1
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Zhang Y, Lillo JV, Mohamed Abdelrasoul MS, Wang Y, Arrasate P, Frolov VA, Noy A. Nanoscale dynamics of Dynamin 1 helices reveals squeeze-twist deformation mode critical for membrane fission. Proc Natl Acad Sci U S A 2024; 121:e2321514121. [PMID: 39602273 PMCID: PMC11626203 DOI: 10.1073/pnas.2321514121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 10/21/2024] [Indexed: 11/29/2024] Open
Abstract
Dynamin 1 (Dyn1) GTPase, a principal driver of membrane fission during synaptic endocytosis, self-assembles into short mechanoactive helices cleaving the necks of endocytic vesicles. While structural information about Dyn1 helix is abundant, little is known about the nanoscale dynamics of the helical scaffolding at the moment of fission, complicating mechanistic understanding of Dyn1 action. To address the role of the helix dynamics in fission, we used High-Speed Atomic Force Microscopy (HS-AFM) and fluorescence microscopy to track and compare the spatiotemporal characteristics of the helices formed by wild-type Dyn1 and its K44A mutant impaired in GTP hydrolysis on minimal lipid membrane templates. In the absence of nucleotide, membrane-bound WTDyn1 and K44ADyn1 self-assembled into tubular protein scaffolding of similar diameter encaging the lipid bilayer. In both cases, the GTP addition caused scaffold constriction coupled with formation of 20 to 30 nm nanogaps in the protein coverage. While both proteins reached scaffold diameters characteristic for membrane superconstriction causing fission, the fission was detected only with WTDyn1. We associated the fission activity with the dynamic evolution of the nanogaps: K44ADyn1 gaps were static, while WTDyn1 gaps actively evolved via repetitive nonaxisymmetric constriction-bending deformations caused by localized GTP hydrolysis. Modeling of the deformations implicated filament twist as an additional deformation mode which combines with superconstriction to facilitate membrane fission. Our results thus show that the dynamics of the Dyn1 helical scaffold goes beyond radial constriction and involves nonaxisymmetric deformations, where filament twist emerges as a critical driver of membrane fission.
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Affiliation(s)
- Yuliang Zhang
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA94550
| | - Javier Vera Lillo
- Biofisika Institute Consejo Superior de Investigaciones Científicas, Universidad del País Vasco, Euskal Herriko Unibersitatea (CSIC, UPV/EHU), University of the Basque Country, Leioa, 48940, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, 48940, Spain
| | | | - Yaqing Wang
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA94550
| | - Pedro Arrasate
- Biofisika Institute Consejo Superior de Investigaciones Científicas, Universidad del País Vasco, Euskal Herriko Unibersitatea (CSIC, UPV/EHU), University of the Basque Country, Leioa, 48940, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, 48940, Spain
| | - Vadim A. Frolov
- Biofisika Institute Consejo Superior de Investigaciones Científicas, Universidad del País Vasco, Euskal Herriko Unibersitatea (CSIC, UPV/EHU), University of the Basque Country, Leioa, 48940, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, 48940, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48009, Spain
| | - Aleksandr Noy
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA94550
- School of Natural Sciences, University of California Merced, Merced, CA93434
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2
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Zhao Y, Hu K, Wang F, Zhao L, Su Y, Chen J, Zou G, Yang L, Wei L, Deng M, He Y, Wang P, Ruan XZ, Chen Y, Yu C. Guanidine-Derived Polymeric Nanoinhibitors Target the Lysosomal V-ATPase and Activate AMPK Pathway to Ameliorate Liver Lipid Accumulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2408906. [PMID: 39499772 DOI: 10.1002/advs.202408906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 10/14/2024] [Indexed: 11/07/2024]
Abstract
Current research efforts in polymer and nanotechnology applications are primarily focused on cargo delivery to enhance the therapeutic index, with limited attention being paid to self-molecularly targeted nanoparticles, which may also exhibit significant therapeutic potential. Long-term and anomalous lipid accumulation in the liver is a highly relevant factor contributing to liver diseases. However, the development of the reliable medications and their pharmacological mechanisms remain insufficient. Herein, a polyguanide nanoinhibitors (PGNI) depot is constructed by copolymerizing biguanide derivatives in different proportions onto prepolymers. The nanoinhibitors for their ability to ameliorate lipid accumulation in vitro and in vivo is screened, and subsequently demonstrated that covalently polymeric guanidine chains exhibit superior efficacy in ameliorating hepatic lipid accumulation via heterogeneous mechanisms compared to small-molecule guanidine. It is found that PGNIs stabilize guanidine metabolism in the liver, preferably for biosafety. More importantly, PGNI is ingested and localized in hepatocyte lysosomes and is locked to interact with vesicular adenosine triphosphatase (V-ATPase) on lysosomes, leading to the inhibition of V-ATPase and lysosomal acidification, thereby activating the AMPK pathway, reducing fatty acid synthesis, and enhancing lipolysis and fatty acid oxidation. These results imply that polymer-formed nanoparticles can serve as targeted inhibitors, offering a novel approach for therapeutic applications.
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Affiliation(s)
- Yunfei Zhao
- Chongqing Medical University, College of Pharmacy, Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, Chongqing, 400016, P. R. China
| | - Ke Hu
- Centre for Lipid Research & Chongqing Key Laboratory of Metabolism on Lipid and Glucose, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Fangliang Wang
- Chongqing Medical University, College of Pharmacy, Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, Chongqing, 400016, P. R. China
| | - Lulu Zhao
- Chongqing Medical University, College of Pharmacy, Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, Chongqing, 400016, P. R. China
| | - Yu Su
- Centre for Lipid Research & Chongqing Key Laboratory of Metabolism on Lipid and Glucose, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Jun Chen
- Chongqing Medical University, College of Pharmacy, Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, Chongqing, 400016, P. R. China
| | - Gang Zou
- Chongqing Medical University, College of Pharmacy, Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, Chongqing, 400016, P. R. China
| | - Liming Yang
- Chongqing Medical University, College of Pharmacy, Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, Chongqing, 400016, P. R. China
| | - Li Wei
- Centre for Lipid Research & Chongqing Key Laboratory of Metabolism on Lipid and Glucose, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Mengjiao Deng
- Chongqing Medical University, College of Pharmacy, Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, Chongqing, 400016, P. R. China
| | - Yunyu He
- Chongqing Medical University, College of Pharmacy, Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, Chongqing, 400016, P. R. China
| | - Ping Wang
- Centre for Lipid Research & Chongqing Key Laboratory of Metabolism on Lipid and Glucose, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Xiong Z Ruan
- Centre for Lipid Research & Chongqing Key Laboratory of Metabolism on Lipid and Glucose, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Yaxi Chen
- Centre for Lipid Research & Chongqing Key Laboratory of Metabolism on Lipid and Glucose, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, the Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Chao Yu
- Chongqing Medical University, College of Pharmacy, Chongqing Key Laboratory for Pharmaceutical Metabolism Research, Chongqing Pharmacodynamic Evaluation Engineering Technology Research Center, Chongqing, 400016, P. R. China
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3
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Tábara LC, Segawa M, Prudent J. Molecular mechanisms of mitochondrial dynamics. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00785-1. [PMID: 39420231 DOI: 10.1038/s41580-024-00785-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2024] [Indexed: 10/19/2024]
Abstract
Mitochondria not only synthesize energy required for cellular functions but are also involved in numerous cellular pathways including apoptosis, calcium homoeostasis, inflammation and immunity. Mitochondria are dynamic organelles that undergo cycles of fission and fusion, and these transitions between fragmented and hyperfused networks ensure mitochondrial function, enabling adaptations to metabolic changes or cellular stress. Defects in mitochondrial morphology have been associated with numerous diseases, highlighting the importance of elucidating the molecular mechanisms regulating mitochondrial morphology. Here, we discuss recent structural insights into the assembly and mechanism of action of the core mitochondrial dynamics proteins, such as the dynamin-related protein 1 (DRP1) that controls division, and the mitofusins (MFN1 and MFN2) and optic atrophy 1 (OPA1) driving membrane fusion. Furthermore, we provide an updated view of the complex interplay between different proteins, lipids and organelles during the processes of mitochondrial membrane fusion and fission. Overall, we aim to present a valuable framework reflecting current perspectives on how mitochondrial membrane remodelling is regulated.
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Affiliation(s)
- Luis-Carlos Tábara
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Mayuko Segawa
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Julien Prudent
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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4
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Boopathy S, Luce BE, Lugo CM, Hakim P, McDonald J, Kim HL, Ponce J, Ueberheide BM, Chao LH. Identification of SLC25A46 interaction interfaces with mitochondrial membrane fusogens Opa1 and Mfn2. J Biol Chem 2024; 300:107740. [PMID: 39222684 PMCID: PMC11459905 DOI: 10.1016/j.jbc.2024.107740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 07/27/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024] Open
Abstract
Mitochondrial fusion requires the sequential merger of four bilayers to two. The outer-membrane solute carrier family 25 member (SLC25A46) interacts with both the outer and inner membrane dynamin family GTPases mitofusin 1/2 and optic atrophy 1 (Opa1). While SLC25A46 levels are known to affect mitochondrial morphology, how SLC25A46 interacts with mitofusin 1/2 and Opa1 to regulate membrane fusion is not understood. In this study, we use crosslinking mass spectrometry and AlphaFold 2 modeling to identify interfaces mediating an SLC25A46 interaction with Opa1 and Mfn2. We reveal that the bundle signaling element of Opa1 interacts with SLC25A46, and present evidence of an Mfn2 interaction involving the SLC25A46 cytosolic face. We validate these newly identified interaction interfaces and show that they play a role in mitochondrial network maintenance.
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Affiliation(s)
- Sivakumar Boopathy
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston Massachusetts, USA
| | - Bridget E Luce
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA
| | - Camila Makhlouta Lugo
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA
| | - Pusparanee Hakim
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA
| | - Julie McDonald
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA
| | - Ha Lin Kim
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA
| | - Jackeline Ponce
- Proteomics Resource Center, Division of Advanced Research Technologies, New York University Langone Health Center, New York New York, USA
| | - Beatrix M Ueberheide
- Proteomics Resource Center, Division of Advanced Research Technologies, New York University Langone Health Center, New York New York, USA; Department of Biochemistry and Molecular Pharmacology, New York University Langone Health Center, New York New York, USA
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston Massachusetts, USA.
