utility or specifically addressing lysosomal features. We also review animal models of LSDs together with cutting-edge technology that may reduce the need for animals in the study of these devastating diseases.
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Affiliation(s)
- Ángel Gaudioso
- Centro Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Teresa P Silva
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
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5
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Identification of putative binding interface of PI(3,5)P2 lipid on rice black-streaked dwarf virus (RBSDV) P10 protein. Virology 2022; 570:81-95. [DOI: 10.1016/j.virol.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/15/2022] [Accepted: 03/27/2022] [Indexed: 11/18/2022]
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6
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Unraveling the Cardiac Effects Induced by Carvacrol in Spontaneously Hypertensive Rats: Involvement of Transient Receptor Potential Melastatin Subfamily 4 and 7 Channels. J Cardiovasc Pharmacol 2022; 79:206-216. [PMID: 35099165 DOI: 10.1097/fjc.0000000000001165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/05/2021] [Indexed: 11/26/2022]
Abstract
ABSTRACT Accumulating evidence indicates that transient receptor potential (TRP) channels are involved in the pathophysiological process in the heart, and monoterpenes, such as carvacrol, are able to modulate these channels activity. In this article, our purpose was to evaluate the direct cardiac effect of carvacrol on the contractility of cardiomyocytes and isolated right atria from spontaneously hypertensive and Wistar Kyoto rats. In this way, in vitro experiments were used to evaluate the ventricular cardiomyocytes contractility and the Ca2+ transient measuring, in addition to heart rhythm in the right atria. The role of TRPM channels in carvacrol-mediated cardiac activities was also investigated. The results demonstrated that carvacrol induced a significant reduction in ventricular cell contractility, without changes in transient Ca2+. In addition, carvacrol promoted a significant negative chronotropic response in spontaneously hypertensive and Wistar Kyoto rats' atria. Selective blockage of TRPM channels suggests the involvement of TRP melastatin subfamily 2 (TRPM2), TRPM4, and TRPM7 in the carvacrol-mediated cardiac effects. In silico studies were conducted to further investigate the putative role of TRPM4 in carvacrol-mediated cardiac action. FTMap underscores a conserved pocket in both TRPM4 and TRPM7, revealing a potential carvacrol binding site, and morphological similarity analysis demonstrated that carvacrol shares a more than 85% similarity to 9-phenanthrol. Taken together, these results suggest that carvacrol has direct cardiac actions, leading to reduced cellular contractility and inducing a negative chronotropic effect, which may be related to TRPM7 and TRPM4 modulation.
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7
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Cai R, Chen XZ. Roles of Intramolecular Interactions in the Regulation of TRP Channels. Rev Physiol Biochem Pharmacol 2022; 186:29-56. [PMID: 35882668 DOI: 10.1007/112_2022_74] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The transient receptor potential (TRP) channels, classified into six (-A, -V, -P, -C, -M, -ML, -N and -Y) subfamilies, are important membrane sensors and mediators of diverse stimuli including pH, light, mechano-force, temperature, pain, taste, and smell. The mammalian TRP superfamily of 28 members share similar membrane topology with six membrane-spanning helices (S1-S6) and cytosolic N-/C-terminus. Abnormal function or expression of TRP channels is associated with cancer, skeletal dysplasia, immunodeficiency, and cardiac, renal, and neuronal diseases. The majority of TRP members share common functional regulators such as phospholipid PIP2, 2-aminoethoxydiphenyl borate (2-APB), and cannabinoid, while other ligands are more specific, such as allyl isothiocyanate (TRPA1), vanilloids (TRPV1), menthol (TRPM8), ADP-ribose (TRPM2), and ML-SA1 (TRPML1). The mechanisms underlying the gating and regulation of TRP channels remain largely unclear. Recent advances in cryogenic electron microscopy provided structural insights into 19 different TRP channels which all revealed close proximity of the C-terminus with the N-terminus and intracellular S4-S5 linker. Further studies found that some highly conserved residues in these regions of TRPV, -P, -C and -M members mediate functionally critical intramolecular interactions (i.e., within one subunit) between these regions. This review provides an overview on (1) intramolecular interactions in TRP channels and their effect on channel function; (2) functional roles of interplays between PIP2 (and other ligands) and TRP intramolecular interactions; and (3) relevance of the ligand-induced modulation of intramolecular interaction to diseases.
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Affiliation(s)
- Ruiqi Cai
- Program in Cell Biology, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, ON, Canada.,Department of Physiology, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Xing-Zhen Chen
- Department of Physiology, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada.
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8
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Schmiege P, Fine M, Li X. Atomic insights into ML-SI3 mediated human TRPML1 inhibition. Structure 2021; 29:1295-1302.e3. [PMID: 34171299 DOI: 10.1016/j.str.2021.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/28/2021] [Accepted: 06/04/2021] [Indexed: 11/19/2022]
Abstract
Transient receptor potential mucolipin 1 (TRPML1) regulates lysosomal calcium signaling, lipid trafficking, and autophagy-related processes. This channel is regulated by phosphoinositides and the low pH environment of the lysosome, maintaining calcium levels essential for proper lysosomal function. Recently, several small molecules specifically targeting the TRPML family have been demonstrated to modulate channel activity. One of these, a synthetic antagonist ML-SI3, can prevent lysosomal calcium efflux and has been reported to block downstream TRPML1-mediated induction of autophagy. Here, we report a cryo-electron microscopy structure of human TRPML1 with ML-SI3 at 2.9-Å resolution. ML-SI3 binds to the hydrophobic cavity created by S5, S6, and PH1, the same cavity where the synthetic agonist ML-SA1 binds. Electrophysiological characterizations show that ML-SI3 can compete with ML-SA1, blocking channel activation yet does not inhibit PI(3,5)P2-dependent activation of the channel. Consequently, this work provides molecular insight into how ML-SI3 and native lipids regulate TRPML1 activity.
