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Ismatullah H, Jabeen I, Kiani YS. Structural and functional insight into a new emerging target IP 3R in cancer. J Biomol Struct Dyn 2024; 42:2170-2196. [PMID: 37070253 DOI: 10.1080/07391102.2023.2201332] [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: 01/27/2023] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Calcium signaling has been identified as an important phenomenon in a plethora of cellular processes. Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ER-residing intracellular calcium (Ca2+) release channels responsible for cell bioenergetics by transferring calcium from the ER to the mitochondria. The recent availability of full-length IP3R channel structure has enabled the researchers to design the IP3 competitive ligands and reveal the channel gating mechanism by elucidating the conformational changes induced by ligands. However, limited knowledge is available for IP3R antagonists and the exact mechanism of action of these antagonists within a tumorigenic environment of a cell. Here in this review a summarized information about the role of IP3R in cell proliferation and apoptosis has been discussed. Moreover, structure and gating mechanism of IP3R in the presence of antagonists have been provided in this review. Additionally, compelling information about ligand-based studies (both agonists and antagonists) has been discussed. The shortcomings of these studies and the challenges toward the design of potent IP3R modulators have also been provided in this review. However, the conformational changes induced by antagonists for channel gating mechanism still display some major drawbacks that need to be addressed. However, the design, synthesis and availability of isoform-specific antagonists is a rather challenging one due to intra-structural similarity within the binding domain of each isoform. HighlightsThe intricate complexity of IP3R's in cellular processes declares them an important target whereby, the recently solved structure depicts the receptor's potential involvement in a complex network of processes spanning from cell proliferation to cell death.Pharmacological inhibition of IP3R attenuates the proliferation or invasiveness of cancers, thus inducing necrotic cell death.Despite significant advancements, there is a tremendous need to design new potential hits to target IP3R, based upon 3D structural features and pharmacophoric patterns.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Humaira Ismatullah
- Department of Sciences, School of Interdisciplinary Engineering and Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Ishrat Jabeen
- Department of Sciences, School of Interdisciplinary Engineering and Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Yusra Sajid Kiani
- Department of Sciences, School of Interdisciplinary Engineering and Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan
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2
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Baker MR, Fan G, Arige V, Yule DI, Serysheva II. Understanding IP 3R channels: From structural underpinnings to ligand-dependent conformational landscape. Cell Calcium 2023; 114:102770. [PMID: 37393815 PMCID: PMC10529787 DOI: 10.1016/j.ceca.2023.102770] [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: 05/08/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/04/2023]
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ubiquitously expressed large-conductance Ca2+-permeable channels predominantly localized to the endoplasmic reticulum (ER) membranes of virtually all eukaryotic cell types. IP3Rs work as Ca2+ signaling hubs through which diverse extracellular stimuli and intracellular inputs are processed and then integrated to result in delivery of Ca2+ from the ER lumen to generate cytosolic Ca2+ signals with precise temporal and spatial properties. IP3R-mediated Ca2+ signals control a vast repertoire of cellular functions ranging from gene transcription and secretion to the more enigmatic brain activities such as learning and memory. IP3Rs open and release Ca2+ when they bind both IP3 and Ca2+, the primary channel agonists. Despite overwhelming evidence supporting functional interplay between IP3 and Ca2+ in activation and inhibition of IP3Rs, the mechanistic understanding of how IP3R channels convey their gating through the interplay of two primary agonists remains one of the major puzzles in the field. The last decade has seen much progress in the use of cryogenic electron microscopy to elucidate the molecular mechanisms of ligand binding, ion permeation, ion selectivity and gating of the IP3R channels. The results of these studies, summarized in this review, provide a prospective view of what the future holds in structural and functional research of IP3Rs.
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Affiliation(s)
- Mariah R Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Vikas Arige
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - David I Yule
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA.
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA.
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3
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Smith HA, Thillaiappan NB, Rossi AM. IP 3 receptors: An "elementary" journey from structure to signals. Cell Calcium 2023; 113:102761. [PMID: 37271052 DOI: 10.1016/j.ceca.2023.102761] [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: 03/07/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/06/2023]
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are large tetrameric channels which sit mostly in the membrane of the endoplasmic reticulum (ER) and mediate Ca2+ release from intracellular stores in response to extracellular stimuli in almost all cells. Dual regulation of IP3Rs by IP3 and Ca2+ itself, upstream "licensing", and the arrangement of IP3Rs into small clusters in the ER membrane, allow IP3Rs to generate spatially and temporally diverse Ca2+ signals. The characteristic biphasic regulation of IP3Rs by cytosolic Ca2+ concentration underpins regenerative Ca2+ signals by Ca2+-induced Ca2+-release, while also preventing uncontrolled explosive Ca2+ release. In this way, cells can harness a simple ion such as Ca2+ as a near-universal intracellular messenger to regulate diverse cellular functions, including those with conflicting outcomes such as cell survival and cell death. High-resolution structures of the IP3R bound to IP3 and Ca2+ in different combinations have together started to unravel the workings of this giant channel. Here we discuss, in the context of recently published structures, how the tight regulation of IP3Rs and their cellular geography lead to generation of "elementary" local Ca2+ signals known as Ca2+ "puffs", which form the fundamental bottleneck through which all IP3-mediated cytosolic Ca2+ signals must first pass.
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Affiliation(s)
- Holly A Smith
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | | | - Ana M Rossi
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom.
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4
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Han B, Zhen F, Zheng XS, Hu J, Chen XS. Systematic analysis of the expression and prognostic value of ITPR1 and correlation with tumor infiltrating immune cells in breast cancer. BMC Cancer 2022; 22:297. [PMID: 35313846 PMCID: PMC8939201 DOI: 10.1186/s12885-022-09410-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 03/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND ITPR1 is a key gene for autophagy, but its biological function is still unclear, and there are few studies on the correlation between ITPR1 gene expression and the occurrence and development of breast cancer. METHODS Analyze the expression of ITPR1 through online databases such as Oncomine and TIMER. Kaplan-Meier plotter and other databases were used to evaluate the impact of ITPR1 on clinical prognosis. The expression of ITPR1 in analysis of 145 cases of breast cancer and 30 cases of adjacent normal tissue was detected by Immunohistochemistry. Statistical analysis was used to evaluate the clinical relevance and prognostic significance of abnormally expressed proteins. And the Western Blot was used to detect the expression of ITPR1 between breast cancer tissues and cells. The TIMER database studied the relationship between ITPR1 and cancer immune infiltration. And used the ROC plotter database to predict the response of ITPR1 to chemotherapy, endocrine therapy and anti-HER2 therapy in patients with breast cancer. RESULTS Compared with normal breast samples, ITPR1 was significantly lower in patients with breast cancer. And the increased expression of ITPR1 mRNA was closely related to longer overall survival (OS), distant metastasis free survival (DMFS), disease specific survival (DSS) and relapse free survival (RFS) in breast cancer. And the expression level of ITPR1 was higher in patients treated with chemotherapy than untreated patients. In addition, the expression of ITPR1 was positively correlated with related gene markers of immune cells in different types of breast cancer, especially with BRCA basal tissue breast cancer. CONCLUSION ITPR1 was lower expressed in breast cancer. The higher expression of ITPR1 suggested favorable prognosis for patients. ITPR1 was related to the level of immune infiltration, especially in BRCA-Basal patients. All research results indicated that ITPR1 might affect breast cancer prognosis and participate in immune regulation. In short, ITPR1 might be a potential target for breast cancer therapy.
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Affiliation(s)
- Bing Han
- Department of Breast Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Fang Zhen
- Department of Breast Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Xiu-Shuang Zheng
- Department of Reproductive Medicine, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, Harbin, 150001, China
| | - Jing Hu
- Department of Breast Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China.
| | - Xue-Song Chen
- Department of Breast Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China.
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5
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Woll KA, Van Petegem F. Calcium Release Channels: Structure and Function of IP3 Receptors and Ryanodine Receptors. Physiol Rev 2021; 102:209-268. [PMID: 34280054 DOI: 10.1152/physrev.00033.2020] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ca2+-release channels are giant membrane proteins that control the release of Ca2+ from the endoplasmic and sarcoplasmic reticulum. The two members, ryanodine receptors (RyRs) and inositol-1,4,5-trisphosphate Receptors (IP3Rs), are evolutionarily related and are both activated by cytosolic Ca2+. They share a common architecture, but RyRs have evolved additional modules in the cytosolic region. Their massive size allows for the regulation by tens of proteins and small molecules, which can affect the opening and closing of the channels. In addition to Ca2+, other major triggers include IP3 for the IP3Rs, and depolarization of the plasma membrane for a particular RyR subtype. Their size has made them popular targets for study via electron microscopic methods, with current structures culminating near 3Å. The available structures have provided many new mechanistic insights int the binding of auxiliary proteins and small molecules, how these can regulate channel opening, and the mechanisms of disease-associated mutations. They also help scrutinize previously proposed binding sites, as some of these are now incompatible with the structures. Many questions remain around the structural effects of post-translational modifications, additional binding partners, and the higher-order complexes these channels can make in situ. This review summarizes our current knowledge about the structures of Ca2+-release channels and how this informs on their function.