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5
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Gopaldass N, Chen KE, Collins B, Mayer A. Assembly and fission of tubular carriers mediating protein sorting in endosomes. Nat Rev Mol Cell Biol 2024; 25:765-783. [PMID: 38886588 DOI: 10.1038/s41580-024-00746-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2024] [Indexed: 06/20/2024]
Abstract
Endosomes are central protein-sorting stations at the crossroads of numerous membrane trafficking pathways in all eukaryotes. They have a key role in protein homeostasis and cellular signalling and are involved in the pathogenesis of numerous diseases. Endosome-associated protein assemblies or coats collect transmembrane cargo proteins and concentrate them into retrieval domains. These domains can extend into tubular carriers, which then pinch off from the endosomal membrane and deliver the cargoes to appropriate subcellular compartments. Here we discuss novel insights into the structure of a number of tubular membrane coats that mediate the recruitment of cargoes into these carriers, focusing on sorting nexin-based coats such as Retromer, Commander and ESCPE-1. We summarize current and emerging views of how selective tubular endosomal carriers form and detach from endosomes by fission, highlighting structural aspects, conceptual challenges and open questions.
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Affiliation(s)
- Navin Gopaldass
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
| | - Kai-En Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Brett Collins
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Andreas Mayer
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
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6
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Junglas B, Gewehr L, Mernberger L, Schönnenbeck P, Jilly R, Hellmann N, Schneider D, Sachse C. Structural basis for GTPase activity and conformational changes of the bacterial dynamin-like protein SynDLP. Cell Rep 2024; 43:114657. [PMID: 39207903 DOI: 10.1016/j.celrep.2024.114657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 04/23/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
SynDLP, a dynamin-like protein (DLP) encoded in the cyanobacterium Synechocystis sp. PCC 6803, has recently been identified to be structurally highly similar to eukaryotic dynamins. To elucidate structural changes during guanosine triphosphate (GTP) hydrolysis, we solved the cryoelectron microscopy (cryo-EM) structures of oligomeric full-length SynDLP after addition of guanosine diphosphate (GDP) at 4.1 Å and GTP at 3.6-Å resolution as well as a GMPPNP-bound dimer structure of a minimal G-domain construct of SynDLP at 3.8-Å resolution. In comparison with what has been seen in the previously resolved apo structure, we found that the G-domain is tilted upward relative to the stalk upon GTP hydrolysis and that the G-domain dimerizes via an additional extended dimerization domain not present in canonical G-domains. When incubated with lipid vesicles, we observed formation of irregular tubular SynDLP assemblies that interact with negatively charged lipids. Here, we provide the structural framework of a series of different functional SynDLP assembly states during GTP turnover.
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Affiliation(s)
- Benedikt Junglas
- Ernst Ruska-Center for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Lucas Gewehr
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Lara Mernberger
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Philipp Schönnenbeck
- Ernst Ruska-Center for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ruven Jilly
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany; Institute of Molecular Physiology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany.
| | - Carsten Sachse
- Ernst Ruska-Center for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Department of Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.
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7
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Fan Z, Mao X, Zhu M, Hu X, Li M, Huang L, Li J, Maimaiti T, Zuo X, Fan C, Li Q, Liu M, Tian Y. Probing Twist-Induced Endocytotic Membrane Fission using Anisotropic Gold Homodimers. Angew Chem Int Ed Engl 2024:e202413244. [PMID: 39227862 DOI: 10.1002/anie.202413244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 08/31/2024] [Accepted: 09/02/2024] [Indexed: 09/05/2024]
Abstract
Membrane fission involves a crucial step of lipid remodeling, in which the dynamin collar constricts and severs the tubulated lipid membrane at the neck of budding vesicles. Nevertheless, the difficulty in accurately determining the rotational dynamics of live endocytotic vesicles poses a limit on the elucidation of dynamin-induced membrane remodeling for endocytotic vesicle scission. Herein, we designed a DNA-modified gold homodimer (AuHD)-based anisotropic plasmonic probe with uniform surface chemistry, minimizing orientational fluctuation within vesicle encapsulation. Using AuHDs as cargos to image the dynamics of cargo-containing vesicles during endocytosis, we showed that, prior to detachment from plasma membrane, the cargo-containing vesicles underwent multiple intermittent twists of ~4° angular orientation relative to plasma membrane with a ~0.2 s dwell time. These findings suggest that the membrane torques resulting from dynamin actions in vivo constitute the pathway to membrane fission, potentially shedding light on how dynamin-mediated lipid remodeling orchestrates membrane fission.
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Affiliation(s)
- Zhiying Fan
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Meng Zhu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, China
| | - Xingjie Hu
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Lulu Huang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, China
| | - Jie Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, China
| | - Tumala Maimaiti
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Mengmeng Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, China
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8
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Boopathy S, Luce BE, Lugo CM, Hakim P, McDonald J, Kim HL, Ponce J, Ueberheide BM, Chao LH. Identification of SLC25A46 interaction interfaces with mitochondrial membrane fusogens Opa1 and Mfn2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.29.573615. [PMID: 38234813 PMCID: PMC10793391 DOI: 10.1101/2023.12.29.573615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Mitochondrial fusion requires the sequential merger of four bilayers to two. The outer-membrane solute carrier protein SLC25A46 interacts with both the outer and inner-membrane dynamin family GTPases Mfn1/2 and Opa1. While SLC25A46 levels are known to affect mitochondrial morphology, how SLC25A46 interacts with Mfn1/2 and Opa1 to regulate membrane fusion is not understood. In this study, we use crosslinking mass-spectrometry and AlphaFold 2 modeling to identify interfaces mediating a SLC25A46 interactions with Opa1 and Mfn2. We reveal that the bundle signaling element of Opa1 interacts with SLC25A46, and present evidence of a Mfn2 interaction involving the SLC25A46 cytosolic face. We validate these newly identified interaction interfaces and show that they play a role in mitochondrial network maintenance.
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9
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Jimah JR, Kundu N, Stanton AE, Sochacki KA, Canagarajah B, Chan L, Strub MP, Wang H, Taraska JW, Hinshaw JE. Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission. Dev Cell 2024; 59:1783-1793.e5. [PMID: 38663399 PMCID: PMC11265984 DOI: 10.1016/j.devcel.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/29/2023] [Accepted: 04/04/2024] [Indexed: 07/25/2024]
Abstract
Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlying membrane as it progresses through the GTPase cycle to sever vesicles from the plasma membrane. Although atomic models of the dynamin helical polymer bound to guanosine triphosphate (GTP) analogs define earlier stages of membrane constriction, there are no atomic models of the assembled state post-GTP hydrolysis. Here, we used cryo-EM methods to determine atomic structures of the dynamin helical polymer assembled on lipid tubules, akin to necks of budding endocytic vesicles, in a guanosine diphosphate (GDP)-bound, super-constricted state. In this state, dynamin is assembled as a 2-start helix with an inner lumen of 3.4 nm, primed for spontaneous fission. Additionally, by cryo-electron tomography, we trapped dynamin helical assemblies within HeLa cells using the GTPase-defective dynamin K44A mutant and observed diverse dynamin helices, demonstrating that dynamin can accommodate a range of assembled complexes in cells that likely precede membrane fission.
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Affiliation(s)
- John R Jimah
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Nidhi Kundu
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abigail E Stanton
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kem A Sochacki
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bertram Canagarajah
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lieza Chan
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marie-Paule Strub
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jenny E Hinshaw
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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10
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Sun WW, Michalak DJ, Sochacki KA, Kunamaneni P, Alfonzo-Méndez MA, Arnold AM, Strub MP, Hinshaw JE, Taraska JW. Cryo-electron tomography pipeline for plasma membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.600657. [PMID: 39372776 PMCID: PMC11451596 DOI: 10.1101/2024.06.27.600657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Cryo-electron tomography (cryoET) provides sub-nanometer protein structure within the dense cellular environment. Existing sample preparation methods are insufficient at accessing the plasma membrane and its associated proteins. Here, we present a correlative cryo-electron tomography pipeline optimally suited to image large ultra-thin areas of isolated basal and apical plasma membranes. The pipeline allows for angstrom-scale structure determination with sub-tomogram averaging and employs a genetically-encodable rapid chemically-induced electron microscopy visible tag for marking specific proteins within the complex cell environment. The pipeline provides fast, efficient, distributable, low-cost sample preparation and enables targeted structural studies of identified proteins at the plasma membrane of cells.
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Affiliation(s)
- Willy W. Sun
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
- These authors contributed equally
| | - Dennis J. Michalak
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
- These authors contributed equally
| | - Kem A. Sochacki
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
- These authors contributed equally
| | - Prasanthi Kunamaneni
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
- National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Marco A. Alfonzo-Méndez
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Andreas M. Arnold
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Marie-Paule Strub
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Jenny E. Hinshaw
- National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, Maryland, USA
| | - Justin W. Taraska
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland, USA
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11
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Bussoletti M, Gallo M, Bottacchiari M, Abbondanza D, Casciola CM. Mesoscopic elasticity controls dynamin-driven fission of lipid tubules. Sci Rep 2024; 14:14003. [PMID: 38890460 PMCID: PMC11189461 DOI: 10.1038/s41598-024-64685-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
Mesoscale physics bridges the gap between the microscopic degrees of freedom of a system and its large-scale continuous behavior and highlights the role of a few key quantities in complex and multiscale phenomena, like dynamin-driven fission of lipid membranes. The dynamin protein wraps the neck formed during clathrin-mediated endocytosis, for instance, and constricts it until severing occurs. Although ubiquitous and fundamental for life, the cooperation between the GTP-consuming conformational changes within the protein and the full-scale response of the underlying lipid substrate is yet to be unraveled. In this work, we build an effective mesoscopic model from constriction to fission of lipid tubules based on continuum membrane elasticity and implicitly accounting for ratchet-like power strokes of dynamins. Localization of the fission event, the overall geometry, and the energy expenditure we predict comply with the major experimental findings. This bolsters the idea that a continuous picture emerges soon enough to relate dynamin polymerization length and membrane rigidity and tension with the optimal pathway to fission. We therefore suggest that dynamins found in in vivo processes may optimize their structure accordingly. Ultimately, we shed light on real-time conductance measurements available in literature and predict the fission time dependency on elastic parameters.
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Affiliation(s)
- Marco Bussoletti
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy
| | - Mirko Gallo
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy
| | - Matteo Bottacchiari
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, Rome, Italy
| | - Dario Abbondanza
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy
| | - Carlo Massimo Casciola
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy.
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12
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Peng R, Rochon K, Stagg SM, Mears JA. The Structure of the Drp1 Lattice on Membrane. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588123. [PMID: 38617273 PMCID: PMC11014616 DOI: 10.1101/2024.04.04.588123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Mitochondrial health relies on the membrane fission mediated by dynamin-related protein 1 (Drp1). Previous structural studies of Drp1 on remodeled membranes were hampered by heterogeneity, leaving a critical gap in the understanding of the mitochondrial fission mechanism. Here we present a cryo-electron microscopy structure of full-length human Drp1 decorated on membrane tubules. Using the reconstruction of average subtracted tubular regions (RASTR) technique, we report that Drp1 forms a locally ordered lattice along the tubule without global helical symmetry. The filaments in the lattice are similar to dynamin rungs with conserved stalk interactions. Adjacent filaments are connected by GTPase domain interactions in a novel stacked conformation. Additionally, we observed contact between Drp1 and membrane that can be assigned to variable domain sequence. We identified two states of the Drp1 lattice representing conformational changes related to membrane curvature differences. Together these structures revealed a putative mechanism by which Drp1 constricts mitochondria membranes in a stepwise, "ratchet" manner.
