1
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Vuillemot R, Rouiller I, Jonić S. MDTOMO method for continuous conformational variability analysis in cryo electron subtomograms based on molecular dynamics simulations. Sci Rep 2023; 13:10596. [PMID: 37391578 PMCID: PMC10313669 DOI: 10.1038/s41598-023-37037-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/14/2023] [Indexed: 07/02/2023] Open
Abstract
Cryo electron tomography (cryo-ET) allows observing macromolecular complexes in their native environment. The common routine of subtomogram averaging (STA) allows obtaining the three-dimensional (3D) structure of abundant macromolecular complexes, and can be coupled with discrete classification to reveal conformational heterogeneity of the sample. However, the number of complexes extracted from cryo-ET data is usually small, which restricts the discrete-classification results to a small number of enough populated states and, thus, results in a largely incomplete conformational landscape. Alternative approaches are currently being investigated to explore the continuity of the conformational landscapes that in situ cryo-ET studies could provide. In this article, we present MDTOMO, a method for analyzing continuous conformational variability in cryo-ET subtomograms based on Molecular Dynamics (MD) simulations. MDTOMO allows obtaining an atomic-scale model of conformational variability and the corresponding free-energy landscape, from a given set of cryo-ET subtomograms. The article presents the performance of MDTOMO on a synthetic ABC exporter dataset and an in situ SARS-CoV-2 spike dataset. MDTOMO allows analyzing dynamic properties of molecular complexes to understand their biological functions, which could also be useful for structure-based drug discovery.
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Affiliation(s)
- Rémi Vuillemot
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, CC 115, 4 Place Jussieu, 75005, Paris, France
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Isabelle Rouiller
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Australian Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins, Parkville, VIC, 3052, Australia
| | - Slavica Jonić
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, CC 115, 4 Place Jussieu, 75005, Paris, France.
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2
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Valimehr S, Sethi A, Shukla M, Bhattacharyya S, Kazemi M, Rouiller I. Molecular Mechanisms Driving and Regulating the AAA+ ATPase VCP/p97, an Important Therapeutic Target for Treating Cancer, Neurological and Infectious Diseases. Biomolecules 2023; 13:biom13050737. [PMID: 37238606 DOI: 10.3390/biom13050737] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/15/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023] Open
Abstract
p97/VCP, a highly conserved type II ATPase associated with diverse cellular activities (AAA+ ATPase), is an important therapeutic target in the treatment of neurodegenerative diseases and cancer. p97 performs a variety of functions in the cell and facilitates virus replication. It is a mechanochemical enzyme that generates mechanical force from ATP-binding and hydrolysis to perform several functions, including unfolding of protein substrates. Several dozens of cofactors/adaptors interact with p97 and define the multifunctionality of p97. This review presents the current understanding of the molecular mechanism of p97 during the ATPase cycle and its regulation by cofactors and small-molecule inhibitors. We compare detailed structural information obtained in different nucleotide states in the presence and absence of substrates and inhibitors. We also review how pathogenic gain-of-function mutations modify the conformational changes of p97 during the ATPase cycle. Overall, the review highlights how the mechanistic knowledge of p97 helps in designing pathway-specific modulators and inhibitors.
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Affiliation(s)
- Sepideh Valimehr
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Ian Holmes Imaging Centre, Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Ashish Sethi
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- Australian Nuclear Science Technology Organisation, The Australian Synchrotron, 800 Blackburn Rd, Clayton, VIC 3168, Australia
| | - Manjari Shukla
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Jodhpur 342030, Rajasthan, India
| | - Sudipta Bhattacharyya
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Jodhpur 342030, Rajasthan, India
| | - Mohsen Kazemi
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Isabelle Rouiller
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, The University of Melbourne, Melbourne, VIC 3010, Australia
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3
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Vuillemot R, Mirzaei A, Harastani M, Hamitouche I, Fréchin L, Klaholz BP, Miyashita O, Tama F, Rouiller I, Jonic S. MDSPACE: Extracting Continuous Conformational Landscapes from Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation. J Mol Biol 2023; 435:167951. [PMID: 36638910 DOI: 10.1016/j.jmb.2023.167951] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/08/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
This article presents an original approach for extracting atomic-resolution landscapes of continuous conformational variability of biomolecular complexes from cryo electron microscopy (cryo-EM) single particle images. This approach is based on a new 3D-to-2D flexible fitting method, which uses molecular dynamics (MD) simulation and is embedded in an iterative conformational-landscape refinement scheme. This new approach is referred to as MDSPACE, which stands for Molecular Dynamics simulation for Single Particle Analysis of Continuous Conformational hEterogeneity. The article describes the MDSPACE approach and shows its performance using synthetic and experimental datasets.
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Affiliation(s)
- Rémi Vuillemot
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France; Department of Biochemistry & Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Alex Mirzaei
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Mohamad Harastani
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Ilyes Hamitouche
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
| | - Léo Fréchin
- Centre for Integrative Biology, Department of Integrated Structural Biology, IGBMC-UMR 7104 CNRS, U964 Inserm, Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology, Department of Integrated Structural Biology, IGBMC-UMR 7104 CNRS, U964 Inserm, Université de Strasbourg, Strasbourg, France
| | | | - Florence Tama
- RIKEN Center for Computational Science, Kobe, Japan; Institute of Transformative Biomolecules, Graduate School of Science, Nagoya University, Nagoya, Japan; Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Isabelle Rouiller
- Department of Biochemistry & Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Slavica Jonic
- IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France.
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Mirzadeh A, Kobakhidze G, Vuillemot R, Jonic S, Rouiller I. In silico prediction, characterization, docking studies and molecular dynamics simulation of human p97 in complex with p37 cofactor. BMC Mol Cell Biol 2022; 23:39. [PMID: 36088301 PMCID: PMC9464413 DOI: 10.1186/s12860-022-00437-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/13/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The AAA + ATPase p97 is an essential unfoldase/segragase involved in a multitude of cellular processes. It functions as a molecular machine critical for protein homeostasis, homotypic membrane fusion events and organelle biogenesis during mitosis in which it acts in concert with cofactors p47 and p37. Cofactors assist p97 in extracting and unfolding protein substrates through ATP hydrolysis. In contrast to other p97ʼs cofactors, p37 uniquely increases the ATPase activity of p97. Disease-causing mutations in p97, including mutations that cause neurodegenerative diseases, increase cofactor association with its N-domain, ATPase activity and improper substrate processing. Upregulation of p97 has also been observed in various cancers. This study aims towards the characterization of the protein–protein interaction between p97 and p37 at the atomic level. We defined the interacting residues in p97 and p37. The knowledge will facilitate the design of unique small molecules inhibiting this interaction with insights into cancer therapy and drug design.
Results
The homology model of human p37 UBX domain was built from the X-ray crystal structure of p47 C-terminus from rat (PDB code:1S3S, G) as a template and assessed by model validation analysis. According to the HDOCK, HAWKDOCK, MM-GBSA binding free energy calculations and Arpeggio, we found that there are several hydrophobic and two hydrogen-bonding interactions between p37 UBX and p97 N-D1 domain. Residues of p37 UBX predicted to be involved in the interactions with p97 N-D1 domain interface are highly conserved among UBX cofactors.
Conclusion
This study provides a reliable structural insight into the p37-p97 complex binding sites at the atomic level though molecular docking coupled with molecular dynamics simulation. This can guide the rational design of small molecule drugs for inhibiting mutant p97 activity.
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Heydarchi B, Fong DS, Gao H, Salazar-Quiroz NA, Edwards JM, Gonelli CA, Grimley S, Aktepe TE, Mackenzie C, Wales WJ, van Gils MJ, Cupo A, Rouiller I, Gooley PR, Moore JP, Sanders RW, Montefiori D, Sethi A, Purcell DFJ. Broad and ultra-potent cross-clade neutralization of HIV-1 by a vaccine-induced CD4 binding site bovine antibody. Cell Rep Med 2022; 3:100635. [PMID: 35584627 PMCID: PMC9133467 DOI: 10.1016/j.xcrm.2022.100635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/27/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) vaccination of cows has elicited broadly neutralizing antibodies (bNAbs). In this study, monoclonal antibodies (mAbs) are isolated from a clade A (KNH1144 and BG505) vaccinated cow using a heterologous clade B antigen (AD8). CD4 binding site (CD4bs) bNAb (MEL-1872) is more potent than a majority of CD4bs bNAbs isolated so far. MEL-1872 mAb with CDRH3 of 57 amino acids shows more potency (geometric mean half-maximal inhibitory concentration [IC50]: 0.009 μg/mL; breadth: 66%) than VRC01 against clade B viruses (29-fold) and than CHO1-31 against tested clade A viruses (21-fold). It also shows more breadth and potency than NC-Cow1, the only other reported anti-HIV-1 bovine bNAb, which has 60% breadth with geometric mean IC50 of 0.090 μg/mL in this study. Using successive different stable-structured SOSIP trimers in bovines can elicit bNAbs focusing on epitopes ubiquitous across subtypes. Furthermore, the cross-clade selection strategy also results in ultra-potent bNAbs. Sequential vaccine with different SOSIP trimers could elicit bNAbs Cross-clade B-cell-sorting probe could select ultra-potent bNAbs Bovine CD4bs monoclonal antibody neutralizes HIV-1 isolates potently
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Affiliation(s)
- Behnaz Heydarchi
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Danielle S Fong
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Hongmei Gao
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Natalia A Salazar-Quiroz
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Jack M Edwards
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Christopher A Gonelli
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Samantha Grimley
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Turgut E Aktepe
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Charlene Mackenzie
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - William J Wales
- Dairy Production Sciences, Victorian Department of Jobs, Precincts and Resources, Ellinbank, VIC, Australia; Centre for Agricultural Innovation, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, the Netherlands
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Isabelle Rouiller
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia; Australian Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins, Parkville, VIC, Australia
| | - Paul R Gooley
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - David Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Ashish Sethi
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Damian F J Purcell
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia.