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Affiliation(s)
- Kellie A Woll
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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Azumaya CM, Linton EA, Risener CJ, Nakagawa T, Karakas E. Cryo-EM structure of human type-3 inositol triphosphate receptor reveals the presence of a self-binding peptide that acts as an antagonist. J Biol Chem 2020; 295:1743-1753. [PMID: 31915246 PMCID: PMC7008357 DOI: 10.1074/jbc.ra119.011570] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/06/2020] [Indexed: 01/04/2023] Open
Abstract
Calcium-mediated signaling through inositol 1,4,5-triphosphate receptors (IP3Rs) is essential for the regulation of numerous physiological processes, including fertilization, muscle contraction, apoptosis, secretion, and synaptic plasticity. Deregulation of IP3Rs leads to pathological calcium signaling and is implicated in many common diseases, including cancer and neurodegenerative, autoimmune, and metabolic diseases. Revealing the mechanism of activation and inhibition of this ion channel will be critical to an improved understanding of the biological processes that are controlled by IP3Rs. Here, we report structural findings of the human type-3 IP3R (IP3R-3) obtained by cryo-EM (at an overall resolution of 3.8 Å), revealing an unanticipated regulatory mechanism where a loop distantly located in the primary sequence occupies the IP3-binding site and competitively inhibits IP3 binding. We propose that this inhibitory mechanism must differ qualitatively among IP3R subtypes because of their diverse loop sequences, potentially serving as a key molecular determinant of subtype-specific calcium signaling in IP3Rs. In summary, our structural characterization of human IP3R-3 provides critical insights into the mechanistic function of IP3Rs and into subtype-specific regulation of these important calcium-regulatory channels.
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MESH Headings
- Binding Sites
- Calcium Signaling
- Cryoelectron Microscopy
- Humans
- Inositol 1,4,5-Trisphosphate/metabolism
- Inositol 1,4,5-Trisphosphate Receptors/antagonists & inhibitors
- Inositol 1,4,5-Trisphosphate Receptors/chemistry
- Inositol 1,4,5-Trisphosphate Receptors/metabolism
- Inositol 1,4,5-Trisphosphate Receptors/ultrastructure
- Models, Molecular
- Peptides/metabolism
- Protein Conformation
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Affiliation(s)
- Caleigh M Azumaya
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232
| | - Emily A Linton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232
| | - Caitlin J Risener
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232
| | - Terunaga Nakagawa
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232; Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232; Vanderbilt Brain Institute, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232
| | - Erkan Karakas
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232; Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232.
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Berenguer-Escuder C, Grossmann D, Massart F, Antony P, Burbulla LF, Glaab E, Imhoff S, Trinh J, Seibler P, Grünewald A, Krüger R. Variants in Miro1 Cause Alterations of ER-Mitochondria Contact Sites in Fibroblasts from Parkinson's Disease Patients. J Clin Med 2019; 8:jcm8122226. [PMID: 31888276 PMCID: PMC6947516 DOI: 10.3390/jcm8122226] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 01/03/2023] Open
Abstract
Background: Although most cases of Parkinson´s disease (PD) are idiopathic with unknown cause, an increasing number of genes and genetic risk factors have been discovered that play a role in PD pathogenesis. Many of the PD-associated proteins are involved in mitochondrial quality control, e.g., PINK1, Parkin, and LRRK2, which were recently identified as regulators of mitochondrial-endoplasmic reticulum (ER) contact sites (MERCs) linking mitochondrial homeostasis to intracellular calcium handling. In this context, Miro1 is increasingly recognized to play a role in PD pathology. Recently, we identified the first PD patients carrying mutations in RHOT1, the gene coding for Miro1. Here, we describe two novel RHOT1 mutations identified in two PD patients and the characterization of the cellular phenotypes. Methods: Using whole exome sequencing we identified two PD patients carrying heterozygous mutations leading to the amino acid exchanges T351A and T610A in Miro1. We analyzed calcium homeostasis and MERCs in detail by live cell imaging and immunocytochemistry in patient-derived fibroblasts. Results: We show that fibroblasts expressing mutant T351A or T610A Miro1 display impaired calcium homeostasis and a reduced amount of MERCs. All fibroblast lines from patients with pathogenic variants in Miro1, revealed alterations of the structure of MERCs. Conclusion: Our data suggest that Miro1 is important for the regulation of the structure and function of MERCs. Moreover, our study supports the role of MERCs in the pathogenesis of PD and further establishes variants in RHOT1 as rare genetic risk factors for neurodegeneration.
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Affiliation(s)
- Clara Berenguer-Escuder
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4367 Belvaux, Luxembourg; (D.G.); (F.M.); (P.A.); (E.G.); (A.G.)
- Correspondence: (C.B.E.); (R.K.); Tel.: +352-46-66-44-5401 (R.K.)
| | - Dajana Grossmann
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4367 Belvaux, Luxembourg; (D.G.); (F.M.); (P.A.); (E.G.); (A.G.)
| | - Franҫois Massart
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4367 Belvaux, Luxembourg; (D.G.); (F.M.); (P.A.); (E.G.); (A.G.)
| | - Paul Antony
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4367 Belvaux, Luxembourg; (D.G.); (F.M.); (P.A.); (E.G.); (A.G.)
| | - Lena F. Burbulla
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA;
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4367 Belvaux, Luxembourg; (D.G.); (F.M.); (P.A.); (E.G.); (A.G.)
| | - Sophie Imhoff
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany; (S.I.); (J.T.); (P.S.)
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany; (S.I.); (J.T.); (P.S.)
| | - Philip Seibler
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany; (S.I.); (J.T.); (P.S.)
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4367 Belvaux, Luxembourg; (D.G.); (F.M.); (P.A.); (E.G.); (A.G.)
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany; (S.I.); (J.T.); (P.S.)
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4367 Belvaux, Luxembourg; (D.G.); (F.M.); (P.A.); (E.G.); (A.G.)
- Luxembourg Institute of Health (LIH), 1445 Strassen, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), 1460 Luxembourg, Luxembourg
- Correspondence: (C.B.E.); (R.K.); Tel.: +352-46-66-44-5401 (R.K.)
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8
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Lemos FDO, Florentino RM, Lima Filho ACM, Santos MLD, Leite MF. Inositol 1,4,5-trisphosphate receptor in the liver: Expression and function. World J Gastroenterol 2019; 25:6483-6494. [PMID: 31802829 PMCID: PMC6886013 DOI: 10.3748/wjg.v25.i44.6483] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/22/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
The liver is a complex organ that performs several functions to maintain homeostasis. These functions are modulated by calcium, a second messenger that regulates several intracellular events. In hepatocytes and cholangiocytes, which are the epithelial cell types in the liver, inositol 1,4,5-trisphosphate (InsP3) receptors (ITPR) are the only intracellular calcium release channels. Three isoforms of the ITPR have been described, named type 1, type 2 and type 3. These ITPR isoforms are differentially expressed in liver cells where they regulate distinct physiological functions. Changes in the expression level of these receptors correlate with several liver diseases and hepatic dysfunctions. In this review, we highlight how the expression level, modulation, and localization of ITPR isoforms in hepatocytes and cholangiocytes play a role in hepatic homeostasis and liver pathology.
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Affiliation(s)
- Fernanda de Oliveira Lemos
- Department of Physiology and Biophysics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Rodrigo M Florentino
- Department of Physiology and Biophysics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Antônio Carlos Melo Lima Filho
- Department of Physiology and Biophysics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Marcone Loiola dos Santos
- Department of Cell Biology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - M Fatima Leite
- Department of Physiology and Biophysics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
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9
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Abstract
In the body, extracellular stimuli produce inositol 1,4,5-trisphosphate (IP3), an intracellular chemical signal that binds to the IP3 receptor (IP3R) to release calcium ions (Ca2+) from the endoplasmic reticulum. In the past 40 years, the wide-ranging functions mediated by IP3R and its genetic defects causing a variety of disorders have been unveiled. Recent cryo-electron microscopy and X-ray crystallography have resolved IP3R structures and begun to integrate with concurrent functional studies, which can explicate IP3-dependent opening of Ca2+-conducting gates placed ∼90 Å away from IP3-binding sites and its regulation by Ca2+. This review highlights recent research progress on the IP3R structure and function. We also propose how protein plasticity within IP3R, which involves allosteric gating and assembly transformations accompanied by rapid and chronic structural changes, would enable it to regulate diverse functions at cellular microdomains in pathophysiological states.