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Affiliation(s)
- Ruizhi Peng
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
| | - Kristy Rochon
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - Scott M Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
- Department of Biological Sciences, Florida State University, Tallahassee, Florida, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
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13
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Pang X, Zhang Y, Park K, Liao Z, Li J, Xu J, Hong MT, Yin G, Zhang T, Wang Y, Egelman EH, Fan J, Park SY, Hsu VW, Sun F. Structural elucidation of how ARF small GTPases induce membrane tubulation for vesicle fission. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572083. [PMID: 38187566 PMCID: PMC10769218 DOI: 10.1101/2023.12.19.572083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The ADP-Ribosylation Factor (ARF) small GTPases have been found to act in vesicle fission through a direct ability to tubulate membrane. Here, we have used cryo-electron microscopy (EM) to solve the structure of an ARF6 protein lattice assembled on tubulated membrane to 3.9 Å resolution. ARF6 forms tetramers that polymerize into helical arrays to form this lattice. We identify, and confirm functionally, protein contacts critical for this lattice formation. The solved structure also suggests how the ARF amphipathic helix is positioned in the lattice for membrane insertion, and how a GTPase-activating protein (GAP) docks onto the lattice to catalyze ARF-GTP hydrolysis in completing membrane fission. As ARF1 and ARF6 are structurally conserved, we have also modeled ARF1 onto the ARF6 lattice, which has allowed us to pursue the reconstitution of Coat Protein I (COPI) vesicles to confirm more definitively that the ARF lattice acts in vesicle fission. Our findings are notable for having achieved the first detailed glimpse of how a small GTPase bends membrane and having provided a molecular understanding of how an ARF protein acts in vesicle fission.
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Affiliation(s)
- Xiaoyun Pang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Equal contribution
| | - Yan Zhang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Equal contribution
| | - Kunyou Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
- Equal contribution
| | - Zhenyu Liao
- City University of Hong Kong, Hong Kong, China
| | - Jian Li
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115 USA
| | - Jiashu Xu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minh-Triet Hong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Guoliang Yin
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tongming Zhang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaoyu Wang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, VA 22908 USA
| | - Jun Fan
- City University of Hong Kong, Hong Kong, China
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Victor W Hsu
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115 USA
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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14
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S Cannon K, Sarsam RD, Tedamrongwanish T, Zhang K, Baker RW. Lipid nanodiscs as a template for high-resolution cryo-EM structures of peripheral membrane proteins. J Struct Biol 2023; 215:107989. [PMID: 37364761 DOI: 10.1016/j.jsb.2023.107989] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/05/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Peripheral membrane proteins are ubiquitous throughout cell biology and are required for a variety of cellular processes such as signal transduction, membrane trafficking, and autophagy. Transient binding to the membrane has a profound impact on protein function, serving to induce conformational changes and alter biochemical and biophysical parameters by increasing the local concentration of factors and restricting diffusion to two dimensions. Despite the centrality of the membrane in serving as a template for cell biology, there are few reported high-resolution structures of peripheral membrane proteins bound to the membrane. We analyzed the utility of lipid nanodiscs to serve as a template for cryo-EM analysis of peripheral membrane proteins. We tested a variety of nanodiscs and we report a 3.3 Å structure of the AP2 clathrin adaptor complex bound to a 17-nm nanodisc, with sufficient resolution to visualize a bound lipid head group. Our data demonstrate that lipid nanodiscs are amenable to high-resolution structure determination of peripheral membrane proteins and provide a framework for extending this analysis to other systems.
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Affiliation(s)
- Kevin S Cannon
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA
| | - Reta D Sarsam
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA
| | - Tanita Tedamrongwanish
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA
| | - Kevin Zhang
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA
| | - Richard W Baker
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA; UNC Lineberger Comprehensive Cancer Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA.
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15
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Álvarez D, Sapia J, Vanni S. Computational modeling of membrane trafficking processes: From large molecular assemblies to chemical specificity. Curr Opin Cell Biol 2023; 83:102205. [PMID: 37451175 DOI: 10.1016/j.ceb.2023.102205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
In the last decade, molecular dynamics (MD) simulations have become an essential tool to investigate the molecular properties of membrane trafficking processes, often in conjunction with experimental approaches. The combination of MD simulations with recent developments in structural biology, such as cryo-electron microscopy and artificial intelligence-based structure determination, opens new, exciting possibilities for future investigations. However, the full potential of MD simulations to provide a molecular view of the complex and dynamic processes involving membrane trafficking can only be realized if certain limitations are addressed, and especially those concerning the quality of coarse-grain models, which, despite recent successes in describing large-scale systems, still suffer from far-from-ideal chemical accuracy. In this review, we will highlight recent success stories of MD simulations in the investigation of membrane trafficking processes, their implications for future research, and the challenges that lie ahead in this specific research domain.
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Affiliation(s)
- Daniel Álvarez
- Department of Biology, University of Fribourg, Switzerland; Departamento de Química Física y Analítica, Universidad de Oviedo, Spain
| | - Jennifer Sapia
- Department of Biology, University of Fribourg, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Switzerland; Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France.
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16
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Gewehr L, Junglas B, Jilly R, Franz J, Zhu WE, Weidner T, Bonn M, Sachse C, Schneider D. SynDLP is a dynamin-like protein of Synechocystis sp. PCC 6803 with eukaryotic features. Nat Commun 2023; 14:2156. [PMID: 37059718 PMCID: PMC10104851 DOI: 10.1038/s41467-023-37746-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/29/2023] [Indexed: 04/16/2023] Open
Abstract
Dynamin-like proteins are membrane remodeling GTPases with well-understood functions in eukaryotic cells. However, bacterial dynamin-like proteins are still poorly investigated. SynDLP, the dynamin-like protein of the cyanobacterium Synechocystis sp. PCC 6803, forms ordered oligomers in solution. The 3.7 Å resolution cryo-EM structure of SynDLP oligomers reveals the presence of oligomeric stalk interfaces typical for eukaryotic dynamin-like proteins. The bundle signaling element domain shows distinct features, such as an intramolecular disulfide bridge that affects the GTPase activity, or an expanded intermolecular interface with the GTPase domain. In addition to typical GD-GD contacts, such atypical GTPase domain interfaces might be a GTPase activity regulating tool in oligomerized SynDLP. Furthermore, we show that SynDLP interacts with and intercalates into membranes containing negatively charged thylakoid membrane lipids independent of nucleotides. The structural characteristics of SynDLP oligomers suggest it to be the closest known bacterial ancestor of eukaryotic dynamin.
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Affiliation(s)
- Lucas Gewehr
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Benedikt Junglas
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Jülich, Germany
- Institute for Biological Information Processing (IBI-6): Cellular Structural Biology, Jülich, Germany
| | - Ruven Jilly
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Johannes Franz
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Wenyu Eva Zhu
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Carsten Sachse
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Jülich, Germany.
- Institute for Biological Information Processing (IBI-6): Cellular Structural Biology, Jülich, Germany.
- Department of Biology, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, Germany.
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany.
- Institute of Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany.
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17
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Laiman J, Lin SS, Liu YW. Dynamins in human diseases: differential requirement of dynamin activity in distinct tissues. Curr Opin Cell Biol 2023; 81:102174. [PMID: 37230036 DOI: 10.1016/j.ceb.2023.102174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/12/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023]
Abstract
Dynamin, a 100-kDa GTPase, is one of the most-characterized membrane fission machineries catalyzing vesicle release from plasma membrane during endocytosis. The human genome encodes three dynamins: DNM1, DNM2 and DNM3, with high amino acid similarity but distinct expression patterns. Ever since the discoveries of dynamin mutations associated with human diseases in 2005, dynamin has become a paradigm for studying pathogenic mechanisms of mutant proteins from the aspects of structural biology, cell biology, model organisms as well as therapeutic strategy development. Here, we review the diseases and pathogenic mechanisms caused by mutations of DNM1 and DNM2, focusing on the activity requirement and regulation of dynamins in different tissues.
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Affiliation(s)
- Jessica Laiman
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shan-Shan Lin
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Wen Liu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
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18
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Khurana H, Baratam K, Bhattacharyya S, Srivastava A, Pucadyil TJ. Mechanistic analysis of a novel membrane-interacting variable loop in the pleckstrin-homology domain critical for dynamin function. Proc Natl Acad Sci U S A 2023; 120:e2215250120. [PMID: 36888655 PMCID: PMC10089193 DOI: 10.1073/pnas.2215250120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/08/2023] [Indexed: 03/09/2023] Open
Abstract
Classical dynamins are best understood for their ability to generate vesicles by membrane fission. During clathrin-mediated endocytosis (CME), dynamin is recruited to the membrane through multivalent protein and lipid interactions between its proline-rich domain (PRD) with SRC Homology 3 (SH3) domains in endocytic proteins and its pleckstrin-homology domain (PHD) with membrane lipids. Variable loops (VL) in the PHD bind lipids and partially insert into the membrane thereby anchoring the PHD to the membrane. Recent molecular dynamics (MD) simulations reveal a novel VL4 that interacts with the membrane. Importantly, a missense mutation that reduces VL4 hydrophobicity is linked to an autosomal dominant form of Charcot-Marie-Tooth (CMT) neuropathy. We analyzed the orientation and function of the VL4 to mechanistically link data from simulations with the CMT neuropathy. Structural modeling of PHDs in the cryo-electron microscopy (cryo-EM) cryoEM map of the membrane-bound dynamin polymer confirms VL4 as a membrane-interacting loop. In assays that rely solely on lipid-based membrane recruitment, VL4 mutants with reduced hydrophobicity showed an acute membrane curvature-dependent binding and a catalytic defect in fission. Remarkably, in assays that mimic a physiological multivalent lipid- and protein-based recruitment, VL4 mutants were completely defective in fission across a range of membrane curvatures. Importantly, expression of these mutants in cells inhibited CME, consistent with the autosomal dominant phenotype associated with the CMT neuropathy. Together, our results emphasize the significance of finely tuned lipid and protein interactions for efficient dynamin function.