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Affiliation(s)
- Philip Schmiege
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael Fine
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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9
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Goretzki B, Guhl C, Tebbe F, Harder JM, Hellmich UA. Unstructural Biology of TRP Ion Channels: The Role of Intrinsically Disordered Regions in Channel Function and Regulation. J Mol Biol 2021; 433:166931. [PMID: 33741410 DOI: 10.1016/j.jmb.2021.166931] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/02/2021] [Accepted: 03/06/2021] [Indexed: 12/13/2022]
Abstract
The first genuine high-resolution single particle cryo-electron microscopy structure of a membrane protein determined was a transient receptor potential (TRP) ion channel, TRPV1, in 2013. This methodical breakthrough opened up a whole new world for structural biology and ion channel aficionados alike. TRP channels capture the imagination due to the sheer endless number of tasks they carry out in all aspects of animal physiology. To date, structures of at least one representative member of each of the six mammalian TRP channel subfamilies as well as of a few non-mammalian families have been determined. These structures were instrumental for a better understanding of TRP channel function and regulation. However, all of the TRP channel structures solved so far are incomplete since they miss important information about highly flexible regions found mostly in the channel N- and C-termini. These intrinsically disordered regions (IDRs) can represent between a quarter to almost half of the entire protein sequence and act as important recruitment hubs for lipids and regulatory proteins. Here, we analyze the currently available TRP channel structures with regard to the extent of these "missing" regions and compare these findings to disorder predictions. We discuss select examples of intra- and intermolecular crosstalk of TRP channel IDRs with proteins and lipids as well as the effect of splicing and post-translational modifications, to illuminate their importance for channel function and to complement the prevalently discussed structural biology of these versatile and fascinating proteins with their equally relevant 'unstructural' biology.
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Affiliation(s)
- Benedikt Goretzki
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Charlotte Guhl
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany; TransMED - Mainz Research School of Translational Medicine, Johannes Gutenberg-University, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Frederike Tebbe
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Jean-Martin Harder
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany
| | - Ute A Hellmich
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstrasse 10, 07743 Jena, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany; TransMED - Mainz Research School of Translational Medicine, Johannes Gutenberg-University, University Medical Center, Langenbeckstr. 1, 55131 Mainz, Germany; Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University, 07743 Jena, Germany.
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10
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Rindi G, Wiedenmann B. Neuroendocrine neoplasia of the gastrointestinal tract revisited: towards precision medicine. Nat Rev Endocrinol 2020; 16:590-607. [PMID: 32839579 DOI: 10.1038/s41574-020-0391-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 02/06/2023]
Abstract
Over the past 5 years, a number of notable research advances have been made in the field of neuroendocrine cancer, specifically with regard to neuroendocrine cancer of the gastrointestinal tract. The aim of this Review is to provide an update on current knowledge that has proven effective for the clinical management of patients with these tumours. For example, for the first time in the tubular gastrointestinal tract, well-differentiated high-grade (grade 3) tumours and mixed neuroendocrine-non-neuroendocrine neoplasms (MiNENs) are defined in the WHO classification. This novel classification enables efficient identification of the most aggressive well-differentiated neuroendocrine tumours and helps in defining the degree of aggressiveness of MiNENs. The Review also discusses updates to epidemiology, cell biology (including vesicle-specific components) and the as-yet-unresolved complex genetic background that varies according to site and differentiation status. The Review summarizes novel diagnostic instruments, including molecules associated with the secretory machinery, novel radiological approaches (including pattern recognition techniques), novel PET tracers and liquid biopsy combined with DNA or RNA assays. Surgery remains the treatment mainstay; however, peptide receptor radionuclide therapy with novel radioligands and new emerging medical therapies (including vaccination and immunotherapy) are evolving and being tested in clinical trials, which are summarized and critically reviewed here.
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Affiliation(s)
- Guido Rindi
- Università Cattolica del Sacro Cuore, Rome, Italy.
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.
| | - Bertram Wiedenmann
- Charité, Campus Virchow Klinikum and Charité Mitte, University Medicine Berlin, Berlin, Germany
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11
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Kalienkova V, Alvadia C, Clerico Mosina V, Paulino C. Single-Particle Cryo-EM of Membrane Proteins in Lipid Nanodiscs. Methods Mol Biol 2020; 2127:245-273. [PMID: 32112327 DOI: 10.1007/978-1-0716-0373-4_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Single-particle cryo-electron microscopy has become an indispensable technique in structural biology. In particular when studying membrane proteins, it allows the use of membrane-mimicking tools, which can be crucial for a comprehensive understanding of the structure-function relationship of the protein in its native environment. In this chapter we focus on the application of nanodiscs and use our recent studies on the TMEM16 family as an example.