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Affiliation(s)
- Kozo Hamada
- Laboratory of Cell Calcium Signaling, Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, 201210, China; ,
| | - Katsuhiko Mikoshiba
- Laboratory of Cell Calcium Signaling, Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, 201210, China; ,
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10
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Sayed ME, Cheng A, Yadav GP, Ludlow AT, Shay JW, Wright WE, Jiang QX. Catalysis-dependent inactivation of human telomerase and its reactivation by intracellular telomerase-activating factors (iTAFs). J Biol Chem 2019; 294:11579-11596. [PMID: 31186347 DOI: 10.1074/jbc.ra118.007234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 06/04/2019] [Indexed: 12/17/2022] Open
Abstract
Human telomerase maintains genome stability by adding telomeric repeats to the ends of linear chromosomes. Although previous studies have revealed profound insights into telomerase functions, the low cellular abundance of functional telomerase and the difficulties in quantifying its activity leave its thermodynamic and kinetic properties only partially characterized. Employing a stable cell line overexpressing both the human telomerase RNA component and the N-terminally biotinylated human telomerase reverse transcriptase and using a newly developed method to count individual extension products, we demonstrate here that human telomerase holoenzymes contain fast- and slow-acting catalytic sites. Surprisingly, both active sites became inactive after two consecutive rounds of catalysis, named single-run catalysis. The fast active sites turned off ∼40-fold quicker than the slow ones and exhibited higher affinities to DNA substrates. In a dimeric enzyme, the two active sites work in tandem, with the faster site functioning before the slower one, and in the monomeric enzyme, the active sites also perform single-run catalysis. Interestingly, inactive enzymes could be reactivated by intracellular telomerase-activating factors (iTAFs) from multiple cell types. We conclude that the single-run catalysis and the iTAF-triggered reactivation serve as an unprecedented control circuit for dynamic regulation of telomerase. They endow native telomerase holoenzymes with the ability to match their total number of active sites to the number of telomeres they extend. We propose that the exquisite kinetic control of telomerase activity may play important roles in both cell division and cell aging.
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Affiliation(s)
- Mohammed E Sayed
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390.,School of Kinesiology Integrative Molecular Genetics Lab, University of Michigan, Ann Arbor, Michigan 48109
| | - Ao Cheng
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390.,Department of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, Minnesota 55455
| | - Gaya P Yadav
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390.,Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Andrew T Ludlow
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390.,School of Kinesiology Integrative Molecular Genetics Lab, University of Michigan, Ann Arbor, Michigan 48109
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Woodring E Wright
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Qiu-Xing Jiang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390 .,Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
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11
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Yadav GP, Zheng H, Yang Q, Douma LG, Bloom LB, Jiang QX. Secretory granule protein chromogranin B (CHGB) forms an anion channel in membranes. Life Sci Alliance 2018; 1:e201800139. [PMID: 30456382 PMCID: PMC6238609 DOI: 10.26508/lsa.201800139] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/29/2018] [Accepted: 09/11/2018] [Indexed: 12/14/2022] Open
Abstract
The CHGB subfamily of secretory granule proteins forms a new family of anion-selective channels by interacting with membranes via two amphipathic α-helices. The channel exhibits higher anion selectivity, larger conductance, higher DIDS-binding affinity, and higher Cl− sensitivity than other known anion channels. Regulated secretion is an intracellular pathway that is highly conserved from protists to humans. Granin family proteins were proposed to participate in the biogenesis, maturation and release of secretory granules in this pathway. However, the exact molecular mechanisms underlying the intracellular functions of the granin family proteins remain unclear. Here, we show that chromogranin B (CHGB), a secretory granule protein, inserts itself into membrane and forms a chloride-conducting channel. CHGB interacts strongly with phospholipid membranes through two amphipathic α helices. At a high local concentration, CHGB insertion in membrane causes significant bilayer remodeling, producing protein-coated nanoparticles and nanotubules. Fast kinetics and high cooperativity for anion efflux from CHGB vesicles suggest that CHGB tetramerizes to form a functional channel with a single-channel conductance of ∼125 pS (150/150 mM Cl−). The CHGB channel is sensitive to an anion channel blocker and exhibits higher anion selectivity than the other six known families of Cl− channels. Our data suggest that the CHGB subfamily of granin proteins forms a new family of organelle chloride channels.
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Affiliation(s)
- Gaya P Yadav
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Hui Zheng
- Department of Physiology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Qing Yang
- Crop Designing Center, Henan Academy of Agricultural Sciences, Zhengzhou, PR China
| | - Lauren G Douma
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Linda B Bloom
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Qiu-Xing Jiang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
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12
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The genetic architecture of aniridia and Gillespie syndrome. Hum Genet 2018; 138:881-898. [PMID: 30242502 PMCID: PMC6710220 DOI: 10.1007/s00439-018-1934-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 09/06/2018] [Indexed: 12/13/2022]
Abstract
Absence of part or all of the iris, aniridia, is a feature of several genetically distinct conditions. This review focuses on iris development and then the clinical features and molecular genetics of these iris malformations. Classical aniridia, a panocular eye malformation including foveal hypoplasia, is the archetypal phenotype associated with heterozygous PAX6 loss-of-function mutations. Since this was identified in 1991, many genetic mechanisms of PAX6 inactivation have been elucidated, the commonest alleles being intragenic mutations causing premature stop codons, followed by those causing C-terminal extensions. Rarely, aniridia cases are associated with FOXC1, PITX2 and/or their regulatory regions. Aniridia can also occur as a component of many severe global eye malformations. Gillespie syndrome—a triad of partial aniridia, non-progressive cerebellar ataxia and intellectual disability—is phenotypically and genotypically distinct from classical aniridia. The causative gene has recently been identified as ITPR1. The same characteristic Gillespie syndrome-like iris, with aplasia of the pupillary sphincter and a scalloped margin, is seen in ACTA2-related multisystemic smooth muscle dysfunction syndrome. WAGR syndrome (Wilms tumour, aniridia, genitourinary anomalies and mental retardation/intellectual disability), is caused by contiguous deletion of PAX6 and WT1 on chromosome 11p. Deletions encompassing BDNF have been causally implicated in the obesity and intellectual disability associated with the condition. Lastly, we outline a genetic investigation strategy for aniridia in light of recent developments, suggesting an approach based principally on chromosomal array and gene panel testing. This strategy aims to test all known aniridia loci—including the rarer, life-limiting causes—whilst remaining simple and practical.
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13
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Ca 2+ signaling and spinocerebellar ataxia. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1733-1744. [PMID: 29777722 DOI: 10.1016/j.bbamcr.2018.05.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 11/22/2022]
Abstract
Spinocerebellar ataxia (SCA) is a neural disorder, which is caused by degenerative changes in the cerebellum. SCA is primarily characterized by gait ataxia, and additional clinical features include nystagmus, dysarthria, tremors and cerebellar atrophy. Forty-four hereditary SCAs have been identified to date, along with >35 SCA-associated genes. Despite the great diversity and distinct functionalities of the SCA-related genes, accumulating evidence supports the occurrence of a common pathophysiological event among several hereditary SCAs. Altered calcium (Ca2+) homeostasis in the Purkinje cells (PCs) of the cerebellum has been proposed as a possible pathological SCA trigger. In support of this, signaling events that are initiated from or lead to aberrant Ca2+ release from the type 1 inositol 1,4,5-trisphosphate receptor (IP3R1), which is highly expressed in cerebellar PCs, seem to be closely associated with the pathogenesis of several SCA types. In this review, we summarize the current research on pathological hereditary SCA events, which involve altered Ca2+ homeostasis in PCs, through IP3R1 signaling.
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Structural Insights into IP3R Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 981:121-147. [DOI: 10.1007/978-3-319-55858-5_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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15
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Baker MR, Fan G, Serysheva II. Structure of IP 3R channel: high-resolution insights from cryo-EM. Curr Opin Struct Biol 2017; 46:38-47. [PMID: 28618351 PMCID: PMC5683905 DOI: 10.1016/j.sbi.2017.05.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 05/08/2017] [Accepted: 05/25/2017] [Indexed: 01/19/2023]
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ubiquitously expressed intracellular Ca2+ channels and the major mediators of cellular Ca2+ signals generated by the release of Ca2+ ions from intracellular stores in response to a variety of extracellular stimuli. Despite established physiological significance and proven involvements of IP3R channels in many human diseases, detailed structural basis for signal detection by these ion channels and their gating remain obscure. Recently, single particle electron cryomicroscopy (cryo-EM) has yielded a long-awaited near-atomic resolution structure of the entire full-length type 1 IP3R. This structure provided exciting mechanistic insights into the molecular assembly of IP3R, revealing the pronounced structural conservation of Ca2+ release channels and raising many fundamental and controversial questions on their activation and gating. Here we summarize the major technological advances that propelled our cryo-EM analysis of IP3R to near-atomic resolution and discuss what the future holds for structural biology of Ca2+ release channels.
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Affiliation(s)
- Mariah R Baker
- Structural Biology Imaging Center, Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Guizhen Fan
- Structural Biology Imaging Center, Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Irina I Serysheva
- Structural Biology Imaging Center, Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA.