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6
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Kobakhidze G, Sethi A, Valimehr S, Ralph SA, Rouiller I. The AAA+ ATPase p97 as a novel parasite and tuberculosis drug target. Trends Parasitol 2022; 38:572-590. [DOI: 10.1016/j.pt.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 10/18/2022]
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7
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Vuillemot R, Miyashita O, Tama F, Rouiller I, Jonic S. NMMD: Efficient cryo-EM flexible fitting based on simultaneous Normal Mode and Molecular Dynamics atomic displacements. J Mol Biol 2022; 434:167483. [PMID: 35150654 DOI: 10.1016/j.jmb.2022.167483] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/18/2022] [Accepted: 01/31/2022] [Indexed: 11/28/2022]
Abstract
Atomic models of cryo electron microscopy (cryo-EM) maps of biomolecular conformations are often obtained by flexible fitting of the maps with available atomic structures of other conformations (e.g., obtained by X-ray crystallography). This article presents a new flexible fitting method, NMMD, which combines normal mode analysis (NMA) and molecular dynamics simulation (MD). Given an atomic structure and a cryo-EM map to fit, NMMD simultaneously estimates global atomic displacements based on NMA and local displacements based on MD. NMMD was implemented by modifying EMfit, a flexible fitting method using MD only, in GENESIS 1.4. As EMfit, NMMD can be run with replica exchange umbrella sampling procedure. The new method was tested using a variety of EM maps (synthetic and experimental, with different noise levels and resolutions). The results of the tests show that adding normal modes to MD-based fitting makes the fitting faster (40% in average) and, in the majority of cases, more accurate.
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Affiliation(s)
- Rémi Vuillemot
- IMPMC - UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
| | | | - Florence Tama
- Institute of Transformative Biomolecules and Department of Physics, Graduate School of Science, Nagoya University, Japan
| | - Isabelle Rouiller
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
| | - Slavica Jonic
- IMPMC - UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France.
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Fabre L, Ntreh AT, Yazidi A, Leus IV, Weeks JW, Bhattacharyya S, Ruickoldt J, Rouiller I, Zgurskaya HI, Sygusch J. A "Drug Sweeping" State of the TriABC Triclosan Efflux Pump from Pseudomonas aeruginosa. Structure 2020; 29:261-274.e6. [PMID: 32966762 DOI: 10.1016/j.str.2020.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/30/2020] [Accepted: 08/29/2020] [Indexed: 12/01/2022]
Abstract
The structure of the TriABC inner membrane component of the triclosan/SDS-specific efflux pump from Pseudomonas aeruginosa was determined by cryoelectron microscopy to 4.5 Å resolution. The complete structure of the inner membrane transporter TriC of the resistance-nodulation-division (RND) superfamily was solved, including a partial structure of the fused periplasmic membrane fusion subunits, TriA and TriB. The substrate-free conformation of TriABC represents an intermediate step in efflux complex assembly before the engagement of the outer membrane channel. Structural analysis identified a tunnel network whose constriction impedes substrate efflux, indicating inhibition of TriABC in the unengaged state. Blind docking studies revealed binding to TriC at the same loci by substrates and bulkier non-substrates. Together with functional analyses, we propose that selective substrate translocation involves conformational gating at the tunnel narrowing that, together with conformational ordering of TriA and TriB, creates an engaged state capable of mediating substrate efflux.
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Affiliation(s)
- Lucien Fabre
- McGill University, Department of Anatomy and Cell Biology, Montreal, QC H3A 0G4, Canada
| | - Abigail T Ntreh
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Amira Yazidi
- University of Montreal, Department of Biochemistry and Molecular Medicine, Medicine, CP 6128, Station Centre-ville, Montreal, QC H3C 3J7, Canada
| | - Inga V Leus
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Jon W Weeks
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Sudipta Bhattacharyya
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, India
| | - Jakob Ruickoldt
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Isabelle Rouiller
- McGill University, Department of Anatomy and Cell Biology, Montreal, QC H3A 0G4, Canada; Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Helen I Zgurskaya
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA.
| | - Jurgen Sygusch
- University of Montreal, Department of Biochemistry and Molecular Medicine, Medicine, CP 6128, Station Centre-ville, Montreal, QC H3C 3J7, Canada.
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Alsahafi N, Bakouche N, Kazemi M, Richard J, Ding S, Bhattacharyya S, Das D, Anand SP, Prévost J, Tolbert WD, Lu H, Medjahed H, Gendron-Lepage G, Ortega Delgado GG, Kirk S, Melillo B, Mothes W, Sodroski J, Smith AB, Kaufmann DE, Wu X, Pazgier M, Rouiller I, Finzi A, Munro JB. An Asymmetric Opening of HIV-1 Envelope Mediates Antibody-Dependent Cellular Cytotoxicity. Cell Host Microbe 2019; 25:578-587.e5. [PMID: 30974085 DOI: 10.1016/j.chom.2019.03.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/03/2018] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
Abstract
The HIV-1 envelope glycoprotein (Env) (gp120-gp41)3 is the target for neutralizing antibodies and antibody-dependent cellular cytotoxicity (ADCC). HIV-1 Env is flexible, sampling different conformational states. Before engaging CD4, Env adopts a closed conformation (State 1) that is largely antibody resistant. CD4 binding induces an intermediate state (State 2), followed by an open conformation (State 3) that is susceptible to engagement by antibodies that recognize otherwise occluded epitopes. We investigate conformational changes in Env that induce ADCC in the presence of a small-molecule CD4-mimetic compound (CD4mc). We uncover an asymmetric Env conformation (State 2A) recognized by antibodies targeting the conserved gp120 inner domain and mediating ADCC. Sera from HIV+ individuals contain these antibodies, which can stabilize Env State 2A in combination with CD4mc. Additionally, triggering State 2A on HIV-infected primary CD4+ T cells exposes epitopes that induce ADCC. Strategies that induce this Env conformation may represent approaches to fight HIV-1 infection.
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Affiliation(s)
- Nirmin Alsahafi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Nordine Bakouche
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Mohsen Kazemi
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Sudipta Bhattacharyya
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Durba Das
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Sai Priya Anand
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - William D Tolbert
- Infectious Diseases Division, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Hong Lu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, USA
| | | | | | | | - Sharon Kirk
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Bruno Melillo
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Amos B Smith
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Department of Medicine, Université de Montréal, Montreal, QC, Canada; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, USA
| | - Marzena Pazgier
- Infectious Diseases Division, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Isabelle Rouiller
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada.
| | - James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
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10
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Carlson ML, Young JW, Zhao Z, Fabre L, Jun D, Li J, Li J, Dhupar HS, Wason I, Mills AT, Beatty JT, Klassen JS, Rouiller I, Duong F. The Peptidisc, a simple method for stabilizing membrane proteins in detergent-free solution. eLife 2018; 7:34085. [PMID: 30109849 PMCID: PMC6093710 DOI: 10.7554/elife.34085] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/05/2018] [Indexed: 12/15/2022] Open
Abstract
Membrane proteins are difficult to work with due to their insolubility in aqueous solution and quite often their poor stability in detergent micelles. Here, we present the peptidisc for their facile capture into water-soluble particles. Unlike the nanodisc, which requires scaffold proteins of different lengths and precise amounts of matching lipids, reconstitution of detergent solubilized proteins in peptidisc only requires a short amphipathic bi-helical peptide (NSPr) and no extra lipids. Multiple copies of the peptide wrap around to shield the membrane-exposed part of the target protein. We demonstrate the effectiveness of this ‘one size fits all’ method using five different membrane protein assemblies (MalFGK2, FhuA, SecYEG, OmpF, BRC) during ‘on-column’, ‘in-gel’, and ‘on-bead’ reconstitution embedded within the membrane protein purification protocol. The peptidisc method is rapid and cost-effective, and it may emerge as a universal tool for high-throughput stabilization of membrane proteins to advance modern biological studies. Surrounding every living cell is a biological membrane that is largely impermeable to water-soluble molecules. This hydrophobic (or “water-hating”) barrier preserves the contents of the cell and also regulates how the cell interacts with its environment. This latter function is critical and relies on a class of proteins that are embedded within the membrane and are also hydrophobic. The hydrophobic nature of membrane proteins is however inconvenient for biochemical studies which usually take place in water-based solutions. Therefore, membrane proteins are under-represented in biological research compared to the water-soluble ones, even though roughly one quarter of a cell’s proteins are membrane proteins. Researchers have developed a few tricks to keep membrane proteins soluble after they have been extracted from the membrane. An old but popular technique makes use of detergents, which are chemicals with opposing hydrophobic and hydrophilic properties (hydrophilic literally means “water-loving”). However, even mild detergents can damage membrane proteins and will sometimes lead to experimental artifacts. More recent tricks to stabilize membrane proteins without detergents have been described but remain laborious, costly or difficult to perform. To overcome these limitations, Carlson et al. developed a simple method to stabilize membrane proteins without detergent. Called the “peptidisc”, the method uses multiple copies of a unique peptide – a short sequence of the building blocks of protein – that had been redesigned to have optimal hydrophobic and hydrophilic properties. The idea was that the peptides would wrap around the hydrophobic parts of the membrane protein, and shield them from the watery solution. Indeed, when Carlson et al. mixed this peptide with five different membrane proteins from bacteria, all were perfectly soluble and functional without detergent. The ideal ratio of peptide needed to form a peptidisc around each membrane protein was reached automatically, without having to test many different conditions. This indicates that the peptidisc acts like a “one size fits all” scaffold. The peptidisc is a new tool that will allow more researchers, including those who are not expert biochemists, to study membrane proteins. This will yield a better understanding of the structure of a cell’s membrane and how it interacts with the environment. Since the approach is both simple and easy to apply, more membrane proteins can now also be included in high-throughput searches for potential new drugs for various medical conditions.