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Affiliation(s)
- Valeria Kalienkova
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Carolina Alvadia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Vanessa Clerico Mosina
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Cristina Paulino
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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12
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Brillault L, Landsberg MJ. Preparation of Proteins and Macromolecular Assemblies for Cryo-electron Microscopy. Methods Mol Biol 2020; 2073:221-246. [PMID: 31612445 DOI: 10.1007/978-1-4939-9869-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cryo-electron microscopy has become popular as the penultimate step on the road to structure determination for many proteins and macromolecular assemblies. The process of obtaining high-resolution images of a purified biomolecular complex in an electron microscope often follows a long, and in many cases exhaustive screening process in which many iterative rounds of protein purification are employed and the sample preparation procedure progressively re-evaluated in order to improve the distribution of particles visualized under the electron microscope, and thus maximize the opportunity for high-resolution structure determination. Typically, negative stain electron microscopy is employed to obtain a preliminary assessment of the sample quality, followed by cryo-EM which first requires the identification of optimal vitrification conditions. The original methods for frozen-hydrated specimen preparation developed over 40 years ago still enjoy widespread use today, although recent developments have set the scene for a future where more systematic and high-throughput approaches to the preparation of vitrified biomolecular complexes may be routinely employed. Here we summarize current approaches and ongoing innovations for the preparation of frozen-hydrated single particle specimens for cryo-EM, highlighting some of the commonly encountered problems and approaches that may help overcome these.
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Affiliation(s)
- Lou Brillault
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
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13
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Scotto Rosato A, Montefusco S, Soldati C, Di Paola S, Capuozzo A, Monfregola J, Polishchuk E, Amabile A, Grimm C, Lombardo A, De Matteis MA, Ballabio A, Medina DL. TRPML1 links lysosomal calcium to autophagosome biogenesis through the activation of the CaMKKβ/VPS34 pathway. Nat Commun 2019; 10:5630. [PMID: 31822666 PMCID: PMC6904751 DOI: 10.1038/s41467-019-13572-w] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 11/14/2019] [Indexed: 12/24/2022] Open
Abstract
The lysosomal calcium channel TRPML1, whose mutations cause the lysosomal storage disorder (LSD) mucolipidosis type IV (MLIV), contributes to upregulate autophagic genes by inducing the nuclear translocation of the transcription factor EB (TFEB). Here we show that TRPML1 activation also induces autophagic vesicle (AV) biogenesis through the generation of phosphatidylinositol 3-phosphate (PI3P) and the recruitment of essential PI3P-binding proteins to the nascent phagophore in a TFEB-independent manner. Thus, TRPML1 activation of phagophore formation requires the calcium-dependent kinase CaMKKβ and AMPK, which increase the activation of ULK1 and VPS34 autophagic protein complexes. Consistently, cells from MLIV patients show a reduced recruitment of PI3P-binding proteins to the phagophore during autophagy induction, suggesting that altered AV biogenesis is part of the pathological features of this disease. Together, we show that TRPML1 is a multistep regulator of autophagy that may be targeted for therapeutic purposes to treat LSDs and other autophagic disorders. It was known that prolonged TRMPL1 activation induces TFEB translocation and upregulates autophagic gene regulation. Here, the authors show that acute TRMPL1 activation also induces autophagy through VPS34 and by lysosomal calcium release independent of TFEB.
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Affiliation(s)
- A Scotto Rosato
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy.,Faculty of Medicine, Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität, Munich, Germany
| | - S Montefusco
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - C Soldati
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - S Di Paola
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - A Capuozzo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - J Monfregola
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - E Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - A Amabile
- Telethon Institute for Gene Therapy (SR-Tiget), Division of Regenerative Medicine, Stem Cells, and Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, 20132, Milan, Italy
| | - C Grimm
- Faculty of Medicine, Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität, Munich, Germany
| | - A Lombardo
- Telethon Institute for Gene Therapy (SR-Tiget), Division of Regenerative Medicine, Stem Cells, and Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, 20132, Milan, Italy
| | - M A De Matteis
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy.,Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - A Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy.,Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy.,Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - D L Medina
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy. .,Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy.
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14
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Yu J, Yang J. Ion channels as potential redox sensors in lysosomes. Channels (Austin) 2019; 13:477-482. [PMID: 31662029 PMCID: PMC6833971 DOI: 10.1080/19336950.2019.1684428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/26/2019] [Accepted: 09/15/2019] [Indexed: 02/08/2023] Open
Abstract
Lysosomes are central organelles that recycle materials and energy to maintain intracellular homeostasis. Lysosomes are capable of sensing environmental cues such as nutrition to regulate their function accordingly. Whether lysosomes can sense redox signaling, however, was unclear. Here in this review, we summarized recent evidence of lysosomal ion channel as redox sensors for this organelle. We also discussed their roles in lysosomal diseases that features imbalanced redox.
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Affiliation(s)
- Jie Yu
- Sports Science Research Center, Zhejiang College of Sports, Hangzhou, China
| | - Junsheng Yang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
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15
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Structural insights into group II TRP channels. Cell Calcium 2019; 86:102107. [PMID: 31841954 DOI: 10.1016/j.ceca.2019.102107] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 01/01/2023]
Abstract
The seven members of the TRP channel superfamily are divided into two main groups with five members comprising group I (TRPC/V/M/N/A) and TRPML (TRP MucoLipin) and TRPP (TRP Polycystin) making up group II. Group II channels share a high sequence homology on their transmembrane domains and are distinct from group I members as they contain a large luminal/extracellular domain between transmembrane helix 1 (S1) and S2. Since 2016, there are more than ten research papers reporting various structures of group II channels by either cryo-EM or X-ray crystallography. These studies along with recent functional analysis by the other groups have considerably strengthened our knowledge on TRPML and TRPP channels. In this review, we summarize and discuss these reports providing molecular insights into the group II TRP channel family.