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Affiliation(s)
- Himani Khurana
- Indian Institute of Science Education and Research, Pune411008, India
| | | | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru560012, India
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19
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Moss FR, Lincoff J, Tucker M, Mohammed A, Grabe M, Frost A. Brominated lipid probes expose structural asymmetries in constricted membranes. Nat Struct Mol Biol 2023; 30:167-175. [PMID: 36624348 PMCID: PMC9935397 DOI: 10.1038/s41594-022-00898-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 11/11/2022] [Indexed: 01/11/2023]
Abstract
Lipids in biological membranes are thought to be functionally organized, but few experimental tools can probe nanoscale membrane structure. Using brominated lipids as contrast probes for cryo-EM and a model ESCRT-III membrane-remodeling system composed of human CHMP1B and IST1, we observed leaflet-level and protein-localized structural lipid patterns within highly constricted and thinned membrane nanotubes. These nanotubes differed markedly from protein-free, flat bilayers in leaflet thickness, lipid diffusion rates and lipid compositional and conformational asymmetries. Simulations and cryo-EM imaging of brominated stearoyl-docosahexanenoyl-phosphocholine showed how a pair of phenylalanine residues scored the outer leaflet with a helical hydrophobic defect where polyunsaturated docosahexaenoyl tails accumulated at the bilayer surface. Combining cryo-EM of halogenated lipids with molecular dynamics thus enables new characterizations of the composition and structure of membranes on molecular length scales.
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Affiliation(s)
- Frank R Moss
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Altos Labs, Redwood City, CA, USA
| | - James Lincoff
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Maxwell Tucker
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Arshad Mohammed
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- University of California Berkeley, Berkeley, CA, USA
- Altos Labs, Redwood City, CA, USA
| | - Michael Grabe
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA.
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
- Altos Labs, Redwood City, CA, USA.
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20
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Cryo-electron tomography reveals structural insights into the membrane remodeling mode of dynamin-like EHD filaments. Nat Commun 2022; 13:7641. [PMID: 36496453 PMCID: PMC9741607 DOI: 10.1038/s41467-022-35164-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Eps15-homology domain containing proteins (EHDs) are eukaryotic, dynamin-related ATPases involved in cellular membrane trafficking. They oligomerize on membranes into filaments that induce membrane tubulation. While EHD crystal structures in open and closed conformations were previously reported, little structural information is available for the membrane-bound oligomeric form. Consequently, mechanistic insights into the membrane remodeling mechanism have remained sparse. Here, by using cryo-electron tomography and subtomogram averaging, we determined structures of nucleotide-bound EHD4 filaments on membrane tubes of various diameters at an average resolution of 7.6 Å. Assembly of EHD4 is mediated via interfaces in the G-domain and the helical domain. The oligomerized EHD4 structure resembles the closed conformation, where the tips of the helical domains protrude into the membrane. The variation in filament geometry and tube radius suggests a spontaneous filament curvature of approximately 1/70 nm-1. Combining the available structural and functional data, we suggest a model for EHD-mediated membrane remodeling.
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21
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Jani RA, Di Cicco A, Keren-Kaplan T, Vale-Costa S, Hamaoui D, Hurbain I, Tsai FC, Di Marco M, Macé AS, Zhu Y, Amorim MJ, Bassereau P, Bonifacino JS, Subtil A, Marks MS, Lévy D, Raposo G, Delevoye C. PI4P and BLOC-1 remodel endosomal membranes into tubules. J Biophys Biochem Cytol 2022; 221:213508. [PMID: 36169638 PMCID: PMC9524204 DOI: 10.1083/jcb.202110132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 07/25/2022] [Accepted: 08/31/2022] [Indexed: 12/11/2022] Open
Abstract
Intracellular trafficking is mediated by transport carriers that originate by membrane remodeling from donor organelles. Tubular carriers contribute to the flux of membrane lipids and proteins to acceptor organelles, but how lipids and proteins impose a tubular geometry on the carriers is incompletely understood. Using imaging approaches on cells and in vitro membrane systems, we show that phosphatidylinositol-4-phosphate (PI4P) and biogenesis of lysosome-related organelles complex 1 (BLOC-1) govern the formation, stability, and functions of recycling endosomal tubules. In vitro, BLOC-1 binds and tubulates negatively charged membranes, including those containing PI4P. In cells, endosomal PI4P production by type II PI4-kinases is needed to form and stabilize BLOC-1-dependent recycling endosomal tubules. Decreased PI4KIIs expression impairs the recycling of endosomal cargoes and the life cycles of intracellular pathogens such as Chlamydia bacteria and influenza virus that exploit the membrane dynamics of recycling endosomes. This study demonstrates how a phospholipid and a protein complex coordinate the remodeling of cellular membranes into functional tubules.
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Affiliation(s)
- Riddhi Atul Jani
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France
| | - Aurélie Di Cicco
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Tal Keren-Kaplan
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Silvia Vale-Costa
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Daniel Hamaoui
- Institut Pasteur, Université de Paris Cité, CNRS UMR3691, Cellular biology of microbial infection, Paris, France
| | - Ilse Hurbain
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Feng-Ching Tsai
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France
| | - Mathilde Di Marco
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France
| | - Anne-Sophie Macé
- Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Yueyao Zhu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Universidade Católica Portuguesa, Católica Medical School, Católica Biomedical Research Centre, Palma de Cima, Lisboa, Portugal
| | - Patricia Bassereau
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Agathe Subtil
- Institut Pasteur, Université de Paris Cité, CNRS UMR3691, Cellular biology of microbial infection, Paris, France
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Daniel Lévy
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Graça Raposo
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Cédric Delevoye
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
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22
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Abstract
Monitoring the proteins and lipids that mediate all cellular processes requires imaging methods with increased spatial and temporal resolution. STED (stimulated emission depletion) nanoscopy enables fast imaging of nanoscale structures in living cells but is limited by photobleaching. Here, we present event-triggered STED, an automated multiscale method capable of rapidly initiating two-dimensional (2D) and 3D STED imaging after detecting cellular events such as protein recruitment, vesicle trafficking and second messengers activity using biosensors. STED is applied in the vicinity of detected events to maximize the temporal resolution. We imaged synaptic vesicle dynamics at up to 24 Hz, 40 ms after local calcium activity; endocytosis and exocytosis events at up to 11 Hz, 40 ms after local protein recruitment or pH changes; and the interaction between endosomal vesicles at up to 3 Hz, 70 ms after approaching one another. Event-triggered STED extends the capabilities of live nanoscale imaging, enabling novel biological observations in real time.
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Affiliation(s)
- Jonatan Alvelid
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Martina Damenti
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Chiara Sgattoni
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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23
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Yamada H, Abe T, Nagaoka H, Takashima E, Nitta R, Yamamoto M, Takei K. Recruitment of Irgb6 to the membrane is a direct trigger for membrane deformation. Front Cell Infect Microbiol 2022; 12:992198. [PMID: 36159643 PMCID: PMC9504060 DOI: 10.3389/fcimb.2022.992198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
Irgb6 is a member of interferon γ-induced immunity related GTPase (IRG), and one of twenty “effector” IRGs, which coordinately attack parasitophorous vacuole membrane (PVM), causing death of intracellular pathogen. Although Irgb6 plays a pivotal role as a pioneer in the process of PVM disruption, the direct effect of Irgb6 on membrane remained to be elucidated. Here, we utilized artificial lipid membranes to reconstitute Irgb6-membrane interaction in vitro, and revealed that Irgb6 directly deformed the membranes. Liposomes incubated with recombinant Irgb6 were drastically deformed generating massive tubular protrusions in the absence of guanine nucleotide, or with GMP-PNP. Liposome deformation was abolished by incubating with Irgb6-K275A/R371A, point mutations at membrane targeting residues. The membrane tubules generated by Irgb6 were mostly disappeared by the addition of GTP or GDP, which are caused by detachment of Irgb6 from membrane. Binding of Irgb6 to the membrane, which was reconstituted in vitro using lipid monolayer, was stimulated at GTP-bound state. Irgb6 GTPase activity was stimulated by the presence of liposomes more than eightfold. Irgb6 GTPase activity in the absence of membrane was also slightly stimulated, by lowering ionic strength, or by increasing protein concentration, indicating synergistic stimulation of the GTPase activity. These results suggest that membrane targeting of Irgb6 and resulting membrane deformation does not require GTP, but converting into GTP-bound state is crucial for detaching Irgb6 from the membrane, which might coincident with local membrane disruption.
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Affiliation(s)
- Hiroshi Yamada
- Department of Neuroscience, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
- *Correspondence: Hiroshi Yamada, ; Kohji Takei,
| | - Tadashi Abe
- Department of Neuroscience, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Hikaru Nagaoka
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Ryo Nitta
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masahiro Yamamoto
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Kohji Takei
- Department of Neuroscience, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
- *Correspondence: Hiroshi Yamada, ; Kohji Takei,
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24
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Imoto Y, Raychaudhuri S, Ma Y, Fenske P, Sandoval E, Itoh K, Blumrich EM, Matsubayashi HT, Mamer L, Zarebidaki F, Söhl-Kielczynski B, Trimbuch T, Nayak S, Iwasa JH, Liu J, Wu B, Ha T, Inoue T, Jorgensen EM, Cousin MA, Rosenmund C, Watanabe S. Dynamin is primed at endocytic sites for ultrafast endocytosis. Neuron 2022; 110:2815-2835.e13. [PMID: 35809574 PMCID: PMC9464723 DOI: 10.1016/j.neuron.2022.06.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 03/24/2022] [Accepted: 06/09/2022] [Indexed: 02/06/2023]
Abstract
Dynamin mediates fission of vesicles from the plasma membrane during endocytosis. Typically, dynamin is recruited from the cytosol to endocytic sites, requiring seconds to tens of seconds. However, ultrafast endocytosis in neurons internalizes vesicles as quickly as 50 ms during synaptic vesicle recycling. Here, we demonstrate that Dynamin 1 is pre-recruited to endocytic sites for ultrafast endocytosis. Specifically, Dynamin 1xA, a splice variant of Dynamin 1, interacts with Syndapin 1 to form molecular condensates on the plasma membrane. Single-particle tracking of Dynamin 1xA molecules confirms the liquid-like property of condensates in vivo. When Dynamin 1xA is mutated to disrupt its interaction with Syndapin 1, the condensates do not form, and consequently, ultrafast endocytosis slows down by 100-fold. Mechanistically, Syndapin 1 acts as an adaptor by binding the plasma membrane and stores Dynamin 1xA at endocytic sites. This cache bypasses the recruitment step and accelerates endocytosis at synapses.