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Affiliation(s)
- Michael Luke Carlson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - John William Young
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Lucien Fabre
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Daniel Jun
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Jianing Li
- Glycomics Centre and Department of Chemistry, University of Alberta, Alberta, Canada
| | - Jun Li
- Glycomics Centre and Department of Chemistry, University of Alberta, Alberta, Canada
| | - Harveer Singh Dhupar
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Irvin Wason
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Allan T Mills
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - John S Klassen
- Glycomics Centre and Department of Chemistry, University of Alberta, Alberta, Canada
| | - Isabelle Rouiller
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
| | - Franck Duong
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
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11
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McLelland GL, Goiran T, Yi W, Dorval G, Chen CX, Lauinger ND, Krahn AI, Valimehr S, Rakovic A, Rouiller I, Durcan TM, Trempe JF, Fon EA. Mfn2 ubiquitination by PINK1/parkin gates the p97-dependent release of ER from mitochondria to drive mitophagy. eLife 2018; 7:32866. [PMID: 29676259 PMCID: PMC5927771 DOI: 10.7554/elife.32866] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/19/2018] [Indexed: 12/23/2022] Open
Abstract
Despite their importance as signaling hubs, the function of mitochondria-ER contact sites in mitochondrial quality control pathways remains unexplored. Here we describe a mechanism by which Mfn2, a mitochondria-ER tether, gates the autophagic turnover of mitochondria by PINK1 and parkin. Mitochondria-ER appositions are destroyed during mitophagy, and reducing mitochondria-ER contacts increases the rate of mitochondrial degradation. Mechanistically, parkin/PINK1 catalyze a rapid burst of Mfn2 phosphoubiquitination to trigger p97-dependent disassembly of Mfn2 complexes from the outer mitochondrial membrane, dissociating mitochondria from the ER. We additionally demonstrate that a major portion of the facilitatory effect of p97 on mitophagy is epistatic to Mfn2 and promotes the availability of other parkin substrates such as VDAC1. Finally, we reconstitute the action of these factors on Mfn2 and VDAC1 ubiquitination in a cell-free assay. We show that mitochondria-ER tethering suppresses mitophagy and describe a parkin-/PINK1-dependent mechanism that regulates the destruction of mitochondria-ER contact sites.
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Affiliation(s)
- Gian-Luca McLelland
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Thomas Goiran
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Wei Yi
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Geneviève Dorval
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada.,iPSC-CRISPR Platform, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Carol X Chen
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada.,iPSC-CRISPR Platform, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Nadine D Lauinger
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada.,iPSC-CRISPR Platform, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Andrea I Krahn
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Sepideh Valimehr
- Department of Anatomy & Cell Biology, McGill University, Montreal, Canada
| | | | - Isabelle Rouiller
- Department of Anatomy & Cell Biology, McGill University, Montreal, Canada
| | - Thomas M Durcan
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada.,iPSC-CRISPR Platform, Montreal Neurological Institute, McGill University, Montreal, Canada
| | | | - Edward A Fon
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada.,Neurodegenerative Diseases Group, Montreal Neurological Institute, McGill University, Montreal, Canada.,iPSC-CRISPR Platform, Montreal Neurological Institute, McGill University, Montreal, Canada
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12
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Fabre L, Santelli E, Mountassif D, Donoghue A, Biswas A, Blunck R, Hanein D, Volkmann N, Liddington R, Rouiller I. Structure of anthrax lethal toxin prepore complex suggests a pathway for efficient cell entry. J Gen Physiol 2017; 148:313-24. [PMID: 27670897 PMCID: PMC5037343 DOI: 10.1085/jgp.201611617] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/25/2016] [Indexed: 01/20/2023] Open
Abstract
Anthrax toxin comprises three soluble proteins: protective antigen (PA), lethal factor (LF), and edema factor (EF). PA must be cleaved by host proteases before it oligomerizes and forms a prepore, to which LF and EF bind. After endocytosis of this tripartite complex, the prepore transforms into a narrow transmembrane pore that delivers unfolded LF and EF into the host cytosol. Here, we find that translocation of multiple 90-kD LF molecules is rapid and efficient. To probe the molecular basis of this translocation, we calculated a three-dimensional map of the fully loaded (PA63)7-(LF)3 prepore complex by cryo-electron microscopy (cryo-EM). The map shows three LFs bound in a similar way to one another, via their N-terminal domains, to the surface of the PA heptamer. The model also reveals contacts between the N- and C-terminal domains of adjacent LF molecules. We propose that this molecular arrangement plays an important role in the maintenance of translocation efficiency through the narrow PA pore.
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Affiliation(s)
- Lucien Fabre
- Department of Anatomy and Cell Biology, McGill University, Montréal, Québec H3A 0C7, Canada Groupe de Recherche Axé sur la Structure des Protéines (GRASP), Groupe d'Étude des Protéines Membranaires (GÉPROM), McGill University, Montréal, Québec H3A 0C7, Canada
| | - Eugenio Santelli
- Bioinformatics and Structural Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Driss Mountassif
- Department of Anatomy and Cell Biology, McGill University, Montréal, Québec H3A 0C7, Canada Groupe de Recherche Axé sur la Structure des Protéines (GRASP), Groupe d'Étude des Protéines Membranaires (GÉPROM), McGill University, Montréal, Québec H3A 0C7, Canada
| | - Annemarie Donoghue
- Departments of Physics, Université de Montréal, Montréal, Québec H3T 1J4, Canada Department of Physiology, Université de Montréal, Montréal, Québec H3T 1J4, Canada Groupe d'Étude des Protéines Membranaires (GÉPROM), Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Aviroop Biswas
- Department of Anatomy and Cell Biology, McGill University, Montréal, Québec H3A 0C7, Canada Groupe de Recherche Axé sur la Structure des Protéines (GRASP), Groupe d'Étude des Protéines Membranaires (GÉPROM), McGill University, Montréal, Québec H3A 0C7, Canada
| | - Rikard Blunck
- Departments of Physics, Université de Montréal, Montréal, Québec H3T 1J4, Canada Department of Physiology, Université de Montréal, Montréal, Québec H3T 1J4, Canada Groupe d'Étude des Protéines Membranaires (GÉPROM), Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Dorit Hanein
- Bioinformatics and Structural Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Niels Volkmann
- Bioinformatics and Structural Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Robert Liddington
- Bioinformatics and Structural Biology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Isabelle Rouiller
- Department of Anatomy and Cell Biology, McGill University, Montréal, Québec H3A 0C7, Canada Groupe de Recherche Axé sur la Structure des Protéines (GRASP), Groupe d'Étude des Protéines Membranaires (GÉPROM), McGill University, Montréal, Québec H3A 0C7, Canada
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13
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Remoué A, Flavien B, Dessomme B, Caillon J, Boutoille D, Rouiller I, Huon J, Navas D. Revue de pertinence des prescriptions de carbapénèmes au sein d’un centre hospitalo-universitaire. Med Mal Infect 2017. [DOI: 10.1016/j.medmal.2017.03.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Fabre L, Bao H, Innes J, Duong F, Rouiller I. Negative Stain Single-particle EM of the Maltose Transporter in Nanodiscs Reveals Asymmetric Closure of MalK 2 and Catalytic Roles of ATP, MalE, and Maltose. J Biol Chem 2017; 292:5457-5464. [PMID: 28188291 DOI: 10.1074/jbc.m116.757898] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 02/08/2017] [Indexed: 12/26/2022] Open
Abstract
The Escherichia coli MalE-MalFGK2 complex is one of the best characterized members of the large and ubiquitous family of ATP-binding cassette (ABC) transporters. It is composed of a membrane-spanning heterodimer, MalF-MalG; a homodimeric ATPase, MalK2; and a periplasmic maltose receptor, MalE. Opening and closure of MalK2 is coupled to conformational changes in MalF-MalG and the alternate exposition of the substrate-binding site to either side of the membrane. To further define this alternate access mechanism and the impact of ATP, MalE, and maltose on the conformation of the transporter during the transport cycle, we have reconstituted MalFGK2 in nanodiscs and analyzed its conformations under 10 different biochemical conditions using negative stain single-particle EM. EM map results (at 15-25 Å resolution) indicate that binding of ATP to MalK2 promotes an asymmetric, semi-closed conformation in accordance with the low ATPase activity of MalFGK2 In the presence of MalE, the MalK dimer becomes fully closed, gaining the ability to hydrolyze ATP. In the presence of ADP or maltose, MalE·MalFGK2 remains essentially in a semi-closed symmetric conformation, indicating that release of these ligands is required for the return to the initial state. Taken together, this structural information provides a rationale for the stimulation of MalK ATPase activity by MalE as well as by maltose.
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Affiliation(s)
- Lucien Fabre
- From the Department of Anatomy and Cell Biology, Groupe de Recherche Axé sur la Structure des Protéines, Groupe d'Étude des Protéines Membranaires, McGill University, Montreal, Quebec H3A 2B2, Canada and
| | - Huan Bao
- the Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - James Innes
- From the Department of Anatomy and Cell Biology, Groupe de Recherche Axé sur la Structure des Protéines, Groupe d'Étude des Protéines Membranaires, McGill University, Montreal, Quebec H3A 2B2, Canada and
| | - Franck Duong
- the Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Isabelle Rouiller
- From the Department of Anatomy and Cell Biology, Groupe de Recherche Axé sur la Structure des Protéines, Groupe d'Étude des Protéines Membranaires, McGill University, Montreal, Quebec H3A 2B2, Canada and
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15
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Belardinelli JM, Yazidi A, Yang L, Fabre L, Li W, Jacques B, Angala SK, Rouiller I, Zgurskaya HI, Sygusch J, Jackson M. Structure-Function Profile of MmpL3, the Essential Mycolic Acid Transporter from Mycobacterium tuberculosis. ACS Infect Dis 2016; 2:702-713. [PMID: 27737557 DOI: 10.1021/acsinfecdis.6b00095] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The MmpL family of proteins translocates complex (glyco)lipids and siderophores across the cell envelope of mycobacteria and closely related Corynebacteriaceae and plays important roles in the biogenesis of the outer membrane of these organisms. Despite their significance in the physiology and virulence of Mycobacterium tuberculosis, and from the perspective of developing novel antituberculosis agents, little is known about their structure and mechanism of translocation. In this study, the essential mycobacterial mycolic acid transporter, MmpL3, and its orthologue in Corynebacterium glutamicum, CmpL1, were investigated as prototypical MmpL proteins to gain insight into the transmembrane topology, tertiary and quaternary structures, and functional regions of this transporter family. The combined genetic, biochemical, and biophysical studies indicate that MmpL3 and CmpL1 are structurally similar to Gram-negative resistance-nodulation and division efflux pumps. They harbor 12 transmembrane segments interrupted by two large soluble periplasmic domains and function as homotrimers to export long-chain (C22-C90) mycolic acids, possibly in their acetylated form, esterified to trehalose. The mapping of a number of functional residues within the middle region of the transmembrane domain of MmpL3 shows a striking overlap with mutations associated with resistance to MmpL3 inhibitors. The results suggest that structurally diverse inhibitors of MmpL3 all target the proton translocation path of the transporter and that multiresistance to these inhibitors is enabled by conformational changes in MmpL3.