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16
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Xie T, Wu Z, Gu J, Guo R, Yan X, Duan H, Liu X, Liu W, Liang L, Wan H, Luo Y, Tang D, Shi H, Hu J. The global motion affecting electron transfer in Plasmodium falciparum type II NADH dehydrogenases: a novel non-competitive mechanism for quinoline ketone derivative inhibitors. Phys Chem Chem Phys 2019; 21:18105-18118. [PMID: 31396604 DOI: 10.1039/c9cp02645b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
With the emergence of drug-resistant Plasmodium falciparum, the treatment of malaria has become a significant challenge; therefore, the development of antimalarial drugs acting on new targets is extremely urgent. In Plasmodium falciparum, type II nicotinamide adenine dinucleotide (NADH) dehydrogenase (NDH-2) is responsible for catalyzing the transfer of two electrons from NADH to flavin adenine dinucleotide (FAD), which in turn transfers the electrons to coenzyme Q (CoQ). As an entry enzyme for oxidative phosphorylation, NDH-2 has become one of the popular targets for the development of new antimalarial drugs. In this study, reliable motion trajectories of the NDH-2 complex with its co-factors (NADH and FAD) and inhibitor, RYL-552, were obtained by comparative molecular dynamics simulations. The influence of cofactor binding on the global motion of NDH-2 was explored through conformational clustering, principal component analysis and free energy landscape. The molecular interactions of NDH-2 before and after its binding with the inhibitor RYL-552 were analyzed, and the key residues and important hydrogen bonds were also determined. The results show that the association of RYL-552 results in the weakening of intramolecular hydrogen bonds and large allosterism of NDH-2. There was a significant positive correlation between the angular change of the key pocket residues in the NADH-FAD-pockets that represents the global functional motion and the change in distance between NADH-C4 and FAD-N5 that represents the electron transfer efficiency. Finally, the possible non-competitive inhibitory mechanism of RYL-552 was proposed. Specifically, the association of inhibitors with NDH-2 significantly affects the global motion mode of NDH-2, leading to widening of the distance between NADH and FAD through cooperative motion induction; this reduces the electron transfer efficiency of the mitochondrial respiratory chain. The simulation results provide useful theoretical guidance for subsequent antimalarial drug design based on the NDH-2 structure and the respiratory chain electron transfer mechanism.
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Affiliation(s)
- Tao Xie
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Chengdu University, Chengdu, 610106, China.
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17
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Yin S, Liu J, Kang Y, Lin Y, Li D, Shao L. Interactions of nanomaterials with ion channels and related mechanisms. Br J Pharmacol 2019; 176:3754-3774. [PMID: 31290152 DOI: 10.1111/bph.14792] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 06/10/2019] [Accepted: 07/01/2019] [Indexed: 12/15/2022] Open
Abstract
The pharmacological potential of nanotechnology, especially in drug delivery and bioengineering, has developed rapidly in recent decades. Ion channels, which are easily targeted by external agents, such as nanomaterials (NMs) and synthetic drugs, due to their unique structures, have attracted increasing attention in the fields of nanotechnology and pharmacology for the treatment of ion channel-related diseases. NMs have significant effects on ion channels, and these effects are manifested in many ways, including changes in ion currents, kinetic characteristics and channel distribution. Subsequently, intracellular ion homeostasis, signalling pathways, and intracellular ion stores are affected, leading to the initiation of a range of biological processes. However, the effect of the interactions of NMs with ion channels is an interesting topic that remains obscure. In this review, we have summarized the recent research progress on the direct and indirect interactions between NMs and ion channels and discussed the related molecular mechanisms, which are crucial to the further development of ion channel-related nanotechnological applications.
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Affiliation(s)
- Suhan Yin
- Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, China
| | - Jia Liu
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yiyuan Kang
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yuqing Lin
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dongjian Li
- Liwan District Stomatology Hospital, Guangzhou, China
| | - Longquan Shao
- Nanfang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, China
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18
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Viet KK, Wagner A, Schwickert K, Hellwig N, Brennich M, Bader N, Schirmeister T, Morgner N, Schindelin H, Hellmich UA. Structure of the Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain. Structure 2019; 27:1246-1257.e5. [DOI: 10.1016/j.str.2019.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/16/2019] [Accepted: 04/29/2019] [Indexed: 11/28/2022]
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19
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Abstract
The opening of voltage-gated ion channels is initiated by transfer of gating charges that sense the electric field across the membrane. Although transient receptor potential ion channels (TRP) are members of this family, their opening is not intrinsically linked to membrane potential, and they are generally not considered voltage gated. Here we demonstrate that TRPP2, a member of the polycystin subfamily of TRP channels encoded by the PKD2L1 gene, is an exception to this rule. TRPP2 borrows a biophysical riff from canonical voltage-gated ion channels, using 2 gating charges found in its fourth transmembrane segment (S4) to control its conductive state. Rosetta structural prediction demonstrates that the S4 undergoes ∼3- to 5-Å transitional and lateral movements during depolarization, which are coupled to opening of the channel pore. Here both gating charges form state-dependent cation-π interactions within the voltage sensor domain (VSD) during membrane depolarization. Our data demonstrate that the transfer of a single gating charge per channel subunit is requisite for voltage, temperature, and osmotic swell polymodal gating of TRPP2. Taken together, we find that irrespective of stimuli, TRPP2 channel opening is dependent on activation of its VSDs.