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Affiliation(s)
- Yuuta Imoto
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA.
| | - Sumana Raychaudhuri
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ye Ma
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Pascal Fenske
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Eduardo Sandoval
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Kie Itoh
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Eva-Maria Blumrich
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK; The Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK; Simons Initiatives for the Developing Brain, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK
| | - Hideaki T Matsubayashi
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lauren Mamer
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Fereshteh Zarebidaki
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | | | - Thorsten Trimbuch
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Shraddha Nayak
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-0840, USA
| | - Janet H Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-0840, USA
| | - Jian Liu
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA; Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK
| | - Bin Wu
- The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Takanari Inoue
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Erik M Jorgensen
- HHMI, Department of Biology, University of Utah, Salt Lake City, UT 84112-0840, USA
| | - Michael A Cousin
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK; The Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK; Simons Initiatives for the Developing Brain, University of Edinburgh, Edinburgh, Scotland EH8 9XD, UK
| | - Christian Rosenmund
- Institute of Neurophysiology, Charité Universitätsmedizin Berlin, Berlin, Germany.
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA.
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25
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Shin W, Zucker B, Kundu N, Lee SH, Shi B, Chan CY, Guo X, Harrison JT, Turechek JM, Hinshaw JE, Kozlov MM, Wu LG. Molecular mechanics underlying flat-to-round membrane budding in live secretory cells. Nat Commun 2022; 13:3697. [PMID: 35760780 PMCID: PMC9237132 DOI: 10.1038/s41467-022-31286-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/10/2022] [Indexed: 12/21/2022] Open
Abstract
Membrane budding entails forces to transform flat membrane into vesicles essential for cell survival. Accumulated studies have identified coat-proteins (e.g., clathrin) as potential budding factors. However, forces mediating many non-coated membrane buddings remain unclear. By visualizing proteins in mediating endocytic budding in live neuroendocrine cells, performing in vitro protein reconstitution and physical modeling, we discovered how non-coated-membrane budding is mediated: actin filaments and dynamin generate a pulling force transforming flat membrane into Λ-shape; subsequently, dynamin helices surround and constrict Λ-profile's base, transforming Λ- to Ω-profile, and then constrict Ω-profile's pore, converting Ω-profiles to vesicles. These mechanisms control budding speed, vesicle size and number, generating diverse endocytic modes differing in these parameters. Their impact is widespread beyond secretory cells, as the unexpectedly powerful functions of dynamin and actin, previously thought to mediate fission and overcome tension, respectively, may contribute to many dynamin/actin-dependent non-coated-membrane buddings, coated-membrane buddings, and other membrane remodeling processes.
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Affiliation(s)
- Wonchul Shin
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Ben Zucker
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978, Ramat Aviv, Israel
| | - Nidhi Kundu
- Structural Cell Biology Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Sung Hoon Lee
- Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Bo Shi
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Chung Yu Chan
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Xiaoli Guo
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Jonathan T Harrison
- Structural Cell Biology Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | | | - Jenny E Hinshaw
- Structural Cell Biology Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978, Ramat Aviv, Israel.
| | - Ling-Gang Wu
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
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26
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Hamasaki E, Wakita N, Yasuoka H, Nagaoka H, Morita M, Takashima E, Uchihashi T, Takeda T, Abe T, Lee JW, Iimura T, Saleem MA, Ogo N, Asai A, Narita A, Takei K, Yamada H. The Lipid-Binding Defective Dynamin 2 Mutant in Charcot-Marie-Tooth Disease Impairs Proper Actin Bundling and Actin Organization in Glomerular Podocytes. Front Cell Dev Biol 2022; 10:884509. [PMID: 35620056 PMCID: PMC9127447 DOI: 10.3389/fcell.2022.884509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Dynamin is an endocytic protein that functions in vesicle formation by scission of invaginated membranes. Dynamin maintains the structure of foot processes in glomerular podocytes by directly and indirectly interacting with actin filaments. However, molecular mechanisms underlying dynamin-mediated actin regulation are largely unknown. Here, biochemical and cell biological experiments were conducted to uncover how dynamin modulates interactions between membranes and actin in human podocytes. Actin-bundling, membrane tubulating, and GTPase activities of dynamin were examined in vitro using recombinant dynamin 2-wild-type (WT) or dynamin 2-K562E, which is a mutant found in Charcot-Marie-Tooth patients. Dynamin 2-WT and dynamin 2-K562E led to the formation of prominent actin bundles with constant diameters. Whereas liposomes incubated with dynamin 2-WT resulted in tubule formation, dynamin 2-K562E reduced tubulation. Actin filaments and liposomes stimulated dynamin 2-WT GTPase activity by 6- and 20-fold, respectively. Actin-filaments, but not liposomes, stimulated dynamin 2-K562E GTPase activity by 4-fold. Self-assembly-dependent GTPase activity of dynamin 2-K562E was reduced to one-third compared to that of dynamin 2-WT. Incubation of liposomes and actin with dynamin 2-WT led to the formation of thick actin bundles, which often bound to liposomes. The interaction between lipid membranes and actin bundles by dynamin 2-K562E was lower than that by dynamin 2-WT. Dynamin 2-WT partially colocalized with stress fibers and actin bundles based on double immunofluorescence of human podocytes. Dynamin 2-K562E expression resulted in decreased stress fiber density and the formation of aberrant actin clusters. Dynamin 2-K562E colocalized with α-actinin-4 in aberrant actin clusters. Reformation of stress fibers after cytochalasin D-induced actin depolymerization and washout was less effective in dynamin 2-K562E-expressing cells than that in dynamin 2-WT. Bis-T-23, a dynamin self-assembly enhancer, was unable to rescue the decreased focal adhesion numbers and reduced stress fiber density induced by dynamin 2-K562E expression. These results suggest that the low affinity of the K562E mutant for lipid membranes, and atypical self-assembling properties, lead to actin disorganization in HPCs. Moreover, lipid-binding and self-assembly of dynamin 2 along actin filaments are required for podocyte morphology and functions. Finally, dynamin 2-mediated interactions between actin and membranes are critical for actin bundle formation in HPCs.
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Affiliation(s)
- Eriko Hamasaki
- Department of Neuroscience, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Natsuki Wakita
- Department of Neuroscience, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Hiroki Yasuoka
- Department of Neuroscience, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Hikaru Nagaoka
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Masayuki Morita
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | | | - Tetsuya Takeda
- Department of Neuroscience, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Tadashi Abe
- Department of Neuroscience, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Ji-Won Lee
- Department of Pharmacology, Faculty and Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
| | - Tadahiro Iimura
- Department of Pharmacology, Faculty and Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
| | - Moin A Saleem
- Bristol Renal, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Naohisa Ogo
- Center for Drug Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Akira Asai
- Center for Drug Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Akihiro Narita
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kohji Takei
- Department of Neuroscience, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Hiroshi Yamada
- Department of Neuroscience, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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27
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Hori T, Eguchi K, Wang HY, Miyasaka T, Guillaud L, Taoufiq Z, Mahapatra S, Yamada H, Takei K, Takahashi T. Microtubule assembly by soluble tau impairs vesicle endocytosis and excitatory neurotransmission via dynamin sequestration in Alzheimer's disease mice synapse model. eLife 2022; 11:73542. [PMID: 35471147 PMCID: PMC9071263 DOI: 10.7554/elife.73542] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 04/20/2022] [Indexed: 11/27/2022] Open
Abstract
Elevation of soluble wild-type (WT) tau occurs in synaptic compartments in Alzheimer’s disease. We addressed whether tau elevation affects synaptic transmission at the calyx of Held in slices from mice brainstem. Whole-cell loading of WT human tau (h-tau) in presynaptic terminals at 10–20 µM caused microtubule (MT) assembly and activity-dependent rundown of excitatory neurotransmission. Capacitance measurements revealed that the primary target of WT h-tau is vesicle endocytosis. Blocking MT assembly using nocodazole prevented tau-induced impairments of endocytosis and neurotransmission. Immunofluorescence imaging analyses revealed that MT assembly by WT h-tau loading was associated with an increased MT-bound fraction of the endocytic protein dynamin. A synthetic dodecapeptide corresponding to dynamin 1-pleckstrin-homology domain inhibited MT-dynamin interaction and rescued tau-induced impairments of endocytosis and neurotransmission. We conclude that elevation of presynaptic WT tau induces de novo assembly of MTs, thereby sequestering free dynamins. As a result, endocytosis and subsequent vesicle replenishment are impaired, causing activity-dependent rundown of neurotransmission.
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Affiliation(s)
- Tetsuya Hori
- Cellular and Molecular Synaptic Function Unit, Okinawa Institute of Science and Technology - Graduate University, Okinawa, Japan
| | - Kohgaku Eguchi
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Han-Ying Wang
- Cellular and Molecular Synaptic Function Unit, Okinawa Institute of Science and Technology - Graduate University, Okinawa, Japan
| | - Tomohiro Miyasaka
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Laurent Guillaud
- Cellular and Molecular Synaptic Function Unit, Okinawa Institute of Science and Technology - Graduate University, Okinawa, Japan
| | - Zacharie Taoufiq
- Cellular and Molecular Synaptic Function Unit,, Okinawa Institute of Science and Technology - Graduate University, Okinawa, Japan
| | - Satyajit Mahapatra
- Cellular and Molecular Synaptic Function Unit,, Okinawa Institute of Science and Technology - Graduate University, Okinawa, Japan
| | - Hiroshi Yamada
- Department of Neuroscience, Okayama University, Okayama, Japan
| | - Kohji Takei
- Department of Neuroscience, Okayama University, Okayama, Japan
| | - Tomoyuki Takahashi
- Cellular and Molecular Synaptic Function Unit, Okinawa Institute of Science and Technology - Graduate University, Okinawa, Japan
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28
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Synthesis and Effect of Conformationally Locked Carbocyclic Guanine Nucleotides on Dynamin. Biomolecules 2022; 12:biom12040584. [PMID: 35454173 PMCID: PMC9031165 DOI: 10.3390/biom12040584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
Guanine nucleotides can flip between a North and South conformation in the ribose moiety. To test the enzymatic activity of GTPases bound to nucleotides in the two conformations, we generated methanocarba guanine nucleotides in the North or South envelope conformations, i.e., (N)-GTP and (S)-GTP, respectively. With dynamin as a model system, we examined the effects of (N)-GTP and (S)-GTP on dynamin-mediated membrane constriction, an activity essential for endocytosis. Dynamin membrane constriction and fission activity are dependent on GTP binding and hydrolysis, but the effect of the conformational state of the GTP nucleotide on dynamin activity is not known. After reconstituting dynamin-mediated lipid tubulation and membrane constriction in vitro, we observed via cryo-electron microscopy (cryo-EM) that (N)-GTP, but not (S)-GTP, enables the constriction of dynamin-decorated lipid tubules. These findings suggest that the activity of dynamin is dependent on the conformational state of the GTP nucleotide. However, a survey of nucleotide ribose conformations associated with dynamin structures in nature shows almost exclusively the (S)-conformation. The explanation for this mismatch of (N) vs. (S) required for GTP analogues in a dynamin-mediated process will be addressed in future studies.
