151
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Schmidt C, Urlaub H. Combining cryo-electron microscopy (cryo-EM) and cross-linking mass spectrometry (CX-MS) for structural elucidation of large protein assemblies. Curr Opin Struct Biol 2017; 46:157-168. [DOI: 10.1016/j.sbi.2017.10.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/21/2017] [Accepted: 10/05/2017] [Indexed: 01/11/2023]
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152
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Mahato DR, Fischer WB. Specification of binding modes between a transmembrane peptide mimic of ATP6V0C and polytopic E5 of human papillomavirus-16. J Biomol Struct Dyn 2017; 36:2618-2627. [DOI: 10.1080/07391102.2017.1364671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Dhani Ram Mahato
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, 155, Li-Nong St., Sec. 2, Taipei 112, Taiwan
| | - Wolfgang B. Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, 155, Li-Nong St., Sec. 2, Taipei 112, Taiwan
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153
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Bodzęta A, Kahms M, Klingauf J. The Presynaptic v-ATPase Reversibly Disassembles and Thereby Modulates Exocytosis but Is Not Part of the Fusion Machinery. Cell Rep 2017; 20:1348-1359. [DOI: 10.1016/j.celrep.2017.07.040] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/23/2017] [Accepted: 07/14/2017] [Indexed: 11/15/2022] Open
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154
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Murata K, Wolf M. Cryo-electron microscopy for structural analysis of dynamic biological macromolecules. Biochim Biophys Acta Gen Subj 2017; 1862:324-334. [PMID: 28756276 DOI: 10.1016/j.bbagen.2017.07.020] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Since the introduction of what became today's standard for cryo-embedding of biological macromolecules at native conditions more than 30years ago, techniques and equipment have been drastically improved and the structure of biomolecules can now be studied at near atomic resolution by cryo-electron microscopy (cryo-EM) while capturing multiple dynamic states. Here we review the recent progress in cryo-EM for structural studies of dynamic biological macromolecules. SCOPE OF REVIEW We provide an overview of the cryo-EM method and introduce contemporary studies to investigate biomolecular structure and dynamics, including examples from the recent literature. MAJOR CONCLUSIONS Cryo-EM is a powerful tool for the investigation of biological macromolecular structures including analysis of their dynamics by using advanced image-processing algorithms. The method has become even more widely applicable with present-day single particle analysis and electron tomography. GENERAL SIGNIFICANCE The cryo-EM method can be used to determine the three-dimensional structure of biomacromolecules in near native condition at close to atomic resolution, and has the potential to reveal conformations of dynamic molecular complexes. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Kazuyoshi Murata
- National Institute for Physiological Sciences, 38 Myodaiji, Okazaki, Aichi 444-8585, Japan.
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology, 7542 Onna, Onna-Son, Kunigami, Okinawa 904-0411, Japan.
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155
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Isaka Y, Ekimoto T, Kokabu Y, Yamato I, Murata T, Ikeguchi M. Rotation Mechanism of Molecular Motor V 1-ATPase Studied by Multiscale Molecular Dynamics Simulation. Biophys J 2017; 112:911-920. [PMID: 28297650 PMCID: PMC5355535 DOI: 10.1016/j.bpj.2017.01.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/06/2017] [Accepted: 01/30/2017] [Indexed: 11/28/2022] Open
Abstract
Enterococcus hirae V1-ATPase is a molecular motor composed of the A3B3 hexamer ring and the central stalk. In association with ATP hydrolysis, three catalytic AB pairs in the A3B3 ring undergo conformational changes, which lead to a 120° rotation of the central stalk. To understand how the conformational changes of three catalytic pairs induce the 120° rotation of the central stalk, we performed multiscale molecular dynamics (MD) simulations in which coarse-grained and all-atom MD simulations were combined using a fluctuation matching methodology. During the rotation, a catalytic AB pair spontaneously adopted an intermediate conformation, which was not included in the initial inputs of the simulations and was essentially close to the “bindable-like” structure observed in a recently solved crystal structure. Furthermore, the creation of a space between the bindable-like and tight pairs was required for the central stalk to rotate without steric hindrance. These cooperative rearrangements of the three catalytic pairs are crucial for the rotation of the central stalk.
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Affiliation(s)
- Yuta Isaka
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Japan
| | - Yuichi Kokabu
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Japan
| | - Ichiro Yamato
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika-ku, Tokyo, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, Japan; JST, PRESTO, Inage, Chiba, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Japan.
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156
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Banerjee S, Kane PM. Direct interaction of the Golgi V-ATPase a-subunit isoform with PI(4)P drives localization of Golgi V-ATPases in yeast. Mol Biol Cell 2017; 28:2518-2530. [PMID: 28720663 PMCID: PMC5597324 DOI: 10.1091/mbc.e17-05-0316] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/03/2017] [Accepted: 07/14/2017] [Indexed: 12/11/2022] Open
Abstract
PI(4)P directly interacts with the cytosolic domain of yeast Golgi vacuolar H+-ATPase (V-ATPase) a-isoform, Stv1, and the human Golgi a-subunit isoform. Lys-84 of Stv1 is essential for PI(4)P interaction, and localization of Stv1-containing V-ATPases in vivo requires the PI(4)P interaction. We propose that phosphatidylinositol binding exerts organelle-specific control over V-ATPases. Luminal pH and phosphoinositide content are fundamental features of organelle identity. Vacuolar H+-ATPases (V-ATPases) drive organelle acidification in all eukaryotes, and membrane-bound a-subunit isoforms of the V-ATPase are implicated in organelle-specific targeting and regulation. Earlier work demonstrated that the endolysosomal lipid PI(3,5)P2 activates V-ATPases containing the vacuolar a-subunit isoform in Saccharomyces cerevisiae. Here we demonstrate that PI(4)P, the predominant Golgi phosphatidylinositol (PI) species, directly interacts with the cytosolic amino terminal (NT) domain of the yeast Golgi V-ATPase a-isoform Stv1. Lysine-84 of Stv1NT is essential for interaction with PI(4)P in vitro and in vivo, and interaction with PI(4)P is required for efficient localization of Stv1-containing V-ATPases. The cytosolic NT domain of the human V-ATPase a2 isoform specifically interacts with PI(4)P in vitro, consistent with its Golgi localization and function. We propose that NT domains of Vo a-subunit isoforms interact specifically with PI lipids in their organelles of residence. These interactions can transmit organelle-specific targeting or regulation information to V-ATPases.
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Affiliation(s)
- Subhrajit Banerjee
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210
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157
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Li S, Hong T, Wang K, Lu Y, Zhou M. Dissociation and purification of the endogenous membrane-bound Vo complex from Pichia pastoris. Protein Expr Purif 2017; 138:76-80. [PMID: 28709863 DOI: 10.1016/j.pep.2017.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/29/2017] [Accepted: 07/11/2017] [Indexed: 01/22/2023]
Abstract
Most proteins occur and function in complexes rather than as isolated entities in membranes. In most cases macromolecules with multiple subunits are purified from endogenous sources. In this study, an endogenous membrane-protein complex was obtained from Pichia pastoris, which can be grown at high densities to significantly improve the membrane protein yield. We successfully isolated the membrane-bound Vo complex of V-ATPase from P. pastoris using a fusion FLAG tag attached to the C-terminus of subunit a to generate the vph-tag strain, which was used for dissociation and purification. After FLAG affinity and size exclusion chromatography purification, the production quantity and purity of the membrane-bound Vo complex was 20 μg l-1 and >98%, respectively. The subunits of the endogenous membrane-bound Vo complex observed in P. pastoris were similar to those obtained from S. cerevisiae, as demonstrated by liquid chromatography-tandem mass spectrometry (LC-MS-MS). Therefore, successful dissociation and purification of the membrane-bound Vo complex at a high purity and sufficient quantity was achieved via a rapid and simple procedure that can be used to obtain the endogenous membrane-protein complexes from P. pastoris.
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Affiliation(s)
- Sumei Li
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China.
| | - Tao Hong
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China
| | - Kun Wang
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China
| | - Yinghong Lu
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China
| | - Min Zhou
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, People's Republic of China.
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158
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Sánchez-Vásquez L, Vázquez-Acevedo M, de la Mora J, Vega-deLuna F, Cardol P, Remacle C, Dreyfus G, González-Halphen D. Near-neighbor interactions of the membrane-embedded subunits of the mitochondrial ATP synthase of a chlorophycean alga. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:497-509. [DOI: 10.1016/j.bbabio.2017.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/25/2017] [Accepted: 04/29/2017] [Indexed: 12/24/2022]
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159
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Abstract
In this issue of Cell, Hite and MacKinnon (2017) report the open conformation structure of Slo2.2, a neuronal Na+-activated K+ channel. More importantly, 3D classification of electron cryomicroscopy (cryo-EM) images allows visualization of the structural transition that occurs as the open probability of individual channels increases with added sodium.
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Affiliation(s)
- John L Rubinstein
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Canada M5G 0A4; Department of Biochemistry, The University of Toronto, Canada M5S 1A8; Department of Medical Biophysics, The University of Toronto, Canada M5G 1L7.