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Affiliation(s)
- Juan Manuel Belardinelli
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Amira Yazidi
- Biochimie et Médecine Moléculaire, Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
- Groupe d’Étude des Protéines Membranaires
(GÉPROM), Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
| | - Liang Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Lucien Fabre
- Groupe d’Étude des Protéines Membranaires
(GÉPROM), Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, Quebec H3A 2B2, Canada
| | - Wei Li
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Benoit Jacques
- Biochimie et Médecine Moléculaire, Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
| | - Shiva kumar Angala
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Isabelle Rouiller
- Groupe d’Étude des Protéines Membranaires
(GÉPROM), Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
- Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, Quebec H3A 2B2, Canada
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Jurgen Sygusch
- Biochimie et Médecine Moléculaire, Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
- Groupe d’Étude des Protéines Membranaires
(GÉPROM), Université de Montréal, CP 6128, Station Centre-Ville, Montréal, Quebec H3C 3J7, Canada
| | - Mary Jackson
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
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16
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Mountassif D, Fabre L, Zaid Y, Halawani D, Rouiller I. Cryo-EM of the pathogenic VCP variant R155P reveals long-range conformational changes in the D2 ATPase ring. Biochem Biophys Res Commun 2015; 468:636-41. [PMID: 26549226 DOI: 10.1016/j.bbrc.2015.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/02/2015] [Indexed: 11/25/2022]
Abstract
Single amino acid mutations in valosin containing protein (VCP/p97), a highly conserved member of the ATPases associated with diverse cellular activities (AAA) family of ATPases has been linked to a severe degenerative disease affecting brain, muscle and bone tissue. Previous studies have demonstrated the role of VCP mutations in altering the ATPase activity of the D2 ring; however the structural consequences of these mutations remain unclear. In this study, we report the three-dimensional (3D) map of the pathogenic VCP variant, R155P, as revealed by single-particle Cryo-Electron Microscopy (EM) analysis at 14 Å resolution. We show that the N-terminal R155P mutation induces a large structural reorganisation of the D2 ATPase ring. Results from docking studies using crystal structure data of available wild-type VCP in the EM density maps indicate that the major difference is localized at the interface between two protomers within the D2 ring. Consistent with a conformational change, the VCP R155P variant shifted the isoelectric point of the protein and reduced its interaction with its well-characterized cofactor, nuclear protein localization-4 (Npl4). Together, our results demonstrate that a single amino acid substitution in the N-terminal domain can relay long-range conformational changes to the distal D2 ATPase ring. Our results provide the first structural clues of how VCP mutations may influence the activity and function of the D2 ATPase ring.
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Affiliation(s)
- Driss Mountassif
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada
| | - Lucien Fabre
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada
| | - Younes Zaid
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada; Current address: Laboratory of Thrombosis and Hemostasis, Montreal Heart Institute, Montreal, Quebec, Canada
| | - Dalia Halawani
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada; Current address: Department of Cell Biology, Lerner Research Institute, 9500 Euclid Avenue NC10, Cleveland, OH 44195, USA
| | - Isabelle Rouiller
- Department of Anatomy and Cell Biology, McGill University, Groupe de recherche axé sur la structure des protéines (GRASP), Groupe d'Étude des Proteines Membranaires (GÉPROM), 3640 University Street, Montreal H3A 0C7, Canada.
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17
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Kalynych S, Cherney M, Bostina M, Rouiller I, Cygler M. Quaternary structure of WzzB and WzzE polysaccharide copolymerases. Protein Sci 2014; 24:58-69. [PMID: 25307743 DOI: 10.1002/pro.2586] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/06/2014] [Accepted: 10/09/2014] [Indexed: 01/02/2023]
Abstract
Bacteria have evolved cellular control mechanisms to ensure proper length specification for surface-bound polysaccharides. Members of the Polysaccharide Copolymerase (PCP) family are central to this process. PCP-1 family members are anchored to the inner membrane through two transmembrane helices and contain a large periplasm-exposed domain. PCPs are known to form homooligomers but their exact stoichiometry is controversial in view of conflicting structural and biochemical data. Several prior investigations addressing this question indicated a nonameric, hexameric, or tetrameric organization of several PCP-1 family members. In this work, we gathered additional evidence that E.coli WzzB and WzzE PCPs form octameric homo-oligomeric complexes. Detergent-solubilized PCPs were purified to homogeneity and subjected to blue native gel analysis, which indicated the presence of a predominant high-molecular product of over 500 kDa in mass. Molecular mass of WzzE and WzzB-detergent oligomers was estimated to be 550 kDA by size-exclusion coupled to multiangle laser light scattering (SEC-MALLS). Oligomeric organization of purified WzzB and WzzE was further investigated by negative stain electron microscopy and by X-ray crystallography, respectively. Analysis of EM-derived molecular envelope of WzzB indicated that the full-length protein is composed of eight protomers. Crystal structure of LDAO-solubilized WzzE was solved to 6 Å resolutions and revealed its octameric subunit stoichiometry. In summary, we identified a possible biological unit utilized for the glycan chain length determination by two PCP-1 family members. This provides an important step toward further unraveling of the mechanistic basis of chain length control of the O-antigen and the enterobacterial common antigen.
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Affiliation(s)
- Sergei Kalynych
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
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18
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Mountassif D, Fabre L, Basu K, Bostina M, Jonic S, Rouiller I. Conformational heterogeneity of the AAA ATPase p97 characterized by single particle cryo-EM. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314091463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
p97, a member of the AAA (ATPase Associated with various Activities) ATPase family, is essential and centrally involved in a wide variety of cellular processes. Single amino-acid substitutions in p97 have been associated with the severe degenerative disorder of Inclusion Body Myopathy associated with Paget disease of bone and Frontotemporal Dementia (IBMPFD) as well as amytropic leteral sclerosis (ALS). Current models propose that p97 acts as a motor transmitting the energy from the ATPase cycle to conformational changes of substrate protein complexes causing segregation, remodeling or translocation. Mutations at the interface between the N and the D1 domains impact the ATPase activity and the conformation of D2 on the opposite side of the protein complex, suggesting intermolecular communication. Because of limited structural information, the molecular mechanisms on how p97 drives its activities and the molecular basis for transmission of information within the molecule remain elusive. Structural heterogeneity is observed in vitro and is likely relevant for the in vivo biological function of p97. Single particle cryo-EM is the method of choice to study a flexible complex. The technique allows study in solution and also deals with sample heterogeneity by image classification. We have set-up the characterization of the conformational heterogeneity in WT and disease relevant p97 mutant using multi-likelihood classification and Hybrid Electron Microscopy Normal Mode Analysis HEMNMA. The multi-likelihood analysis shows a link between the conformations of the N and D2 domains. HEMNMA allows the analysis of the asymmetry of the conformational changes. Together these studies describe the structural flexibility of p97 and the coupling of the ATPase activity with conformational changes in health and in disease. Study of this model system also allows the development of new methods to understand the conformational heterogeneity of other protein complexes.
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Sverzhinsky A, Fabre L, Cottreau AL, Biot-Pelletier DMP, Khalil S, Bostina M, Rouiller I, Coulton JW. Coordinated rearrangements between cytoplasmic and periplasmic domains of the membrane protein complex ExbB-ExbD of Escherichia coli. Structure 2014; 22:791-7. [PMID: 24657092 DOI: 10.1016/j.str.2014.02.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/05/2014] [Accepted: 02/11/2014] [Indexed: 10/25/2022]
Abstract
Gram-negative bacteria rely on the ExbB-ExbD-TonB system for the import of essential nutrients. Despite decades of research, the stoichiometry, subunit organization, and mechanism of action of the membrane proteins of the Ton system remain unclear. We copurified ExbB with ExbD as an ∼240 kDa protein-detergent complex, measured by light scattering and by native gels. Quantitative Coomassie staining revealed a stoichiometry of ExbB4-ExbD2. Negative stain electron microscopy and 2D analysis showed particles of ∼10 nm diameter in multiple structural states. Nanogold labeling identified the position of the ExbD periplasmic domain. Random conical tilt was used to reconstruct the particles in three structural states followed by sorting of the single particles and refinement of each state. The different states are interpreted by coordinated structural rearrangements between the cytoplasmic domain and the periplasmic domain, concordant with in vivo predictions.
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Affiliation(s)
- Aleksandr Sverzhinsky
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Lucien Fabre
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Andrew L Cottreau
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | - Sofia Khalil
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Mihnea Bostina
- Facility for Electron Microscope Research, McGill University, Montreal, QC H3A 2B4, Canada
| | - Isabelle Rouiller
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 2B4, Canada
| | - James W Coulton
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada; Microbiome and Disease Tolerance Centre, McGill University, Montreal, QC H3A 2B4, Canada.
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20
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Kovács K, Basu K, Rouiller I, Sík A. Regional differences in the expression of K(+)-Cl(-) 2 cotransporter in the developing rat cortex. Brain Struct Funct 2014; 219:527-38. [PMID: 23420348 PMCID: PMC3933751 DOI: 10.1007/s00429-013-0515-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 01/31/2013] [Indexed: 12/12/2022]
Abstract
The type 2 potassium-chloride cotransporter (KCC2) is the main regulator of intracellular chloride concentration in CNS neurons, and plays a crucial role in spine development that is independent of its ion cotransport function. The expression pattern of KCC2 is upregulated during postnatal development showing area and layer-specific differences in distinct brain areas. We examined the regional and ultrastructural localisation of KCC2 in various areas of developing neocortex and paleocortex during the first two postnatal weeks. Light-microscopy examination revealed diffuse neuropil and discrete funnel-shaped dendritic labelling in the piriform and entorhinal cortices at birth. Subsequently, during the beginning of the first postnatal week, diffuse KCC2 labelling gradually started to appear in the superficial layers of the neocortex while the punctate-like labelling of dendrites in the piriform, entorhinal and perirhinal cortices become more pronounced. By the end of the first postnatal week, discrete dendritic expression of KCC2 was visible in all neocortical and paleocortical areas. The expression level did not change during the second postnatal week suggesting that, in contrast to hippocampus, adult pattern of KCC2 in the cortical cells is already established by the end of the first postnatal week. Quantitative electron microscopy examination revealed that in superficial layers of both neo- and paleocortex, the majority of KCC2 signal was plasma membrane associated but the number of transport vesicle-associated immunosignal increased with development. In deep layers, KCC2 immunolabeling was evenly distributed in plasma membrane and transport vesicles showing no obvious change with maturation. The number of KCC2 immunogold particles increased in dendritic spines with no association with synapses. This observation points to the dual role of KCC2 in spine genesis and ion cotransport.