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29
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Schiano Lomoriello I, Sigismund S, Day KJ. Biophysics of endocytic vesicle formation: A focus on liquid–liquid phase separation. Curr Opin Cell Biol 2022; 75:102068. [DOI: 10.1016/j.ceb.2022.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 02/07/2023]
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30
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Mehrani A, Stagg SM. Probing intracellular vesicle trafficking and membrane remodelling by cryo-EM. J Struct Biol 2022; 214:107836. [PMID: 35101600 PMCID: PMC8923612 DOI: 10.1016/j.jsb.2022.107836] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/07/2022] [Accepted: 01/24/2022] [Indexed: 11/25/2022]
Abstract
Protein transport between the membranous compartments of the eukaryotic cells is mediated by the constant fission and fusion of the membrane-bounded vesicles from a donor to an acceptor membrane. While there are many membrane remodelling complexes in eukaryotes, COPII, COPI, and clathrin-coated vesicles are the three principal classes of coat protein complexes that participate in vesicle trafficking in the endocytic and secretory pathways. These vesicle-coat proteins perform two key functions: deforming lipid bilayers into vesicles and encasing selective cargoes. The three trafficking complexes share some commonalities in their structural features but differ in their coat structures, mechanisms of cargo sorting, vesicle formation, and scission. While the structures of many of the proteins involved in vesicle formation have been determined in isolation by X-ray crystallography, elucidating the proteins' structures together with the membrane is better suited for cryogenic electron microscopy (cryo-EM). In recent years, advances in cryo-EM have led to solving the structures and mechanisms of several vesicle trafficking complexes and associated proteins.
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Affiliation(s)
- Atousa Mehrani
- Department of Chemistry and Biochemistry, Florida State University
| | - Scott M. Stagg
- Department of Biological Sciences, Florida State University,Institute of Molecular Biophysics, Florida State University
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31
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Prichard KL, O'Brien NS, Murcia SR, Baker JR, McCluskey A. Role of Clathrin and Dynamin in Clathrin Mediated Endocytosis/Synaptic Vesicle Recycling and Implications in Neurological Diseases. Front Cell Neurosci 2022; 15:754110. [PMID: 35115907 PMCID: PMC8805674 DOI: 10.3389/fncel.2021.754110] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/10/2021] [Indexed: 12/17/2022] Open
Abstract
Endocytosis is a process essential to the health and well-being of cell. It is required for the internalisation and sorting of “cargo”—the macromolecules, proteins, receptors and lipids of cell signalling. Clathrin mediated endocytosis (CME) is one of the key processes required for cellular well-being and signalling pathway activation. CME is key role to the recycling of synaptic vesicles [synaptic vesicle recycling (SVR)] in the brain, it is pivotal to signalling across synapses enabling intracellular communication in the sensory and nervous systems. In this review we provide an overview of the general process of CME with a particular focus on two key proteins: clathrin and dynamin that have a central role to play in ensuing successful completion of CME. We examine these two proteins as they are the two endocytotic proteins for which small molecule inhibitors, often of known mechanism of action, have been identified. Inhibition of CME offers the potential to develop therapeutic interventions into conditions involving defects in CME. This review will discuss the roles and the current scope of inhibitors of clathrin and dynamin, providing an insight into how further developments could affect neurological disease treatments.
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32
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Sych T, Levental KR, Sezgin E. Lipid–Protein Interactions in Plasma Membrane Organization and Function. Annu Rev Biophys 2022; 51:135-156. [DOI: 10.1146/annurev-biophys-090721-072718] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lipid–protein interactions in cells are involved in various biological processes, including metabolism, trafficking, signaling, host–pathogen interactions, and transmembrane transport. At the plasma membrane, lipid–protein interactions play major roles in membrane organization and function. Several membrane proteins have motifs for specific lipid binding, which modulate protein conformation and consequent function. In addition to such specific lipid–protein interactions, protein function can be regulated by the dynamic, collective behavior of lipids in membranes. Emerging analytical, biochemical, and computational technologies allow us to study the influence of specific lipid–protein interactions, as well as the collective behavior of membranes on protein function. In this article, we review the recent literature on lipid–protein interactions with a specific focus on the current state-of-the-art technologies that enable novel insights into these interactions. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden;,
| | - Kandice R. Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden;,
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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33
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Baker JR, O'Brien NS, Prichard KL, Robinson PJ, McCluskey A, Russell CC. Dynole 34-2 and Acrylo-Dyn 2-30, Novel Dynamin GTPase Chemical Biology Probes. Methods Mol Biol 2022; 2417:221-238. [PMID: 35099803 DOI: 10.1007/978-1-0716-1916-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This protocol describes the chemical synthesis of the dynamin inhibitors Dynole 34-2 and Acrylo-Dyn 2-30, and their chemical scaffold matched partner inactive compounds. The chosen active and inactive paired compounds represent potent dynamin inhibitors and very closely related dynamin-inactive compounds, with the synthesis of three of the four compounds readily possible via a common intermediate. Combined with the assay data provided, this allows the interrogation of dynamin in vitro and potentially in vivo.
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Affiliation(s)
- Jennifer R Baker
- Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Nicholas S O'Brien
- Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Kate L Prichard
- Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Phillip J Robinson
- Cell Signaling Unit, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, Australia
| | - Adam McCluskey
- Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Cecilia C Russell
- Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia.
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34
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Yin CF, Chang YW, Huang HC, Juan HF. Targeting protein interaction networks in mitochondrial dynamics for cancer therapy. Drug Discov Today 2021; 27:1077-1087. [PMID: 34774766 DOI: 10.1016/j.drudis.2021.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/07/2021] [Accepted: 11/03/2021] [Indexed: 11/16/2022]
Abstract
Mitochondria are crucial organelles that provide energy via oxidative phosphorylation in eukaryotic cells and also have critical roles in growth, division, and the cell cycle, as well as the rapid adaptation required to meet the metabolic needs of the cell. Mitochondrial processes are highly dynamic; fusion and fission can vary with cell type, cellular context, and stress levels. Accumulating evidence demonstrates that an imbalance in mitochondrial dynamics leads to death in numerous types of human cancer cells. Therefore, modulating mitochondrial dynamics could be a therapeutic target. In this review, we provide an overview of the protein interaction networks involved in mitochondrial dynamics as effective and feasible drug targets and discuss the related potential therapeutic strategies for cancer.
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Affiliation(s)
- Chieh-Fan Yin
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Wen Chang
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
| | - Hsueh-Fen Juan
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan; Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan; Center for Computational and Systems Biology, National Taiwan University, Taipei 106, Taiwan; Taiwan AI Labs, Taipei 103, Taiwan.
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35
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Kelly CM, Byrnes LJ, Neela N, Sondermann H, O'Donnell JP. The hypervariable region of atlastin-1 is a site for intrinsic and extrinsic regulation. J Cell Biol 2021; 220:212648. [PMID: 34546351 PMCID: PMC8563291 DOI: 10.1083/jcb.202104128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/03/2021] [Accepted: 09/02/2021] [Indexed: 11/30/2022] Open
Abstract
Atlastin (ATL) GTPases catalyze homotypic membrane fusion of the peripheral endoplasmic reticulum (ER). GTP-hydrolysis–driven conformational changes and membrane tethering are prerequisites for proper membrane fusion. However, the molecular basis for regulation of these processes is poorly understood. Here we establish intrinsic and extrinsic modes of ATL1 regulation that involve the N-terminal hypervariable region (HVR) of ATLs. Crystal structures of ATL1 and ATL3 exhibit the HVR as a distinct, isoform-specific structural feature. Characterizing the functional role of ATL1’s HVR uncovered its positive effect on membrane tethering and on ATL1’s cellular function. The HVR is post-translationally regulated through phosphorylation-dependent modification. A kinase screen identified candidates that modify the HVR site specifically, corresponding to the modifications on ATL1 detected in cells. This work reveals how the HVR contributes to efficient and potentially regulated activity of ATLs, laying the foundation for the identification of cellular effectors of ATL-mediated membrane processes.
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Affiliation(s)
- Carolyn M Kelly
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Laura J Byrnes
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Niharika Neela
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Holger Sondermann
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY.,CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Kiel University, Kiel, Germany
| | - John P O'Donnell
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY.,Cell Biology Division, Medical Research Counsil (MRC) Laboratory of Molecular Biology, Cambridge, UK
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36
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Auddya D, Zhang X, Gulati R, Vasan R, Garikipati K, Rangamani P, Rudraraju S. Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff-Love kinematicsand revealed by a three-dimensional computational framework. Proc Math Phys Eng Sci 2021; 477:20210246. [PMID: 35153593 PMCID: PMC8580429 DOI: 10.1098/rspa.2021.0246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/11/2021] [Indexed: 01/10/2023] Open
Abstract
Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging and transport of nutrients, transmission of nerve impulses, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo significant morphological changes through deformation, scission, and fusion. Modelling the underlying mechanics of such morphological changes has traditionally relied on reduced order axisymmetric representations of membrane geometry and deformation. Axisymmetric representations, while robust and extensively deployed, suffer from their inability to model-symmetry breaking deformations and structural bifurcations. To address this limitation, a three-dimensional computational mechanics framework for high fidelity modelling of biomembrane deformation is presented. The proposed framework brings together Kirchhoff–Love thin-shell kinematics, Helfrich-energy-based mechanics, and state-of-the-art numerical techniques for modelling deformation of surface geometries. Lipid bilayers are represented as spline-based surface discretizations immersed in a three-dimensional space; this enables modelling of a wide spectrum of membrane geometries, boundary conditions, and deformations that are physically admissible in a three-dimensional space. The mathematical basis of the framework and its numerical machinery are presented, and their utility is demonstrated by modelling three classical, yet non-trivial, membrane deformation problems: formation of tubular shapes and their lateral constriction, Piezo1-induced membrane footprint generation and gating response, and the budding of membranes by protein coats during endocytosis. For each problem, the full three-dimensional membrane deformation is captured, potential symmetry-breaking deformation paths identified, and various case studies of boundary and load conditions are presented. Using the endocytic vesicle budding as a case study, we also present a ‘phase diagram’ for its symmetric and broken-symmetry states.