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160
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Rotating with the brakes on and other unresolved features of the vacuolar ATPase. Biochem Soc Trans 2017; 44:851-5. [PMID: 27284051 PMCID: PMC4900747 DOI: 10.1042/bst20160043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Indexed: 12/31/2022]
Abstract
The rotary ATPase family comprises the ATP synthase (F-ATPase), vacuolar ATPase (V-ATPase) and archaeal ATPase (A-ATPase). These either predominantly utilize a proton gradient for ATP synthesis or use ATP to produce a proton gradient, driving secondary transport and acidifying organelles. With advances in EM has come a significant increase in our understanding of the rotary ATPase family. Following the sub nm resolution reconstructions of both the F- and V-ATPases, the secondary structure organization of the elusive subunit a has now been resolved, revealing a novel helical arrangement. Despite these significant developments in our understanding of the rotary ATPases, there are still a number of unresolved questions about the mechanism, regulation and overall architecture, which this mini-review aims to highlight and discuss.
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161
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Zhao J, Beyrakhova K, Liu Y, Alvarez CP, Bueler SA, Xu L, Xu C, Boniecki MT, Kanelis V, Luo ZQ, Cygler M, Rubinstein JL. Molecular basis for the binding and modulation of V-ATPase by a bacterial effector protein. PLoS Pathog 2017; 13:e1006394. [PMID: 28570695 PMCID: PMC5469503 DOI: 10.1371/journal.ppat.1006394] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 06/13/2017] [Accepted: 05/01/2017] [Indexed: 12/16/2022] Open
Abstract
Intracellular pathogenic bacteria evade the immune response by replicating within host cells. Legionella pneumophila, the causative agent of Legionnaires’ Disease, makes use of numerous effector proteins to construct a niche supportive of its replication within phagocytic cells. The L. pneumophila effector SidK was identified in a screen for proteins that reduce the activity of the proton pumping vacuolar-type ATPases (V-ATPases) when expressed in the yeast Saccharomyces cerevisae. SidK is secreted by L. pneumophila in the early stages of infection and by binding to and inhibiting the V-ATPase, SidK reduces phagosomal acidification and promotes survival of the bacterium inside macrophages. We determined crystal structures of the N-terminal region of SidK at 2.3 Å resolution and used single particle electron cryomicroscopy (cryo-EM) to determine structures of V-ATPase:SidK complexes at ~6.8 Å resolution. SidK is a flexible and elongated protein composed of an α-helical region that interacts with subunit A of the V-ATPase and a second region of unknown function that is flexibly-tethered to the first. SidK binds V-ATPase strongly by interacting via two α-helical bundles at its N terminus with subunit A. In vitro activity assays show that SidK does not inhibit the V-ATPase completely, but reduces its activity by ~40%, consistent with the partial V-ATPase deficiency phenotype its expression causes in yeast. The cryo-EM analysis shows that SidK reduces the flexibility of the A-subunit that is in the ‘open’ conformation. Fluorescence experiments indicate that SidK binding decreases the affinity of V-ATPase for a fluorescent analogue of ATP. Together, these results reveal the structural basis for the fine-tuning of V-ATPase activity by SidK. V-ATPase-driven acidification of lysosomes in phagocytic cells activates enzymes important for killing of phagocytized pathogens. Successful pathogens can subvert host defenses by secreting effectors that target V-ATPases to inhibit lysosomal acidification or lysosomal fusion with other cell compartments. This study reveals the structure of the V-ATPase:SidK complex, an assembly formed from the interaction of host and pathogen proteins involved in the infection of phagocytic white blood cells by Legionella pneumophila. The structure and activity of the V-ATPase is altered upon SidK binding, providing insight into the infection strategy used by L. pneumophila and possibly other intravacuolar pathogens.
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Affiliation(s)
- Jianhua Zhao
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ksenia Beyrakhova
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yao Liu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Claudia P. Alvarez
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | | | - Li Xu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Caishuang Xu
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Michal T. Boniecki
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Voula Kanelis
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail: (JLR); (MC)
| | - John L. Rubinstein
- The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (JLR); (MC)
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162
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Rawson S, McPhillie MJ, Johnson RM, Fishwick CWG, Muench SP. The potential use of single-particle electron microscopy as a tool for structure-based inhibitor design. Acta Crystallogr D Struct Biol 2017; 73:534-540. [PMID: 28580915 PMCID: PMC5458495 DOI: 10.1107/s2059798317004077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/13/2017] [Indexed: 12/14/2022] Open
Abstract
Recent developments in electron microscopy (EM) have led to a step change in our ability to solve the structures of previously intractable systems, especially membrane proteins and large protein complexes. This has provided new opportunities in the field of structure-based drug design, with a number of high-profile publications resolving the binding sites of small molecules and peptide inhibitors. There are a number of advantages of EM over the more traditional X-ray crystallographic approach, such as resolving different conformational states and permitting the dynamics of a system to be better resolved when not constrained by a crystal lattice. There are still significant challenges to be overcome using an EM approach, not least the speed of structure determination, difficulties with low-occupancy ligands and the modest resolution that is available. However, with the anticipated developments in the field of EM, the potential of EM to become a key tool for structure-based drug design, often complementing X-ray and NMR studies, seems promising.
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Affiliation(s)
- S. Rawson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - M. J. McPhillie
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - R. M. Johnson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - C. W. G. Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - S. P. Muench
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
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163
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Abstract
The vacuolar ATPases (V-ATPases) are a family of proton pumps that couple ATP hydrolysis to proton transport into intracellular compartments and across the plasma membrane. They function in a wide array of normal cellular processes, including membrane traffic, protein processing and degradation, and the coupled transport of small molecules, as well as such physiological processes as urinary acidification and bone resorption. The V-ATPases have also been implicated in a number of disease processes, including viral infection, renal disease, and bone resorption defects. This review is focused on the growing evidence for the important role of V-ATPases in cancer. This includes functions in cellular signaling (particularly Wnt, Notch, and mTOR signaling), cancer cell survival in the highly acidic environment of tumors, aiding the development of drug resistance, as well as crucial roles in tumor cell invasion, migration, and metastasis. Of greatest excitement is evidence that at least some tumors express isoforms of V-ATPase subunits whose disruption is not lethal, leading to the possibility of developing anti-cancer therapeutics that selectively target V-ATPases that function in cancer cells.
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Affiliation(s)
- Laura Stransky
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, and Program in Cellular and Molecular Physiology, Program in Biochemistry, and Program in Cell, Molecular and Developmental Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts
| | - Kristina Cotter
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, and Program in Cellular and Molecular Physiology, Program in Biochemistry, and Program in Cell, Molecular and Developmental Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts
| | - Michael Forgac
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, and Program in Cellular and Molecular Physiology, Program in Biochemistry, and Program in Cell, Molecular and Developmental Biology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts
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164
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Abstract
Major developments in cryo-electron microscopy in the past three or four years have led to the solution of a number of spliceosome structures at high resolution, e.g., the fully assembled but not yet active spliceosome (Bact), the spliceosome just after the first step of splicing (C), and the spliceosome activated for the second step (C*). Therefore 30 years of genetics and biochemistry of the spliceosome can now be interpreted at the structural level. I have closely examined the RNase H domain of Prp8 in each of the structures. Interestingly, the RNase H domain has different and unexpected roles in each of the catalytic steps of splicing.
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Affiliation(s)
- John Abelson
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
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165
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Cuniasse P, Tavares P, Orlova EV, Zinn-Justin S. Structures of biomolecular complexes by combination of NMR and cryoEM methods. Curr Opin Struct Biol 2017; 43:104-113. [DOI: 10.1016/j.sbi.2016.12.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/08/2016] [Accepted: 12/13/2016] [Indexed: 11/28/2022]
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166
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Ferencz CM, Petrovszki P, Dér A, Sebők-Nagy K, Kóta Z, Páli T. Oscillating Electric Field Measures the Rotation Rate in a Native Rotary Enzyme. Sci Rep 2017; 7:45309. [PMID: 28345665 PMCID: PMC5366918 DOI: 10.1038/srep45309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 02/21/2017] [Indexed: 11/09/2022] Open
Abstract
Rotary enzymes are complex, highly challenging biomolecular machines whose biochemical working mechanism involves intersubunit rotation. The true intrinsic rate of rotation of any rotary enzyme is not known in a native, unmodified state. Here we use the effect of an oscillating electric (AC) field on the biochemical activity of a rotary enzyme, the vacuolar proton-ATPase (V-ATPase), to directly measure its mean rate of rotation in its native membrane environment, without any genetic, chemical or mechanical modification of the enzyme, for the first time. The results suggest that a transmembrane AC field is able to synchronise the steps of ion-pumping in individual enzymes via a hold-and-release mechanism, which opens up the possibility of biotechnological exploitation. Our approach is likely to work for other transmembrane ion-transporting assemblies, not only rotary enzymes, to determine intrinsic in situ rates of ion pumping.