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20
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Thakore P, Earley S. Transient Receptor Potential Channels and Endothelial Cell Calcium Signaling. Compr Physiol 2019; 9:1249-1277. [PMID: 31187891 DOI: 10.1002/cphy.c180034] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The vascular endothelium is a broadly distributed and highly specialized organ. The endothelium has a number of functions including the control of blood vessels diameter through the production and release of potent vasoactive substances or direct electrical communication with underlying smooth muscle cells, regulates the permeability of the vascular barrier, stimulates the formation of new blood vessels, and influences inflammatory and thrombotic processes. Endothelial cells that make up the endothelium express a variety of cell-surface receptors and ion channels on the plasma membrane that are capable of detecting circulating hormones, neurotransmitters, oxygen tension, and shear stress across the vascular wall. Changes in these stimuli activate signaling cascades that initiate an appropriate physiological response. Increases in the global intracellular Ca2+ concentration and localized Ca2+ signals that occur within specialized subcellular microdomains are fundamentally important components of many signaling pathways in the endothelium. The transient receptor potential (TRP) channels are a superfamily of cation-permeable ion channels that act as a primary means of increasing cytosolic Ca2+ in endothelial cells. Consequently, TRP channels are vitally important for the major functions of the endothelium. In this review, we provide an in-depth discussion of Ca2+ -permeable TRP channels in the endothelium and their role in vascular regulation. © 2019 American Physiological Society. Compr Physiol 9:1249-1277, 2019.
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Affiliation(s)
- Pratish Thakore
- Department of Pharmacology, Center for Cardiovascular Research, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Scott Earley
- Department of Pharmacology, Center for Cardiovascular Research, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
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21
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Vangeel L, Voets T. Transient Receptor Potential Channels and Calcium Signaling. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a035048. [PMID: 30910771 DOI: 10.1101/cshperspect.a035048] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Transient receptor potential (TRP) cation channels play diverse roles in cellular Ca2+ signaling. First, as Ca2+-permeable channels that respond to a variety of stimuli, TRP channels can directly initiate cellular Ca2+ signals. Second, as nonselective cation channels, TRP channel activation leads to membrane depolarization, influencing Ca2+ influx via voltage-gated and store-operated Ca2+ channels. Finally, Ca2+ modulates the activity of most TRP channels, allowing them to function as molecular effectors downstream of intracellular Ca2+ signals. Whereas the TRP channel field has long been devoid of detailed channel structures, recent advances, particularly in cryo-electron microscopy-based structural approaches, have yielded a flurry of TRP channel structures, including members from all seven subfamilies. These structures, in conjunction with mutagenesis-based functional approaches, provided important new insights into the mechanisms whereby TRP channels permeate and sense Ca2+ These insights will be highly instrumental in the rational design of novel treatments for the multitude of TRP channel-related diseases.
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Affiliation(s)
- Laura Vangeel
- Laboratory of Ion Channel Research, VIB Center for Brain and Disease Research & Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Thomas Voets
- Laboratory of Ion Channel Research, VIB Center for Brain and Disease Research & Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
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22
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Boudewyn LC, Walkley SU. Current concepts in the neuropathogenesis of mucolipidosis type IV. J Neurochem 2019; 148:669-689. [PMID: 29770442 PMCID: PMC6239999 DOI: 10.1111/jnc.14462] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/29/2018] [Accepted: 05/02/2018] [Indexed: 12/11/2022]
Abstract
Mucolipidosis type IV (MLIV) is an autosomal recessive, lysosomal storage disorder causing progressively severe intellectual disability, motor and speech deficits, retinal degeneration often culminating in blindness, and systemic disease causing a shortened lifespan. MLIV results from mutations in the gene MCOLN1 encoding the transient receptor potential channel mucolipin-1. It is an ultra-rare disease and is currently known to affect just over 100 diagnosed individuals. The last decade has provided a wealth of research focused on understanding the role of the enigmatic mucolipin-1 protein in cell and brain function and how its absence causes disease. This review explores our current understanding of the mucolipin-1 protein in relation to neuropathogenesis in MLIV and describes recent findings implicating mucolipin-1's important role in mechanistic target of rapamycin and TFEB (transcription factor EB) signaling feedback loops as well as in the function of the greater endosomal/lysosomal system. In addition to addressing the vital role of mucolipin-1 in the brain, we also report new data on the question of whether haploinsufficiency as would be anticipated in MCOLN1 heterozygotes is associated with any evidence of neuron dysfunction or disease. Greater insights into the role of mucolipin-1 in the nervous system can be expected to shed light not only on MLIV disease but also on numerous processes governing normal brain function. This article is part of the Special Issue "Lysosomal Storage Disorders".