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Affiliation(s)
- Debabrata Auddya
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xiaoxuan Zhang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rahul Gulati
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ritvik Vasan
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Krishna Garikipati
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA.,Michigan Institute for Computational Discovery and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Shiva Rudraraju
- Department of Mechanical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
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37
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Tassin TC, Barylko B, Hedde PN, Chen Y, Binns DD, James NG, Mueller JD, Jameson DM, Taussig R, Albanesi JP. Gain-of-Function Properties of a Dynamin 2 Mutant Implicated in Charcot-Marie-Tooth Disease. Front Cell Neurosci 2021; 15:745940. [PMID: 34744632 PMCID: PMC8563704 DOI: 10.3389/fncel.2021.745940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
Mutations in the gene encoding dynamin 2 (DNM2), a GTPase that catalyzes membrane constriction and fission, are associated with two autosomal-dominant motor disorders, Charcot-Marie-Tooth disease (CMT) and centronuclear myopathy (CNM), which affect nerve and muscle, respectively. Many of these mutations affect the pleckstrin homology domain of DNM2, yet there is almost no overlap between the sets of mutations that cause CMT or CNM. A subset of CMT-linked mutations inhibit the interaction of DNM2 with phosphatidylinositol (4,5) bisphosphate, which is essential for DNM2 function in endocytosis. In contrast, CNM-linked mutations inhibit intramolecular interactions that normally suppress dynamin self-assembly and GTPase activation. Hence, CNM-linked DNM2 mutants form abnormally stable polymers and express enhanced assembly-dependent GTPase activation. These distinct effects of CMT and CNM mutations are consistent with current findings that DNM2-dependent CMT and CNM are loss-of-function and gain-of-function diseases, respectively. In this study, we present evidence that at least one CMT-causing DNM2 mutant (ΔDEE; lacking residues 555DEE557) forms polymers that, like the CNM mutants, are resistant to disassembly and display enhanced GTPase activation. We further show that the ΔDEE mutant undergoes 2-3-fold higher levels of tyrosine phosphorylation than wild-type DNM2. These results suggest that molecular mechanisms underlying the absence of pathogenic overlap between DNM2-dependent CMT and CNM should be re-examined.
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Affiliation(s)
- Tara C. Tassin
- Department of Pharmacology, U.T. Southwestern Medical Center, Dallas, TX, United States
| | - Barbara Barylko
- Department of Pharmacology, U.T. Southwestern Medical Center, Dallas, TX, United States
| | - Per Niklas Hedde
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA, United States
| | - Yan Chen
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, United States
| | - Derk D. Binns
- Department of Pharmacology, U.T. Southwestern Medical Center, Dallas, TX, United States
| | - Nicholas G. James
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Joachim D. Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, United States
| | - David M. Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Ronald Taussig
- Department of Pharmacology, U.T. Southwestern Medical Center, Dallas, TX, United States
| | - Joseph P. Albanesi
- Department of Pharmacology, U.T. Southwestern Medical Center, Dallas, TX, United States
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38
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Liu J, Alvarez FJD, Clare DK, Noel JK, Zhang P. CryoEM structure of the super-constricted two-start dynamin 1 filament. Nat Commun 2021; 12:5393. [PMID: 34518553 PMCID: PMC8437954 DOI: 10.1038/s41467-021-25741-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 08/26/2021] [Indexed: 11/23/2022] Open
Abstract
Dynamin belongs to the large GTPase superfamily, and mediates the fission of vesicles during endocytosis. Dynamin molecules are recruited to the neck of budding vesicles to assemble into a helical collar and to constrict the underlying membrane. Two helical forms were observed: the one-start helix in the constricted state and the two-start helix in the super-constricted state. Here we report the cryoEM structure of a super-constricted two-start dynamin 1 filament at 3.74 Å resolution. The two strands are joined by the conserved GTPase dimeric interface. In comparison with the one-start structure, a rotation around Hinge 1 is observed, essential for communicating the chemical power of the GTPase domain and the mechanical force of the Stalk and PH domain onto the underlying membrane. The Stalk interfaces are well conserved and serve as fulcrums for adapting to changing curvatures. Relative to one-start, small rotations per interface accumulate to bring a drastic change in the helical pitch. Elasticity theory rationalizes the diversity of dynamin helical symmetries and suggests corresponding functional significance.
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Affiliation(s)
- Jiwei Liu
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Frances Joan D Alvarez
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Daniel K Clare
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | | | - Peijun Zhang
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA.
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
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39
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Deisl C, Hilgemann DW, Syeda R, Fine M. TMEM16F and dynamins control expansive plasma membrane reservoirs. Nat Commun 2021; 12:4990. [PMID: 34404808 PMCID: PMC8371123 DOI: 10.1038/s41467-021-25286-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/29/2021] [Indexed: 11/09/2022] Open
Abstract
Cells can expand their plasma membrane laterally by unfolding membrane undulations and by exocytosis. Here, we describe a third mechanism involving invaginations held shut by the membrane adapter, dynamin. Compartments open when Ca activates the lipid scramblase, TMEM16F, anionic phospholipids escape from the cytoplasmic monolayer in exchange for neutral lipids, and dynamins relax. Deletion of TMEM16F or dynamins blocks expansion, with loss of dynamin expression generating a maximally expanded basal plasma membrane state. Re-expression of dynamin2 or its GTPase-inactivated mutant, but not a lipid binding mutant, regenerates reserve compartments and rescues expansion. Dynamin2-GFP fusion proteins form punctae that rapidly dissipate from these compartments during TMEM16F activation. Newly exposed compartments extend deeply into the cytoplasm, lack numerous organellar markers, and remain closure-competent for many seconds. Without Ca, compartments open slowly when dynamins are sequestered by cytoplasmic dynamin antibodies or when scrambling is mimicked by neutralizing anionic phospholipids and supplementing neutral lipids. Activation of Ca-permeable mechanosensitive channels via cell swelling or channel agonists opens the compartments in parallel with phospholipid scrambling. Thus, dynamins and TMEM16F control large plasma membrane reserves that open in response to lateral membrane stress and Ca influx.
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Affiliation(s)
- Christine Deisl
- University of Texas Southwestern Medical Center, Department of Physiology, Dallas, TX, USA
| | - Donald W Hilgemann
- University of Texas Southwestern Medical Center, Department of Physiology, Dallas, TX, USA.
| | - Ruhma Syeda
- University of Texas Southwestern Medical Center, Department of Neuroscience, Dallas, TX, USA
| | - Michael Fine
- University of Texas Southwestern Medical Center, Department of Physiology, Dallas, TX, USA.
- University of Texas Southwestern Medical Center, Department of Molecular Genetics, Dallas, TX, USA.
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40
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Mahajan M, Bharambe N, Shang Y, Lu B, Mandal A, Madan Mohan P, Wang R, Boatz JC, Manuel Martinez Galvez J, Shnyrova AV, Qi X, Buck M, van der Wel PCA, Ramachandran R. NMR identification of a conserved Drp1 cardiolipin-binding motif essential for stress-induced mitochondrial fission. Proc Natl Acad Sci U S A 2021; 118:e2023079118. [PMID: 34261790 PMCID: PMC8307854 DOI: 10.1073/pnas.2023079118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mitochondria form tubular networks that undergo coordinated cycles of fission and fusion. Emerging evidence suggests that a direct yet unresolved interaction of the mechanoenzymatic GTPase dynamin-related protein 1 (Drp1) with mitochondrial outer membrane-localized cardiolipin (CL), externalized under stress conditions including mitophagy, catalyzes essential mitochondrial hyperfragmentation. Here, using a comprehensive set of structural, biophysical, and cell biological tools, we have uncovered a CL-binding motif (CBM) conserved between the Drp1 variable domain (VD) and the unrelated ADP/ATP carrier (AAC/ANT) that intercalates into the membrane core to effect specific CL interactions. CBM mutations that weaken VD-CL interactions manifestly impair Drp1-dependent fission under stress conditions and induce "donut" mitochondria formation. Importantly, VD membrane insertion and GTP-dependent conformational rearrangements mediate only transient CL nonbilayer topological forays and high local membrane constriction, indicating that Drp1-CL interactions alone are insufficient for fission. Our studies establish the structural and mechanistic bases of Drp1-CL interactions in stress-induced mitochondrial fission.
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Affiliation(s)
- Mukesh Mahajan
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
| | - Nikhil Bharambe
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
| | - Yutong Shang
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
| | - Bin Lu
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
| | - Abhishek Mandal
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Pooja Madan Mohan
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
| | - Rihua Wang
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
| | - Jennifer C Boatz
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Juan Manuel Martinez Galvez
- Instituto Biofisika and Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Anna V Shnyrova
- Instituto Biofisika and Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Xin Qi
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- Zernike Institute for Advanced Materials, University of Groningen, 9700 AB Groningen, The Netherlands
| | - Rajesh Ramachandran
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106;
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106
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41
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Ganichkin OM, Vancraenenbroeck R, Rosenblum G, Hofmann H, Mikhailov AS, Daumke O, Noel JK. Quantification and demonstration of the collective constriction-by-ratchet mechanism in the dynamin molecular motor. Proc Natl Acad Sci U S A 2021; 118:e2101144118. [PMID: 34244431 PMCID: PMC8285958 DOI: 10.1073/pnas.2101144118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Dynamin oligomerizes into helical filaments on tubular membrane templates and, through constriction, cleaves them in a GTPase-driven way. Structural observations of GTP-dependent cross-bridges between neighboring filament turns have led to the suggestion that dynamin operates as a molecular ratchet motor. However, the proof of such mechanism remains absent. Particularly, it is not known whether a powerful enough stroke is produced and how the motor modules would cooperate in the constriction process. Here, we characterized the dynamin motor modules by single-molecule Förster resonance energy transfer (smFRET) and found strong nucleotide-dependent conformational preferences. Integrating smFRET with molecular dynamics simulations allowed us to estimate the forces generated in a power stroke. Subsequently, the quantitative force data and the measured kinetics of the GTPase cycle were incorporated into a model including both a dynamin filament, with explicit motor cross-bridges, and a realistic deformable membrane template. In our simulations, collective constriction of the membrane by dynamin motor modules, based on the ratchet mechanism, is directly reproduced and analyzed. Functional parallels between the dynamin system and actomyosin in the muscle are seen. Through concerted action of the motors, tight membrane constriction to the hemifission radius can be reached. Our experimental and computational study provides an example of how collective motor action in megadalton molecular assemblies can be approached and explicitly resolved.