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Affiliation(s)
- Csilla-Maria Ferencz
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, 6726, Szeged, Hungary
| | - Pál Petrovszki
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, 6726, Szeged, Hungary
| | - András Dér
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, 6726, Szeged, Hungary
| | - Krisztina Sebők-Nagy
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, 6726, Szeged, Hungary
| | - Zoltán Kóta
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, 6726, Szeged, Hungary
| | - Tibor Páli
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, 6726, Szeged, Hungary
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167
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Anandakrishnan R, Zuckerman DM. Biophysical comparison of ATP-driven proton pumping mechanisms suggests a kinetic advantage for the rotary process depending on coupling ratio. PLoS One 2017; 12:e0173500. [PMID: 28319179 PMCID: PMC5358804 DOI: 10.1371/journal.pone.0173500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/21/2017] [Indexed: 12/15/2022] Open
Abstract
ATP-driven proton pumps, which are critical to the operation of a cell, maintain cytosolic and organellar pH levels within a narrow functional range. These pumps employ two very different mechanisms: an elaborate rotary mechanism used by V-ATPase H+ pumps, and a simpler alternating access mechanism used by P-ATPase H+ pumps. Why are two different mechanisms used to perform the same function? Systematic analysis, without parameter fitting, of kinetic models of the rotary, alternating access and other possible mechanisms suggest that, when the ratio of protons transported per ATP hydrolyzed exceeds one, the one-at-a-time proton transport by the rotary mechanism is faster than other possible mechanisms across a wide range of driving conditions. When the ratio is one, there is no intrinsic difference in the free energy landscape between mechanisms, and therefore all mechanisms can exhibit the same kinetic performance. To our knowledge all known rotary pumps have an H+:ATP ratio greater than one, and all known alternating access ATP-driven proton pumps have a ratio of one. Our analysis suggests a possible explanation for this apparent relationship between coupling ratio and mechanism. When the conditions under which the pump must operate permit a coupling ratio greater than one, the rotary mechanism may have been selected for its kinetic advantage. On the other hand, when conditions require a coupling ratio of one or less, the alternating access mechanism may have been selected for other possible advantages resulting from its structural and functional simplicity.
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Affiliation(s)
- Ramu Anandakrishnan
- Dept. of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, United States of America
- * E-mail: (RA); (DMZ)
| | - Daniel M. Zuckerman
- Dept. of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, United States of America
- * E-mail: (RA); (DMZ)
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168
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Oot RA, Couoh-Cardel S, Sharma S, Stam NJ, Wilkens S. Breaking up and making up: The secret life of the vacuolar H + -ATPase. Protein Sci 2017; 26:896-909. [PMID: 28247968 DOI: 10.1002/pro.3147] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 02/21/2017] [Indexed: 01/24/2023]
Abstract
The vacuolar ATPase (V-ATPase; V1 Vo -ATPase) is a large multisubunit proton pump found in the endomembrane system of all eukaryotic cells where it acidifies the lumen of subcellular organelles including lysosomes, endosomes, the Golgi apparatus, and clathrin-coated vesicles. V-ATPase function is essential for pH and ion homeostasis, protein trafficking, endocytosis, mechanistic target of rapamycin (mTOR), and Notch signaling, as well as hormone secretion and neurotransmitter release. V-ATPase can also be found in the plasma membrane of polarized animal cells where its proton pumping function is involved in bone remodeling, urine acidification, and sperm maturation. Aberrant (hypo or hyper) activity has been associated with numerous human diseases and the V-ATPase has therefore been recognized as a potential drug target. Recent progress with moderate to high-resolution structure determination by cryo electron microscopy and X-ray crystallography together with sophisticated single-molecule and biochemical experiments have provided a detailed picture of the structure and unique mode of regulation of the V-ATPase. This review summarizes the recent advances, focusing on the structural and biophysical aspects of the field.
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Affiliation(s)
- Rebecca A Oot
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, 13210
| | - Sergio Couoh-Cardel
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, 13210
| | - Stuti Sharma
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, 13210
| | - Nicholas J Stam
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, 13210
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, 13210
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169
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Sharma S, Wilkens S. Biolayer interferometry of lipid nanodisc-reconstituted yeast vacuolar H + -ATPase. Protein Sci 2017; 26:1070-1079. [PMID: 28241399 DOI: 10.1002/pro.3143] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/15/2017] [Accepted: 02/17/2017] [Indexed: 01/24/2023]
Abstract
Vacuolar H+ -ATPase (V-ATPase) is a large, multisubunit membrane protein complex responsible for the acidification of subcellular compartments and the extracellular space. V-ATPase activity is regulated by reversible disassembly, resulting in cytosolic V1 -ATPase and membrane-integral V0 proton channel sectors. Reversible disassembly is accompanied by transient interaction with cellular factors and assembly chaperones. Quantifying protein-protein interactions involving membrane proteins, however, is challenging. Here we present a novel method to determine kinetic constants of membrane protein-protein interactions using biolayer interferometry (BLI). Yeast vacuoles are solubilized, vacuolar proteins are reconstituted into lipid nanodiscs with native vacuolar lipids and biotinylated membrane scaffold protein (MSP) followed by affinity purification of nanodisc-reconstituted V-ATPase (V1 V0 ND). We show that V1 V0 ND can be immobilized on streptavidin-coated BLI sensors to quantitate binding of a pathogen derived inhibitor and to measure the kinetics of nucleotide dependent enzyme dissociation.
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Affiliation(s)
- Stuti Sharma
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, Syracuse, New York, 13210
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University 750 East Adams Street, Syracuse, New York, 13210
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170
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Schulz S, Wilkes M, Mills DJ, Kühlbrandt W, Meier T. Molecular architecture of the N-type ATPase rotor ring from Burkholderia pseudomallei. EMBO Rep 2017; 18:526-535. [PMID: 28283532 PMCID: PMC5376962 DOI: 10.15252/embr.201643374] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 02/02/2017] [Accepted: 02/09/2017] [Indexed: 11/09/2022] Open
Abstract
The genome of the highly infectious bacterium Burkholderia pseudomallei harbors an atp operon that encodes an N‐type rotary ATPase, in addition to an operon for a regular F‐type rotary ATPase. The molecular architecture of N‐type ATPases is unknown and their biochemical properties and cellular functions are largely unexplored. We studied the B. pseudomallei N1No‐type ATPase and investigated the structure and ion specificity of its membrane‐embedded c‐ring rotor by single‐particle electron cryo‐microscopy. Of several amphiphilic compounds tested for solubilizing the complex, the choice of the low‐density, low‐CMC detergent LDAO was optimal in terms of map quality and resolution. The cryoEM map of the c‐ring at 6.1 Å resolution reveals a heptadecameric oligomer with a molecular mass of ~141 kDa. Biochemical measurements indicate that the c17 ring is H+ specific, demonstrating that the ATPase is proton‐coupled. The c17 ring stoichiometry results in a very high ion‐to‐ATP ratio of 5.7. We propose that this N‐ATPase is a highly efficient proton pump that helps these melioidosis‐causing bacteria to survive in the hostile, acidic environment of phagosomes.
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Affiliation(s)
- Sarah Schulz
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Martin Wilkes
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Thomas Meier
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
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171
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cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods 2017; 14:290-296. [PMID: 28165473 DOI: 10.1038/nmeth.4169] [Citation(s) in RCA: 4367] [Impact Index Per Article: 623.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/27/2016] [Indexed: 01/02/2023]
Abstract
Single-particle electron cryomicroscopy (cryo-EM) is a powerful method for determining the structures of biological macromolecules. With automated microscopes, cryo-EM data can often be obtained in a few days. However, processing cryo-EM image data to reveal heterogeneity in the protein structure and to refine 3D maps to high resolution frequently becomes a severe bottleneck, requiring expert intervention, prior structural knowledge, and weeks of calculations on expensive computer clusters. Here we show that stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms permit the major steps in cryo-EM structure determination to be performed in hours or minutes on an inexpensive desktop computer. Furthermore, SGD with Bayesian marginalization allows ab initio 3D classification, enabling automated analysis and discovery of unexpected structures without bias from a reference map. These algorithms are combined in a user-friendly computer program named cryoSPARC (http://www.cryosparc.com).
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172
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Van Damme T, Gardeitchik T, Mohamed M, Guerrero-Castillo S, Freisinger P, Guillemyn B, Kariminejad A, Dalloyaux D, van Kraaij S, Lefeber DJ, Syx D, Steyaert W, De Rycke R, Hoischen A, Kamsteeg EJ, Wong SY, van Scherpenzeel M, Jamali P, Brandt U, Nijtmans L, Korenke GC, Chung BHY, Mak CCY, Hausser I, Kornak U, Fischer-Zirnsak B, Strom TM, Meitinger T, Alanay Y, Utine GE, Leung PKC, Ghaderi-Sohi S, Coucke P, Symoens S, De Paepe A, Thiel C, Haack TB, Malfait F, Morava E, Callewaert B, Wevers RA. Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa. Am J Hum Genet 2017; 100:216-227. [PMID: 28065471 DOI: 10.1016/j.ajhg.2016.12.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/08/2016] [Indexed: 02/03/2023] Open
Abstract
Defects of the V-type proton (H+) ATPase (V-ATPase) impair acidification and intracellular trafficking of membrane-enclosed compartments, including secretory granules, endosomes, and lysosomes. Whole-exome sequencing in five families affected by mild to severe cutis laxa, dysmorphic facial features, and cardiopulmonary involvement identified biallelic missense mutations in ATP6V1E1 and ATP6V1A, which encode the E1 and A subunits, respectively, of the V1 domain of the heteromultimeric V-ATPase complex. Structural modeling indicated that all substitutions affect critical residues and inter- or intrasubunit interactions. Furthermore, complexome profiling, a method combining blue-native gel electrophoresis and liquid chromatography tandem mass spectrometry, showed that they disturb either the assembly or the stability of the V-ATPase complex. Protein glycosylation was variably affected. Abnormal vesicular trafficking was evidenced by delayed retrograde transport after brefeldin A treatment and abnormal swelling and fragmentation of the Golgi apparatus. In addition to showing reduced and fragmented elastic fibers, the histopathological hallmark of cutis laxa, transmission electron microscopy of the dermis also showed pronounced changes in the structure and organization of the collagen fibers. Our findings expand the clinical and molecular spectrum of metabolic cutis laxa syndromes and further link defective extracellular matrix assembly to faulty protein processing and cellular trafficking caused by genetic defects in the V-ATPase complex.