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16
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IP 3 receptor signaling and endothelial barrier function. Cell Mol Life Sci 2017; 74:4189-4207. [PMID: 28803370 DOI: 10.1007/s00018-017-2624-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/18/2017] [Accepted: 08/08/2017] [Indexed: 12/14/2022]
Abstract
The endothelium, a monolayer of endothelial cells lining vessel walls, maintains tissue-fluid homeostasis by restricting the passage of the plasma proteins and blood cells into the interstitium. The ion Ca2+, a ubiquitous secondary messenger, initiates signal transduction events in endothelial cells that is critical to control of vascular tone and endothelial permeability. The ion Ca2+ is stored inside the intracellular organelles and released into the cytosol in response to environmental cues. The inositol 1,4,5-trisphosphate (IP3) messenger facilitates Ca2+ release through IP3 receptors which are Ca2+-selective intracellular channels located within the membrane of the endoplasmic reticulum. Binding of IP3 to the IP3Rs initiates assembly of IP3R clusters, a key event responsible for amplification of Ca2+ signals in endothelial cells. This review discusses emerging concepts related to architecture and dynamics of IP3R clusters, and their specific role in propagation of Ca2+ signals in endothelial cells.
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17
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Near-membrane electric field calcium ion dehydration. Cell Calcium 2016; 60:415-422. [DOI: 10.1016/j.ceca.2016.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/14/2016] [Accepted: 09/22/2016] [Indexed: 11/18/2022]
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18
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Giacomello M, Pellegrini L. The coming of age of the mitochondria-ER contact: a matter of thickness. Cell Death Differ 2016; 23:1417-27. [PMID: 27341186 DOI: 10.1038/cdd.2016.52] [Citation(s) in RCA: 278] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/02/2016] [Accepted: 05/05/2016] [Indexed: 12/12/2022] Open
Abstract
The sites of near-contact between the mitochondrion and the endoplasmic reticulum (ER) have earned a lot of attention due to their key role in the maintenance of lipid and calcium (Ca(2+)) homeostasis, in the initiation of autophagy and mitochondrial division, and in sensing metabolic shifts. At these sites, typically called MAMs (mitochondria-associated ER membranes) or MERCs (mitochondria-ER contacts), the organelles juxtapose at a distance that can range from ~10 to ~50 nm. The multifunctional role of this subcellular compartment is puzzling; further, recent studies have shown that mitochondria-ER contacts are highly plastic structures that remodel upon metabolic transitions and that their activity in controlling lipid homeostasis could be involved in Alzheimer's disease pathogenesis. This review aims at integrating the functions of this subcellular compartment to its most characterizing and unexplored structural parameter, their 'thickness': that is, the width of the cleft that separates the cytosolic face of the outer mitochondrial membrane from that of the ER. We describe and discuss the reasons why the thickness of a MERC should be considered a regulated structural parameter of the cell that defines and controls its function. Further, we propose a MERC classification that will help organize the expanding field of MERCs biology and of their role in cell physiology and human disease.
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Affiliation(s)
- M Giacomello
- Department of Biology, Università di Padova, Padua, Italy.,Venetian Institute of Molecular Medicine, Padua, Italy
| | - L Pellegrini
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Universitè Laval, Quebec, Québec, Canada.,Mitochondria Biology Laboratory, CRIUSMQ, Quebec, Québec, Canada
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19
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Reboul CF, Bonnet F, Elmlund D, Elmlund H. A Stochastic Hill Climbing Approach for Simultaneous 2D Alignment and Clustering of Cryogenic Electron Microscopy Images. Structure 2016; 24:988-96. [PMID: 27184214 DOI: 10.1016/j.str.2016.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 04/11/2016] [Accepted: 04/14/2016] [Indexed: 01/10/2023]
Abstract
A critical step in the analysis of novel cryogenic electron microscopy (cryo-EM) single-particle datasets is the identification of homogeneous subsets of images. Methods for solving this problem are important for data quality assessment, ab initio 3D reconstruction, and analysis of population diversity due to the heterogeneous nature of macromolecules. Here we formulate a stochastic algorithm for identification of homogeneous subsets of images. The purpose of the method is to generate improved 2D class averages that can be used to produce a reliable 3D starting model in a rapid and unbiased fashion. We show that our method overcomes inherent limitations of widely used clustering approaches and proceed to test the approach on six publicly available experimental cryo-EM datasets. We conclude that, in each instance, ab initio 3D reconstructions of quality suitable for initialization of high-resolution refinement are produced from the cluster centers.
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Affiliation(s)
- Cyril F Reboul
- Department of Biochemistry Molecular Biology, Monash University, Clayton 3800, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Clayton 3800, Australia
| | - Frederic Bonnet
- Department of Biochemistry Molecular Biology, Monash University, Clayton 3800, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Clayton 3800, Australia
| | - Dominika Elmlund
- Department of Biochemistry Molecular Biology, Monash University, Clayton 3800, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Clayton 3800, Australia.
| | - Hans Elmlund
- Department of Biochemistry Molecular Biology, Monash University, Clayton 3800, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Clayton 3800, Australia.
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20
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De Zorzi R, Mi W, Liao M, Walz T. Single-particle electron microscopy in the study of membrane protein structure. Microscopy (Oxf) 2015; 65:81-96. [PMID: 26470917 DOI: 10.1093/jmicro/dfv058] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/20/2015] [Indexed: 01/13/2023] Open
Abstract
Single-particle electron microscopy (EM) provides the great advantage that protein structure can be studied without the need to grow crystals. However, due to technical limitations, this approach played only a minor role in the study of membrane protein structure. This situation has recently changed dramatically with the introduction of direct electron detection device cameras, which allow images of unprecedented quality to be recorded, also making software algorithms, such as three-dimensional classification and structure refinement, much more powerful. The enhanced potential of single-particle EM was impressively demonstrated by delivering the first long-sought atomic model of a member of the biomedically important transient receptor potential channel family. Structures of several more membrane proteins followed in short order. This review recounts the history of single-particle EM in the study of membrane proteins, describes the technical advances that now allow this approach to generate atomic models of membrane proteins and provides a brief overview of some of the membrane protein structures that have been studied by single-particle EM to date.
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Affiliation(s)
- Rita De Zorzi
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA Howard Hughes Medical Institute, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Wei Mi
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA Howard Hughes Medical Institute, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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21
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Van Petegem F. Ryanodine Receptors: Allosteric Ion Channel Giants. J Mol Biol 2015; 427:31-53. [DOI: 10.1016/j.jmb.2014.08.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/02/2014] [Accepted: 08/05/2014] [Indexed: 01/27/2023]
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22
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Baker MR, Fan G, Serysheva II. Single-particle cryo-EM of the ryanodine receptor channel in an aqueous environment. Eur J Transl Myol 2015; 25:4803. [PMID: 25844145 PMCID: PMC4748972 DOI: 10.4081/ejtm.2015.4803] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/22/2014] [Accepted: 12/31/2014] [Indexed: 12/31/2022] Open
Abstract
Ryanodine receptors (RyRs) are tetrameric ligand-gated Ca2+ release channels that are responsible for the increase of cytosolic Ca2+ concentration leading to muscle contraction. Our current understanding of RyR channel gating and regulation is greatly limited due to the lack of a high-resolution structure of the channel protein. The enormous size and unwieldy shape of Ca2+ release channels make X-ray or NMR methods difficult to apply for high-resolution structural analysis of the full-length functional channel. Single-particle electron cryo-microscopy (cryo-EM) is one of the only effective techniques for the study of such a large integral membrane protein and its molecular interactions. Despite recent developments in cryo-EM technologies and break-through single-particle cryo-EM studies of ion channels, cryospecimen preparation, particularly the presence of detergent in the buffer, remains the main impediment to obtaining atomic-resolution structures of ion channels and a multitude of other integral membrane protein complexes. In this review we will discuss properties of several detergents that have been successfully utilized in cryo-EM studies of ion channels and the emergence of the detergent alternative amphipol to stabilize ion channels for structure-function characterization. Future structural studies of challenging specimen like ion channels are likely to be facilitated by cryo-EM amenable detergents or alternative surfactants.