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Affiliation(s)
- Krisztina Kovács
- Neuroscience Networks Group, Neurobiology and Neuropharmacology, College of Medical and Dental Sciences, School of Clinical and Experimental Medicine, University of Birmingham, Birmingham, B15 2TT UK
| | - Kaustuv Basu
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7 Canada
| | - Isabelle Rouiller
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7 Canada
| | - Attila Sík
- Neuroscience Networks Group, Neurobiology and Neuropharmacology, College of Medical and Dental Sciences, School of Clinical and Experimental Medicine, University of Birmingham, Birmingham, B15 2TT UK
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7 Canada
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21
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Grishin AM, Ajamian E, Tao L, Bostina M, Zhang L, Trempe JF, Menard R, Rouiller I, Cygler M. Family of phenylacetyl-CoA monooxygenases differs in subunit organization from other monooxygenases. J Struct Biol 2013; 184:147-54. [PMID: 24055609 DOI: 10.1016/j.jsb.2013.09.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 09/12/2013] [Accepted: 09/14/2013] [Indexed: 11/25/2022]
Abstract
The phenylacetate degradation pathway is present in a wide range of microbes. A key component of this pathway is the four-subunit phenylacetyl-coenzyme A monooxygenase complex (PA-CoA MO, PaaACBE) that catalyzes the insertion of an oxygen in the aromatic ring of PA. This multicomponent enzyme represents a new family of monooxygenases. We have previously determined the structure of the PaaAC subcomplex of catalytic (A) and structural (C) subunits and shown that PaaACB form a stable complex. The PaaB subunit is unrelated to the small subunits of homologous monooxygenases and its role and organization of the PaaACB complex is unknown. From low-resolution crystal structure, electron microscopy and small angle X-ray scattering we show that the PaaACB complex forms heterohexamers, with a homodimer of PaaB bridging two PaaAC heterodimers. Modeling the interactions of reductase subunit PaaE with PaaACB suggested that a unique and conserved 'lysine bridge' constellation near the Fe-binding site in the PaaA subunit (Lys68, Glu49, Glu72 and Asp126) may form part of the electron transfer path from PaaE to the iron center. The crystal structure of the PaaA(K68Q/E49Q)-PaaC is very similar to the wild-type enzyme structure, but when combined with the PaaE subunit the mutant showed 20-50 times reduced activity, supporting the functional importance of the 'lysine bridge'.
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Affiliation(s)
- Andrey M Grishin
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
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22
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Bao H, Dalal K, Wang V, Rouiller I, Duong F. The maltose ABC transporter: action of membrane lipids on the transporter stability, coupling and ATPase activity. Biochim Biophys Acta 2013; 1828:1723-30. [PMID: 23562402 DOI: 10.1016/j.bbamem.2013.03.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/13/2013] [Accepted: 03/25/2013] [Indexed: 01/25/2023]
Abstract
The coupling between ATP hydrolysis and substrate transport remains a key question in the understanding of ABC-mediated transport. We show using the MalFGK2 complex reconstituted into nanodiscs, that membrane lipids participate directly to the coupling reaction by stabilizing the transporter in a low energy conformation. When surrounded by short acyl chain phospholipids, the transporter is unstable and hydrolyzes large amounts of ATP without inducing maltose. The presence of long acyl chain phospholipids stabilizes the conformational dynamics of the transporter, reduces its ATPase activity and restores dependence on maltose. Membrane lipids therefore play an essential allosteric function, they restrict the transporter ATPase activity to increase coupling to the substrate. In support to the notion, we show that increasing the conformational dynamics of MalFGK2 with mutations in MalF increases the transporter ATPase activity but decreases the maltose transport efficiency.
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Affiliation(s)
- Huan Bao
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada
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23
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Grishin AM, Ajamian E, Zhang L, Rouiller I, Bostina M, Cygler M. Protein-protein interactions in the β-oxidation part of the phenylacetate utilization pathway: crystal structure of the PaaF-PaaG hydratase-isomerase complex. J Biol Chem 2012; 287:37986-96. [PMID: 22961985 DOI: 10.1074/jbc.m112.388231] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microbial anaerobic and so-called hybrid pathways for degradation of aromatic compounds contain β-oxidation-like steps. These reactions convert the product of the opening of the aromatic ring to common metabolites. The hybrid phenylacetate degradation pathway is encoded in Escherichia coli by the paa operon containing genes for 10 enzymes. Previously, we have analyzed protein-protein interactions among the enzymes catalyzing the initial oxidation steps in the paa pathway (Grishin, A. M., Ajamian, E., Tao, L., Zhang, L., Menard, R., and Cygler, M. (2011) J. Biol. Chem. 286, 10735-10743). Here we report characterization of interactions between the remaining enzymes of this pathway and show another stable complex, PaaFG, an enoyl-CoA hydratase and enoyl-Coa isomerase, both belonging to the crotonase superfamily. These steps are biochemically similar to the well studied fatty acid β-oxidation, which can be catalyzed by individual monofunctional enzymes, multifunctional enzymes comprising several domains, or enzymatic complexes such as the bacterial fatty acid β-oxidation complex. We have determined the structure of the PaaFG complex and determined that although individually PaaF and PaaG are similar to enzymes from the fatty acid β-oxidation pathway, the structure of the complex is dissimilar from bacterial fatty acid β-oxidation complexes. The PaaFG complex has a four-layered structure composed of homotrimeric discs of PaaF and PaaG. The active sites of PaaF and PaaG are adapted to accept the intermediary components of the Paa pathway, different from those of the fatty acid β-oxidation. The association of PaaF and PaaG into a stable complex might serve to speed up the steps of the pathway following the conversion of phenylacetyl-CoA to a toxic and unstable epoxide-CoA by PaaABCE monooxygenase.
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Affiliation(s)
- Andrey M Grishin
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
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24
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Karimzadeh F, Primeau M, Mountassif D, Rouiller I, Lamarche-Vane N. A stretch of polybasic residues mediates Cdc42 GTPase-activating protein (CdGAP) binding to phosphatidylinositol 3,4,5-trisphosphate and regulates its GAP activity. J Biol Chem 2012; 287:19610-21. [PMID: 22518840 DOI: 10.1074/jbc.m112.344606] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Rho family of small GTPases are membrane-associated molecular switches involved in the control of a wide range of cellular activities, including cell migration, adhesion, and proliferation. Cdc42 GTPase-activating protein (CdGAP) is a phosphoprotein showing GAP activity toward Rac1 and Cdc42. CdGAP activity is regulated in an adhesion-dependent manner and more recently, we have identified CdGAP as a novel molecular target in signaling and an essential component in the synergistic interaction between TGFβ and Neu/ErbB-2 signaling pathways in breast cancer cells. In this study, we identified a small polybasic region (PBR) preceding the RhoGAP domain that mediates specific binding to negatively charged phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3). In vitro reconstitution of membrane vesicles loaded with prenylated Rac1 demonstrates that the PBR is required for full activation of CdGAP in the presence of PI(3,4,5)P3. In fibroblast cells, the expression of CdGAP protein mutants lacking an intact PBR shows a significant reduced ability of the protein mutants to induce cell rounding or to mediate negative effects on cell spreading. Furthermore, an intact PBR is required for CdGAP to inactivate Rac1 signaling into cells, whereas it is not essential in an in vitro context. Altogether, these studies reveal that specific interaction between negatively charged phospholipid PI(3,4,5)P3 and the stretch of polybasic residues preceding the RhoGAP domain regulates CdGAP activity in vivo and is required for its cellular functions.
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Affiliation(s)
- Fereshteh Karimzadeh
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 2B2, Canada
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25
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Gopalakrishnan G, Yam PT, Madwar C, Bostina M, Rouiller I, Colman DR, Lennox RB. Label-free visualization of ultrastructural features of artificial synapses via cryo-EM. ACS Chem Neurosci 2011; 2:700-4. [PMID: 22860164 PMCID: PMC3369721 DOI: 10.1021/cn200094j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Accepted: 10/04/2011] [Indexed: 01/26/2023] Open
Abstract
The ultrastructural details of presynapses formed between artificial substrates of submicrometer silica beads and hippocampal neurons are visualized via cryo-electron microscopy (cryo-EM). The silica beads are derivatized by poly-d-lysine or lipid bilayers. Molecular features known to exist at presynapses are clearly present at these artificial synapses, as visualized by cryo-EM. Key synaptic features such as the membrane contact area at synaptic junctions, the presynaptic bouton containing presynaptic vesicles, as well as microtubular structures can be identified. This is the first report of the direct, label-free observation of ultrastructural details of artificial synapses.