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Affiliation(s)
- Tim Van Damme
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent 9000, Belgium
| | - Thatjana Gardeitchik
- Department of Pediatrics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Miski Mohamed
- Department of Pediatrics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Sergio Guerrero-Castillo
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Peter Freisinger
- Childrens' Hospital, Klinikum am Steinenberg, Reutlingen 72764, Germany
| | - Brecht Guillemyn
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent 9000, Belgium
| | | | - Daisy Dalloyaux
- Department of Pediatrics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Sanne van Kraaij
- Department of Pediatrics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Dirk J Lefeber
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Department of Neurology, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Delfien Syx
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent 9000, Belgium
| | - Wouter Steyaert
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent 9000, Belgium
| | - Riet De Rycke
- Department of Biomedical Molecular Biology, Ghent University, Ghent 9000, Belgium; Inflammation Research Center, VIB, Ghent 9000, Belgium
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Sunnie Y Wong
- Hayward Genetics Center, Tulane University Medical School, New Orleans, LA 70112, USA
| | - Monique van Scherpenzeel
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Department of Neurology, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Payman Jamali
- Shahrood Genetic Counseling Center, Semnan 36156, Iran
| | - Ulrich Brandt
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - Leo Nijtmans
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands; Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands
| | - G Christoph Korenke
- Department of Neuropediatrics, Children's Hospital Klinikum Oldenburg, Oldenburg 26133, Germany
| | - Brian H Y Chung
- Department of Paediatrics & Adolescent Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Christopher C Y Mak
- Department of Paediatrics & Adolescent Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Ingrid Hausser
- Institute of Pathology, Universitätsklinikum Heidelberg, Heidelberg 69120, Germany
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitaetsmedizin Berlin, Berlin 13353, Germany; Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Charité - Universitaetsmedizin Berlin, Berlin 13353, Germany; Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Yasemin Alanay
- Pediatric Genetics Unit, Department of Pediatrics, Acibadem University School of Medicine, Istanbul 34752, Turkey
| | - Gulen E Utine
- Pediatric Genetics Unit, Department of Pediatrics, Ihsan Doğramacı Children's Hospital, Hacettepe School of Medicine, Ankara 06100, Turkey
| | - Peter K C Leung
- Department of Paediatrics & Adolescent Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | | | - Paul Coucke
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent 9000, Belgium
| | - Sofie Symoens
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent 9000, Belgium
| | - Anne De Paepe
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent 9000, Belgium
| | - Christian Thiel
- Center for Child and Adolescent Medicine, Klinik Kinderheilkunde I, Universitätsklinikum Heidelberg, Heidelberg 69120, Germany
| | - Tobias B Haack
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg 85764, Germany; Institute of Human Genetics, Technische Universität München, Munich 81675, Germany; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
| | - Fransiska Malfait
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent 9000, Belgium
| | - Eva Morava
- Hayward Genetics Center, Tulane University Medical School, New Orleans, LA 70112, USA; Department of Pediatrics, University Hospital Leuven, Leuven 3000, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent 9000, Belgium.
| | - Ron A Wevers
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen 6500 HB, the Netherlands.
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173
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Davies RB, Smits C, Wong ASW, Stock D, Christie M, Sandin S, Stewart AG. Cryo-EM analysis of a domain antibody bound rotary ATPase complex. J Struct Biol 2017; 197:350-353. [PMID: 28115258 DOI: 10.1016/j.jsb.2017.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 01/11/2023]
Abstract
The bacterial A/V-type ATPase/synthase rotary motor couples ATP hydrolysis/synthesis with proton translocation across biological membranes. The A/V-type ATPase/synthase from Thermus thermophilus has been extensively studied both structurally and functionally for many years. Here we provide an 8.7Å resolution cryo-electron microscopy 3D reconstruction of this complex bound to single-domain antibody fragments, small monomeric antibodies containing just the variable heavy domain. Docking of known structures into the density revealed the molecular orientation of the domain antibodies, suggesting that structure determination of co-domain antibody:protein complexes could be a useful avenue for unstable or smaller proteins. Although previous studies suggested that the presence of fluoroaluminate in this complex could change the rotary state of this enzyme, we observed no gross structural rearrangements under these conditions.
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Affiliation(s)
- Roberta B Davies
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Callum Smits
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Andrew S W Wong
- NTU Institute of Structural Biology, Nanyang Technological University, 636921, Singapore
| | - Daniela Stock
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculty of Medicine, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Mary Christie
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculty of Medicine, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Sara Sandin
- NTU Institute of Structural Biology, Nanyang Technological University, 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Alastair G Stewart
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculty of Medicine, The University of New South Wales, Sydney, NSW 2052, Australia.
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174
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Higashida H, Yokoyama S, Tsuji C, Muramatsu SI. Neurotransmitter release: vacuolar ATPase V0 sector c-subunits in possible gene or cell therapies for Parkinson's, Alzheimer's, and psychiatric diseases. J Physiol Sci 2017; 67:11-17. [PMID: 27289535 PMCID: PMC10717279 DOI: 10.1007/s12576-016-0462-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/27/2016] [Indexed: 12/13/2022]
Abstract
We overview the 16-kDa proteolipid mediatophore, the transmembrane c-subunit of the V0 sector of the vacuolar proton ATPase (ATP6V0C) that was shown to mediate the secretion of acetylcholine. Acetylcholine, serotonin, and dopamine (DA) are released from cell soma and/or dendrites if ATP6V0C is expressed in cultured cells. Adeno-associated viral vector-mediated gene transfer of ATP6V0C into the caudate putamen enhanced the depolarization-induced overflow of endogenous DA in Parkinson-model mice. Motor impairment was ameliorated in hemiparkinsonian model mice when ATP6V0C was expressed with DA-synthesizing enzymes. The review discusses application in the future as a potential tool for gene therapy, cell transplantation therapy, and inducible pluripotent stem cell therapy in neurological diseases, from the view point of recent findings regarding vacuolar ATPase.
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Affiliation(s)
- Haruhiro Higashida
- Kanazawa University Research Center for Child Mental Development, Kanazawa, 920-8640, Japan.