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Affiliation(s)
| | | | - Irina I. Serysheva
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA
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23
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Fos C, Becart S, Canonigo Balancio AJ, Boehning D, Altman A. Association of the EF-hand and PH domains of the guanine nucleotide exchange factor SLAT with IP₃ receptor 1 promotes Ca²⁺ signaling in T cells. Sci Signal 2014; 7:ra93. [PMID: 25270259 DOI: 10.1126/scisignal.2005565] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The guanine nucleotide exchange factor SLAT (SWAP-70-like adaptor of T cells) regulates T cell activation and differentiation by enabling Ca(2+) release from intracellular stores in response to stimulation of the T cell receptor (TCR). We found a TCR-induced association between SLAT and inositol 1,4,5-trisphosphate (IP3) receptor type 1 (IP3R1). The N-terminal region of SLAT, which contains two EF-hand motifs that we determined bound Ca(2+), and the SLAT pleckstrin homology (PH) domain independently bound to IP3R1 by associating with a conserved motif within the IP3R1 ligand-binding domain. Disruption of the SLAT-IP3R1 interaction with cell-permeable, IP3R1-based fusion peptides inhibited TCR-stimulated Ca(2+) signaling, activation of the transcription factor NFAT (nuclear factor of activated T cells), and production of cytokines, suggesting that this interaction is required for optimal T cell activation. The finding that SLAT is an IP3R1-interacting protein required for T cell activation suggests that this interaction could be a potential target for a selective immunosuppressive drug.
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Affiliation(s)
- Camille Fos
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Stephane Becart
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Ann J Canonigo Balancio
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Darren Boehning
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Amnon Altman
- Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
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24
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Serysheva II. Toward a high-resolution structure of IP₃R channel. Cell Calcium 2014; 56:125-32. [PMID: 25159857 DOI: 10.1016/j.ceca.2014.08.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 08/01/2014] [Accepted: 08/02/2014] [Indexed: 12/11/2022]
Abstract
The ability of cells to maintain low levels of Ca(2+) under resting conditions and to create rapid and transient increases in Ca(2+) upon stimulation is a fundamental property of cellular Ca(2+) signaling mechanism. An increase of cytosolic Ca(2+) level in response to diverse stimuli is largely accounted for by the inositol 1,4,5-trisphosphate receptor (IP3R) present in the endoplasmic reticulum membranes of virtually all eukaryotic cells. Extensive information is currently available on the function of IP3Rs and their interaction with modulators. Very little, however, is known about their molecular architecture and therefore most critical issues surrounding gating of IP3R channels are still ambiguous, including the central question of how opening of the IP3R pore is initiated by IP3 and Ca(2+). Membrane proteins such as IP3R channels have proven to be exceptionally difficult targets for structural analysis due to their large size, their location in the membrane environment, and their dynamic nature. To date, a 3D structure of complete IP3R channel is determined by single-particle cryo-EM at intermediate resolution, and the best crystal structures of IP3R are limited to a soluble portion of the cytoplasmic region representing ∼15% of the entire channel protein. Together these efforts provide the important structural information for this class of ion channels and serve as the basis for further studies aiming at understanding of the IP3R function.
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Affiliation(s)
- Irina I Serysheva
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA.
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25
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ResLog plots as an empirical metric of the quality of cryo-EM reconstructions. J Struct Biol 2013; 185:418-26. [PMID: 24384117 DOI: 10.1016/j.jsb.2013.12.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 12/19/2013] [Accepted: 12/23/2013] [Indexed: 12/13/2022]
Abstract
Compared to the field of X-ray crystallography, the field of single particle three-dimensional electron microscopy has few reliable metrics for assessing the quality of 3D reconstructions. New metrics are needed that can determine whether a given 3D reconstruction accurately reflects the structure of the particles from which it was derived or instead depicts a plausible though incorrect structure due to coarse misalignment of particles. Here an empirical procedure is presented for differentiating between a reconstruction with well-aligned particles and a reconstruction with grossly misclassified particles. For a given dataset, 3D reconstructions are computed from subsets of particles with decreasing numbers of particles contributing to the reconstruction. A plot of inverse resolution vs. the logarithm of the number of particles (a "ResLog" plot) provides metrics for the reliability of the reconstruction and the overall quality of the dataset and processing. Specifically, the y-intercept of a regression line provides a measure of the relative accuracy of the particle alignment and classification, and the slope is an indicator of the overall data quality including the imaging conditions and processing steps. ResLog plots can also be used to optimize conditions for data collection and reconstruction parameters. Although resolution estimates can vary by method of calculation, ResLog-derived parameters are consistent whether calculated by Fourier shell correlation or Fourier neighbor correlation, or a new coordinate-based metric that serves as a yardstick for structures where atomic coordinates are available. ResLog plots could become part of a standard set of parameters to be included in 3D reconstruction reports.
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26
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Fedorenko OA, Popugaeva E, Enomoto M, Stathopulos PB, Ikura M, Bezprozvanny I. Intracellular calcium channels: inositol-1,4,5-trisphosphate receptors. Eur J Pharmacol 2013; 739:39-48. [PMID: 24300389 DOI: 10.1016/j.ejphar.2013.10.074] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 09/28/2013] [Accepted: 10/17/2013] [Indexed: 01/13/2023]
Abstract
The inositol-1,4,5-trisphosphate receptors (InsP3Rs) are the major intracellular Ca(2+)-release channels in cells. Activity of InsP3Rs is essential for elementary and global Ca(2+) events in the cell. There are three InsP3Rs isoforms that are present in mammalian cells. In this review we will focus primarily on InsP3R type 1. The InsP3R1 is a predominant isoform in neurons and it is the most extensively studied isoform. Combination of biophysical and structural methods revealed key mechanisms of InsP3R function and modulation. Cell biological and biochemical studies lead to identification of a large number of InsP3R-binding proteins. InsP3Rs are involved in the regulation of numerous physiological processes, including learning and memory, proliferation, differentiation, development and cell death. Malfunction of InsP3R1 play a role in a number of neurodegenerative disorders and other disease states. InsP3Rs represent a potentially valuable drug target for treatment of these disorders and for modulating activity of neurons and other cells. Future studies will provide better understanding of physiological functions of InsP3Rs in health and disease.
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Affiliation(s)
- Olena A Fedorenko
- Department of Brain Physiology, Bogomoletz Institute of Physiology, 01024 Kiev, Ukraine; State Key Laboratory of Molecular and Cellular Biology, 01024 Kiev, Ukraine
| | - Elena Popugaeva
- Laboratory of Molecular Neurodegeneration, Department of Medical Physics, St. Petersburg State Polytechnical University, 195251 St. Petersburg, Russia
| | - Masahiro Enomoto
- Princess Margaret Cancer Centre, Department of Medical Biophysics, University of Toronto, M5G1L7 Toronto, Ontario, Canada
| | - Peter B Stathopulos
- Princess Margaret Cancer Centre, Department of Medical Biophysics, University of Toronto, M5G1L7 Toronto, Ontario, Canada
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, Department of Medical Biophysics, University of Toronto, M5G1L7 Toronto, Ontario, Canada
| | - Ilya Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Department of Medical Physics, St. Petersburg State Polytechnical University, 195251 St. Petersburg, Russia; Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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27
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Christian N, Skupin A, Morante S, Jansen K, Rossi G, Ebenhöh O. Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels. J Theor Biol 2013; 343:102-12. [PMID: 24270093 DOI: 10.1016/j.jtbi.2013.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 09/03/2013] [Accepted: 11/13/2013] [Indexed: 11/19/2022]
Abstract
A major challenge in biology is to understand how molecular processes determine phenotypic features. We address this fundamental problem in a class of model systems by developing a general mathematical framework that allows the calculation of mesoscopic properties from the knowledge of microscopic Markovian transition probabilities. We show how exact analytic formulae for the first and second moments of resident time distributions in mesostates can be derived from microscopic resident times and transition probabilities even for systems with a large number of microstates. We apply our formalism to models of the inositol trisphosphate receptor, which plays a key role in generating calcium signals triggering a wide variety of cellular responses. We demonstrate how experimentally accessible quantities, such as opening and closing times and the coefficient of variation of inter-spike intervals, and other, more elaborated, quantities can be analytically calculated from the underlying microscopic Markovian dynamics. A virtue of our approach is that we do not need to follow the detailed time evolution of the whole system, as we derive the relevant properties of its steady state without having to take into account the often extremely complicated transient features. We emphasize that our formulae fully agree with results obtained by stochastic simulations and approaches based on a full determination of the microscopic system's time evolution. We also illustrate how experiments can be devised to discriminate between alternative molecular models of the inositol trisphosphate receptor. The developed approach is applicable to any system described by a Markov process and, owing to the analytic nature of the resulting formulae, provides an easy way to characterize also rare events that are of particular importance to understand the intermittency properties of complex dynamic systems.
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Affiliation(s)
- Nils Christian
- University of Aberdeen, Department of Physics, Meston Walk, Aberdeen AB24 3UE, UK; University Luxembourg, Luxembourg Centre for Systems Biomedicine, 7, Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
| | - Alexander Skupin
- University Luxembourg, Luxembourg Centre for Systems Biomedicine, 7, Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg; Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Silvia Morante
- Università di Roma Tor Vergata and INFN, Sezione di Roma 2, Via della Ricerca Scientifica, I-00133 Roma, Italy
| | - Karl Jansen
- NIC/DESY Zeuthen, Platanenallee 6, D-15738 Zeuthen, Germany
| | - Giancarlo Rossi
- Università di Roma Tor Vergata and INFN, Sezione di Roma 2, Via della Ricerca Scientifica, I-00133 Roma, Italy
| | - Oliver Ebenhöh
- University of Aberdeen, Department of Physics, Meston Walk, Aberdeen AB24 3UE, UK; Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, 14473 Potsdam, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, D-40225 Düsseldorf, Germany.