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Affiliation(s)
- Lauren C. Boudewyn
- Dominick P. Purpura Department of Neuroscience, Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, New York
| | - Steven U. Walkley
- Dominick P. Purpura Department of Neuroscience, Rose F. Kennedy Intellectual and Developmental Disabilities Research Center, Albert Einstein College of Medicine, Bronx, New York
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23
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Combining Structural Data with Computational Methodologies to Investigate Structure-Function Relationships in TRP Channels. Methods Mol Biol 2019; 1987:65-82. [PMID: 31028674 DOI: 10.1007/978-1-4939-9446-5_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Since the emergence of high-resolution three-dimensional structures of membrane proteins, and the increasing availability of state-of-the-art algorithms and high-performance-computing facilities, classical molecular dynamics (MD) simulations have become a routine device to explore the molecular behavior of these proteins. The rise of cryo-electron microscopy (cryo-EM) as a credible experimental tool to resolve structures at an atomic level has revolutionized structural biology in recent years, culminating in the disclosure of the first high-resolution three-dimensional structure of a transient receptor potential (TRP) channel, the vanilloid receptor 1 (TRPV1). As a result, the number of research articles investigating the molecular behavior of TRP channels using macromolecular simulation techniques has proliferated. This review provides an overview of the current state of this field, including our understanding of TRP channel structure, the framework of classical MD simulations, and how to perform such simulations to investigate structure-function relationships in TRP channels.
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24
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Jiang QX. Structural Variability in the RLR-MAVS Pathway and Sensitive Detection of Viral RNAs. Med Chem 2019; 15:443-458. [PMID: 30569868 PMCID: PMC6858087 DOI: 10.2174/1573406415666181219101613] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/23/2018] [Accepted: 12/12/2018] [Indexed: 12/25/2022]
Abstract
Cells need high-sensitivity detection of non-self molecules in order to fight against pathogens. These cellular sensors are thus of significant importance to medicinal purposes, especially for treating novel emerging pathogens. RIG-I-like receptors (RLRs) are intracellular sensors for viral RNAs (vRNAs). Their active forms activate mitochondrial antiviral signaling protein (MAVS) and trigger downstream immune responses against viral infection. Functional and structural studies of the RLR-MAVS signaling pathway have revealed significant supramolecular variability in the past few years, which revealed different aspects of the functional signaling pathway. Here I will discuss the molecular events of RLR-MAVS pathway from the angle of detecting single copy or a very low copy number of vRNAs in the presence of non-specific competition from cytosolic RNAs, and review key structural variability in the RLR / vRNA complexes, the MAVS helical polymers, and the adapter-mediated interactions between the active RLR / vRNA complex and the inactive MAVS in triggering the initiation of the MAVS filaments. These structural variations may not be exclusive to each other, but instead may reflect the adaptation of the signaling pathways to different conditions or reach different levels of sensitivity in its response to exogenous vRNAs.
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Affiliation(s)
- Qiu-Xing Jiang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, United States
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25
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Overduin M, Esmaili M. Memtein: The fundamental unit of membrane-protein structure and function. Chem Phys Lipids 2019; 218:73-84. [DOI: 10.1016/j.chemphyslip.2018.11.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/24/2018] [Accepted: 11/28/2018] [Indexed: 12/14/2022]
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26
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Endolysosomal Ca 2+ Signalling and Cancer Hallmarks: Two-Pore Channels on the Move, TRPML1 Lags Behind! Cancers (Basel) 2018; 11:cancers11010027. [PMID: 30591696 PMCID: PMC6356888 DOI: 10.3390/cancers11010027] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 12/22/2022] Open
Abstract
The acidic vesicles of the endolysosomal (EL) system are emerging as an intracellular Ca2+ store implicated in the regulation of multiple cellular functions. The EL Ca2+ store releases Ca2+ through a variety of Ca2+-permeable channels, including Transient Receptor Potential (TRP) Mucolipin 1-3 (TRPML1-3) and two-pore channels 1-2 (TPC1-2), whereas EL Ca2+ refilling is sustained by the proton gradient across the EL membrane and/or by the endoplasmic reticulum (ER). EL Ca2+ signals may be either spatially restricted to control vesicle trafficking, autophagy and membrane repair or may be amplified into a global Ca2+ signal through the Ca2+-dependent recruitment of ER-embedded channels. Emerging evidence suggested that nicotinic acid adenine dinucleotide phosphate (NAADP)-gated TPCs sustain multiple cancer hallmarks, such as migration, invasiveness and angiogenesis. Herein, we first survey the EL Ca2+ refilling and release mechanisms and then focus on the oncogenic role of EL Ca2+ signaling. While the evidence in favor of TRPML1 involvement in neoplastic transformation is yet to be clearly provided, TPCs are emerging as an alternative target for anticancer therapies.
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27
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Plesch E, Chen CC, Butz E, Scotto Rosato A, Krogsaeter EK, Yinan H, Bartel K, Keller M, Robaa D, Teupser D, Holdt LM, Vollmar AM, Sippl W, Puertollano R, Medina D, Biel M, Wahl-Schott C, Bracher F, Grimm C. Selective agonist of TRPML2 reveals direct role in chemokine release from innate immune cells. eLife 2018; 7:39720. [PMID: 30479274 PMCID: PMC6257821 DOI: 10.7554/elife.39720] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 10/26/2018] [Indexed: 12/21/2022] Open
Abstract
Cytokines and chemokines are produced and secreted by a broad range of immune cells including macrophages. Remarkably, little is known about how these inflammatory mediators are released from the various immune cells. Here, the endolysosomal cation channel TRPML2 is shown to play a direct role in chemokine trafficking and secretion from murine macrophages. To demonstrate acute and direct involvement of TRPML2 in these processes, the first isoform-selective TRPML2 channel agonist was generated, ML2-SA1. ML2-SA1 was not only found to directly stimulate release of the chemokine CCL2 from macrophages but also to stimulate macrophage migration, thus mimicking CCL2 function. Endogenous TRPML2 is expressed in early/recycling endosomes as demonstrated by endolysosomal patch-clamp experimentation and ML2-SA1 promotes trafficking through early/recycling endosomes, suggesting CCL2 being transported and secreted via this pathway. These data provide a direct link between TRPML2 activation, CCL2 release and stimulation of macrophage migration in the innate immune response.