| | - Shigeru Yokoyama
- Kanazawa University Research Center for Child Mental Development, Kanazawa, 920-8640, Japan
| | - Chiharu Tsuji
- Kanazawa University Research Center for Child Mental Development, Kanazawa, 920-8640, Japan
| | - Shin-Ichi Muramatsu
- Division of Neurology, Department of Medicine, Jichi Medical University, Tochigi, 329-0498, Japan
- Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
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175
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Sobti M, Smits C, Wong AS, Ishmukhametov R, Stock D, Sandin S, Stewart AG. Cryo-EM structures of the autoinhibited E. coli ATP synthase in three rotational states. eLife 2016; 5. [PMID: 28001127 PMCID: PMC5214741 DOI: 10.7554/elife.21598] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/15/2016] [Indexed: 12/28/2022] Open
Abstract
A molecular model that provides a framework for interpreting the wealth of functional information obtained on the E. coli F-ATP synthase has been generated using cryo-electron microscopy. Three different states that relate to rotation of the enzyme were observed, with the central stalk’s ε subunit in an extended autoinhibitory conformation in all three states. The Fo motor comprises of seven transmembrane helices and a decameric c-ring and invaginations on either side of the membrane indicate the entry and exit channels for protons. The proton translocating subunit contains near parallel helices inclined by ~30° to the membrane, a feature now synonymous with rotary ATPases. For the first time in this rotary ATPase subtype, the peripheral stalk is resolved over its entire length of the complex, revealing the F1 attachment points and a coiled-coil that bifurcates toward the membrane with its helices separating to embrace subunit a from two sides. DOI:http://dx.doi.org/10.7554/eLife.21598.001 ATP synthase is a biological motor that produces a molecule called adenosine tri-phosphate (ATP for short), which acts as the major store of chemical energy in cells. A single molecule of ATP contains three phosphate groups: the cell can remove one of these phosphates to make a molecule called adenosine di-phosphate (ADP) and release energy to drive a variety of biological processes. ATP synthase sits in the membranes that separate cell compartments or form barriers around cells. When cells break down food they transport hydrogen ions across these membranes so that each side of the membrane has a different level (or “concentration”) of hydrogen ions. Movement of hydrogen ions from an area with a high concentration to a low concentration causes ATP synthase to rotate like a turbine. This rotation of the enzyme results in ATP synthase adding a phosphate group to ADP to make a new molecule of ATP. In certain conditions cells need to switch off the ATP synthase and this is done by changing the shape of the central shaft in a process called autoinhibition, which blocks the rotation. The ATP synthase from a bacterium known as E. coli – which is commonly found in the human gut –has been used as a model to study how this biological motor works. However, since the precise details of the three-dimensional structure of ATP synthase have remained unclear it has been difficult to interpret the results of these studies. Sobti et al. used a technique called Cryo-electron microscopy to investigate the structure of ATP synthase from E. coli. This made it possible to develop a three-dimensional model of the ATP synthase in its autoinhibited form. The structural data could also be split into three distinct shapes that relate to dwell points in the rotation of the motor where the rotation has been inhibited. These models further our understanding of ATP synthases and provide a template to understand the findings of previous studies. Further work will be needed to understand this essential biological process at the atomic level in both its inhibited and uninhibited form. This will reveal the inner workings of a marvel of the natural world and may also lead to the discovery of new antibiotics against related bacteria that cause diseases in humans. DOI:http://dx.doi.org/10.7554/eLife.21598.002
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Affiliation(s)
- Meghna Sobti
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Callum Smits
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Andrew Sw Wong
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Robert Ishmukhametov
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, United Kingdom
| | - Daniela Stock
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,Faculty of Medicine, The University of New South Wales, Sydney, Australia
| | - Sara Sandin
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Alastair G Stewart
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,Faculty of Medicine, The University of New South Wales, Sydney, Australia
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176
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Stam NJ, Wilkens S. Structure of the Lipid Nanodisc-reconstituted Vacuolar ATPase Proton Channel: DEFINITION OF THE INTERACTION OF ROTOR AND STATOR AND IMPLICATIONS FOR ENZYME REGULATION BY REVERSIBLE DISSOCIATION. J Biol Chem 2016; 292:1749-1761. [PMID: 27965356 DOI: 10.1074/jbc.m116.766790] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/11/2016] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic vacuolar H+-ATPase (V-ATPase) is a multisubunit enzyme complex that acidifies subcellular organelles and the extracellular space. V-ATPase consists of soluble V1-ATPase and membrane-integral Vo proton channel sectors. To investigate the mechanism of V-ATPase regulation by reversible disassembly, we recently determined a cryo-EM reconstruction of yeast Vo The structure indicated that, when V1 is released from Vo, the N-terminal cytoplasmic domain of subunit a (aNT) changes conformation to bind rotor subunit d However, insufficient resolution precluded a precise definition of the aNT-d interface. Here we reconstituted Vo into lipid nanodiscs for single-particle EM. 3D reconstructions calculated at ∼15-Å resolution revealed two sites of contact between aNT and d that are mediated by highly conserved charged residues. Alanine mutagenesis of some of these residues disrupted the aNT-d interaction, as shown by isothermal titration calorimetry and gel filtration of recombinant subunits. A recent cryo-EM study of holo V-ATPase revealed three major conformations corresponding to three rotational states of the central rotor of the enzyme. Comparison of the three V-ATPase conformations with the structure of nanodisc-bound Vo revealed that Vo is halted in rotational state 3. Combined with our prior work that showed autoinhibited V1-ATPase to be arrested in state 2, we propose a model in which the conformational mismatch between free V1 and Vo functions to prevent unintended reassembly of holo V-ATPase when activity is not needed.
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Affiliation(s)
- Nicholas J Stam
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Stephan Wilkens
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210.
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177
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Marcoline FV, Ishida Y, Mindell JA, Nayak S, Grabe M. A mathematical model of osteoclast acidification during bone resorption. Bone 2016; 93:167-180. [PMID: 27650914 PMCID: PMC5077641 DOI: 10.1016/j.bone.2016.09.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 08/16/2016] [Accepted: 09/09/2016] [Indexed: 12/01/2022]
Abstract
Bone resorption by osteoclasts occurs through the creation of a sealed extracellular compartment (ECC), or pit, adjacent to the bone that is subsequently acidified through a complex biological process. The low pH of the pit dissolves the bone mineral and activates acid proteases that further break down the bone matrix. There are many ion channels, transporters, and soluble proteins involved in osteoclast mediated resorption, and in the past few years, there has been an increased understanding of the identity and properties of some key proteins such as the ClC-7 Cl-/H+ antiporter and the HV1 proton channel. Here we present a detailed mathematical model of osteoclast acidification that includes the influence of many of the key regulatory proteins. The primary enzyme responsible for acidification is the vacuolar H+-ATPase (V-ATPase), which pumps protons from the cytoplasm into the pit. Unlike the acidification of small lysosomes, the pit is so large that protons become depleted from the cytoplasm. Hence, proton buffering and production in the cytoplasm by carbonic anhydrase II (CAII) is potentially important for proper acidification. We employ an ordinary differential equations (ODE)-based model that accounts for the changes in ionic species in the cytoplasm and the resorptive pit. Additionally, our model tracks ionic flow between the cytoplasm and the extracellular solution surrounding the cell. Whenever possible, the properties of individual channels and transporters are calibrated based on electrophysiological measurements, and physical properties of the cell, such as buffering capacity, surface areas, and volumes, are estimated based on available data. Our model reproduces many of the experimental findings regarding the role of key proteins in the acidification process, and it allows us to estimate, among other things, number of active pumps, protons moved, and the influence of particular mutations implicated in disease.
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Affiliation(s)
- Frank V Marcoline
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Yoichi Ishida
- Department of Philosophy, Ohio University, Athens, OH 45701, USA
| | - Joseph A Mindell
- Membrane Transport Biophysics Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Smita Nayak
- Swedish Center for Research and Innovation, Swedish Health Services, Seattle, WA 98122, USA
| | - Michael Grabe
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
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178
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Pandey A, Shin K, Patterson RE, Liu XQ, Rainey JK. Current strategies for protein production and purification enabling membrane protein structural biology. Biochem Cell Biol 2016; 94:507-527. [PMID: 27010607 PMCID: PMC5752365 DOI: 10.1139/bcb-2015-0143] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10-15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).
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Affiliation(s)
- Aditya Pandey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyungsoo Shin
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Robin E. Patterson
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Xiang-Qin Liu
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jan K. Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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179
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Suzuki K, Mizutani K, Maruyama S, Shimono K, Imai FL, Muneyuki E, Kakinuma Y, Ishizuka-Katsura Y, Shirouzu M, Yokoyama S, Yamato I, Murata T. Crystal structures of the ATP-binding and ADP-release dwells of the V 1 rotary motor. Nat Commun 2016; 7:13235. [PMID: 27807367 PMCID: PMC5095293 DOI: 10.1038/ncomms13235] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 09/14/2016] [Indexed: 12/21/2022] Open
Abstract
V1-ATPases are highly conserved ATP-driven rotary molecular motors found in various membrane systems. We recently reported the crystal structures for the Enterococcus hirae A3B3DF (V1) complex, corresponding to the catalytic dwell state waiting for ATP hydrolysis. Here we present the crystal structures for two other dwell states obtained by soaking nucleotide-free V1 crystals in ADP. In the presence of 20 μM ADP, two ADP molecules bind to two of three binding sites and cooperatively induce conformational changes of the third site to an ATP-binding mode, corresponding to the ATP-binding dwell. In the presence of 2 mM ADP, all nucleotide-binding sites are occupied by ADP to induce conformational changes corresponding to the ADP-release dwell. Based on these and previous findings, we propose a V1-ATPase rotational mechanism model.
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Affiliation(s)
- Kano Suzuki
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Kenji Mizutani
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan
| | - Shintaro Maruyama
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Kazumi Shimono
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Fabiana L. Imai
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Eiro Muneyuki
- Department of Physics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Tokyo 112-8551, Japan
| | - Yoshimi Kakinuma
- Laboratory of Molecular Physiology and Genetics, Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
| | - Yoshiko Ishizuka-Katsura
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Ichiro Yamato
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- JST, PRESTO, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
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180
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Mazhab-Jafari MT, Rohou A, Schmidt C, Bueler SA, Benlekbir S, Robinson CV, Rubinstein JL. Atomic model for the membrane-embedded V O motor of a eukaryotic V-ATPase. Nature 2016; 539:118-122. [PMID: 27776355 DOI: 10.1038/nature19828] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/06/2016] [Indexed: 12/15/2022]
Abstract
Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney function. ATP hydrolysis in the soluble catalytic V1 region drives proton translocation through the membrane-embedded VO region via rotation of a rotor subcomplex. Variability in the structure of the intact enzyme has prevented construction of an atomic model for the membrane-embedded motor of any rotary ATPase. We induced dissociation and auto-inhibition of the V1 and VO regions of the V-ATPase by starving the yeast Saccharomyces cerevisiae, allowing us to obtain a ~3.9-Å resolution electron cryomicroscopy map of the VO complex and build atomic models for the majority of its subunits. The analysis reveals the structures of subunits ac8c'c″de and a protein that we identify and propose to be a new subunit (subunit f). A large cavity between subunit a and the c-ring creates a cytoplasmic half-channel for protons. The c-ring has an asymmetric distribution of proton-carrying Glu residues, with the Glu residue of subunit c″ interacting with Arg735 of subunit a. The structure suggests sequential protonation and deprotonation of the c-ring, with ATP-hydrolysis-driven rotation causing protonation of a Glu residue at the cytoplasmic half-channel and subsequent deprotonation of a Glu residue at a luminal half-channel.