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Affiliation(s)
- Oleg M Ganichkin
- Crystallography, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Renee Vancraenenbroeck
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Gabriel Rosenblum
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Hagen Hofmann
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Alexander S Mikhailov
- Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
- Computational Molecular Biophysics, Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Oliver Daumke
- Crystallography, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany;
- Institute for Chemistry and Biochemistry, Free University of Berlin, 14195 Berlin, Germany
| | - Jeffrey K Noel
- Crystallography, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany;
- Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
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42
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Cheng X, Chen K, Dong B, Yang M, Filbrun SL, Myoung Y, Huang TX, Gu Y, Wang G, Fang N. Dynamin-dependent vesicle twist at the final stage of clathrin-mediated endocytosis. Nat Cell Biol 2021; 23:859-869. [PMID: 34253896 PMCID: PMC8355216 DOI: 10.1038/s41556-021-00713-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/09/2021] [Indexed: 12/11/2022]
Abstract
Dynamin plays an important role in clathrin-mediated endocytosis (CME) by cutting the neck of nascent vesicles from the cell membrane. Here through using gold nanorods as cargos to image dynamin action during live CME, we show that near the peak of dynamin accumulation, the cargo-containing vesicles always exhibit abrupt, right-handed rotations that finish in a short time (~0.28 s). The large and quick twist, herein named the super twist, is the result of the coordinated dynamin helix action upon GTP hydrolysis. After the super twist, the rotational freedom of the vesicle drastically increases, accompanied with simultaneous or delayed translational movement, indicating that it detaches from the cell membrane. These observations suggest that dynamin-mediated scission involves a large torque generated by coordinated actions of multiple dynamins in the helix, which is the main driving force for vesicle scission.
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Affiliation(s)
- Xiaodong Cheng
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.,State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Kuangcai Chen
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Bin Dong
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Meek Yang
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Seth L Filbrun
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Yong Myoung
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Teng-Xiang Huang
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Yan Gu
- The Bristol-Myers Squibb Company, Devens, MA, USA
| | - Gufeng Wang
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.
| | - Ning Fang
- Department of Chemistry, Georgia State University, Atlanta, GA, USA. .,State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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43
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Size, geometry and mobility of protein assemblage regulate the kinetics of membrane wrapping on nanoparticles. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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44
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Baratam K, Jha K, Srivastava A. Flexible pivoting of dynamin pleckstrin homology domain catalyzes fission: insights into molecular degrees of freedom. Mol Biol Cell 2021; 32:1306-1319. [PMID: 33979205 PMCID: PMC8351549 DOI: 10.1091/mbc.e20-12-0794] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The neuronal dynamin1 functions in the release of synaptic vesicles by orchestrating the process of GTPase-dependent membrane fission. Dynamin1 associates with the plasma membrane–localized phosphatidylinositol-4,5-bisphosphate (PIP2) through the centrally located pleckstrin homology domain (PHD). The PHD is dispensable as fission (in model membranes) can be managed, even when the PHD-PIP2 interaction is replaced by a generic polyhistidine- or polylysine-lipid interaction. However, the absence of the PHD renders a dramatic dampening of the rate of fission. These observations suggest that the PHD-PIP2–containing membrane interaction could have evolved to expedite fission to fulfill the requirement of rapid kinetics of synaptic vesicle recycling. Here, we use a suite of multiscale modeling approaches to explore PHD–membrane interactions. Our results reveal that 1) the binding of PHD to PIP2-containing membranes modulates the lipids toward fission-favoring conformations and softens the membrane, and 2) PHD associates with membrane in multiple orientations using variable loops as pivots. We identify a new loop (VL4), which acts as an auxiliary pivot and modulates the orientation flexibility of PHD on the membrane—a mechanism that we believe may be important for high-fidelity dynamin collar assembly. Together, these insights provide a molecular-level understanding of the catalytic role of PHD in dynamin-mediated membrane fission.
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Affiliation(s)
| | - Kirtika Jha
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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45
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46
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Function and regulation of the divisome for mitochondrial fission. Nature 2021; 590:57-66. [PMID: 33536648 DOI: 10.1038/s41586-021-03214-x] [Citation(s) in RCA: 211] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/04/2020] [Indexed: 01/30/2023]
Abstract
Mitochondria form dynamic networks in the cell that are balanced by the flux of iterative fusion and fission events of the organelles. It is now appreciated that mitochondrial fission also represents an end-point event in a signalling axis that allows cells to sense and respond to external cues. The fission process is orchestrated by membrane-associated adaptors, influenced by organellar and cytoskeletal interactions and ultimately executed by the dynamin-like GTPase DRP1. Here we invoke the framework of the 'mitochondrial divisome', which is conceptually and operationally similar to the bacterial cell-division machinery. We review the functional and regulatory aspects of the mitochondrial divisome and, within this framework, parse the core from the accessory machinery. In so doing, we transition from a phenomenological to a mechanistic understanding of the fission process.
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Matthaeus C, Taraska JW. Energy and Dynamics of Caveolae Trafficking. Front Cell Dev Biol 2021; 8:614472. [PMID: 33692993 PMCID: PMC7939723 DOI: 10.3389/fcell.2020.614472] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Caveolae are 70–100 nm diameter plasma membrane invaginations found in abundance in adipocytes, endothelial cells, myocytes, and fibroblasts. Their bulb-shaped membrane domain is characterized and formed by specific lipid binding proteins including Caveolins, Cavins, Pacsin2, and EHD2. Likewise, an enrichment of cholesterol and other lipids makes caveolae a distinct membrane environment that supports proteins involved in cell-type specific signaling pathways. Their ability to detach from the plasma membrane and move through the cytosol has been shown to be important for lipid trafficking and metabolism. Here, we review recent concepts in caveolae trafficking and dynamics. Second, we discuss how ATP and GTP-regulated proteins including dynamin and EHD2 control caveolae behavior. Throughout, we summarize the potential physiological and cell biological roles of caveolae internalization and trafficking and highlight open questions in the field and future directions for study.
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Affiliation(s)
- Claudia Matthaeus
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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48
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Mass photometry enables label-free tracking and mass measurement of single proteins on lipid bilayers. Nat Methods 2021; 18:1247-1252. [PMID: 34608319 PMCID: PMC8490153 DOI: 10.1038/s41592-021-01261-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/04/2021] [Indexed: 02/08/2023]
Abstract
The quantification of membrane-associated biomolecular interactions is crucial to our understanding of various cellular processes. State-of-the-art single-molecule approaches rely largely on the addition of fluorescent labels, which complicates the quantification of the involved stoichiometries and dynamics because of low temporal resolution and the inherent limitations associated with labeling efficiency, photoblinking and photobleaching. Here, we demonstrate dynamic mass photometry, a method for label-free imaging, tracking and mass measurement of individual membrane-associated proteins diffusing on supported lipid bilayers. Application of this method to the membrane remodeling GTPase, dynamin-1, reveals heterogeneous mixtures of dimer-based oligomers, oligomer-dependent mobilities, membrane affinities and (dis)association of individual complexes. These capabilities, together with assay-based advances for studying integral membrane proteins, will enable the elucidation of biomolecular mechanisms in and on lipid bilayers.
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Arriagada-Diaz J, Prado-Vega L, Cárdenas Díaz AM, Ardiles AO, Gonzalez-Jamett AM. Dynamin Superfamily at Pre- and Postsynapses: Master Regulators of Synaptic Transmission and Plasticity in Health and Disease. Neuroscientist 2020; 28:41-58. [PMID: 33300419 DOI: 10.1177/1073858420974313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Dynamin superfamily proteins (DSPs) comprise a large group of GTP-ases that orchestrate membrane fusion and fission, and cytoskeleton remodeling in different cell-types. At the central nervous system, they regulate synaptic vesicle recycling and signaling-receptor turnover, allowing the maintenance of synaptic transmission. In the presynapses, these GTP-ases control the recycling of synaptic vesicles influencing the size of the ready-releasable pool and the release of neurotransmitters from nerve terminals, whereas in the postsynapses, they are involved in AMPA-receptor trafficking to and from postsynaptic densities, supporting excitatory synaptic plasticity, and consequently learning and memory formation. In agreement with these relevant roles, an important number of neurological disorders are associated with mutations and/or dysfunction of these GTP-ases. Along the present review we discuss the importance of DSPs at synapses and their implication in different neuropathological contexts.
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Affiliation(s)
- Jorge Arriagada-Diaz
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile.,Programa de Magister en Ciencias, mención Neurociencia, Universidad de Valparaíso, Valparaíso, Chile
| | - Lorena Prado-Vega
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile.,Programa de Magister en Ciencias, mención Neurociencia, Universidad de Valparaíso, Valparaíso, Chile
| | - Ana M Cárdenas Díaz
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile
| | - Alvaro O Ardiles
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile.,Centro de Neurología Traslacional, Facultad de Medicina, Universidad de Valparaíso, Valparaíso, Chile.,Centro Interdisciplinario de Estudios en Salud, Facultad de Medicina, Universidad de Valparaíso, Viña del Mar, Chile
| | - Arlek M Gonzalez-Jamett
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile
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50
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Hinostroza F, Neely A, Araya-Duran I, Marabolí V, Canan J, Rojas M, Aguayo D, Latorre R, González-Nilo FD, Cárdenas AM. Dynamin-2 R465W mutation induces long range perturbation in highly ordered oligomeric structures. Sci Rep 2020; 10:18151. [PMID: 33097808 PMCID: PMC7584598 DOI: 10.1038/s41598-020-75216-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/13/2020] [Indexed: 11/09/2022] Open
Abstract
High order oligomers are crucial for normal cell physiology, and protein function perturbed by missense mutations underlies several autosomal dominant diseases. Dynamin-2 is one of such protein forming helical oligomers that catalyze membrane fission. Mutations in this protein, where R465W is the most frequent, cause dominant centronuclear myopathy, but the molecular mechanisms underpinning the functional modifications remain to be investigated. To unveil the structural impact of this mutation in dynamin-2, we used full-atom molecular dynamics simulations and coarse-grained models and built dimers and helices of wild-type (WT) monomers, mutant monomers, or both WT and mutant monomers combined. Our results show that the mutation R465W causes changes in the interactions with neighbor amino acids that propagate through the oligomer. These new interactions perturb the contact between monomers and favor an extended conformation of the bundle signaling element (BSE), a dynamin region that transmits the conformational changes from the GTPase domain to the rest of the protein. This extended configuration of the BSE that is only relevant in the helices illustrates how a small change in the microenvironment surrounding a single residue can propagate through the oligomer structures of dynamin explaining how dominance emerges in large protein complexes.
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Affiliation(s)
- Fernando Hinostroza
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Valparaiso, Chile.,Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Av. San Miguel 3605, Talca, Chile
| | - Alan Neely
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Valparaiso, Chile
| | - Ingrid Araya-Duran
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello, Av. República 330, Santiago, Chile
| | - Vanessa Marabolí
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello, Av. República 330, Santiago, Chile
| | - Jonathan Canan
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello, Av. República 330, Santiago, Chile
| | - Maximiliano Rojas
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello, Av. República 330, Santiago, Chile
| | - Daniel Aguayo
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello, Av. República 330, Santiago, Chile
| | - Ramón Latorre
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Valparaiso, Chile
| | - Fernando D González-Nilo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Valparaiso, Chile. .,Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello, Av. República 330, Santiago, Chile.
| | - Ana M Cárdenas
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Valparaiso, Chile.
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