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Affiliation(s)
- Eva Plesch
- Department of Pharmacy, Center for Drug Research and Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, Munich, Germany
| | - Cheng-Chang Chen
- Department of Pharmacy, Center for Drug Research and Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, Munich, Germany
| | - Elisabeth Butz
- Department of Pharmacy, Center for Drug Research and Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Einar K Krogsaeter
- Department of Pharmacology and Toxicology, Medical Faculty, Ludwig Maximilian University of Munich, Munich, Germany
| | - Hua Yinan
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Karin Bartel
- Department of Pharmacy, Center for Drug Research and Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, Munich, Germany
| | - Marco Keller
- Department of Pharmacy, Center for Drug Research and Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, Munich, Germany
| | - Dina Robaa
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, University Hospital Munich, Munich, Germany
| | - Lesca M Holdt
- Institute of Laboratory Medicine, University Hospital Munich, Munich, Germany
| | - Angelika M Vollmar
- Department of Pharmacy, Center for Drug Research and Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, Munich, Germany
| | - Wolfgang Sippl
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Rosa Puertollano
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Diego Medina
- Telethon Institute of Genetics and Medicine, Naples, Italy
| | - Martin Biel
- Department of Pharmacy, Center for Drug Research and Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Franz Bracher
- Department of Pharmacy, Center for Drug Research and Center for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, Munich, Germany
| | - Christian Grimm
- Department of Pharmacology and Toxicology, Medical Faculty, Ludwig Maximilian University of Munich, Munich, Germany
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28
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Fine M, Schmiege P, Li X. Structural basis for PtdInsP 2-mediated human TRPML1 regulation. Nat Commun 2018; 9:4192. [PMID: 30305615 PMCID: PMC6180102 DOI: 10.1038/s41467-018-06493-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/05/2018] [Indexed: 12/27/2022] Open
Abstract
Transient receptor potential mucolipin 1 (TRPML1), a lysosomal channel, maintains the low pH and calcium levels for lysosomal function. Several small molecules modulate TRPML1 activity. ML-SA1, a synthetic agonist, binds to the pore region and phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P2), a natural lipid, stimulates channel activity to a lesser extent than ML-SA1; moreover, PtdIns(4,5)P2, another natural lipid, prevents TRPML1-mediated calcium release. Notably, PtdIns(3,5)P2 and ML-SA1 cooperate further increasing calcium efflux. Here we report the structures of human TRPML1 at pH 5.0 with PtdIns(3,5)P2, PtdIns(4,5)P2, or ML-SA1 and PtdIns(3,5)P2, revealing a unique lipid-binding site. PtdIns(3,5)P2 and PtdIns(4,5)P2 bind to the extended helices of S1, S2, and S3. The phosphate group of PtdIns(3,5)P2 induces Y355 to form a π-cation interaction with R403, moving the S4-S5 linker, thus allosterically activating the channel. Our structures and electrophysiological characterizations reveal an allosteric site and provide molecular insight into how lipids regulate TRP channels.
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Affiliation(s)
- Michael Fine
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Philip Schmiege
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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29
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Membrane protein structural biology in the era of single particle cryo-EM. Curr Opin Struct Biol 2018; 52:58-63. [PMID: 30219656 DOI: 10.1016/j.sbi.2018.08.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 05/15/2018] [Accepted: 08/29/2018] [Indexed: 11/22/2022]
Abstract
In the past few years, significant technological breakthroughs in single particle cryo-electron microscopy enabled a 'resolution revolution' of this technique. It also changed structural biology in an unprecedented way. For many biological macromolecules, obtaining well-ordered crystals of suitable size is no longer a prerequisite for determining their atomic structures. One of the most impacted areas is the structural biology of integral membrane proteins. New structures are now determined at a rapid pace. Despite these advances, further technological developments are still required to overcome new technical challenges that face membrane protein structural biology. In this review, I attempt to discuss some of these challenges.
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30
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Thonghin N, Kargas V, Clews J, Ford RC. Cryo-electron microscopy of membrane proteins. Methods 2018; 147:176-186. [DOI: 10.1016/j.ymeth.2018.04.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 10/17/2022] Open
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31
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Schmiege P, Fine M, Li X. The regulatory mechanism of mammalian TRPMLs revealed by cryo-EM. FEBS J 2018; 285:2579-2585. [PMID: 29577631 DOI: 10.1111/febs.14443] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/15/2018] [Accepted: 03/20/2018] [Indexed: 01/18/2023]
Abstract
Transient receptor potential mucolipin (TRPML) channels are the most recently identified subfamily of TRP channels and have seen a surge of new reports revealing both structural and functional insight. In 2017, several groups published multiple conformations of TRPML channels using cryo-EM. Similar to other TRP channels, the ML subfamily consists of six transmembrane helices (S1-S6), and a pore region including S5, S6, and two pore helices (PH1 and PH2). However, these reports also reveal distinct structural characteristics of the ML subfamily. Asp residues within the luminal pore may function to control calcium/pH regulation. A synthetic agonist, ML-SA1, can bind to the pore region of TRPMLs to force a direct dilation of the lower gate. Finally, biophysical and electrophysiological characterizations reveal another natural agonist binding site in the unique domain of TRPMLs, presumably regulating the conformation of the S4-S5 linker to open the channel. This work elucidates the molecular architecture and provides insights into how multiple ligands regulate TRPMLs.