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Affiliation(s)
- Mohammad T Mazhab-Jafari
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Alexis Rohou
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Carla Schmidt
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Stephanie A Bueler
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Samir Benlekbir
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - John L Rubinstein
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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181
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Takizawa Y, Binshtein E, Erwin AL, Pyburn TM, Mittendorf KF, Ohi MD. While the revolution will not be crystallized, biochemistry reigns supreme. Protein Sci 2016; 26:69-81. [PMID: 27673321 DOI: 10.1002/pro.3054] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 09/22/2016] [Indexed: 12/14/2022]
Abstract
Single-particle cryo-electron microscopy (EM) is currently gaining attention for the ability to calculate structures that reach sub-5 Å resolutions; however, the technique is more than just an alternative approach to X-ray crystallography. Molecular machines work via dynamic conformational changes, making structural flexibility the hallmark of function. While the dynamic regions in molecules are essential, they are also the most challenging to structurally characterize. Single-particle EM has the distinct advantage of being able to directly visualize purified molecules without the formation of ordered arrays of molecules locked into identical conformations. Additionally, structures determined using single-particle EM can span resolution ranges from very low- to atomic-levels (>30-1.8 Å), sometimes even in the same structure. The ability to accommodate various resolutions gives single-particle EM the unique capacity to structurally characterize dynamic regions of biological molecules, thereby contributing essential structural information needed for the development of molecular models that explain function. Further, many important molecular machines are intrinsically dynamic and compositionally heterogeneous. Structures of these complexes may never reach sub-5 Å resolutions due to this flexibility required for function. Thus, the biochemical quality of the sample, as well as, the calculation and interpretation of low- to mid-resolution cryo-EM structures (30-8 Å) remains critical for generating insights into the architecture of many challenging biological samples that cannot be visualized using alternative techniques.
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Affiliation(s)
- Yoshimasa Takizawa
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Elad Binshtein
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Amanda L Erwin
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Tasia M Pyburn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center Vanderbilt University Medical Center, Nashville, Tennessee, 37232
| | - Melanie D Ohi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
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182
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Abstract
The lysosome has long been viewed as the recycling center of the cell. However, recent discoveries have challenged this simple view and have established a central role of the lysosome in nutrient-dependent signal transduction. The degradative role of the lysosome and its newly discovered signaling functions are not in conflict but rather cooperate extensively to mediate fundamental cellular activities such as nutrient sensing, metabolic adaptation, and quality control of proteins and organelles. Moreover, lysosome-based signaling and degradation are subject to reciprocal regulation. Transcriptional programs of increasing complexity control the biogenesis, composition, and abundance of lysosomes and fine-tune their activity to match the evolving needs of the cell. Alterations in these essential activities are, not surprisingly, central to the pathophysiology of an ever-expanding spectrum of conditions, including storage disorders, neurodegenerative diseases, and cancer. Thus, unraveling the functions of this fascinating organelle will contribute to our understanding of the fundamental logic of metabolic organization and will point to novel therapeutic avenues in several human diseases.
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Affiliation(s)
- Rushika M Perera
- Department of Anatomy and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94143;
| | - Roberto Zoncu
- Department of Molecular and Cellular Biology and Paul F. Glenn Center for Aging Research, University of California, Berkeley, California 94720;
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183
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Unravelling biological macromolecules with cryo-electron microscopy. Nature 2016; 537:339-46. [PMID: 27629640 DOI: 10.1038/nature19948] [Citation(s) in RCA: 262] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/15/2016] [Indexed: 12/11/2022]
Abstract
Knowledge of the three-dimensional structures of proteins and other biological macromolecules often aids understanding of how they perform complicated tasks in the cell. Because many such tasks involve the cleavage or formation of chemical bonds, structural characterization at the atomic level is most useful. Developments in the electron microscopy of frozen hydrated samples (cryo-electron microscopy) are providing unprecedented opportunities for the structural characterization of biological macromolecules. This is resulting in a wave of information about processes in the cell that were impossible to characterize with existing techniques in structural biology.
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184
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185
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Magnani F, Serrano-Vega MJ, Shibata Y, Abdul-Hussein S, Lebon G, Miller-Gallacher J, Singhal A, Strege A, Thomas JA, Tate CG. A mutagenesis and screening strategy to generate optimally thermostabilized membrane proteins for structural studies. Nat Protoc 2016; 11:1554-71. [PMID: 27466713 PMCID: PMC5268090 DOI: 10.1038/nprot.2016.088] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The thermostability of an integral membrane protein (MP) in detergent solution is a key parameter that dictates the likelihood of obtaining well-diffracting crystals that are suitable for structure determination. However, many mammalian MPs are too unstable for crystallization. We developed a thermostabilization strategy based on systematic mutagenesis coupled to a radioligand-binding thermostability assay that can be applied to receptors, ion channels and transporters. It takes ∼6-12 months to thermostabilize a G-protein-coupled receptor (GPCR) containing 300 amino acid (aa) residues. The resulting thermostabilized MPs are more easily crystallized and result in high-quality structures. This methodology has facilitated structure-based drug design applied to GPCRs because it is possible to determine multiple structures of the thermostabilized receptors bound to low-affinity ligands. Protocols and advice are given on how to develop thermostability assays for MPs and how to combine mutations to make an optimally stable mutant suitable for structural studies. The steps in the procedure include the generation of ∼300 site-directed mutants by Ala/Leu scanning mutagenesis, the expression of each mutant in mammalian cells by transient transfection and the identification of thermostable mutants using a thermostability assay that is based on binding of an (125)I-labeled radioligand to the unpurified, detergent-solubilized MP. Individual thermostabilizing point mutations are then combined to make an optimally stable MP that is suitable for structural biology and other biophysical studies.
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Affiliation(s)
| | | | | | | | | | | | - Ankita Singhal
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Annette Strege
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jennifer A. Thomas
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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186
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Tresguerres M. Novel and potential physiological roles of vacuolar-type H+-ATPase in marine organisms. J Exp Biol 2016; 219:2088-97. [DOI: 10.1242/jeb.128389] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
ABSTRACT
The vacuolar-type H+-ATPase (VHA) is a multi-subunit enzyme that uses the energy from ATP hydrolysis to transport H+ across biological membranes. VHA plays a universal role in essential cellular functions, such as the acidification of lysosomes and endosomes. In addition, the VHA-generated H+-motive force can drive the transport of diverse molecules across cell membranes and epithelia for specialized physiological functions. Here, I discuss diverse physiological functions of VHA in marine animals, focusing on recent discoveries about base secretion in shark gills, potential bone dissolution by Osedax bone-eating worms and its participation in a carbon-concentrating mechanism that promotes coral photosynthesis. Because VHA is evolutionarily conserved among eukaryotes, it is likely to play many other essential physiological roles in diverse marine organisms. Elucidating and characterizing basic VHA-dependent mechanisms could help to determine species responses to environmental stress, including (but not limited to) that resulting from climate change.
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Affiliation(s)
- Martin Tresguerres
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, SIO mail code 0202, La Jolla, CA 92093, USA
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187
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Wang F, Gong H, Liu G, Li M, Yan C, Xia T, Li X, Zeng J. DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM. J Struct Biol 2016; 195:325-336. [PMID: 27424268 DOI: 10.1016/j.jsb.2016.07.006] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 01/12/2023]
Abstract
Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep learning framework, called DeepPicker, to address this problem and fill the current gaps toward a fully automated cryo-EM pipeline. DeepPicker employs a novel cross-molecule training strategy to capture common features of particles from previously-analyzed micrographs, and thus does not require any human intervention during particle picking. Tests on the recently-published cryo-EM data of three complexes have demonstrated that our deep learning based scheme can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those picked manually by human experts. These results indicate that DeepPicker can provide a practically useful tool to significantly reduce the time and manual effort spent in single-particle analysis and thus greatly facilitate high-resolution cryo-EM structure determination. DeepPicker is released as an open-source program, which can be downloaded from https://github.com/nejyeah/DeepPicker-python.
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Affiliation(s)
- Feng Wang
- School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Huichao Gong
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China
| | - Gaochao Liu
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structure Biology, Tsinghua University, Beijing 100084, China
| | - Meijing Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structure Biology, Tsinghua University, Beijing 100084, China
| | - Chuangye Yan
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tian Xia
- School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Xueming Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structure Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China.
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188
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Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study. Proc Natl Acad Sci U S A 2016; 113:E4190-9. [PMID: 27402735 DOI: 10.1073/pnas.1603980113] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The AAA+ (ATPases associated with a variety of cellular activities) enzymes play critical roles in a variety of homeostatic processes in all kingdoms of life. Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), the archaeal homolog of the ubiquitous AAA+ protein Cdc48/p97, functions in concert with the 20S proteasome by unfolding substrates and passing them on for degradation. Here, we present electron cryomicroscopy (cryo-EM) maps showing that VAT undergoes large conformational rearrangements during its ATP hydrolysis cycle that differ dramatically from the conformational states observed for Cdc48/p97. We validate key features of the model with biochemical and solution methyl-transverse relaxation optimized spectroscopY (TROSY) NMR experiments and suggest a mechanism for coupling the energy of nucleotide hydrolysis to substrate unfolding. These findings illustrate the unique complementarity between cryo-EM and solution NMR for studies of molecular machines, showing that the structural properties of VAT, as well as the population distributions of conformers, are similar in the frozen specimens used for cryo-EM and in the solution phase where NMR spectra are recorded.