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28
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Abstract
Intracellular free Ca(2+) ([Ca(2+)]i) is a highly versatile second messenger that regulates a wide range of functions in every type of cell and tissue. To achieve this versatility, the Ca(2+) signaling system operates in a variety of ways to regulate cellular processes that function over a wide dynamic range. This is particularly well exemplified for Ca(2+) signals in the liver, which modulate diverse and specialized functions such as bile secretion, glucose metabolism, cell proliferation, and apoptosis. These Ca(2+) signals are organized to control distinct cellular processes through tight spatial and temporal coordination of [Ca(2+)]i signals, both within and between cells. This article will review the machinery responsible for the formation of Ca(2+) signals in the liver, the types of subcellular, cellular, and intercellular signals that occur, the physiological role of Ca(2+) signaling in the liver, and the role of Ca(2+) signaling in liver disease.
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Affiliation(s)
- Maria Jimena Amaya
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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Amenitsch H, Benetti F, Ramos A, Legname G, Requena JR. SAXS structural study of PrP(Sc) reveals ~11 nm diameter of basic double intertwined fibers. Prion 2013; 7:496-500. [PMID: 24247356 DOI: 10.4161/pri.27190] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A sample of purified Syrian hamster PrP27-30 prion fibers was analyzed by synchrotron small-angle X-ray scattering (SAXS). The SAXS pattern obtained was fitted to a model based on infinitely long cylinders with a log-normal intensity distribution, a hard-sphere structure factor and a general Porod term for larger aggregates. The diameter calculated for the cylinders determined from the fit was 11.0 ± 0.2 nm. This measurement offers an estimation of the diameter of PrP(Sc) fibers in suspension, i.e., free of errors derived from estimations based on 2D projections in transmission electron microscopy images, subjected to further possible distortions from the negative stain. This diameter, which corresponds to a maximum diameter of approximately 5.5 nm for each of the two intertwined protofilaments making up the fibers, rules out the possibility that PrP(Sc) conforms to a stack of in-register, single-rung flat PrP(Sc) monomers; rather, PrP(Sc) subunits must necessarily coil, most likely several times, into themselves.
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Affiliation(s)
- Heinz Amenitsch
- Institute of Inorganic Chemistry; Graz University of Technology; Graz, Austria
| | - Federico Benetti
- Laboratory of Prion Biology; Department of Neuroscience; Scuola Internazionale Superiore di Studi Avanzati (SISSA); Trieste, Italy
| | - Adriana Ramos
- CIMUS Biomedical Research Institute & Department of Medicine; University of Santiago de Compostela-IDIS; Santiago de Compostela, Spain
| | - Giuseppe Legname
- Laboratory of Prion Biology; Department of Neuroscience; Scuola Internazionale Superiore di Studi Avanzati (SISSA); Trieste, Italy
| | - Jesús R Requena
- CIMUS Biomedical Research Institute & Department of Medicine; University of Santiago de Compostela-IDIS; Santiago de Compostela, Spain
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30
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Stathopulos PB, Seo MD, Enomoto M, Amador FJ, Ishiyama N, Ikura M. Themes and variations in ER/SR calcium release channels: structure and function. Physiology (Bethesda) 2013; 27:331-42. [PMID: 23223627 DOI: 10.1152/physiol.00013.2012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Calcium (Ca(2+)) release from reticular stores is a vital regulatory signal in eukaryotes. Recent structural data on large NH(2)-terminal regions of IP(3)Rs and RyRs and their tetrameric arrangement in the full-length context reveal striking mechanistic similarities in Ca(2+) release channel function. A common ancestor found in unicellular genomes underscores the fundamentality of these elements to Ca(2+) release channels.
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Affiliation(s)
- Peter B Stathopulos
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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31
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Lyumkis D, Vinterbo S, Potter CS, Carragher B. Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy. J Struct Biol 2013; 184:417-26. [PMID: 24161732 DOI: 10.1016/j.jsb.2013.10.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/04/2013] [Accepted: 10/08/2013] [Indexed: 12/13/2022]
Abstract
Single-particle cryo-electron microscopy is now well established as a technique for the structural characterization of large macromolecules and macromolecular complexes. The raw data is very noisy and consists of two-dimensional projections, from which the 3D biological object must be reconstructed. The 3D object depends upon knowledge of proper angular orientations assigned to the 2D projection images. Numerous algorithms have been developed for determining relative angular orientations between 2D images, but the transition from 2D to 3D remains challenging and can result in erroneous and conflicting results. Here we describe a general, automated procedure, called OptiMod, for reconstructing and optimizing 3D models using common-lines methodologies. OptiMod approximates orientation angles and reconstructs independent maps from 2D class averages. It then iterates the procedure, while considering each map as a raw solution that needs to be compared with other possible outcomes. We incorporate procedures for 3D alignment, clustering, and refinement to optimize each map, as well as standard scoring metrics to facilitate the selection of the optimal model. We also show that small angle tilt-pair data can be included as one of the scoring metrics to improve the selection of the optimal initial model, and also to provide a validation check. The overall approach is demonstrated using two experimental cryo-EM data sets--the 80S ribosome that represents a relatively straightforward case for ab initio reconstruction, and the Tf-TfR complex that represents a challenging case in that it has previously been shown to provide multiple equally plausible solutions to the initial model problem.
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Affiliation(s)
- Dmitry Lyumkis
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Institute, La Jolla, CA 92037, United States
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32
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Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise. Proc Natl Acad Sci U S A 2013; 110:18037-41. [PMID: 24106306 DOI: 10.1073/pnas.1314449110] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single particle cryo-electron microscopy is currently poised to produce high-resolution structures of many biological assemblies, but several pitfalls can trap the unwary. This critique highlights one problem that is particularly relevant when smaller structures are being studied. It is known as "Einstein from noise," in which the experimenter honestly believes they have recorded images of their particles, whereas in reality, most if not all of their data consist of pure noise. Selection of particles using cross-correlation methods can then lead to 3D maps that resemble the model used in the initial selection and provide the illusion of progress. Suggestions are given about how to circumvent the problem.
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33
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Ludtke SJ, Serysheva II. Single-particle cryo-EM of calcium release channels: structural validation. Curr Opin Struct Biol 2013; 23:755-62. [PMID: 23831288 PMCID: PMC3805725 DOI: 10.1016/j.sbi.2013.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 06/10/2013] [Indexed: 11/23/2022]
Abstract
Few tools are available to determine the structure of large integral membrane proteins such as intracellular Ca(2+) release channels, RyRs and IP3Rs. Single particle cryo-EM can readily determine the structure of such channels to intermediate resolution, and can be used to quantitatively assess conformational variability. However, due to the, often low, image contrast of these cryospecimens, methods for validation are critical to insure the accuracy of such structures, and to put limits on their interpretability. The low-resolution structure of RyR has been well established for some time, but high-resolution has been slow to emerge. The structure of IP3R channel by cryo-EM had a number of false-starts, but improved validation methods have recently lead to a demonstrably accurate reconstruction.
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Affiliation(s)
- Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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34
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Murray SC, Flanagan J, Popova OB, Chiu W, Ludtke SJ, Serysheva II. Validation of cryo-EM structure of IP₃R1 channel. Structure 2013; 21:900-9. [PMID: 23707684 DOI: 10.1016/j.str.2013.04.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 04/15/2013] [Accepted: 04/18/2013] [Indexed: 10/26/2022]
Abstract
About a decade ago, three electron cryomicroscopy (cryo-EM) single-particle reconstructions of IP3R1 were reported at low resolution. It was disturbing that these structures bore little similarity to one another, even at the level of quaternary structure. Recently, we published an improved structure of IP3R1 at ∼1 nm resolution. However, this structure did not bear any resemblance to any of the three previously published structures, leading to the question of why the structure should be considered more reliable than the original three. Here, we apply several methods, including class-average/map comparisons, tilt-pair validation, and use of multiple refinement software packages, to give strong evidence for the reliability of our recent structure. The map resolution and feature resolvability are assessed with the gold standard criterion. This approach is generally applicable to assessing the validity of cryo-EM maps of other molecular machines.