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Affiliation(s)
- Philip Schmiege
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Fine
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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32
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Sterea AM, Almasi S, El Hiani Y. The hidden potential of lysosomal ion channels: A new era of oncogenes. Cell Calcium 2018; 72:91-103. [PMID: 29748137 DOI: 10.1016/j.ceca.2018.02.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 01/14/2023]
Abstract
Lysosomes serve as the control centre for cellular clearance. These membrane-bound organelles receive biomolecules destined for degradation from intracellular and extracellular pathways; thus, facilitating the production of energy and shaping the fate of the cell. At the base of their functionality are the lysosomal ion channels which mediate the function of the lysosome through the modulation of ion influx and efflux. Ion channels form pores in the membrane of lysosomes and allow the passage of ions, a seemingly simple task which harbours the potential of overthrowing the cell's stability. Considered the master regulators of ion homeostasis, these integral membrane proteins enable the proper operation of the lysosome. Defects in the structure or function of these ion channels lead to the development of lysosomal storage diseases, neurodegenerative diseases and cancer. Although more than 50 years have passed since their discovery, lysosomes are not yet fully understood, with their ion channels being even less well characterized. However, significant improvements have been made in the development of drugs targeted against these ion channels as a means of combating diseases. In this review, we will examine how Ca2+, K+, Na+ and Cl- ion channels affect the function of the lysosome, their involvement in hereditary and spontaneous diseases, and current ion channel-based therapies.
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Affiliation(s)
- Andra M Sterea
- Departments of Physiology & Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Shekoufeh Almasi
- Departments of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Yassine El Hiani
- Departments of Physiology & Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada.
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33
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Madej MG, Ziegler CM. Dawning of a new era in TRP channel structural biology by cryo-electron microscopy. Pflugers Arch 2018; 470:213-225. [PMID: 29344776 DOI: 10.1007/s00424-018-2107-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 01/03/2018] [Indexed: 12/20/2022]
Abstract
Cryo-electron microscopy (cryo-EM) permits the determination of atomic protein structures by averaging large numbers of individual projection images recorded at cryogenic temperatures-a method termed single-particle analysis. The cryo-preservation traps proteins within a thin glass-like ice layer, making literally a freeze image of proteins in solution. Projections of randomly adopted orientations are merged to reconstruct a 3D density map. While atomic resolution for highly symmetric viruses was achieved already in 2009, the development of new sensitive and fast electron detectors has enabled cryo-EM for smaller and asymmetrical proteins including fragile membrane proteins. As one of the most important structural biology methods at present, cryo-EM was awarded in October 2017 with the Nobel Prize in Chemistry. The molecular understanding of Transient-Receptor-Potential (TRP) channels has been boosted tremendously by cryo-EM single-particle analysis. Several near-atomic and atomic structures gave important mechanistic insights, e.g., into ion permeation and selectivity, gating, as well as into the activation of this enigmatic and medically important membrane protein family by various chemical and physical stimuli. Lastly, these structures have set the starting point for the rational design of TRP channel-targeted therapeutics to counteract life-threatening channelopathies. Here, we attempt a brief introduction to the method, review the latest advances in cryo-EM structure determination of TRP channels, and discuss molecular insights into the channel function based on the wealth of TRP channel cryo-EM structures.
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Affiliation(s)
- M Gregor Madej
- Department of Structural Biology, Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053, Regensburg, Germany
| | - Christine M Ziegler
- Department of Structural Biology, Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053, Regensburg, Germany.
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Zhou X, Li M, Su D, Jia Q, Li H, Li X, Yang J. Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states. Nat Struct Mol Biol 2017; 24:1146-1154. [PMID: 29106414 PMCID: PMC5747366 DOI: 10.1038/nsmb.3502] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/10/2017] [Indexed: 12/23/2022]
Abstract
TRPML3 channels are mainly localized to endolysosomes and play a critical role in the endocytic pathway. Their dysfunction causes deafness and pigmentation defects in mice. TRPML3 activity is inhibited by low endolysosomal pH. Here we present cryo-electron microscopy (cryo-EM) structures of human TRPML3 in the closed, agonist-activated, and low-pH-inhibited states, with resolutions of 4.06, 3.62, and 4.65 Å, respectively. The agonist ML-SA1 lodges between S5 and S6 and opens an S6 gate. A polycystin-mucolipin domain (PMD) forms a luminal cap. S1 extends into this cap, forming a 'gating rod' that connects directly to a luminal pore loop, which undergoes dramatic conformational changes in response to low pH. S2 extends intracellularly and interacts with several intracellular regions to form a 'gating knob'. These unique structural features, combined with the results of electrophysiological studies, indicate a new mechanism by which luminal pH and other physiological modulators such as PIP2 regulate TRPML3 by changing S1 and S2 conformations.
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Affiliation(s)
- Xiaoyuan Zhou
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Minghui Li
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Deyuan Su
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, and Ion Channel Research and Drug Development Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qi Jia
- Department of Orthopedic Oncology, Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai 200003, China
| | - Huan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, and Ion Channel Research and Drug Development Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xueming Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jian Yang
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, and Ion Channel Research and Drug Development Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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