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189
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Mazhab-Jafari MT, Rubinstein JL. Cryo-EM studies of the structure and dynamics of vacuolar-type ATPases. SCIENCE ADVANCES 2016; 2:e1600725. [PMID: 27532044 PMCID: PMC4985227 DOI: 10.1126/sciadv.1600725] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/15/2016] [Indexed: 06/06/2023]
Abstract
Electron cryomicroscopy (cryo-EM) has significantly advanced our understanding of molecular structure in biology. Recent innovations in both hardware and software have made cryo-EM a viable alternative for targets that are not amenable to x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Cryo-EM has even become the method of choice in some situations where x-ray crystallography and NMR spectroscopy are possible but where cryo-EM can determine structures at higher resolution or with less time or effort. Rotary adenosine triphosphatases (ATPases) are crucial to the maintenance of cellular homeostasis. These enzymes couple the synthesis or hydrolysis of adenosine triphosphate to the use or production of a transmembrane electrochemical ion gradient, respectively. However, the membrane-embedded nature and conformational heterogeneity of intact rotary ATPases have prevented their high-resolution structural analysis to date. Recent application of cryo-EM methods to the different types of rotary ATPase has led to sudden advances in understanding the structure and function of these enzymes, revealing significant conformational heterogeneity and characteristic transmembrane α helices that are highly tilted with respect to the membrane. In this Review, we will discuss what has been learned recently about rotary ATPase structure and function, with a particular focus on the vacuolar-type ATPases.
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Affiliation(s)
- Mohammad T. Mazhab-Jafari
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - John L. Rubinstein
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, The University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
- Department of Medical Biophysics, The University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
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190
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Hahn A, Parey K, Bublitz M, Mills DJ, Zickermann V, Vonck J, Kühlbrandt W, Meier T. Structure of a Complete ATP Synthase Dimer Reveals the Molecular Basis of Inner Mitochondrial Membrane Morphology. Mol Cell 2016; 63:445-56. [PMID: 27373333 PMCID: PMC4980432 DOI: 10.1016/j.molcel.2016.05.037] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/21/2016] [Accepted: 05/26/2016] [Indexed: 11/28/2022]
Abstract
We determined the structure of a complete, dimeric F1Fo-ATP synthase from yeast Yarrowia lipolytica mitochondria by a combination of cryo-EM and X-ray crystallography. The final structure resolves 58 of the 60 dimer subunits. Horizontal helices of subunit a in Fo wrap around the c-ring rotor, and a total of six vertical helices assigned to subunits a, b, f, i, and 8 span the membrane. Subunit 8 (A6L in human) is an evolutionary derivative of the bacterial b subunit. On the lumenal membrane surface, subunit f establishes direct contact between the two monomers. Comparison with a cryo-EM map of the F1Fo monomer identifies subunits e and g at the lateral dimer interface. They do not form dimer contacts but enable dimer formation by inducing a strong membrane curvature of ∼100°. Our structure explains the structural basis of cristae formation in mitochondria, a landmark signature of eukaryotic cell morphology. Cryo-EM structure of a yeast F1Fo-ATP synthase dimer Inhibitor-free X-ray structure of the F1 head and rotor complex Mechanism of ATP generation by rotary catalysis Structural basis of cristae formation in the inner mitochondrial membrane
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Affiliation(s)
- Alexander Hahn
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Kristian Parey
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Maike Bublitz
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, Medical School, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany.
| | - Thomas Meier
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany.
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191
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Oot RA, Kane PM, Berry EA, Wilkens S. Crystal structure of yeast V1-ATPase in the autoinhibited state. EMBO J 2016; 35:1694-706. [PMID: 27295975 DOI: 10.15252/embj.201593447] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 05/12/2016] [Indexed: 01/23/2023] Open
Abstract
Vacuolar ATPases (V-ATPases) are essential proton pumps that acidify the lumen of subcellular organelles in all eukaryotic cells and the extracellular space in some tissues. V-ATPase activity is regulated by a unique mechanism referred to as reversible disassembly, wherein the soluble catalytic sector, V1, is released from the membrane and its MgATPase activity silenced. The crystal structure of yeast V1 presented here shows that activity silencing involves a large conformational change of subunit H, with its C-terminal domain rotating ~150° from a position near the membrane in holo V-ATPase to a position at the bottom of V1 near an open catalytic site. Together with biochemical data, the structure supports a mechanistic model wherein subunit H inhibits ATPase activity by stabilizing an open catalytic site that results in tight binding of inhibitory ADP at another site.
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Affiliation(s)
- Rebecca A Oot
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Edward A Berry
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
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192
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Papachristos K, Muench SP, Paci E. Characterization of the flexibility of the peripheral stalk of prokaryotic rotary A-ATPases by atomistic simulations. Proteins 2016; 84:1203-12. [PMID: 27177595 PMCID: PMC4988496 DOI: 10.1002/prot.25066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/03/2016] [Accepted: 05/09/2016] [Indexed: 12/31/2022]
Abstract
Rotary ATPases are involved in numerous physiological processes, with the three distinct types (F/A/V‐ATPases) sharing functional properties and structural features. The basic mechanism involves the counter rotation of two motors, a soluble ATP hydrolyzing/synthesizing domain and a membrane‐embedded ion pump connected through a central rotor axle and a stator complex. Within the A/V‐ATPase family conformational flexibility of the EG stators has been shown to accommodate catalytic cycling and is considered to be important to function. For the A‐ATPase three EG structures have been reported, thought to represent conformational states of the stator during different stages of rotary catalysis. Here we use long, detailed atomistic simulations to show that those structures are conformers explored through thermal fluctuations, but do not represent highly populated states of the EG stator in solution. We show that the coiled coil tail domain has a high persistence length (∼100 nm), but retains the ability to adapt to different conformational states through the presence of two hinge regions. Moreover, the stator network of the related V‐ATPase has been suggested to adapt to subunit interactions in the collar region in addition to the nucleotide occupancy of the catalytic domain. The MD simulations reported here, reinforce this observation showing that the EG stators have enough flexibility to adapt to significantly different structural re‐arrangements and accommodate structural changes in the catalytic domain whilst resisting the large torque generated by catalytic cycling. These results are important to understand the role the stators play in the rotary‐ATPase mechanism. Proteins 2016; 84:1203–1212. © 2016 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Kostas Papachristos
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, England.,School of Molecular and Cellular Biology, University of Leeds, Leeds, England
| | - Stephen P Muench
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, England.,School of Biomedical Sciences, University of Leeds, Leeds, England
| | - Emanuele Paci
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, England.,School of Molecular and Cellular Biology, University of Leeds, Leeds, England
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193
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Chan CY, Dominguez D, Parra KJ. Regulation of Vacuolar H+-ATPase (V-ATPase) Reassembly by Glycolysis Flow in 6-Phosphofructo-1-kinase (PFK-1)-deficient Yeast Cells. J Biol Chem 2016; 291:15820-9. [PMID: 27226568 DOI: 10.1074/jbc.m116.717488] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Indexed: 01/21/2023] Open
Abstract
Yeast 6-phosphofructo-1-kinase (PFK-1) has two subunits, Pfk1p and Pfk2p. Deletion of Pfk2p alters glucose-dependent V-ATPase reassembly and vacuolar acidification (Chan, C. Y., and Parra, K. J. (2014) Yeast phosphofructokinase-1 subunit Pfk2p is necessary for pH homeostasis and glucose-dependent vacuolar ATPase reassembly. J. Biol. Chem. 289, 19448-19457). This study capitalized on the mechanisms suppressing vacuolar H(+)-ATPase (V-ATPase) in pfk2Δ to gain new knowledge of the mechanisms underlying glucose-dependent V-ATPase regulation. Because V-ATPase is fully assembled in pfk2Δ, and glycolysis partially suppressed at steady state, we manipulated glycolysis and assessed its direct involvement on V-ATPase function. At steady state, the ratio of proton transport to ATP hydrolysis increased 24% after increasing the glucose concentration from 2% to 4% to enhance the glycolysis flow in pfk2Δ. Tighter coupling restored vacuolar pH when glucose was abundant and glycolysis operated below capacity. After readdition of glucose to glucose-deprived cells, glucose-dependent V1Vo reassembly was proportional to the glycolysis flow. Readdition of 2% glucose to pfk2Δ cells, which restored 62% of ethanol concentration, led to equivalent 60% V1Vo reassembly levels. Steady-state level of assembly (100% reassembly) was reached at 4% glucose when glycolysis reached a threshold in pfk2Δ (≥40% the wild-type flow). At 4% glucose, the level of Pfk1p co-immunoprecipitated with V-ATPase decreased 58% in pfk2Δ, suggesting that Pfk1p binding to V-ATPase may be inhibitory in the mutant. We concluded that V-ATPase activity at steady state and V-ATPase reassembly after readdition of glucose to glucose-deprived cells are controlled by the glycolysis flow. We propose a new mechanism by which glucose regulates V-ATPase catalytic activity that occurs at steady state without changing V1Vo assembly.