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Affiliation(s)
- Gopakumar Gopalakrishnan
- Department of Chemistry, McGill
University, 801 Sherbrooke Street West, H3A
2K6 Montreal, Canada
- Montreal
Neurological Institute, McGill University, 3801 University Street, H3A 2B4
Montreal, Canada
| | - Patricia T. Yam
- Montreal
Neurological Institute, McGill University, 3801 University Street, H3A 2B4
Montreal, Canada
| | - Carolin Madwar
- Department of Chemistry, McGill
University, 801 Sherbrooke Street West, H3A
2K6 Montreal, Canada
| | - Mihnea Bostina
- Facility
for Electron Microscopy Research (FEMR), Department of Anatomy & Cell
Biology, McGill University, 3640 University Street, H3A
2B2 Montreal, Canada
| | - Isabelle Rouiller
- Facility
for Electron Microscopy Research (FEMR), Department of Anatomy & Cell
Biology, McGill University, 3640 University Street, H3A
2B2 Montreal, Canada
| | - David R. Colman
- Montreal
Neurological Institute, McGill University, 3801 University Street, H3A 2B4
Montreal, Canada
| | - R. Bruce Lennox
- Department of Chemistry, McGill
University, 801 Sherbrooke Street West, H3A
2K6 Montreal, Canada
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26
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Xu XP, Rouiller I, Slaughter BD, Egile C, Kim E, Unruh JR, Fan X, Pollard TD, Li R, Hanein D, Volkmann N. Three-dimensional reconstructions of Arp2/3 complex with bound nucleation promoting factors. EMBO J 2011; 31:236-47. [PMID: 21934650 DOI: 10.1038/emboj.2011.343] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 08/30/2011] [Indexed: 11/09/2022] Open
Abstract
Arp2/3 complex initiates the growth of branched actin-filament networks by inducing actin polymerization from the sides of pre-existing filaments. Nucleation promoting factors (NPFs) are essential for the branching reaction through interactions with the Arp2/3 complex prior to branch formation. The modes by which NPFs bind Arp2/3 complex and associated conformational changes have remained elusive. Here, we used electron microscopy to determine three-dimensional structures at ~2 nm resolution of Arp2/3 complex with three different bound NPFs: N-WASp, Scar-VCA and cortactin. All of these structures adopt a conformation with the two actin-related proteins in an actin-filament-like dimer and the NPF bound to the pointed end. Distance constraints derived by fluorescence resonance energy transfer independently verified the NPF location. Furthermore, all bound NPFs partially occlude the actin-filament binding site, suggesting that additional local structural rearrangements are required in the pathway of Arp2/3 complex activation to allow branch formation.
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Affiliation(s)
- Xiao-Ping Xu
- Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
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27
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Zhang T, Dayanandan B, Rouiller I, Lawrence EJ, Mandato CA. Growth-arrest-specific protein 2 inhibits cell division in Xenopus embryos. PLoS One 2011; 6:e24698. [PMID: 21931817 PMCID: PMC3170402 DOI: 10.1371/journal.pone.0024698] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 08/17/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Growth-arrest-specific 2 gene was originally identified in murine fibroblasts under growth arrest conditions. Furthermore, serum stimulation of quiescent, non-dividing cells leads to the down-regulation of gas2 and results in re-entry into the cell cycle. Cytoskeleton rearrangements are critical for cell cycle progression and cell division and the Gas2 protein has been shown to co-localize with actin and microtubules in interphase mammalian cells. Despite these findings, direct evidence supporting a role for Gas2 in the mechanism of cell division has not been reported. METHODOLOGY AND PRINCIPAL FINDINGS To determine whether the Gas2 protein plays a role in cell division, we over-expressed the full-length Gas2 protein and Gas2 truncations containing either the actin-binding CH domain or the tubulin-binding Gas2 domain in Xenopus laevis embryos. We found that both the full-length Gas2 protein and the Gas2 domain, but not the CH domain, inhibited cell division and resulted in multinucleated cells. The observation that Gas2 domain alone can arrest cell division suggests that Gas2 function is mediated by microtubule binding. Gas2 co-localized with microtubules at the cell cortex of Gas2-injected Xenopus embryos using cryo-confocal microscopy and co-sedimented with microtubules in cytoskeleton co-sedimentation assays. To investigate the mechanism of Gas2-induced cell division arrest, we showed, using a wound-induced contractile array assay, that Gas2 stabilized microtubules. Finally, electron microscopy studies demonstrated that Gas2 bundled microtubules into higher-order structures. CONCLUSION AND SIGNIFICANCE Our experiments show that Gas2 inhibits cell division in Xenopus embryos. We propose that Gas2 function is mediated by binding and bundling microtubules, leading to cell division arrest.
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Affiliation(s)
- Tong Zhang
- Department of Biology, McGill University, Montreal, Quebec, Canada
- * E-mail: (TZ); (CAM)
| | - Bama Dayanandan
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Isabelle Rouiller
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | | | - Craig A. Mandato
- Department of Biology, McGill University, Montreal, Quebec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
- * E-mail: (TZ); (CAM)
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28
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Petrilli⁎ AM, Song W, Bossy B, Liot G, Lubitz S, de Assis V, Johnson J, Poquiz P, Tjong J, Pouladi M, Hayden MR, Masliah E, Ellisman M, Rouiller I, Perkins G, Bossy-Wetzel E. Mutant Huntington interaction with DRP1 impairs the mitochondrial fission and fusion balance and mediates neuronal injury. Mitochondrion 2011. [DOI: 10.1016/j.mito.2011.03.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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29
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Song W, Chen J, Petrilli A, Liot G, Klinglmayr E, Zhou Y, Poquiz P, Tjong J, Pouladi MA, Hayden MR, Masliah E, Ellisman M, Rouiller I, Schwarzenbacher R, Bossy B, Perkins G, Bossy-Wetzel E. Mutant huntingtin binds the mitochondrial fission GTPase dynamin-related protein-1 and increases its enzymatic activity. Nat Med 2011; 17:377-82. [PMID: 21336284 PMCID: PMC3051025 DOI: 10.1038/nm.2313] [Citation(s) in RCA: 406] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 01/18/2011] [Indexed: 02/07/2023]
Abstract
Huntington disease (HD) is an inherited and incurable neurodegenerative disorder caused by an abnormal polyglutamine (polyQ) expansion in huntingtin (HTT). PolyQ length determines disease onset and severity with a longer expansion causing earlier onset. The mechanisms of mutant HTT-mediated neurotoxicity remain unclear; however, mitochondrial dysfunction is a key event in HD pathogenesis1,2. Here we tested whether mutant HTT impairs the mitochondrial fission/fusion balance and thereby causes neuronal injury. We show that mutant HTT triggers mitochondrial fragmentation in neurons and fibroblasts of HD individuals in vitro and HD mice in vivo before the presence of neurological deficits and HTT aggregates. Interestingly, mutant HTT abnormally interacts with the mitochondrial fission GTPase dynamin-related protein 1 (DRP1) in HD mice and individuals which in turn stimulates its enzymatic activity. Importantly, mutant HTT-mediated mitochondrial fragmentation, defects in anterograde and retrograde mitochondrial transport, and neuronal cell death are all rescued by reducing DRP1 GTPase activity with the dominant-negative DRP1K38A mutant. Thus, DRP1 might represent a new therapeutic target to combat neurodegeneration in HD.
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Affiliation(s)
- Wenjun Song
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
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30
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Karam P, Ngo AT, Rouiller I, Cosa G. Unravelling Electronic Energy Transfer in Single Conjugated Polyelectrolytes Encapsulated in Lipid Vesicles. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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31
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Karam P, Ngo AT, Rouiller I, Cosa G. Unraveling electronic energy transfer in single conjugated polyelectrolytes encapsulated in lipid vesicles. Proc Natl Acad Sci U S A 2010; 107:17480-5. [PMID: 20876146 PMCID: PMC2955115 DOI: 10.1073/pnas.1008068107] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A method for the study of conjugated polyelectrolyte (CPE) photophysics in solution at the single-molecule level is described. Extended observation times of single polymer molecules are enabled by the encapsulation of the CPEs within 200-nm lipid vesicles, which are in turn immobilized on a surface. When combined with a molecular-level visualization of vesicles and CPE via cryo-transmission electron microscopy, these single-molecule spectroscopy studies on CPEs enable us to directly correlate the polymer conformation with its spectroscopic features. These studies are conducted with poly[5-methoxy-2-(3-sulfopropoxy)-1,4-phenylene-vinylene] (MPS-PPV, a negatively charged CPE), when encapsulated in neutral and in negatively charged lipid vesicles. MPS-PPV exists as a freely diffusing polymer when confined in negatively charged vesicles. Individual MPS-PPV molecules adopt a collapsed-chain conformation leading to efficient energy migration over multiple chromophores. Both the presence of stepwise photobleaching in fluorescence intensity-time trajectories and emission from low-energy chromophores along the chain are observed. These results correlate with the amplified sensing potential reported for MPS-PPV in aqueous solution. When confined within neutral vesicles, single MPS-PPV molecules adopt an extended conformation upon insertion in the lipid bilayer. In this case emission arises from multiple chromophores within the isolated polymer chains, leading to an exponential decay of the intensity over time and a broad blue-shifted emission spectrum.
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Affiliation(s)
- Pierre Karam
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 2K6
- Centre for Self-Assembled Chemical Structures; and
| | - An Thien Ngo
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 2K6
- Centre for Self-Assembled Chemical Structures; and
| | - Isabelle Rouiller
- Department of Anatomy and Cell Biology, McGill University, Strathcona Anatomy and Dentistry Building, Room 115, 3640 University Street, Montreal, QC, Canada H3A 2B2
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 2K6
- Centre for Self-Assembled Chemical Structures; and
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32
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Gopalakrishnan G, Thostrup P, Rouiller I, Lucido AL, Belkaïd W, Colman DR, Lennox RB. Lipid bilayer membrane-triggered presynaptic vesicle assembly. ACS Chem Neurosci 2010; 1:86-94. [PMID: 22778819 DOI: 10.1021/cn900011n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Accepted: 10/01/2009] [Indexed: 11/30/2022] Open
Abstract
The formation of functional synapses on artificial substrates is a very important step in the development of engineered in vitro neural networks. Spherical supported bilayer lipid membranes (SS-BLMs) are used here as a novel substrate to demonstrate presynaptic vesicle accumulation at an in vitro synaptic junction. Confocal fluorescence microscopy, cryo-transmission electron microscopy (cryo-TEM), and fluorescence recovery after photobleaching (FRAP) experiments have been used to characterize the SS-BLMs. Conventional immunocytochemistry combined with confocal fluorescence microscopy was used to observe the formation of presynaptic vesicles at the neuron-SS-BLM contacts. These results indicate that lipid phases may play a role in the observed phenomenon, in addition to the chemical and electrostatic interactions between the neurons and SS-BLMs. The biocompatibility of lipid bilayers along with their membrane tunability makes the suggested approach a useful "toolkit" for many neuroengineering applications including artificial synapse formation and synaptogenesis in vivo.