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Affiliation(s)
- Stephen C Murray
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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35
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Vais H, Foskett JK, Ullah G, Pearson JE, Mak DOD. Permeant calcium ion feed-through regulation of single inositol 1,4,5-trisphosphate receptor channel gating. ACTA ACUST UNITED AC 2012; 140:697-716. [PMID: 23148262 PMCID: PMC3514735 DOI: 10.1085/jgp.201210804] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The ubiquitous inositol 1,4,5-trisphosphate (InsP(3)) receptor (InsP(3)R) Ca(2+) release channel plays a central role in the generation and modulation of intracellular Ca(2+) signals, and is intricately regulated by multiple mechanisms including cytoplasmic ligand (InsP(3), free Ca(2+), free ATP(4-)) binding, posttranslational modifications, and interactions with cytoplasmic and endoplasmic reticulum (ER) luminal proteins. However, regulation of InsP(3)R channel activity by free Ca(2+) in the ER lumen ([Ca(2+)](ER)) remains poorly understood because of limitations of Ca(2+) flux measurements and imaging techniques. Here, we used nuclear patch-clamp experiments in excised luminal-side-out configuration with perfusion solution exchange to study the effects of [Ca(2+)](ER) on homotetrameric rat type 3 InsP(3)R channel activity. In optimal [Ca(2+)](i) and subsaturating [InsP(3)], jumps of [Ca(2+)](ER) from 70 nM to 300 µM reduced channel activity significantly. This inhibition was abrogated by saturating InsP(3) but restored when [Ca(2+)](ER) was raised to 1.1 mM. In suboptimal [Ca(2+)](i), jumps of [Ca(2+)](ER) (70 nM to 300 µM) enhanced channel activity. Thus, [Ca(2+)](ER) effects on channel activity exhibited a biphasic dependence on [Ca(2+)](i). In addition, the effect of high [Ca(2+)](ER) was attenuated when a voltage was applied to oppose Ca(2+) flux through the channel. These observations can be accounted for by Ca(2+) flux driven through the open InsP(3)R channel by [Ca(2+)](ER), raising local [Ca(2+)](i) around the channel to regulate its activity through its cytoplasmic regulatory Ca(2+)-binding sites. Importantly, [Ca(2+)](ER) regulation of InsP(3)R channel activity depended on cytoplasmic Ca(2+)-buffering conditions: it was more pronounced when [Ca(2+)](i) was weakly buffered but completely abolished in strong Ca(2+)-buffering conditions. With strong cytoplasmic buffering and Ca(2+) flux sufficiently reduced by applied voltage, both activation and inhibition of InsP(3)R channel gating by physiological levels of [Ca(2+)](ER) were completely abolished. Collectively, these results rule out Ca(2+) regulation of channel activity by direct binding to the luminal aspect of the channel.
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Affiliation(s)
- Horia Vais
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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36
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Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. Outcome of the first electron microscopy validation task force meeting. Structure 2012; 20:205-14. [PMID: 22325770 PMCID: PMC3328769 DOI: 10.1016/j.str.2011.12.014] [Citation(s) in RCA: 361] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/29/2011] [Accepted: 12/29/2011] [Indexed: 11/10/2022]
Abstract
This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Task Force organized by the Unified Data Resource for 3DEM (http://www.emdatabank.org) and held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. At the workshop, a group of scientists involved in collecting electron microscopy data, using the data to determine three-dimensional electron microscopy (3DEM) density maps, and building molecular models into the maps explored how to assess maps, models, and other data that are deposited into the Electron Microscopy Data Bank and Protein Data Bank public data archives. The specific recommendations resulting from the workshop aim to increase the impact of 3DEM in biology and medicine.
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Affiliation(s)
- Richard Henderson
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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37
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Membrane electrical properties. Biophysics (Nagoya-shi) 2012. [DOI: 10.1017/cbo9781139035002.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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38
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Szlufcik K, Missiaen L, Parys JB, Callewaert G, De Smedt H. Uncoupled IP3 receptor can function as a Ca2+-leak channel: cell biological and pathological consequences. Biol Cell 2012; 98:1-14. [PMID: 16354157 DOI: 10.1042/bc20050031] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ca(2+) release via intracellular release channels, IP(3)Rs (inositol 1,4,5-trisphosphate receptors) and RyRs (ryanodine receptors), is perhaps the most ubiquitous and versatile cellular signalling mechanism, and is involved in a vast number of cellular processes. In addition to this classical release pathway there is limited, but yet persistent, information about less well-defined Ca(2+)-leak pathways that may play an important role in the control of the Ca(2+) load of the endo(sarco)plasmic reticulum. The mechanisms responsible for this 'basal' leak are not known, but recent data suggest that both IP(3)Rs and RyRs may also operate as Ca(2+)-leak channels, particularly in pathological conditions. Proteolytic cleavage or biochemical modification (such as hyperphosphorylation or nitrosylation), for example, occurring during conditions of cell stress or apoptosis, can functionally uncouple the cytoplasmic control domains from the channel domain of the receptor. Highly significant information has been obtained from studies of malfunctioning channels in various disorders; for example, RyRs in cardiac malfunction or genetic muscle diseases and IP(3)Rs in neurodegenerative diseases. In this review we aim to summarize the existing information about functionally uncoupled IP(3)R and RyR channels, and to discuss the concept that those channels can participate in Ca(2+)-leak pathways.
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39
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Abstract
The Ca(2) (+) signals evoked by inositol 1,4,5-trisphosphate (IP(3)) are built from elementary Ca(2) (+) release events involving progressive recruitment of IP(3) receptors (IP(3)R), intracellular Ca(2) (+) channels that are expressed in almost all animal cells. The smallest events ('blips') result from opening of single IP(3)R. Larger events ('puffs') reflect the near-synchronous opening of a small cluster of IP(3)R. These puffs become more frequent as the stimulus intensity increases and they eventually trigger regenerative Ca(2) (+) waves that propagate across the cell. This hierarchical recruitment of IP(3)R is important in allowing Ca(2) (+) signals to be delivered locally to specific target proteins or more globally to the entire cell. Co-regulation of IP(3)R by Ca(2) (+) and IP(3), the ability of a single IP(3)R rapidly to mediate a large efflux of Ca(2) (+) from the endoplasmic reticulum, and the assembly of IP(3)R into clusters are key features that allow IP(3)R to propagate Ca(2) (+) signals regeneratively. We review these properties of IP(3)R and the structural basis of IP(3)R behavior.
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Affiliation(s)
- Colin W Taylor
- Department of Pharmacology, Tennis Court Road, CB2 1PD, Cambridge, UK,
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40
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The Discovery and Structural Investigation of the IP3 Receptor and the Associated IRBIT Protein. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 740:281-304. [DOI: 10.1007/978-94-007-2888-2_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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41
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Ludtke SJ, Tran TP, Ngo QT, Moiseenkova-Bell VY, Chiu W, Serysheva II. Flexible architecture of IP3R1 by Cryo-EM. Structure 2011; 19:1192-9. [PMID: 21827954 DOI: 10.1016/j.str.2011.05.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Revised: 04/28/2011] [Accepted: 05/02/2011] [Indexed: 11/16/2022]
Abstract
Inositol 1,4,5-trisphosphate receptors (IP3Rs) play a fundamental role in generating Ca2+ signals that trigger many cellular processes in virtually all eukaryotic cells. Thus far, the three-dimensional (3D) structure of these channels has remained extremely controversial. Here, we report a subnanometer resolution electron cryomicroscopy (cryo-EM) structure of a fully functional type 1 IP3R from cerebellum in the closed state. The transmembrane region reveals a twisted bundle of four α helices, one from each subunit, that form a funnel shaped structure around the 4-fold symmetry axis, strikingly similar to the ion-conduction pore of K+ channels. The lumenal face of IP3R1 has prominent densities that surround the pore entrance and similar to the highly structured turrets of Kir channels. 3D statistical analysis of the cryo-EM density map identifies high variance in the cytoplasmic region. This structural variation could be attributed to genuine structural flexibility of IP3R1.
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Affiliation(s)
- Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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42
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Lin CC, Baek K, Lu Z. Apo and InsP₃-bound crystal structures of the ligand-binding domain of an InsP₃ receptor. Nat Struct Mol Biol 2011; 18:1172-4. [PMID: 21892169 PMCID: PMC3242432 DOI: 10.1038/nsmb.2112] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 07/01/2011] [Indexed: 11/09/2022]
Abstract
We report the crystal structures of the ligand-binding domain (LBD) of a rat inositol 1,4,5-trisphosphate receptor (InsP(3)R) in its apo and InsP(3)-bound conformations. Comparison of these two conformations reveals that LBD's first β-trefoil fold (β-TF1) and armadillo repeat fold (ARF) move together as a unit relative to its second β-trefoil fold (β-TF2). Whereas apo LBD may spontaneously transition between gating conformations, InsP(3) binding shifts this equilibrium toward the active state.