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Affiliation(s)
- Chun-Yuan Chan
- From the Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131
| | - Dennis Dominguez
- From the Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131
| | - Karlett J Parra
- From the Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131
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194
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Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8124636. [PMID: 27274991 PMCID: PMC4870676 DOI: 10.1155/2016/8124636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/06/2016] [Indexed: 11/17/2022]
Abstract
Aspergillus oryzae is widely used for the industrial production of enzymes. In A. oryzae metabolism, transporters appear to play crucial roles in controlling the flux of molecules for energy generation, nutrients delivery, and waste elimination in the cell. While the A. oryzae genome sequence is available, transporter annotation remains limited and thus the connectivity of metabolic networks is incomplete. In this study, we developed a metabolic annotation strategy to understand the relationship between the sequence, structure, and function for annotation of A. oryzae metabolic transporters. Sequence-based analysis with manual curation showed that 58 genes of 12,096 total genes in the A. oryzae genome encoded metabolic transporters. Under consensus integrative databases, 55 unambiguous metabolic transporter genes were distributed into channels and pores (7 genes), electrochemical potential-driven transporters (33 genes), and primary active transporters (15 genes). To reveal the transporter functional role, a combination of homology modeling and molecular dynamics simulation was implemented to assess the relationship between sequence to structure and structure to function. As in the energy metabolism of A. oryzae, the H+-ATPase encoded by the AO090005000842 gene was selected as a representative case study of multilevel linkage annotation. Our developed strategy can be used for enhancing metabolic network reconstruction.
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195
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Goh BC, Hadden JA, Bernardi RC, Singharoy A, McGreevy R, Rudack T, Cassidy CK, Schulten K. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes. Annu Rev Biophys 2016; 45:253-78. [PMID: 27145875 DOI: 10.1146/annurev-biophys-062215-011113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving structural details across a range of spatiotemporal resolutions, computational hybrid methods have the unique ability to integrate the diverse data from multimodal techniques such as X-ray crystallography and electron microscopy into consistent, fully atomistic structures. Here, commonly employed strategies for computational real-space structural refinement are reviewed, and their specific applications are illustrated for several large macromolecular complexes: ribosome, virus capsids, chemosensory array, and photosynthetic chromatophore. The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed.
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Affiliation(s)
- Boon Chong Goh
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Jodi A Hadden
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Rafael C Bernardi
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Abhishek Singharoy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Ryan McGreevy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Till Rudack
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - C Keith Cassidy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Klaus Schulten
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801;
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196
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Couoh-Cardel S, Hsueh YC, Wilkens S, Movileanu L. Yeast V-ATPase Proteolipid Ring Acts as a Large-conductance Transmembrane Protein Pore. Sci Rep 2016; 6:24774. [PMID: 27098228 PMCID: PMC4838861 DOI: 10.1038/srep24774] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/04/2016] [Indexed: 12/12/2022] Open
Abstract
The vacuolar H+ -ATPase (V-ATPase) is a rotary motor enzyme that acidifies intracellular organelles and the extracellular milieu in some tissues. Besides its canonical proton-pumping function, V-ATPase’s membrane sector, Vo, has been implicated in non-canonical functions including membrane fusion and neurotransmitter release. Here, we report purification and biophysical characterization of yeast V-ATPase c subunit ring (c-ring) using electron microscopy and single-molecule electrophysiology. We find that yeast c-ring forms dimers mediated by the c subunits’ cytoplasmic loops. Electrophysiology measurements of the c-ring reconstituted into a planar lipid bilayer revealed a large unitary conductance of ~8.3 nS. Thus, the data support a role of V-ATPase c-ring in membrane fusion and neuronal communication.
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Affiliation(s)
- Sergio Couoh-Cardel
- Department of Biochemistry &Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210, USA
| | - Yi-Ching Hsueh
- Department of Physics, Syracuse University, 201 Physics Bldg., Syracuse, New York 13244-1130, USA
| | - Stephan Wilkens
- Department of Biochemistry &Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Bldg., Syracuse, New York 13244-1130, USA.,Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA.,The Syracuse Biomaterials Institute, Syracuse University, 318 Bowne Hall, Syracuse, New York 13244-1200, USA
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197
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Cotter K, Stransky L, McGuire C, Forgac M. Recent Insights into the Structure, Regulation, and Function of the V-ATPases. Trends Biochem Sci 2016; 40:611-622. [PMID: 26410601 DOI: 10.1016/j.tibs.2015.08.005] [Citation(s) in RCA: 211] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/06/2015] [Accepted: 08/07/2015] [Indexed: 10/23/2022]
Abstract
The vacuolar (H(+))-ATPases (V-ATPases) are ATP-dependent proton pumps that acidify intracellular compartments and are also present at the plasma membrane. They function in such processes as membrane traffic, protein degradation, virus and toxin entry, bone resorption, pH homeostasis, and tumor cell invasion. V-ATPases are large multisubunit complexes, composed of an ATP-hydrolytic domain (V1) and a proton translocation domain (V0), and operate by a rotary mechanism. This review focuses on recent insights into their structure and mechanism, the mechanisms that regulate V-ATPase activity (particularly regulated assembly and trafficking), and the role of V-ATPases in processes such as cell signaling and cancer. These developments have highlighted the potential of V-ATPases as a therapeutic target in a variety of human diseases.
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Affiliation(s)
- Kristina Cotter
- Program in Cellular and Molecular Physiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Laura Stransky
- Program in Cellular and Molecular Physiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Christina McGuire
- Program in Biochemistry, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Michael Forgac
- Program in Cellular and Molecular Physiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA; Program in Biochemistry, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA; Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA.
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198
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Rawson S, Iadanza MG, Ranson NA, Muench SP. Methods to account for movement and flexibility in cryo-EM data processing. Methods 2016; 100:35-41. [PMID: 27016144 PMCID: PMC4854228 DOI: 10.1016/j.ymeth.2016.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 12/02/2022] Open
Abstract
Recent advances in direct electron detectors and improved CMOS cameras have been accompanied by the development of a range of software to take advantage of the data they produce. In particular they allow for the correction of two types of motion in cryo electron microscopy samples: motion correction for movements of the sample particles in the ice, and differential masking to account for heterogeneity caused by flexibility within protein complexes. Here we provide several scripts that allow users to move between RELION and standalone motion correction and centring programs. We then compare the computational cost and improvements in data quality with each program. We also describe our masking procedures to account for conformational flexibility. For the different elements of this study we have used three samples; a high symmetry virus, flexible protein complex (∼1 MDa) and a relatively small protein complex (∼550 kDa), to benchmark four widely available motion correction packages. Using these as test cases we demonstrate how motion correction and differential masking, as well as an additional particle re-centring protocol can improve final reconstructions when used within the RELION image-processing package.
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Affiliation(s)
- S Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - M G Iadanza
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - N A Ranson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - S P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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199
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Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance. Proc Natl Acad Sci U S A 2016; 113:3245-50. [PMID: 26951669 DOI: 10.1073/pnas.1521990113] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the membrane-embedded a subunit. The V/A-ATPase from the eubacterium Thermus thermophilus is similar in structure to the eukaryotic V-ATPase but has a simpler subunit composition and functions in vivo to synthesize ATP rather than pump protons. We determined the T. thermophilus V/A-ATPase structure by cryo-EM at 6.4 Å resolution. Evolutionary covariance analysis allowed tracing of the a subunit sequence within the map, providing a complete model of the rotary ATPase. Comparing the membrane-embedded regions of the T. thermophilus V/A-ATPase and eukaryotic V-ATPase from Saccharomyces cerevisiae allowed identification of the α-helices that belong to the a subunit and revealed the existence of previously unknown subunits in the eukaryotic enzyme. Subsequent evolutionary covariance analysis enabled construction of a model of the a subunit in the S. cerevisae V-ATPase that explains numerous biochemical studies of that enzyme. Comparing the two a subunit structures determined here with a structure of the distantly related a subunit from the bovine F-type ATP synthase revealed a conserved pattern of residues, suggesting a common mechanism for proton transport in all rotary ATPases.
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200
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Rawson S, Davies S, Lippiat JD, Muench SP. The changing landscape of membrane protein structural biology through developments in electron microscopy. Mol Membr Biol 2016; 33:12-22. [PMID: 27608730 PMCID: PMC5206964 DOI: 10.1080/09687688.2016.1221533] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/14/2016] [Accepted: 07/19/2016] [Indexed: 11/30/2022]
Abstract
Membrane proteins are ubiquitous in biology and are key targets for therapeutic development. Despite this, our structural understanding has lagged behind that of their soluble counterparts. This review provides an overview of this important field, focusing in particular on the recent resurgence of electron microscopy (EM) and the increasing role it has to play in the structural studies of membrane proteins, and illustrating this through several case studies. In addition, we examine some of the challenges remaining in structural determination, and what steps are underway to enhance our knowledge of these enigmatic proteins.
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Affiliation(s)
- Shaun Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds,
Leeds,
UK
| | - Simon Davies
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds,
Leeds,
UK
| | - Jonathan D. Lippiat
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds,
Leeds,
UK
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds,
Leeds,
UK
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