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Affiliation(s)
- Gopakumar Gopalakrishnan
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, H3A 2K6 Montreal, Canada
- Montreal Neurological Institute & Hospital, McGill University, 3801 University Street, H3A 2B4 Montreal, Canada
- McGill Program in Neuroengineering, McGill University, Montreal, Canada
- FQRNT Centre for Self-Assembled Chemical Structures (CSACS), McGill University, Montreal, Canada
| | - Peter Thostrup
- Department of Physics, McGill University, 3600 University Street, H3A 2T8 Montreal, Canada
- McGill Program in Neuroengineering, McGill University, Montreal, Canada
| | - Isabelle Rouiller
- Department of Anatomy & Cell Biology, McGill University, 3640 University Street, H3A 2B2 Montreal, Canada
| | - Anna Lisa Lucido
- Montreal Neurological Institute & Hospital, McGill University, 3801 University Street, H3A 2B4 Montreal, Canada
- McGill Program in Neuroengineering, McGill University, Montreal, Canada
| | - Wiam Belkaïd
- Montreal Neurological Institute & Hospital, McGill University, 3801 University Street, H3A 2B4 Montreal, Canada
- McGill Program in Neuroengineering, McGill University, Montreal, Canada
| | - David R. Colman
- Montreal Neurological Institute & Hospital, McGill University, 3801 University Street, H3A 2B4 Montreal, Canada
- McGill Program in Neuroengineering, McGill University, Montreal, Canada
| | - R. Bruce Lennox
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, H3A 2K6 Montreal, Canada
- McGill Program in Neuroengineering, McGill University, Montreal, Canada
- FQRNT Centre for Self-Assembled Chemical Structures (CSACS), McGill University, Montreal, Canada
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Affiliation(s)
- Shaoyong Yu
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 2K6, Canada, and Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, H3A 2B2, Canada
| | - Tony Azzam
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 2K6, Canada, and Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, H3A 2B2, Canada
| | - Isabelle Rouiller
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 2K6, Canada, and Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, H3A 2B2, Canada
| | - Adi Eisenberg
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 2K6, Canada, and Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, H3A 2B2, Canada
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Gopalakrishnan G, Rouiller I, Colman DR, Lennox RB. Supported bilayers formed from different phospholipids on spherical silica substrates. Langmuir 2009; 25:5455-5458. [PMID: 19382772 DOI: 10.1021/la9006982] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Spherical supported bilayer membranes (SS-BLMs) are very attractive candidates in modern bioanalytics and biorecognition studies. A uniform, facile method of preparing different SS-BLMs on silica beads is reported. Confocal fluorescence microscopy and cryo-TEM imaging have been used to characterize these SS-BLMs. Thermal analysis data and FRAP experiments show that the bilayer properties of the SS-BLM are consistent with those of lipid vesicles from which they are formed. The possibility of modulating the size, lipid type and functionality, and mechanical stability makes these rigid liposomes very attractive candidates in biosensors, drug screening, and gene delivery-related applications. This is especially true in work with native vesicle membranes derived from living cells because the existing methods can only accommodate anionic membranes to a limited extent.
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Affiliation(s)
- Gopakumar Gopalakrishnan
- Department of Chemistry, Montreal Neurological Institute & Hospital, and McGill Program in Neuroengineering, Centre for Self-Assembled Chemical Structures, Department of Anatomy & Dentistry, McGill University, Montreal, Canada
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35
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Kafaie J, Dolatshahi M, Ajamian L, Song R, Mouland AJ, Rouiller I, Laughrea M. Role of capsid sequence and immature nucleocapsid proteins p9 and p15 in Human Immunodeficiency Virus type 1 genomic RNA dimerization. Virology 2009; 385:233-44. [DOI: 10.1016/j.virol.2008.11.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Revised: 10/18/2008] [Accepted: 11/14/2008] [Indexed: 11/28/2022]
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36
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Rouiller I, Xu XP, Amann KJ, Egile C, Nickell S, Nicastro D, Li R, Pollard TD, Volkmann N, Hanein D. The structural basis of actin filament branching by the Arp2/3 complex. ACTA ACUST UNITED AC 2008; 180:887-95. [PMID: 18316411 PMCID: PMC2265399 DOI: 10.1083/jcb.200709092] [Citation(s) in RCA: 219] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The actin-related protein 2/3 (Arp2/3) complex mediates the formation of branched actin filaments at the leading edge of motile cells and in the comet tails moving certain intracellular pathogens. Crystal structures of the Arp2/3 complex are available, but the architecture of the junction formed by the Arp2/3 complex at the base of the branch was not known. In this study, we use electron tomography to reconstruct the branch junction with sufficient resolution to show how the Arp2/3 complex interacts with the mother filament. Our analysis reveals conformational changes in both the mother filament and Arp2/3 complex upon branch formation. The Arp2 and Arp3 subunits reorganize into a dimer, providing a short-pitch template for elongation of the daughter filament. Two subunits of the mother filament undergo conformational changes that increase stability of the branch. These data provide a rationale for why branch formation requires cooperative interactions among the Arp2/3 complex, nucleation-promoting factors, an actin monomer, and the mother filament.
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37
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Faustin B, Lartigue L, Bruey JM, Luciano F, Sergienko E, Bailly-Maitre B, Volkmann N, Hanein D, Rouiller I, Reed JC. Reconstituted NALP1 inflammasome reveals two-step mechanism of caspase-1 activation. Mol Cell 2007; 25:713-24. [PMID: 17349957 DOI: 10.1016/j.molcel.2007.01.032] [Citation(s) in RCA: 523] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2006] [Revised: 11/21/2006] [Accepted: 01/18/2007] [Indexed: 11/26/2022]
Abstract
Interleukin (IL)-1beta maturation is accomplished by caspase-1-mediated proteolysis, an essential element of innate immunity. NLRs constitute a recently recognized family of caspase-1-activating proteins, which contain a nucleotide-binding oligomerization domain and leucine-rich repeat (LRR) domains and which assemble into multiprotein complexes to create caspase-1-activating platforms called "inflammasomes." Using purified recombinant proteins, we have reconstituted the NALP1 inflammasome and have characterized the requirements for inflammasome assembly and caspase-1 activation. Oligomerization of NALP1 and activation of caspase-1 occur via a two-step mechanism, requiring microbial product, muramyl-dipeptide, a component of peptidoglycan, followed by ribonucleoside triphosphates. Caspase-1 activation by NALP1 does not require but is enhanced by adaptor protein ASC. The findings provide the biochemical basis for understanding how inflammasome assembly and function are regulated, and shed light on NALP1 as a direct sensor of bacterial components in host defense against pathogens.
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Abstract
Formin proteins are regulators of actin dynamics, mediating assembly of unbranched actin filaments. These multidomain proteins are defined by the presence of a Formin Homology 2 (FH2) domain. Previous work has shown that FH2 domains bind to filament barbed ends and move processively at the barbed end as the filament elongates. Here we report that two FH2 domains, from mammalian FRL1 and mDia2, also bundle filaments, whereas the FH2 domain from mDia1 cannot under similar conditions. The FH2 domain alone is sufficient for bundling. Bundled filaments made by either FRL1 or mDia2 are in both parallel and anti-parallel orientations. A novel property that might contribute to bundling is the ability of the dimeric FH2 domains from both FRL1 and mDia2 to dissociate and recombine. This property is not observed for mDia1. A difference between FRL1 and mDia2 is that FRL1-mediated bundling is competitive with barbed end binding, whereas mDia2-mediated bundling is not. Mutation of a highly conserved isoleucine residue in the FH2 domain does not inhibit bundling by either FRL1 or mDia2, but inhibits barbed end activities. However, the severity of this mutation varies between formins. For mDia1 and mDia2, the mutation strongly inhibits all effects of barbed end binding, but affects FRL1 much less strongly. Furthermore, our results suggest that the Ile mutation affects processivity. Taken together, our data suggest that the bundling activities of FRL1 and mDia2, while producing phenotypically similar bundles, differ in mechanistic detail.
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Affiliation(s)
- Elizabeth S Harris
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
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39
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Egile C, Rouiller I, Xu XP, Volkmann N, Li R, Hanein D. Mechanism of filament nucleation and branch stability revealed by the structure of the Arp2/3 complex at actin branch junctions. PLoS Biol 2005; 3:e383. [PMID: 16262445 PMCID: PMC1278936 DOI: 10.1371/journal.pbio.0030383] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Accepted: 09/12/2005] [Indexed: 11/18/2022] Open
Abstract
Actin branch junctions are conserved cytoskeletal elements critical for the generation of protrusive force during actin polymerization-driven cellular motility. Assembly of actin branch junctions requires the Arp2/3 complex, upon activation, to initiate a new actin (daughter) filament branch from the side of an existing (mother) filament, leading to the formation of a dendritic actin network with the fast growing (barbed) ends facing the direction of movement. Using genetic labeling and electron microscopy, we have determined the structural organization of actin branch junctions assembled in vitro with 1-nm precision. We show here that the activators of the Arp2/3 complex, except cortactin, dissociate after branch formation. The Arp2/3 complex associates with the mother filament through a comprehensive network of interactions, with the long axis of the complex aligned nearly perpendicular to the mother filament. The actin-related proteins, Arp2 and Arp3, are positioned with their barbed ends facing the direction of daughter filament growth. This subunit map brings direct structural insights into the mechanism of assembly and mechanical stability of actin branch junctions. Genetic labeling and electron microscopy were used to examine actin branch junctions assembled in vitro. The subunit map obtained offers insights into the assembly of these conserved cytoskeletal elements.