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Affiliation(s)
- Chun-Chi Lin
- Department of Physiology, Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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43
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The structural biology of ryanodine receptors. SCIENCE CHINA-LIFE SCIENCES 2011; 54:712-24. [DOI: 10.1007/s11427-011-4198-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Accepted: 05/30/2011] [Indexed: 10/18/2022]
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44
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Goto JI, Mikoshiba K. Inositol 1,4,5-Trisphosphate Receptor-Mediated Calcium Release in Purkinje Cells: From Molecular Mechanism to Behavior. THE CEREBELLUM 2011; 10:820-33. [DOI: 10.1007/s12311-011-0270-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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45
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Vais H, Foskett JK, Daniel Mak DO. Unitary Ca(2+) current through recombinant type 3 InsP(3) receptor channels under physiological ionic conditions. J Gen Physiol 2010; 136:687-700. [PMID: 21078871 PMCID: PMC2995152 DOI: 10.1085/jgp.201010513] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 10/21/2010] [Indexed: 11/20/2022] Open
Abstract
The ubiquitous inositol 1,4,5-trisphosphate (InsP(3)) receptor (InsP(3)R) channel, localized primarily in the endoplasmic reticulum (ER) membrane, releases Ca(2+) into the cytoplasm upon binding InsP(3), generating and modulating intracellular Ca(2+) signals that regulate numerous physiological processes. Together with the number of channels activated and the open probability of the active channels, the size of the unitary Ca(2+) current (i(Ca)) passing through an open InsP(3)R channel determines the amount of Ca(2+) released from the ER store, and thus the amplitude and the spatial and temporal nature of Ca(2+) signals generated in response to extracellular stimuli. Despite its significance, i(Ca) for InsP(3)R channels in physiological ionic conditions has not been directly measured. Here, we report the first measurement of i(Ca) through an InsP(3)R channel in its native membrane environment under physiological ionic conditions. Nuclear patch clamp electrophysiology with rapid perfusion solution exchanges was used to study the conductance properties of recombinant homotetrameric rat type 3 InsP(3)R channels. Within physiological ranges of free Ca(2+) concentrations in the ER lumen ([Ca(2+)](ER)), free cytoplasmic [Ca(2+)] ([Ca(2+)](i)), and symmetric free [Mg(2+)] ([Mg(2+)](f)), the i(Ca)-[Ca(2+)](ER) relation was linear, with no detectable dependence on [Mg(2+)](f). i(Ca) was 0.15 +/- 0.01 pA for a filled ER store with 500 microM [Ca(2+)](ER). The i(Ca)-[Ca(2+)](ER) relation suggests that Ca(2+) released by an InsP(3)R channel raises [Ca(2+)](i) near the open channel to approximately 13-70 microM, depending on [Ca(2+)](ER). These measurements have implications for the activities of nearby InsP(3)-liganded InsP(3)R channels, and they confirm that Ca(2+) released by an open InsP(3)R channel is sufficient to activate neighboring channels at appropriate distances away, promoting Ca(2+)-induced Ca(2+) release.
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Affiliation(s)
- Horia Vais
- Department of Physiology and Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - J. Kevin Foskett
- Department of Physiology and Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Don-On Daniel Mak
- Department of Physiology and Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
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46
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Rossi AM, Sureshan KM, Riley AM, Potter VL, Taylor CW. Selective determinants of inositol 1,4,5-trisphosphate and adenophostin A interactions with type 1 inositol 1,4,5-trisphosphate receptors. Br J Pharmacol 2010; 161:1070-85. [PMID: 20977457 PMCID: PMC2998688 DOI: 10.1111/j.1476-5381.2010.00947.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 06/01/2010] [Accepted: 06/07/2010] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND AND PURPOSE Adenophostin A (AdA) is a potent agonist of inositol 1,4,5-trisphosphate receptors (IP(3) R). AdA shares with IP(3) the essential features of all IP(3) R agonists, namely structures equivalent to the 4,5-bisphosphate and 6-hydroxyl of IP(3) , but the basis of its increased affinity is unclear. Hitherto, the 2'-phosphate of AdA has been thought to provide a supra-optimal mimic of the 1-phosphate of IP(3) . EXPERIMENTAL APPROACH We examined the structural determinants of AdA binding to type 1 IP(3) R (IP(3) R1). Chemical synthesis and mutational analysis of IP(3) R1 were combined with (3) H-IP(3) binding to full-length IP(3) R1 and its N-terminal fragments, and Ca(2+) release assays from recombinant IP(3) R1 expressed in DT40 cells. KEY RESULTS Adenophostin A is at least 12-fold more potent than IP(3) in functional assays, and the IP(3) -binding core (IBC, residues 224-604 of IP(3) R1) is sufficient for this high-affinity binding of AdA. Removal of the 2'-phosphate from AdA (to give 2'-dephospho-AdA) had significantly lesser effects on its affinity for the IBC than did removal of the 1-phosphate from IP(3) (to give inositol 4,5-bisphosphate). Mutation of the only residue (R568) that interacts directly with the 1-phosphate of IP(3) decreased similarly (by ~30-fold) the affinity for IP(3) and AdA, but mutating R504, which has been proposed to form a cation-π interaction with the adenine of AdA, more profoundly reduced the affinity of IP(3) R for AdA (353-fold) than for IP(3) (13-fold). CONCLUSIONS AND IMPLICATIONS The 2'-phosphate of AdA is not a major determinant of its high affinity. R504 in the receptor, most likely via a cation-π interaction, contributes specifically to AdA binding.
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Affiliation(s)
- Ana M Rossi
- Department of Pharmacology, University of Cambridge, Cambridge, UK
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47
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Taylor CW, Tovey SC. IP(3) receptors: toward understanding their activation. Cold Spring Harb Perspect Biol 2010; 2:a004010. [PMID: 20980441 DOI: 10.1101/cshperspect.a004010] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Inositol 1,4,5-trisphosphate receptors (IP(3)R) and their relatives, ryanodine receptors, are the channels that most often mediate Ca(2+) release from intracellular stores. Their regulation by Ca(2+) allows them also to propagate cytosolic Ca(2+) signals regeneratively. This brief review addresses the structural basis of IP(3)R activation by IP(3) and Ca(2+). IP(3) initiates IP(3)R activation by promoting Ca(2+) binding to a stimulatory Ca(2+)-binding site, the identity of which is unresolved. We suggest that interactions of critical phosphate groups in IP(3) with opposite sides of the clam-like IP(3)-binding core cause it to close and propagate a conformational change toward the pore via the adjacent N-terminal suppressor domain. The pore, assembled from the last pair of transmembrane domains and the intervening pore loop from each of the four IP(3)R subunits, forms a structure in which a luminal selectivity filter and a gate at the cytosolic end of the pore control cation fluxes through the IP(3)R.
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Affiliation(s)
- Colin W Taylor
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, United Kingdom.
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Mio K, Maruyama Y, Ogura T, Kawata M, Moriya T, Mio M, Sato C. Single particle reconstruction of membrane proteins: A tool for understanding the 3D structure of disease-related macromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2010; 103:122-30. [DOI: 10.1016/j.pbiomolbio.2010.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 02/06/2010] [Accepted: 03/07/2010] [Indexed: 11/28/2022]
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Wolfram F, Morris E, Taylor C. Three-dimensional structure of recombinant type 1 inositol 1,4,5-trisphosphate receptor. Biochem J 2010; 428:483-9. [PMID: 20377523 PMCID: PMC3685215 DOI: 10.1042/bj20100143] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 03/29/2010] [Accepted: 04/08/2010] [Indexed: 11/17/2022]
Abstract
IP3Rs (inositol 1,4,5-trisphosphate receptors) are the intracellular channels that mediate release of Ca2+ from the endoplasmic reticulum in response to the many stimuli that evoke Ins(1,4,5)P3 formation. We characterized and purified type 1 IP3R heterologously expressed in Sf9 insect cells, and used the purified IP3R1 to determine its three-dimensional structure by electron microscopy and single-particle analysis. Recombinant IP3R1 has 4-fold symmetry with overall dimensions of approx. 19.5 nm x 19.5 nm x 17.5 nm. It comprises a small domain, which is likely to include the pore, linked by slender bridges to a large cytoplasmic domain with four petal-like regions. Our structures of recombinant IP3R1 and native cerebellar IP3R have similar appearances and dimensions. The only notable difference is the absence of a central stigma-like domain from the cytoplasmic region of recombinant IP3R1. The first structure of a recombinant IP3R is an important step towards developing three-dimensional structures of IP3R that better contribute to our understanding of the structural basis of IP3R activation.
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Key Words
- calcium channel
- electron microscopy (em)
- inositol 1,4,5-trisphosphate receptor (ip3r)
- single-particle analysis (spa)
- clm, cytosol-like medium
- ddm, dodecyl maltoside
- ecfp, enhanced cyan fluorescent protein
- em, electron microscopy
- er, endoplasmic reticulum
- ip3r, inositol 1,4,5-trisphosphate receptor
- pbm, phosphate-buffered medium
- peg, poly(ethylene glycol)
- ryr, ryanodine receptor
- spa, single-particle analysis
- tem, tris/edta medium
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Affiliation(s)
- Francis Wolfram
- *Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Edward Morris
- †Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K
| | - Colin W. Taylor
- *Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
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