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Affiliation(s)
- Coumaran Egile
- 1Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Isabelle Rouiller
- 2Cell Adhesion Program, Burnham Institute for Medical Research, La Jolla, California, United States of America
| | - Xiao-Ping Xu
- 2Cell Adhesion Program, Burnham Institute for Medical Research, La Jolla, California, United States of America
| | - Niels Volkmann
- 2Cell Adhesion Program, Burnham Institute for Medical Research, La Jolla, California, United States of America
| | - Rong Li
- 1Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- 3The Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Dorit Hanein
- 2Cell Adhesion Program, Burnham Institute for Medical Research, La Jolla, California, United States of America
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Martin AC, Xu XP, Rouiller I, Kaksonen M, Sun Y, Belmont L, Volkmann N, Hanein D, Welch M, Drubin DG. Effects of Arp2 and Arp3 nucleotide-binding pocket mutations on Arp2/3 complex function. ACTA ACUST UNITED AC 2005; 168:315-28. [PMID: 15657399 PMCID: PMC2171590 DOI: 10.1083/jcb.200408177] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Contributions of actin-related proteins (Arp) 2 and 3 nucleotide state to Arp2/3 complex function were tested using nucleotide-binding pocket (NBP) mutants in Saccharomyces cerevisiae. ATP binding by Arp2 and Arp3 was required for full Arp2/3 complex nucleation activity in vitro. Analysis of actin dynamics and endocytosis in mutants demonstrated that nucleotide-bound Arp3 is particularly important for Arp2/3 complex function in vivo. Severity of endocytic defects did not correlate with effects on in vitro nucleation activity, suggesting that a critical Arp2/3 complex function during endocytosis may be structural rather than catalytic. A separate class of Arp2 and Arp3 NBP mutants suppressed phenotypes of mutants defective for actin nucleation. An Arp2 suppressor mutant increased Arp2/3 nucleation activity. Electron microscopy of Arp2/3 complex containing this Arp2 suppressor identified a structural change that also occurs upon Arp2/3 activation by nucleation promoting factors. These data demonstrate the importance of Arp2 and Arp3 nucleotide binding for nucleating activity, and Arp3 nucleotide binding for maintenance of cortical actin cytoskeleton cytoarchitecture.
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Affiliation(s)
- Adam C Martin
- Barker Hall, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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41
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Dang TX, Hotze EM, Rouiller I, Tweten RK, Wilson-Kubalek EM. Prepore to pore transition of a cholesterol-dependent cytolysin visualized by electron microscopy. J Struct Biol 2005; 150:100-8. [PMID: 15797734 DOI: 10.1016/j.jsb.2005.02.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2004] [Revised: 01/24/2005] [Indexed: 11/29/2022]
Abstract
Perfringolysin O (PFO), a soluble toxin secreted by the pathogenic Clostridium perfringens, forms large homo-oligomeric pore complexes comprising up to 50 PFO molecules in cholesterol-containing membranes. In this study, electron microscopy (EM) and single-particle image analysis were used to reconstruct two-dimensional (2D) projection maps from images of oligomeric PFO prepore and pore complexes formed on cholesterol-rich lipid layers. The projection maps are characterized by an outer and an inner ring of density peaks. The outer rings of the prepore and pore complexes are very similar; however, the protein densities that make up the inner ring of the pore complex are more intense and discretely resolved than they are for the prepore complex. The change in inner-ring protein density is consistent with a mechanism in which the monomers within the prepore complex make a transition from a partially disordered state to a more ordered transmembrane beta-barrel in the pore complex. Finally, the orientation of the monomers within the oligomeric complexes was determined by visualization of streptavidin (SA) molecules bound to biotinylated cysteine-substituted residues predicted to face either the inner or outer surface of the oligomeric pore complex. This study provides an unprecedented view of the conversion of the PFO prepore to pore complex.
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Affiliation(s)
- Thanh X Dang
- Department of Cell Biology, The Scripps Research Institute, 10550 N.Torrey Pines Rd, La Jolla, CA 92037, USA
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42
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Abstract
We describe an algorithm for finding particle images in cryo-EM micrographs. The algorithm starts from a crude 3D map of the target particle, computed from a relatively small number of manually picked images, and then projects the map in many different directions to give synthetic 2D templates. The templates are clustered and averaged and then cross-correlated with the micrographs. A probabilistic model of the imaging process then scores cross-correlation peaks to produce the final picks. We give quantitative results on two quite different target particles: keyhole limpet hemocyanin and p97 AAA ATPase. On these particles our automatic particle picker shows human performance level, as measured by the Fourier shell correlations of 3D reconstructions.
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Affiliation(s)
- H Chi Wong
- Palo Alto Research Center, 3333 Coyote Hill Rd, Palo Alto, CA 94070, USA.
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43
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Netherton C, Rouiller I, Wileman T. The subcellular distribution of multigene family 110 proteins of African swine fever virus is determined by differences in C-terminal KDEL endoplasmic reticulum retention motifs. J Virol 2004; 78:3710-21. [PMID: 15016891 PMCID: PMC371041 DOI: 10.1128/jvi.78.7.3710-3721.2004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
African swine fever virus (ASFV) is a large double-stranded DNA virus that replicates in discrete areas in the cytosol of infected cells called viral factories. Recent studies have shown that assembling virions acquire their internal envelopes through enwrapment by membranes derived from the endoplasmic reticulum (ER). However, the mechanisms that underlie the formation of viral factories and progenitor viral membranes are as yet unclear. Analysis of the published genome of the virus revealed a conserved multigene family that encodes proteins with hydrophobic signal sequences, indicating possible translocation into the ER lumen. Strikingly, two of these genes, XP124L and Y118L, encoded proteins with KDEL-like ER retention motifs. Analysis of XP124L and Y118L gene product by biochemical and immunofluorescence techniques showed that the proteins were localized to pre-Golgi compartments and that the KEDL motif at the C terminus of pXP124L was functional. XP124L expression, in the absence of other ASFV genes, had a dramatic effect on the contents of the ER that was dependent precisely on the C-terminal sequence KEDL. The normal subcellular distribution of a number of proteins resident to this important, cellular organelle was drastically altered in cells expressing wild-type XP124L gene product. PXP124L formed unusual perinuclear structures that contained resident ER proteins, as well as proteins of the ER-Golgi intermediate compartment. The data presented here hint at a role for MGF110 gene product in preparing the ER for its role in viral morphogenesis; this and other potential functions are discussed.
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Affiliation(s)
- Christopher Netherton
- Division of Immunology, Pirbright Laboratory, Institute for Animal Health, Pirbright, Surrey GU24 0NF, United Kingdom
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Rouiller I, DeLaBarre B, May AP, Weis WI, Brunger AT, Milligan RA, Wilson-Kubalek EM. Conformational changes of the multifunction p97 AAA ATPase during its ATPase cycle. Nat Struct Biol 2002; 9:950-7. [PMID: 12434150 DOI: 10.1038/nsb872] [Citation(s) in RCA: 173] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2002] [Accepted: 10/15/2002] [Indexed: 11/09/2022]
Abstract
p97 (also called VCP), a member of the AAA ATPase family, is involved in several cellular processes, including membrane fusion and extraction of proteins from the endoplasmic reticulum for cytoplasmic degradation. We have studied the conformational changes that p97 undergoes during the ATPase cycle by cryo-EM and single-particle analysis. Three-dimensional maps show that the two AAA domains, D1 and D2, as well as the N-domains, experience conformational changes during ATP binding, ATP hydrolysis, P(i) release and ADP release. The N-domain is flexible in most nucleotide states except after ATP hydrolysis. The rings formed by D1 and D2 rotate with respect to each other, and the size of their axial openings fluctuates. Taken together, our results depict the movements that this and possibly other AAA ATPases can undergo during an ATPase cycle.
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Affiliation(s)
- Isabelle Rouiller
- The Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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Rouiller I, Pulokas J, Butel VM, Milligan RA, Wilson-Kubalek EM, Potter CS, Carragher BO. Automated image acquisition for single-particle reconstruction using p97 as the biological sample. J Struct Biol 2001; 133:102-7. [PMID: 11472082 DOI: 10.1006/jsbi.2001.4367] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have used Leginon, a fully automatic system capable of acquiring cryo-electron micrographs, to collect data of single particles, specifically of the AAA ATPase p97. The images were acquired under low-dose conditions and required no operator intervention other than the initial setup and periodic refilling of the cold-stage dewar. Each image was acquired at two different defocus values. Two-dimensional projection maps of p97 were calculated from these data and compared to results previously obtained using the conventional manual data collection methods to film. The results demonstrate that Leginon performs as well as an experienced microscopist for the acquisition of single-particle data. The general advantages of automation are discussed.
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Affiliation(s)
- I Rouiller
- Department of Cell Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA
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46
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Abstract
AAA ATPases play central roles in cellular activities. The ATPase p97, a prototype of this superfamily, participates in organelle membrane fusion. Cryoelectron microscopy and single-particle analysis revealed that a major conformational change of p97 during the ATPase cycle occurred upon nucleotide binding and not during hydrolysis as previously hypothesized. Furthermore, our study indicates that six p47 adaptor molecules bind to the periphery of the ring-shaped p97 hexamer. Taken together, these results provide a revised model of how this and possibly other AAA ATPases can translate nucleotide binding into conformational changes of associated binding partners.
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Affiliation(s)
- I Rouiller
- Department of Cell Biology, Scripps Research Institute, La Jolla, CA 92037, USA
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47
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Abstract
African swine fever (ASF) virus is a large DNA virus that shares the striking icosahedral symmetry of iridoviruses and the genomic organization of poxviruses. Both groups of viruses have a complex envelope structure. In this study, the mechanism of formation of the inner envelope of ASF virus was investigated. Examination of thin cryosections by electron microscopy showed two internal membranes in mature intracellular virions and all structural intermediates. These membranes were in continuity with intracellular membrane compartments, suggesting that the virus gained two membranes from intracellular membrane cisternae. Immunogold electron microscopy showed the viral structural protein p17 and resident membrane proteins of the endoplasmic reticulum (ER) within virus assembly sites, virus assembly intermediates, and mature virions. Resident ER proteins were also detected by Western blotting of isolated virions. The data suggested the ASF virus was wrapped by the ER. Analysis of the published sequence of ASF virus (R. J. Yanez et al., Virology 208:249-278, 1995) revealed a reading frame, XP124L, that encoded a protein predicted to translocate into the lumen of the ER. Pulse-chase immunoprecipitation and glycosylation analysis of pXP124L, the product of the XP124L gene, showed that pXP124L was retained in the ER lumen after synthesis. When analyzed by immunogold electron microscopy, pXP124L localized to virus assembly intermediates and fully assembled virions. Western blot analysis detected pXP124L in virions isolated from Percoll gradients. The packaging of pXP124L from the lumen of the ER into the virion is consistent with ASF virus being wrapped by ER cisternae: a mechanism which explains the presence of two membranes in the viral envelope.
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Affiliation(s)
- I Rouiller
- Division of Immunology, Pirbright Laboratories, Institute for Animal Health, Surrey, England
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